Comparison of Proteomic Assessment Methods in Multiple Cohort Studies

Novel proteomics platforms, such as the aptamer-based SOMAscan platform, can quantify large numbers of proteins efficiently and cost-effectively and are rapidly growing in popularity. However, comparisons to conventional immunoassays remain underexplored, leaving investigators unsure when cross-assay comparisons are appropriate. The correlation of results from immunoassays with relative protein quantification is explored by SOMAscan. For 63 proteins assessed in two chronic obstructive pulmonary disease (COPD) cohorts, subpopulations and intermediate outcome measures in COPD Study (SPIROMICS), and COPDGene, using myriad rules based medicine multiplex immunoassays and SOMAscan, Spearman correlation coefficients range from -0.13 to 0.97, with a median correlation coefficient of ≈0.5 and consistent results across cohorts. A similar range is observed for immunoassays in the population-based Multi-Ethnic Study of Atherosclerosis and for other assays in COPDGene and SPIROMICS. Comparisons of relative quantification from the antibody-based Olink platform and SOMAscan in a small cohort of myocardial infarction patients also show a wide correlation range. Finally, cis pQTL data, mass spectrometry aptamer confirmation, and other publicly available data are integrated to assess relationships with observed correlations. Correlation between proteomics assays shows a wide range and should be carefully considered when comparing and meta-analyzing proteomics data across assays and studies.

Higher serum levels of systemic inflammatory markers are linked to greater inspiratory muscle dysfunction in COPD

BACKGROUND

Chronic obstructive pulmonary disease (COPD) is associated with an inflammatory response that becomes more pronounced in acute exacerbations. Considerable attention has recently focused on the value of several inflammatory mediators in predicting worsening of COPD-related symptoms. Whereas respiratory muscle dysfunction is also widely present in this population, little is known about how systemic inflammation relates to inspiratory muscle dysfunction in COPD.

METHODS

Fifty-three males with mild-to-very severe airflow obstruction underwent blood sampling for 23 inflammatory markers, including acute-phase proteins, cytokines and adipokines. Inspiratory muscle performance was assessed via the test of incremental respiratory endurance, providing measures of maximal (MIP) and sustained maximal (SMIP) inspiratory pressures.

RESULTS

The mean ± SD MIP and SMIP were 75.32 ± 19.62 cmH₂ O and 406.15 ± 124.55 PTU. MIP negatively correlated with CRP, SAA and cystatin C (r-values from -0.333 to -0.378, P < 0.02), while SMIP was inversely related to SAA and cystatin C (r = -0.534 and r = -0.396, P = 0.00). Significant differences in CRP, SAA, cystatin C and PARC were also found between subjects with and without inspiratory muscle weakness. No additional significant relationships were observed between either MIP or SMIP and other inflammatory markers in the study.

CONCLUSIONS

MIP and SMIP are markedly reduced with greater degrees of inflammation in COPD as expressed by higher levels of CRP, SAA and cystatin C. Future research is needed to further examine the above findings and determine the impact of systemic inflammation along with its underlying mechanisms on inspiratory muscle function in COPD.

Markers of Response to Antiangiogenic Therapies in Colorectal Cancer: Where Are We Now and What Should Be Next?

Despite advances in the treatment of colorectal cancer (CRC), it remains the second most common cause of cancer-related death in the Western world. Angiogenesis is a complex process that involves the formation of new blood vessels from preexisting vessels. It is essential for promoting cancer survival, growth, and dissemination. The inhibition of angiogenesis has been shown to prevent tumor progression experimentally, and several chemotherapeutic targets of tumor angiogenesis have been identified. These include anti-vascular endothelial growth factor (VEGF) treatments, such as bevacizumab (a VEGF-specific binding antibody) and anti-VEGF receptor tyrosine kinase inhibitors, although antiangiogenic therapy has been shown to be effective in the treatment of several cancers, including CRC. However, it is also associated with its own side effects and financial costs. Therefore, the identification of biomarkers that are able to identify patients who are more likely to benefit from antiangiogenic treatment is very important. This article intends to be a concise summary of the potential biomarkers that can predict or prognosticate the benefit of antiangiogenic treatments in CRC, and also what we can expect in the near future.

Total body water in children with cystic fibrosis using bioelectrical impedance

BACKGROUND

The aim of this study was to assess the ability of commercially available single frequency bioelectrical impedance analysis (BIA) to predict total body water and hence body composition in a cohort of children with cystic fibrosis (CF).

METHODS

In 56 (31 girls, 25 boys) children aged 4 to 18 years, total body water was predicted using BIA and measured using a deuterium oxide dilution technique. Each child provided a urine sample before consuming 0.5 g/kg body weight 10% deuterium oxide. A further urine sample was collected between 4 and 6 h later.

RESULTS

There was a mean bias between predicted and measured total body water of 1.1 L. The bias was consistent across the range of total body water measured in this study. The relationship between height2/impedance and measured total body water was TBW=0.35+0.74*height2/impedance. This equation is similar to other equations found in healthy children.

CONCLUSION

We have shown that a commercially available bioelectrical device underestimates measured total body water. We have generated a prediction equation for the population studied, which we believe might enhance the accuracy of the method in children with cystic fibrosis.

Confocal microscopy and multi-photon excitation microscopy of human skin in vivo

This paper compares tandem scanning reflected light confocal microscopy and multi-photon excitation microscopy for the observation of human skin in vivo. Tandem scanning confocal light microscopy based on a white light source can provide video-rate image acquisition from the skin surface to the epidermal-dermal junction. Multi-photon excitation is induced by a 80 MHz pulse train of femtosecond laser pulses at 780 nm wavelength. This nonlinear microscopic technique is inherently suitable for deep tissue fluorescence imaging. The relative merits of these two techniques can be identified by comparing movies of optical sections obtained from the forearm skin of the same volunteer.

Atypical mycobacterial pulmonary disease and bronchial obstruction in HIV-negative children

Atypical mycobacterial infection in HIV-negative children usually presents with cervical lymphadenopathy. We report on 10 children who are HIV-negative and who presented with pulmonary disease, in whom either culture-proven atypical mycobacterium infection (four), positive avian Mantoux test (five), or lack of response to human tuberculosis treatment (one) had been observed. One case was subsequently diagnosed as chronic granulomatous disease and illustrates that children with atypical mycobacterial pulmonary infection should have their immune status fully investigated. Bronchial obstruction was observed in eight cases, and of these, endobronchial disease was found in six children. The diagnosis of atypical mycobacterial disease is difficult, and a negative avian Mantoux test does not exclude the diagnosis. The availability of clarithromycin and rifabutin has offered new therapeutic options in treating atypical mycobacterial pulmonary infection, but management of these cases can be prolonged and difficult.

Three-dimensional confocal microscopy of the human optic nerve in vivo

A scanning laser confocal microscope was used to visualize the human fundus (the back portion of the eyeball, as seen by means of the ophthalmoscope) in vivo from near the retinal surface to deep within the optic nerve head. Thirty two optical sections based on reflected light were acquired, digitized and aligned to compensate for small eye movements. The registered stack of optical sections was reconstructed with three-dimensional volume rendering software and presented as a movie. The three-dimensional rendering presents a new technique to view the optic nerve. This technique is clinically important since morphological changes of the lamina cribrosa of the optic nerve may be involved in glaucoma.

Three-dimensional confocal microscopy of the living in situ rabbit cornea

Three-dimensional confocal microscopy of a living in situ rabbit cornea, in a freshly excised eye, is demonstrated in two movie loops. A specimen chamber for the eye was designed and constructed to maintain the unstained, unfixed, in situ cornea in a viable physiological state during data acquisition. The 400 micron thick, transparent, cornea has been optically sectioned into 365 sections using a laser scanning confocal microscope. A high numerical aperture, water immersion microscope objective minimized the spherical aberrations which would occur with the use of an oil immersion objective. Depth dependent light attenuation due to absorption and scatter within the specimen was manually compensated at each sampled section. Isometric sampling resulted in near-cubic voxels which compensated for the reduced microscopic resolution in the z-axis as compared to x- and y- resolution.

Three-dimensional microscopic tomographic imagings of the cataract in a human lens in vivo

The problem of three-dimensional visualization of a human lens in vivo has been solved by a technique of volume rendering a transformed series of 60 rotated Scheimpflug (a dual slit reflected light microscope) digital images. The data set was obtained by rotating the Scheimpflug camera about the optic axis of the lens in 3 degree increments. The transformed set of optical sections were first aligned to correct for small eye movements, and then rendered into a volume reconstruction with volume rendering computer graphics techniques. To help visualize the distribution of lens opacities (cataracts) in the living, human lens the intensity of light scattering was pseudocolor coded and the cataract opacities were displayed as a movie.

Post-infectious bronchiolitis obliterans: clinical, radiological and pulmonary function sequelae

Background. There are few data on clinical, chest radiograph (CXR) or pulmonary function sequelae in children with post-infectious bronchiolitis obliterans (BO) (pulmonary crepitations, abnormalities on CXR, CT, nuclear medicine scans, or bronchography, with a history of past pulmonary infection and in the absence of other underlying pathology). Objective. To analyse the methodology of diagnosis, long-term clinical imaging and pulmonary function sequelae of post-infectious BO in children. Materials and methods. Imaging (CXRs, CT and nuclear lung scans) and clinical histories of 19 children were analysed. Results. Clinical follow-up (mean 6.8 years), revealed a high incidence of continuing problems (asthma and bronchiectasis). Fixed airway obstruction was the most common pulmonary function sequela. The sequelae on follow-up (mean 5.8 years) CXR were classified into five patterns which are illustrated: unilateral hyperlucency of an enlarged lung/part of lung; complete collapse of the affected lobe; unilateral hyperlucency of a small or normal-sized lung; bilateral hyperlucent lungs and a mixed pattern of persistent collapse, hyperlucency and peribronchial thickening. Conclusion. Long-term observations in children with post-infectious BO should be undertaken to detect bronchiectasis and obstructive airway disease. Sequelae evident on CXR, other than those previously described, can be found. Bronchography and/or lung biopsy are not usually required for the diagnosis of post-infectious BO.

HIV-1 survival kinetics in peritoneal dialysis effluent

Viable and potentially infectious HIV-1 has been recovered from the peritoneal dialysis effluent (PDE) of patients with end-stage renal disease (ESRD) who are infected with the human immunodeficiency virus (HIV). No information had previously been available as to how long HIV-1 could survive in this environment, and no data were available as to how long HIV-1 could survive on peritoneal dialysis exchange tubing (PDET). Therefore, this study was designed to answer these questions. HIV-1 Mn was added to PDE and allowed to incubate at room temperature for 0 to 14 days. Following centrifugation, the cellular component of the PDE mixture was placed in co-culture with peripheral blood mononuclear cells (PBMC) from HIV negative donors. Aliquots from the co-cultures were removed after 14 days and assayed for the HIV-1-P24 antigen. High levels of HIV P24 antigen were recovered up to and including seven days of room temperature incubation. HIV could not be recovered from PDE that had been incubated at room temperature for 10 to 14 days. Ten milliters of HIV-PDE mixture was placed within PDET and incubated at room temperature for 10 minutes. The solution was then removed by gravity drainage. After drying times of 0 to 168 hours, the tubing was flushed with HIV culture medium and placed in co-culture with PBMCs from HIV negative donors. The culture supernatant was assayed for the HIV-1 P24 antigen as a marker of viral replication. High levels of HIV-1 P24 antigen were recovered from the PDET wash for up to and including 48 hours of drying time. No viable virus could be detected for drying times of between 72 and 168 hours. To determine if common disinfectants found in the dialysis unit could inactivate HIV, dilutions of Amukin 50% and household bleach were prepared at final concentrations ranging from 1:32 to 1:2048. These disinfectant solutions were incubated with PDE containing HIV for 10 minutes. The cellular fraction of the PDE was isolated by centrifugation, washed, and placed in co-cultures with peripheral blood mononuclear cells. HIV P24 antigen levels were assayed every three days for 28 days. Amukin 50% and a 10% household bleach solution were effective in killing HIV in PDE at dilutions up to and including 1:512. These results indicate that HIV can survive in PDE at room temperature for up to seven days. HIV can survive on peritoneal dialysis exchange tubing for up to 48 hours. Final dilutions of 1:512 Amukin 50% and 10% household bleach, after 10 minutes of exposure, are effective viricidal agents in disinfecting PDE.

Resting energy expenditure, pulmonary inflammation, and genotype in the early course of cystic fibrosis

To further investigate the early course of cystic fibrosis (CF), specifically to examine factors contributing to energy imbalance, we examined resting energy expenditure (REE) (by indirect calorimetry) per unit body weight and metabolically active body cell mass (by total body potassium), in relation to CF genotype (by genomic DNA analysis), CF pancreatic phenotype, and markers of pulmonary inflammation (from bronchoalveolar lavage fluid). Eighteen subjects with presymptomatic CF who were less than 2 years of age (n = 11, delta F508/ delta F508 genotype; n = 15, pancreatic insufficiency phenotype), identified by newborn screening, were compared with age-, sex-, and length-matched control subjects (n = 13). Those with the delta F508/ delta F508 genotype had significantly higher mean REE expressed per unit body weight (125%) and body cell mass (115%; p < 0.03). Those with other genotypes (n = 7) did not, as a group, have significantly different mean REEs, but individuals with known "severe" genotypes had REEs in the high range and those with a pancreatic-sufficient phenotype had significantly lower REE than those with a pancreatic-insufficient phenotype (p < 0.05), and REEs were in the normal range. Examination of bronchoalveolar lavage fluid revealed positive culture results (7/10) but variable colony counts, neutrophil percentages, and concentrations of interleukin-8 and interleukin-1 beta equally in both CF genotype groups. These markers of pulmonary inflammation were not correlated, individually or collectively, with REE or genotype. We conclude that genotypic variations in energy balance are detectable early in CF unrelated to lung inflammation. Subclinical defects in body composition and pulmonary integrity occur early in CF and, in combination with increased cellular metabolic activity, have important clinical implications with respect to early diagnosis and management.

The management of acute bronchiolitis. Thoracic Society of Australia and New Zealand

The management of acute bronchiolitis is mainly supportive, but infants require minimal handling. Of those who are hospitalized, less than 3% require intensive care and ventilation but in these children the condition is life threatening. Oxygen, fluid replacement and careful observation remain the cornerstones of management. Bronchodilators should be avoided in young infants and antiviral therapy should only be considered in critically ill infants who have an underlying cardiopulmonary condition.

Food safety and inspection service update on food safety of animals derived from biotechnology experiments

Recent progress in the field of biotechnology and the production of transgenic livestock has raised a question regarding the need for the regulation of these animals. There is also the need to regulate nontransgenic animals resulting from transgenic animal research. It is anticipated that several governmental agencies will be involved in regulatory issues pertaining to these animals. The United States Department of Agriculture (USDA), Food Safety and Inspection Service (FSIS) will ultimately be responsible for ensuring that transgenic animals intended for human consumption are wholesome, unadulterated, and properly labeled. The FSIS has implemented a program for the regulation of slaughtering nontransgenic animals resulting from transgenic animal experiments. However, the FSIS has not yet approved any transgenic livestock for slaughter. Scientists from the FSIS, in conjunction with other government agencies, are currently developing guidelines for the slaughter of transgenic animals.

Mycobacterium haemophilum causing perihilar or cervical lymphadenitis in healthy children

We describe five apparently immunologically normal children with infection caused by Mycobacterium haemophilum and resulting in perihilar or cervical lymphadenitis. Clinical distinction from Mycobacterium tuberculosis infection could be made by culture only, because differential Mantoux test results suggested tuberculosis. Treatment of these children involved chemotherapy or surgery or both, and outcome in all cases has been excellent. We believe that M. haemophilum should be added to the list of non-tuberculosis mycobacteria known to cause lymphadenitis in otherwise healthy children.

The management of acute laryngo-tracheo-bronchitis (croup): a consensus view

The management of croup relies upon the traditional clinical skills of observation and examination. Parental involvement is essential and the appropriate reassurance of the patient is important. Endotracheal intubation is required only in a small percentage of children whose airway is compromised to such a degree as to produce fatigue and/or near occlusion.

Pulmonary actinomyces in a child

Pulmonary actinomycosis is rare in Australian children. A patient with the condition is described in whom a diagnosis was made by open lung biopsy. She was treated successfully with penicillin and tetracycline.