Neurodevelopmental outcome in preterm infants with intraventricular hemorrhages: the potential of quantitative brainstem MRI.

OBJECTIVES: This retrospective study aimed to identify quantitative magnetic resonance imaging markers in the brainstem of preterm neonates with intraventricular hemorrhages. It delves into the intricate associations between quantitative brainstem magnetic resonance imaging metrics and neurodevelopmental outcomes in preterm infants with intraventricular hemorrhage, aiming to elucidate potential relationships and their clinical implications. MATERIALS AND METHODS: Neuroimaging was performed on preterm neonates with intraventricular hemorrhage using a multi-dynamic multi-echo sequence to determine T1 relaxation time, T2 relaxation time, and proton density in specific brainstem regions. Neonatal outcome scores were collected using the Bayley Scales of Infant and Toddler Development. Statistical analysis aimed to explore potential correlations between magnetic resonance imaging metrics and neurodevelopmental outcomes. RESULTS: Sixty preterm neonates (mean gestational age at birth 26.26 ± 2.69 wk; n = 24 [40%] females) were included. The T2 relaxation time of the midbrain exhibited significant positive correlations with cognitive (r = 0.538, P < 0.0001, Pearson's correlation), motor (r = 0.530, P < 0.0001), and language (r = 0.449, P = 0.0008) composite scores at 1 yr of age. CONCLUSION: Quantitative magnetic resonance imaging can provide valuable insights into neurodevelopmental outcomes after intraventricular hemorrhage, potentially aiding in identifying at-risk neonates. Multi-dynamic multi-echo sequence sequences hold promise as an adjunct to conventional sequences, enhancing the sensitivity of neonatal magnetic resonance neuroimaging and supporting clinical decision-making for these vulnerable patients.

ImmUniverse Consortium: Multi-omics integrative approach in personalized medicine for immune-mediated inflammatory diseases.

Immune mediated inflammatory diseases (IMIDs) are a heterogeneous group of debilitating, multifactorial and unrelated conditions featured by a dysregulated immune response leading to destructive chronic inflammation. The immune dysregulation can affect various organ systems: gut (e.g., inflammatory bowel disease), joints (e.g., rheumatoid arthritis), skin (e.g., psoriasis, atopic dermatitis), resulting in significant morbidity, reduced quality of life, increased risk for comorbidities, and premature death. As there are no reliable disease progression and therapy response biomarkers currently available, it is very hard to predict how the disease will develop and which treatments will be effective in a given patient. In addition, a considerable proportion of patients do not respond sufficiently to the treatment. ImmUniverse is a large collaborative consortium of 27 partners funded by the Innovative Medicine Initiative (IMI), which is sponsored by the European Union (Horizon 2020) and in-kind contributions of participating pharmaceutical companies within the European Federation of Pharmaceutical Industries and Associations (EFPIA). ImmUniverse aims to advance our understanding of the molecular mechanisms underlying two immune-mediated diseases, ulcerative colitis (UC) and atopic dermatitis (AD), by pursuing an integrative multi-omics approach. As a consequence of the heterogeneity among IMIDs patients, a comprehensive, evidence-based identification of novel biomarkers is necessary to enable appropriate patient stratification that would account for the inter-individual differences in disease severity, drug efficacy, side effects or prognosis. This would guide clinicians in the management of patients and represent a major step towards personalized medicine. ImmUniverse will combine the existing and novel advanced technologies, including multi-omics, to characterize both the tissue microenvironment and blood. This comprehensive, systems biology-oriented approach will allow for identification and validation of tissue and circulating biomarker signatures as well as mechanistic principles, which will provide information about disease severity and future disease progression. This truly makes the ImmUniverse Consortium an unparalleled approach.

Implications and pitfalls for cancer diagnostics exploiting extracellular vesicles.

Early detection of cancer in order to facilitate timely therapeutic interventions is an unsolved problem in today's clinical diagnostics. Tumors are detected so far mostly after pathological symptoms have emerged (usually already in progressed disease states), within preventive screenings, or occasionally as incidental finding. The emergence of extracellular vesicle (EV) analytics in combination with liquid biopsy sampling opened a plethora of new possibilities for the detection of tumors (and other diseases). This review gives an overview of the diversity of currently known EV species and the relevant cargo molecules representing potential biomarkers to detect, identify and characterize tumor cells. A number of molecules reported in recent years to be valuable targets for different aspects of cancer diagnostics, are presented. Furthermore, we discuss (technical) challenges and pitfalls related to the various potential applications (screening, diagnosis, prognosis, monitoring) of liquid biopsy based EV analytics, and give an outlook to possible future directions of this emerging field in oncology.

Salivary biomarkers in cardiovascular disease: An insight into the current evidence.

Cardiovascular diseases (CVDs) are the most common cause of mortality worldwide. In acute cardiovascular conditions, time is a crucial player in the outcomes of disease management. Given the ease and noninvasiveness of obtaining saliva, salivary biomarkers may provide a rapid and efficient diagnosis of CVD. Here, we reviewed the published data on the value of salivary molecules for diagnosis of CVD, especially in acute care settings. In this review, we show that some biomarkers such as salivary creatinine kinase myocardial band, C-reactive protein, troponin-1, and myoglobin exhibited promising diagnostic values that were comparable to their serum counterparts. Other molecules were also investigated and showed controversial results, including myeloperoxidase, brain natriuretic peptide, and some oxidative stress markers. Based on our review, we concluded that the clinical use of salivary biomarkers to diagnose CVD is promising; however, it is still in the early stage of development. Further studies are needed to validate these findings, determine cutoff values for diagnosis, and compare them to other established biomarkers currently in clinical use.

Multiplexed and Sensitive DNA Methylation Testing Using Methylation-Sensitive Restriction Enzymes "MSRE-qPCR".

DNA methylation is a chemically stable key-player in epigenetics. In the vertebrate genome the 5-methyl cytosine (5mC) has been found almost exclusively in the CpG dinucleotide context. CpG dinucleotides are enriched in CpG islands very frequently located within or close to gene promoters. Analyses of DNA methylation changes in human diagnostics have been conducted classically using methylation-sensitive restriction enzymes (MSRE). Since the discovery of bisulfite conversion-based sequencing and PCR assays, MSRE-based PCR assays have been less frequently used, although especially in the field of cancer epigenetics MSRE-based genome-wide discovery and targeted screening applications have been and are still performed successfully. Even though epigenome-wide discovery of altered DNA methylation patterns has found its way into various fields of human disease and molecular genetics research, the validation of findings upon discovery is still a bottleneck. Usually several multiples of 10 up to 100 candidate biomarkers from discovery have to be confirmed or are of interest for further work. In particular, bisulfite PCR assays are often limited in the number of candidates which can be analyzed, due to their low multiplexing capability, especially, if only small amounts of DNA are available from for example clinical specimens. In clinical research and diagnostics a similar situation arises for the analyses of cell-free DNA (cfDNA) in body fluids or circulating tumor cells (CTCs). Although tissue- or disease- (e.g., cancer) specific DNA methylation patterns can be deduced very efficiently in a genome-wide manner if around 100 ng of DNA are available, confirming these candidates and selecting target-sequences for studying methylation changes in liquid biopsies using cfDNA or CTCs remains a big challenge. Along these lines we have developed MSRE-qPCR and introduce here method details, which have been found very suitable for the efficient confirmation and testing of DNA methylation in a quantitative multiplexed manner (e.g., 48-96 plex) from ng amounts of DNA. The method is applicable in a standard qPCR setting as well for nanoliter scaled high-throughput qPCR, enabling detection of <10 copies of targets, thus suitable to pick up 0.1-1% of specific methylated DNA in an unmethylated background.

Plasmonic Hepatitis B Biosensor for the Analysis of Clinical Saliva.

A biosensor for the detection of hepatitis B antibodies in clinical saliva was developed. Compared to conventional analysis of blood serum, it offers the advantage of noninvasive collection of samples. Detection of biomarkers in saliva imposes two major challenges associated with the low analyte concentration and increased surface fouling. The detection of minute amounts of hepatitis B antibodies was performed by plasmonically amplified fluorescence sandwich immunoassay. To have access to specific detection, we prevented the nonspecific adsorption of biomolecules present in saliva by brushes of poly[(N-(2-hydroxypropyl) methacrylamide)-co-(carboxybetaine methacrylamide)] grafted from the gold sensor surface and post modified with hepatitis B surface antigen. Obtained results were validated against the response measured with ELISA at a certified laboratory using serum from the same patients.

High-k Dielectric Passivation: Novel Considerations Enabling Cell Specific Lysis Induced by Electric Fields.

A better understanding of the electrodynamic behavior of cells interacting with electric fields would allow for novel scientific insights and would lead to the next generation of cell manipulation, diagnostics, and treatment. Here, we introduce a promising electrode design by using metal oxide high-k dielectric passivation. The thermally generated dielectric passivation layer enables efficient electric field coupling to the fluid sample comprising cells while simultaneously decoupling the electrode ohmically from the electrolyte, allowing for better control and adjustability of electric field effects due to reduced electrochemical reactions at the electrode surface. This approach demonstrates cell-size specific lysis with electric fields in a microfluidic flow-through design resulting in 99.8% blood cell lysis at 6 s exposure without affecting the viability of Gram-positive and Gram-negative bacterial spike-ins. The advantages of this new approach can support next-generation investigations of electrodynamics in biological systems and their exploitation for cell manipulation in multiple fields of medicine, life science, and industry.

Hepatitis B plasmonic biosensor for the analysis of clinical serum samples.

A plasmonic biosensor for rapid detection of protein biomarkers in complex media is reported. Clinical serum samples were analyzed by using a novel biointerface architecture based on poly[(N-(2-hydroxypropyl) methacrylamide)-co-(carboxybetaine methacrylamide)] brushes functionalized with bioreceptors. This biointerface provided an excellent resistance to fouling even after the functionalization and allowed for the first time the direct detection of antibodies against hepatitis B surface antigen (anti-HBs) in clinical serum samples using surface plasmon resonance (SPR). The fabricated SPR biosensor allowed discrimination of anti-HBs positive and negative clinical samples in 10min. Results are validated by enzyme-linked immunoassays of the sera in a certified laboratory. The sensor could be regenerated by simple treatment with glycine buffer.

Multiplex characterization of human pathogens including species and antibiotic-resistance gene identification.

The efficient medical treatment of infections requires detailed information about the pathogens involved and potential antibiotic-resistance mechanisms. The dramatically increasing incidence of multidrug-resistant bacteria especially highlights the importance of sophisticated diagnostic tests enabling a fast patient-customized therapy. However, the current molecular detection methods are limited to either the detection of species or only a few antibiotic-resistance genes.In this work, we present a human pathogen characterization assay using a rRNA gene microarray identifying 75 species comprising bacteria and fungi. A statistical classifier was developed to facilitate the automated species identification. Additionally, the clinically most important ß-lactamases were identified simultaneously in a 100-plex reaction using padlock probes and the same microarray. The specificity and sensitivity of the combined assay was determined using clinical isolates. The detection limit was 10(5) c.f.u. ml(-1), recovering 89 % of the detectable ß-lactamase-encoding genes specifically. The total assay time was less than 7 hand the modular character of the antibiotic-resistance detection allows the easy integration of further genetic targets. In summary, we present a fast, highly specific and sensitive multiplex pathogen characterization assay.

Strategies for validation and testing of DNA methylation biomarkers.

DNA methylation is a stable covalent epigenetic modification of primarily CpG dinucleotides that has recently gained considerable attention for its use as a biomarker in different clinical settings, including disease diagnosis, prognosis and therapeutic response prediction. Although the advent of genome-wide DNA methylation profiling in primary disease tissue has provided a manifold resource for biomarker development, only a tiny fraction of DNA methylation-based assays have reached clinical testing. Here, we provide a critical overview of different analytical methods that are suitable for biomarker validation, including general study design considerations, which might help to streamline epigenetic marker development. Furthermore, we highlight some of the recent marker validation studies and established markers that are currently commercially available for assisting in clinical management of different cancers.

High diversity of beta-lactamases in the General Hospital Vienna verified by whole genome sequencing and statistical analysis.

The detailed analysis of antibiotic resistance mechanisms is essential for understanding the underlying evolutionary processes, the implementation of appropriate intervention strategies and to guarantee efficient treatment options. In the present study, 110 ß-lactam-resistant, clinical isolates of Enterobacteriaceae sampled in 2011 in one of Europe's largest hospitals, the General Hospital Vienna, were screened for the presence of 31 ß-lactamase genes. Twenty of those isolates were selected for whole genome sequencing (WGS). In addition, the number of ß-lactamase genes was estimated using biostatistical models. The carbapenemase genes blaKPC-2, blaKPC-3, and blaVIM-4 were identified in carbapenem-resistant and intermediate susceptible isolates, blaOXA-72 in an extended-spectrum ß-lactamase (ESBL)-positive one. Furthermore, the observed high prevalence of the acquired blaDHA-1 and blaCMY AmpC ß-lactamase genes (70%) in phenotypically AmpC-positive isolates is alarming due to their capability to become carbapenem-resistant upon changes in membrane permeability. The statistical analyses revealed that approximately 55% of all ß-lactamase genes present in the General Hospital Vienna were detected by this study. In summary, this work gives a very detailed picture on the disseminated ß-lactamases and other resistance genes in one of Europe's largest hospitals.

Multiplex detection of antibiotic resistance genes using padlock probes.

The elucidation of resistance mechanisms is of central importance to providing and maintaining efficient medical treatment. However, molecular detection methods covering the complete set of resistance genes with a single test are still missing. Here, we present a novel 100-plex assay based on padlock probes in combination with a microarray that allows the simultaneous large-scale identification of highly diverse ß-lactamases. The specificity of the assay was performed using 70 clinical bacterial isolates, recovering 98% of the ß-lactamase nucleotide sequences present. Additionally, the sensitivity was evaluated with PCR products and genomic bacterial DNA, revealing a detection limit of 10(4) DNA copies per reaction when using PCR products as the template. Pre-amplification of genomic DNA in a 25-multiplex PCR further facilitated the detection of ß-lactamase genes in dilutions of 10(7) cells/mL. In summary, we present an efficient, highly specific, and highly sensitive multiplex detection method for any gene.

Soluble ST2 is regulated by p75 neurotrophin receptor and predicts mortality in diabetic patients with critical limb ischemia.

OBJECTIVE: The p75 neurotrophin receptor (p75(NTR)) contributes to diabetes mellitus-induced defective postischemic neovascularization. The interleukin-33 receptor ST2 is expressed as transmembrane (ST2L) and soluble (sST2) isoforms. Here, we studied the following: (1) the impact of p75(NTR) in the healing of ischemic and diabetic calf wounds; (2) the link between p75(NTR) and ST2; and (3) circulating sST2 levels in critical limb ischemia (CLI) patients. METHODS AND RESULTS: Diabetes mellitus was induced in p75(NTR) knockout (p75KO) mice and wild-type (WT) littermates by streptozotocin. Diabetic and nondiabetic p75KO and WT mice received left limb ischemia induction and a full-thickness wound on the ipsilateral calf. Diabetes mellitus impaired wound closure and angiogenesis and increased ST2 expression in WT, but not in p75KO wounds. In cultured endothelial cells, p75(NTR) promoted ST2 (both isoforms) expression through p38(MAPK)/activating transcription factor 2 pathway activation. Next, sST2 was measured in the serum of patients with CLI undergoing either revascularization or limb amputation and in the 2 nondiabetic groups (with CLI or nonischemic individuals). Serum sST2 increased in diabetic patients with CLI and was directly associated with higher mortality at 1 year from revascularization. CONCLUSIONS: p75(NTR) inhibits the healing of ischemic lower limb wounds in diabetes mellitus and promotes ST2 expression. Circulating sST2 predicts mortality in diabetic CLI patients.

Establishment of a semi-automated pathogen DNA isolation from whole blood and comparison with commercially available kits.

Molecular methods for bacterial pathogen identification are gaining increased importance in routine clinical diagnostic laboratories. Achieving reliable results using DNA based technologies is strongly dependent on pre-analytical processes including isolation of target cells and their DNA of high quality and purity. In this study a fast and semi-automated method was established for bacterial DNA isolation from whole blood samples and compared to different commercially available kits: Looxster, MolYsis kit, SeptiFast DNA isolation method and standard EasyMAG protocol. The newly established, semi-automated method utilises the EasyMAG device combined with pre-processing steps comprising human cell lysis, centrifugation and bacterial pellet resuspension. Quality of DNA was assessed by a universal PCR targeting the 16S rRNA gene and subsequent microarray hybridisation. The DNA extractions were amplified using two different PCR-mastermixes, to allow comparison of a commercial mastermix with a guaranteed bacterial DNA free PCR mastermix. The modified semi-automated EasyMAG protocol and the Looxster kit gave the most sensitive results. After hybridisation a detection limit of 10(1) to 10(2) bacterial cells per mL whole blood was achieved depending on the isolation method and microbial species lysed. Human DNA present in the isolated DNA suspension did not interfere with PCR and did not lead to non-specific hybridisation events.

DNA microarrays provide new options for allergen testing.

Microarray studies are increasingly used for toxicological research and even for the development of new toxicological test methods. Since gene-expression changes in cultured cells can be conveniently measured with microarrays, this method might be of use for in vitro toxicity testing, for example, in the field of contact sensitization. Allergic contact dermatitis, the clinical manifestation of contact sensitization, may occur when sensitizing chemicals enter the skin and get in contact with epidermal and dermal antigen-presenting cells. The resulting maturation process in these cells can be measured by employing gene-expression analysis. Biomarkers currently known seem to be insufficient to identify all kinds of contact sensitizers, which may partly activate different signaling pathways (e.g., metal or organic sensitizers). Therefore, genome-wide screenings using whole-genome DNA microarrays and extensive data analysis can be performed in order to identify additional genes. Ultimately, marker genes detected in whole-genome experiments can be included in small-scale-targeted microarrays in order to establish the final test method.

RGG: a general GUI Framework for R scripts.

BACKGROUND: R is the leading open source statistics software with a vast number of biostatistical and bioinformatical analysis packages. To exploit the advantages of R, extensive scripting/programming skills are required. RESULTS: We have developed a software tool called R GUI Generator (RGG) which enables the easy generation of Graphical User Interfaces (GUIs) for the programming language R by adding a few Extensible Markup Language (XML) - tags. RGG consists of an XML-based GUI definition language and a Java-based GUI engine. GUIs are generated in runtime from defined GUI tags that are embedded into the R script. User-GUI input is returned to the R code and replaces the XML-tags. RGG files can be developed using any text editor. The current version of RGG is available as a stand-alone software (RGGRunner) and as a plug-in for JGR. CONCLUSION: RGG is a general GUI framework for R that has the potential to introduce R statistics (R packages, built-in functions and scripts) to users with limited programming skills and helps to bridge the gap between R developers and GUI-dependent users. RGG aims to abstract the GUI development from individual GUI toolkits by using an XML-based GUI definition language. Thus RGG can be easily integrated in any software. The RGG project further includes the development of a web-based repository for RGG-GUIs. RGG is an open source project licensed under the Lesser General Public License (LGPL) and can be downloaded freely at (http://rgg.r-forge.r-project.org).

PCR-based analysis of differentially methylated regions of GNAS enables convenient diagnostic testing of pseudohypoparathyroidism type Ib.

BACKGROUND: Pseudohypoparathyroidism type Ib (PHPIb) is characterized by parathyroid hormone (PTH) resistance, which can lead to hypocalcemia, hyperphosphatemia, and increased serum PTH. The disorder is caused by mutations in regulatory regions of the GNAS gene (GNAS complex locus) that lead to interferences in the methylation status of alternative GNAS promoters, such as exon A/B, NESP55, and XL alpha-s. PHPIb comprises disorders that show distinctive changes in methylation status but share the same clinical phenotype: (a) loss of methylation only at exon A/B of the GNAS gene and involving no other obvious epigenetic abnormalities [e.g., those caused by heterozygous microdeletions in the STX16 (syntaxin 16) region and found in many patients with autosomal dominant (AD) PHPIb]; (b) methylation abnormalities at several differentially methylated regions (DMRs), which are observed in most patients with sporadic PHPIb and some families with AD PHPIb. METHODS: To permit early and reliable diagnosis of suspected PHPIb, we designed methylation-sensitive restriction enzyme-based and bisulfite deamination-based PCR tests for exon A/B and NESP55 DMRs. RESULTS: Both PCR strategies permit proper methylation testing of GNAS and NESP55 DMRs and elucidate different disease subtypes. We have identified a novel microsatellite repeat polymorphism within GNAS exon A/B, and pedigree analyses have shown its presence to be conclusive evidence for familial disease. CONCLUSIONS: We provide a simple diagnostic test for PHPIb, an imprinting disorder caused by different molecular changes within the GNAS complex locus. PHPIb, a complex and diagnostically challenging clinical phenotype, can be treated successfully by taking steps before the manifestation of symptoms to avoid clinical complications in affected patients or asymptomatic members of affected families who show positive results in genetic tests.

Microarray-based in vitro test system for the discrimination of contact allergens and irritants: identification of potential marker genes.

BACKGROUND: Animal tests have been used to characterize the potential of chemicals to produce allergic contact dermatitis, but this approach is increasingly a matter of public and political concern. Our aim was to develop and validate an alternative in vitro test that can identify contact allergens. METHODS: We developed a targeted microarray containing oligonucleotide probes for 66 immune-relevant genes and analyzed gene expression in monocyte-derived dendritic cells (Mo-DCs) treated with 1 irritant (SDS) and 2 prominent contact allergens, nickel and Bandrowski's base (BB), which is the oxidation product of the most important hair dye allergen, p-phenylenediamine. RESULTS: Comparing RNA amounts in chemical-treated and solvent-treated cells, we identified significant changes in the expression of 21 genes and 10 genes after exposure of immature DCs (iDCs) to nickel and BB, respectively, but not after exposure to SDS. Eight genes were differentially expressed after application of both nickel and BB. Real-time PCR was used to confirm the results for selected genes. CONCLUSION: We propose a microarray-based in vitro test that might allow the identification of contact allergens. Independently from donor variability, several immune-relevant genes were up- or downregulated after the application of the tested sensitizers to iDCs, therefore presenting potential marker genes. While reducing the number of laboratory animals used, this test would also enable reliable analysis of chemicals using a human system.

Consensus genes of the literature to predict breast cancer recurrence.

BACKGROUND: Extensive efforts have been undertaken to discover genes relevant for breast cancer prognosis. Yet, in current opinion, with little overlap in findings. We aimed to reanalyze molecular prediction of breast cancer recurrence. METHODS: From 44 published gene lists relevant for breast cancer prognosis, we extracted 374 genes, which, besides other quality criteria, are recorded at least twice. From eight published microarray datasets, a single dataset of 1,067 breast cancer patients was created, using transformation to 'probability of expression' scale. For recurrence analysis, the Cox proportional hazards model was applied. RESULTS: The 374 genes, termed '374 Gene Set', are highly enriched in cell cycle genes. The '374 Gene Set' is significantly associated with breast cancer recurrence (p = 2 x 10(-12), log-rank test) in the meta set of 1,067 patients, showing an estimated Hazard Ratio of recurrence for the 'poor' prognosis group compared to the 'good' prognosis group of 2.03 (95% confidence interval, 1.66-2.48). Notably, the '374 Gene Set' is significantly associated with recurrence in untreated patients. In multivariate analysis, including the standard histopathological parameters, only tumor size and the '374 Gene Set' remain independent predictors of recurrence. External validation further confirmed the prognostic relevance of the gene set (253 patients, p = 0.001, log-rank test). CONCLUSIONS: The '374 Gene Set' comprises a molecular basis of metastatic breast cancer progression. Starting from this gene set it might be possible to construct a clinically relevant classifier, which then again needs to be validated.