Transcriptomics resources of human tissues and organs

Quantifying the differential expression of genes in various human organs, tissues, and cell types is vital to understand human physiology and disease. Recently, several large-scale transcriptomics studies have analyzed the expression of protein-coding genes across tissues. These datasets provide a framework for defining the molecular constituents of the human body as well as for generating comprehensive lists of proteins expressed across tissues or in a tissue-restricted manner. Here, we review publicly available human transcriptome resources and discuss body-wide data from independent genome-wide transcriptome analyses of different tissues. Gene expression measurements from these independent datasets, generated using samples from fresh frozen surgical specimens and postmortem tissues, are consistent. Overall, the different genome-wide analyses support a distribution in which many proteins are found in all tissues and relatively few in a tissue-restricted manner. Moreover, we discuss the applications of publicly available omics data for building genome-scale metabolic models, used for analyzing cell and tissue functions both in physiological and in disease contexts

Stratification of responders towards eculizumab using a structural epitope mapping strategy

The complement component 5 (C5)-binding antibody eculizumab is used to treat patients with paroxysmal nocturnal hemoglobinuria (PNH) and atypical haemolytic uremic syndrome (aHUS). As recently reported there is a need for a precise classification of eculizumab responsive patients to allow for a safe and cost-effective treatment. To allow for such stratification, knowledge of the precise binding site of the drug on its target is crucial. Using a structural epitope mapping strategy based on bacterial surface display, flow cytometric sorting and validation via haemolytic activity testing, we identified six residues essential for binding of eculizumab to C5. This epitope co-localizes with the contact area recently identified by crystallography and includes positions in C5 mutated in non-responders. The identified epitope also includes residue W917, which is unique for human C5 and explains the observed lack of cross-reactivity for eculizumab with other primates. We could demonstrate that Ornithodorus moubata complement inhibitor (OmCI), in contrast to eculizumab, maintained anti-haemolytic function for mutations in any of the six epitope residues, thus representing a possible alternative treatment for patients non-responsive to eculizumab. The method for stratification of patients described here allows for precision medicine and should be applicable to several other diseases and therapeutics

Manual for implementation or modification of child vision and hearing screening programmes:EUSCREEN

The euscreen study aimed to compare vision and hearing screening programmes for children in all EU states by using a cost-effectiveness model. The cost-effectiveness model predicts the most cost-effective and affordable way to screen children in each country, given the local circumstances. Representatives of countries in Europe were asked to provide detailed data on the following domains: demography, the general background of screening systems, existing screening systems, coverage/attendance, tests used, follow-up/diagnosis, treatment, benefits and adverse effects. Paediatric ophthalmologists, paediatric otolaryngologists, audiologists and professionals who organise and perform screening in each country were invited to participate in the study and report on the state of screening in their country. An extensive, detailed questionnaire was developed for that purpose. Screening programmes have been tested in the county of Cluj in Romania for vision, and in three counties in Albania for hearing screening. This manual for implementation or modification of child vision and hearing screening programmes was developed by detailed tracking, and from identified requisites, facilitators and barriers. The cost-effectiveness model and this manual for implementation will assist healthcare providers and policy makers worldwide in their decisions to introduce or modify vision and hearing screening programmes, and increase effectiveness, efficiency and equity of child healthcar

Manual for implementation or modification of child vision and hearing screening programmes:EUSCREEN

The euscreen study aimed to compare vision and hearing screening programmes for children in all EU states by using a cost-effectiveness model. The cost-effectiveness model predicts the most cost-effective and affordable way to screen children in each country, given the local circumstances. Representatives of countries in Europe were asked to provide detailed data on the following domains: demography, the general background of screening systems, existing screening systems, coverage/attendance, tests used, follow-up/diagnosis, treatment, benefits and adverse effects. Paediatric ophthalmologists, paediatric otolaryngologists, audiologists and professionals who organise and perform screening in each country were invited to participate in the study and report on the state of screening in their country. An extensive, detailed questionnaire was developed for that purpose. Screening programmes have been tested in the county of Cluj in Romania for vision, and in three counties in Albania for hearing screening. This manual for implementation or modification of child vision and hearing screening programmes was developed by detailed tracking, and from identified requisites, facilitators and barriers. The cost-effectiveness model and this manual for implementation will assist healthcare providers and policy makers worldwide in their decisions to introduce or modify vision and hearing screening programmes, and increase effectiveness, efficiency and equity of child healthcar

Tumour-specific HMG-CoAR is an independent predictor of recurrence free survival in epithelial ovarian cancer

<p>Abstract</p> <p>Background</p> <p>Our group previously reported that tumour-specific expression of the rate-limiting enzyme in the mevalonate pathway, 3-hydroxy-3-methylglutharyl-coenzyme A reductase (HMG-CoAR) is associated with more favourable tumour parameters and a good prognosis in breast cancer. In the present study, the prognostic value of HMG-CoAR expression was examined in tumours from a cohort of patients with primary epithelial ovarian cancer.</p> <p>Methods</p> <p>HMG-CoAR expression was assessed using immunohistochemistry (IHC) on tissue microarrays (TMA) consisting of 76 ovarian cancer cases, analysed using automated algorithms to develop a quantitative scoring model. Kaplan Meier analysis and Cox proportional hazards modelling were used to estimate the risk of recurrence free survival (RFS).</p> <p>Results</p> <p>Seventy-two tumours were suitable for analysis. Cytoplasmic HMG-CoAR expression was present in 65% (n = 46) of tumours. No relationship was seen between HMG-CoAR and age, histological subtype, grade, disease stage, estrogen receptor or Ki-67 status. Patients with tumours expressing HMG-CoAR had a significantly prolonged RFS (p = 0.012). Multivariate Cox regression analysis revealed that HMG-CoAR expression was an independent predictor of improved RFS (RR = 0.49, 95% CI (0.25-0.93); p = 0.03) when adjusted for established prognostic factors such as residual disease, tumour stage and grade.</p> <p>Conclusion</p> <p>HMG-CoAR expression is an independent predictor of prolonged RFS in primary ovarian cancer. As HMG-CoAR inhibitors, also known as statins, have demonstrated anti-neoplastic effects <it>in vitro</it>, further studies are required to evaluate HMG-CoAR expression as a surrogate marker of response to statin treatment, especially in conjunction with current chemotherapeutic regimens.</p

Scalable In Situ Hybridization on Tissue Arrays for Validation of Novel Cancer and Tissue-Specific Biomarkers

Tissue localization of gene expression is increasingly important for accurate interpretation of large scale datasets from expression and mutational analyses. To this end, we have (1) developed a robust and scalable procedure for generation of mRNA hybridization probes, providing >95% first-pass success rate in probe generation to any human target gene and (2) adopted an automated staining procedure for analyses of formalin-fixed paraffin-embedded tissues and tissue microarrays. The in situ mRNA and protein expression patterns for genes with known as well as unknown tissue expression patterns were analyzed in normal and malignant tissues to assess procedure specificity and whether in situ hybridization can be used for validating novel antibodies. We demonstrate concordance between in situ transcript and protein expression patterns of the well-known pathology biomarkers KRT17, CHGA, MKI67, PECAM1 and VIL1, and provide independent validation for novel antibodies to the biomarkers BRD1, EZH2, JUP and SATB2. The present study provides a foundation for comprehensive in situ gene set or transcriptome analyses of human normal and tumor tissues

Association of CSF proteins with tau and amyloid β levels in asymptomatic 70-year-olds

BACKGROUND: Increased knowledge of the evolution of molecular changes in neurodegenerative disorders such as Alzheimer's disease (AD) is important for the understanding of disease pathophysiology and also crucial to be able to identify and validate disease biomarkers. While several biological changes that occur early in the disease development have already been recognized, the need for further characterization of the pathophysiological mechanisms behind AD still remains. METHODS: In this study, we investigated cerebrospinal fluid (CSF) levels of 104 proteins in 307 asymptomatic 70-year-olds from the H70 Gothenburg Birth Cohort Studies using a multiplexed antibody- and bead-based technology. RESULTS: The protein levels were first correlated with the core AD CSF biomarker concentrations of total tau, phospho-tau and amyloid beta (Aβ42) in all individuals. Sixty-three proteins showed significant correlations to either total tau, phospho-tau or Aβ42. Thereafter, individuals were divided based on CSF Aβ42/Aβ40 ratio and Clinical Dementia Rating (CDR) score to determine if early changes in pathology and cognition had an effect on the correlations. We compared the associations of the analysed proteins with CSF markers between groups and found 33 proteins displaying significantly different associations for amyloid-positive individuals and amyloid-negative individuals, as defined by the CSF Aβ42/Aβ40 ratio. No differences in the associations could be seen for individuals divided by CDR score. CONCLUSIONS: We identified a series of transmembrane proteins, proteins associated with or anchored to the plasma membrane, and proteins involved in or connected to synaptic vesicle transport to be associated with CSF biomarkers of amyloid and tau pathology in AD. Further studies are needed to explore these proteins' role in AD pathophysiology