Molecular mechanistic associations of human diseases

<p>Abstract</p> <p>Background</p> <p>The study of relationships between human diseases provides new possibilities for biomedical research. Recent achievements on human genetic diseases have stimulated interest to derive methods to identify disease associations in order to gain further insight into the network of human diseases and to predict disease genes.</p> <p>Results</p> <p>Using about 10000 manually collected causal disease/gene associations, we developed a statistical approach to infer meaningful associations between human morbidities. The derived method clustered cardiometabolic and endocrine disorders, immune system-related diseases, solid tissue neoplasms and neurodegenerative pathologies into prominent disease groups. Analysis of biological functions confirmed characteristic features of corresponding disease clusters. Inference of disease associations was further employed as a starting point for prediction of disease genes. Efforts were made to underpin the validity of results by relevant literature evidence. Interestingly, many inferred disease relationships correspond to known clinical associations and comorbidities, and several predicted disease genes were subjects of therapeutic target research.</p> <p>Conclusions</p> <p>Causal molecular mechanisms present a unifying principle to derive methods for disease classification, analysis of clinical disorder associations, and prediction of disease genes. According to the definition of causal disease genes applied in this study, these results are not restricted to genetic disease/gene relationships. This may be particularly useful for the study of long-term or chronic illnesses, where pathological derangement due to environmental or as part of sequel conditions is of importance and may not be fully explained by genetic background.</p

Cyanobacterial lipopolysaccharides and human health – a review

Cyanobacterial lipopolysaccharide/s (LPS) are frequently cited in the cyanobacteria literature as toxins responsible for a variety of heath effects in humans, from skin rashes to gastrointestinal, respiratory and allergic reactions. The attribution of toxic properties to cyanobacterial LPS dates from the 1970s, when it was thought that lipid A, the toxic moiety of LPS, was structurally and functionally conserved across all Gram-negative bacteria. However, more recent research has shown that this is not the case, and lipid A structures are now known to be very different, expressing properties ranging from LPS agonists, through weak endotoxicity to LPS antagonists. Although cyanobacterial LPS is widely cited as a putative toxin, most of the small number of formal research reports describe cyanobacterial LPS as weakly toxic compared to LPS from the Enterobacteriaceae. We systematically reviewed the literature on cyanobacterial LPS, and also examined the much lager body of literature relating to heterotrophic bacterial LPS and the atypical lipid A structures of some photosynthetic bacteria. While the literature on the biological activity of heterotrophic bacterial LPS is overwhelmingly large and therefore difficult to review for the purposes of exclusion, we were unable to find a convincing body of evidence to suggest that heterotrophic bacterial LPS, in the absence of other virulence factors, is responsible for acute gastrointestinal, dermatological or allergic reactions via natural exposure routes in humans. There is a danger that initial speculation about cyanobacterial LPS may evolve into orthodoxy without basis in research findings. No cyanobacterial lipid A structures have been described and published to date, so a recommendation is made that cyanobacteriologists should not continue to attribute such a diverse range of clinical symptoms to cyanobacterial LPS without research confirmation

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Prognostic significance and phenotypic manifestations of MYC/BCL2 protein expression in diffuse large B-cell lymphoma (DLBCL) with extranodal organ involvement: a report of the International DLBCL Rituximab-CHOP Consortium Program Study

This journal issue is proceedings of ASH Conference 2012Open Access JournalOral Sessions - 622. Non-Hodgkin Lymphoma - Biology, excluding Therapy: MYC And Others, The Usual SuspectsBACKGROUND: In DLBCL, multiple extranodal sites of involvement and MYC/BCL2 translocations (double hit lymphoma) are associated with a poor clinical outcome. The association between the pattern of extranodal involvement and MYC and BCL2 protein expression, as well as the prognostic significance of expression, are unknown. METHODS: We analyzed the clinical data of 487 DLBCL patients treated with R-CHOP. Immunohistochemical (IHC) studies were performed on paraffin-embedded tissue samples for MYC and BCL2. A double-hit score (DHS) of 0, 1, or 2 was assigned to all patients based on protein expression of MYC and BCL2. Those with both MYC and BCL2 expression were DHS 2, with MYC or BCL2 was DHS 1, and neither was DHS 0. Cell-of-origin classification was achieved by combining gene expression profiling (GEP) and IHC data with GEP as the gold standard. Patient characteristics were compared using Fisher's exact test. Survival analyses were performed using Kaplan-Meier curves and compared using log-rank test. The Cox proportional regression model was used for mult…link_to_OA_fulltex

Prognostic significance and phenotypic manifestations of MYC/BCL2 protein expression in diffuse large B-cell lymphoma (DLBCL) with extranodal organ involvement: a report of the International DLBCL Rituximab-CHOP Consortium Program Study

This journal issue is proceedings of ASH Conference 2012Open Access JournalOral Sessions - 622. Non-Hodgkin Lymphoma - Biology, excluding Therapy: MYC And Others, The Usual SuspectsBACKGROUND: In DLBCL, multiple extranodal sites of involvement and MYC/BCL2 translocations (double hit lymphoma) are associated with a poor clinical outcome. The association between the pattern of extranodal involvement and MYC and BCL2 protein expression, as well as the prognostic significance of expression, are unknown. METHODS: We analyzed the clinical data of 487 DLBCL patients treated with R-CHOP. Immunohistochemical (IHC) studies were performed on paraffin-embedded tissue samples for MYC and BCL2. A double-hit score (DHS) of 0, 1, or 2 was assigned to all patients based on protein expression of MYC and BCL2. Those with both MYC and BCL2 expression were DHS 2, with MYC or BCL2 was DHS 1, and neither was DHS 0. Cell-of-origin classification was achieved by combining gene expression profiling (GEP) and IHC data with GEP as the gold standard. Patient characteristics were compared using Fisher's exact test. Survival analyses were performed using Kaplan-Meier curves and compared using log-rank test. The Cox proportional regression model was used for mult…link_to_OA_fulltex

The t(14;18)(q32;q21) characterizes a subset of patients with diffuse large-B cell lymphoma of germinal center origin with poor outcome: report from the International DLBCL Rituximab-CHOP Consortium Program Study

Oral Sessions - 622. Non-Hodgkin Lymphoma - Biology, excluding Therapy: Clinical Determinants and MicroenvironmentOpen Access JournalThis journal issue is proceedings of ASH Conference 2011INTRODUCTION: Diffuse large B cell lymphoma (DLBCL) has a highly variable outcome, and individual risk assessment is largely based on clinical features. Gene expression profiling (GEP) stratifies patients into those with germinal center B-cell (GCB) and activated B-cell subtype (ABC) subtype with different prognoses. These groups have been shown to predict prognosis in patients treated with CHOP or R-CHOP. Conversely, the role of other recognized prognostic markers, such as BCL2 gene abnormalities or Bcl2 expression has been questioned in the new therapeutic era. MATERIALS AND METHODS: In 438 patients treated with R-CHOP for de novo DLBCL, we analyzed the tumors by immunohistochemistry for Bcl2 protein expression and by interphase fluorescence in situ hybridization (FISH) for BCL2 translocation and other abnormalities. All cases were successfully studied by GEP. The cutoff for Bcl2 protein expression, 60%, used as prognostic factor was determined using receiver operating characteristic curves. Progression-free survival (PFS) and overall survival (OS) were assessed. RESULTS: The t(14;18)(q32;q21) was detected in 82 cases (18.7%) and BCL2 gains occurred in 63 cases (14.3%). Both t(14;18) and BCL2 gains strongly correlated with higher levels of Bcl2 protein expression (p60%) tumors had significantly inferior PFS in the GCB subgroup (p=0.03), but not in the ABC subgroup (p=0.54). Multivariate analysis revealed that the presence of the t(14;18), but not Bcl2 protein expression, was independent of the International Prognostic Index in predicting outcome of our patients. CONCLUSIONS: Patients with the GCB subtype and t(14;18) exhibit a significantly worse prognosis than patients without t(14;18) when treated with R-CHOP. The assessment of t(14;18) by FISH approach not only functions as a valuable prognosticator for individual risk estimation in GCB-DLBCL patients in addition to the established parameters, but also provides valuable result for therapeutic intervention.link_to_OA_fulltex