Massively parallel and multiplex blood group genotyping using next-generation-sequencing

OBJECTIVES

Thirty-six blood group systems are listed by the International Society of Blood Transfusion, containing almost 350 antigens. Most of these result from a single nucleotide polymorphism (SNP). Serology is the standard method for blood group typing. However, this technique has some limitations and cannot respond to the growing demand of blood product typing for a large number of antigens. Here we describe a blood group genotyping assay directly from whole blood samples using Next-Generation Sequencing (NGS), allowing the simultaneous identification of 15 SNPs associated with the blood group systems of 95 patients in a single run.

DESIGN AND METHOD

After an automated DNA extraction, targets are amplified by multiplex polymerase chain reaction (PCRm). Two panels addressing 9 groups have been developed (MNS, Lutheran, Kell, Duffy, Kidd, Diego, Yt, Dombrock, and Colton), one for 8 SNPs, the other for 7 SNPs. For each sample, both panels corresponding to 14 amplicons (1 amplicon containing 2 SNPs) are pooled. Then a dual-indexed library is generated from each pool by linking Illumina adaptors directly onto amplicons, followed by sequencing using the MiSeq platform (Illumina).

RESULTS

In a single experiment, 95 blood donor samples have been sequenced for the genes of interest. Among the 1425 targeted single nucleotide polymorphisms, 1420 were identified by sequencing, reflecting a coverage of 99.65%. The obtained data shows a good correlation (99% for all SNPs) with other blood group typing methods. Depending on the allele pairs analyzed, correlations vary between 97.12 and 100%.

CONCLUSION

Next-Generation sequencing would supplement serological and molecular techniques and, in the near future, could replace it with complete and fast results acquisition for pre-screening and identification of rare blood bags.

A novel framework for biomedical entity sense induction

BACKGROUND

Rapid advancements in biomedical research have accelerated the number of relevant electronic documents published online, ranging from scholarly articles to news, blogs, and user-generated social media content. Nevertheless, the vast amount of this information is poorly organized, making it difficult to navigate. Emerging technologies such as ontologies and knowledge bases (KBs) could help organize and track the information associated with biomedical research developments. A major challenge in the automatic construction of ontologies and KBs is the identification of words with its respective sense(s) from a free-text corpus. Word-sense induction (WSI) is a task to automatically induce the different senses of a target word in the different contexts. In the last two decades, there have been several efforts on WSI. However, few methods are effective in biomedicine and life sciences.

METHODS

We developed a framework for biomedical entity sense induction using a mixture of natural language processing, supervised, and unsupervised learning methods with promising results. It is composed of three main steps: (1) a polysemy detection method to determine if a biomedical entity has many possible meanings; (2) a clustering quality index-based approach to predict the number of senses for the biomedical entity; and (3) a method to induce the concept(s) (i.e., senses) of the biomedical entity in a given context.

RESULTS

To evaluate our framework, we used the well-known MSH WSD polysemic dataset that contains 203 annotated ambiguous biomedical entities, where each entity is linked to 2-5 concepts. Our polysemy detection method obtained an F-measure of 98%. Second, our approach for predicting the number of senses achieved an F-measure of 93%. Finally, we induced the concepts of the biomedical entities based on a clustering algorithm and then extracted the keywords of reach cluster to represent the concept.

CONCLUSIONS

We have developed a framework for biomedical entity sense induction with promising results. Our study results can benefit a number of downstream applications, for example, help to resolve concept ambiguities when building Semantic Web KBs from biomedical text.

Down-expression of P2RX2, KCNQ5, ERBB3 and SOCS3 through DNA hypermethylation in elderly women with presbycusis

CONTEXT

Presbycusis, an age-related hearing impairment (ARHI), represents the most common sensory disability in adults. Today, the molecular mechanisms underlying presbycusis remain unclear. This is in particular due to the fact that ARHI is a multifactorial complex disorder resulting from several genomic factors interacting with lifelong cumulative effects of: disease, diet, and environment.

OBJECTIVE

Identification of novel biomarkers for presbycusis.

MATERIALS AND METHODS

We selectively ascertained 18 elderly unrelated women lacking environmental and metabolic risk factors. Subsequently, we screened for methylation map changes in blood samples of women with presbycusis as compared to controls, using reduced representation bisulfite sequencing. We focused on hypermethylated cytosine bases located in gene promoters and the first two exons. To elucidate the related gene expression changes, we performed transcriptomic study using gene expression microarray.

RESULTS

Twenty-seven genes, known to be expressed in adult human cochlea, were found in the blood cells to be differentially hypermethylated with significant (p < 0.01) methylation differences (>30%) and down-expressed with fold change >1.2 (FDR <0.05). Functional annotation and qRT-PCR further identified P2RX2, KCNQ5, ERBB3 and SOCS3 to be associated with the progression of ARHI.

DISCUSSION AND CONCLUSION

Down-expressed genes associated with DNA hypermethylation could be used as biomarkers for understanding complex pathogenic mechanisms underlying presbycusis.

MicroRNAs in pituitary tumors

Since the presence of microRNAs was first observed in normal pituitary, the majority of scientific publications addressing their role and the function of microRNAs in the pituitary have been based on pituitary tumor studies. In this review, we briefly describe the involvement of microRNAs in the synthesis of pituitary hormones and we present a comprehensive inventory of microRNA suppressors and inducers of pituitary tumors. Finally, we summarize the functional role of microRNAs in tumorigenesis, progression and aggressiveness of pituitary tumors, mechanisms contributing to the regulation (transcription factors, genomic modifications or epigenetic) or modulation (pharmacological treatment) of microRNAs in these tumors, and the interest of thoroughly studying the expression of miRNAs in body fluids.

Hepatitis E virus mutations associated with ribavirin treatment failure result in altered viral fitness and ribavirin sensitivity

BACKGROUND & AIMS

Ribavirin monotherapy is the preferred treatment for chronic hepatitis E, although occasional treatment failure occurs. We present a patient with chronic hepatitis E experiencing ribavirin treatment failure with a completely resistant phenotype. We aimed to identify viral mutations associated with treatment failure and explore the underlying mechanisms.

METHODS

Viral genomes were deep-sequenced at different time points and the role of identified mutations was assessed in vitro using mutant replicons, antiviral assays, cell culture of patient-derived virus and deep-sequencing.

RESULTS

Ribavirin resistance was associated with Y1320H, K1383N and G1634R mutations in the viral polymerase, but also an insertion in the hypervariable region comprising a duplication and a polymerase-derived fragment. Analysis of these genome alterations in vitro revealed replication-increasing roles for Y1320H and G1634R mutations and the hypervariable region insertion. In contrast, the K1383N mutation in the polymerase F1-motif suppressed viral replication and increased the in vitro sensitivity to ribavirin, contrary to the clinical phenotype. Analysis of the replication of mutant full-length virus and in vitro culturing of patient-derived virus confirmed that sensitivity to ribavirin was retained. Finally, deep-sequencing of hepatitis E virus genomes revealed that ribavirin is mutagenic to viral replication in vitro and in vivo.

CONCLUSIONS

Mutations Y1320H, G1634R and the hypervariable region insertion compensated for K1383N-associated replication defects. The specific role of the K1383N mutation remains enigmatic, but it appears to be of importance for the ribavirin resistant phenotype in this patient.

LAY SUMMARY

Ribavirin is the most common treatment for chronic hepatitis E and is mostly effective, although some cases of ribavirin treatment failure have been described. Here, we report on a particular case of ribavirin resistance and investigate the underlying causes of treatment failure. Mutations in the viral polymerase, an essential enzyme for viral replication, appear to be responsible.

Distinctive effects of eicosapentaenoic and docosahexaenoic acids in regulating neural stem cell fate are mediated via endocannabinoid signalling pathways

Emerging evidence suggests a complex interplay between the endocannabinoid system, omega-3 fatty acids and the immune system in the promotion of brain self-repair. However, it is unknown if all omega-3 fatty acids elicit similar effects on adult neurogenesis and if such effects are mediated or regulated by interactions with the endocannabinoid system. This study investigated the effects of DHA and EPA on neural stem cell (NSC) fate and the role of the endocannabinoid signalling pathways in these effects. EPA, but not DHA, significantly increased proliferation of NSCs compared to controls, an effect associated with enhanced levels of the endocannabinoid 2-arachidonylglycerol (2-AG) and p-p38 MAPK, effects attenuated by pre-treatment with CB1 (AM251) or CB2 (AM630) receptor antagonists. Furthermore, in NSCs derived from IL-1β deficient mice, EPA significantly decreased proliferation and p-p38 MAPK levels compared to controls, suggesting a key role for IL-1β signalling in the effects observed. Although DHA similarly increased 2-AG levels in wild-type NSCs, there was no concomitant increase in proliferation or p-p38 MAPK activity. In addition, in NSCs from IL-1β deficient mice, DHA significantly increased proliferation without effects on p-P38 MAPK, suggesting effects of DHA are mediated via alternative signalling pathways. These results provide crucial new insights into the divergent effects of EPA and DHA in regulating NSC proliferation and the pathways involved, and highlight the therapeutic potential of their interplay with endocannabinoid signalling in brain repair.

Angular roughshark Oxynotus centrina (Squaliformes: Oxynotidae) in captivity feeding exclusively on elasmobranch eggs: an overlooked feeding niche or a matter of individual taste?

A specimen of angular roughshark Oxynotus centrina has been kept successfully in captivity for the first time. Over a period of 24 months, the specimen preyed exclusively on the contents of elasmobranch egg cases, suggesting a specialized trophic niche.

Survival in patients with primary liver cancer, gallbladder and extrahepatic biliary tract cancer and pancreatic cancer in Europe 1999-2007: Results of EUROCARE-5

BACKGROUND

The EUROCARE study collects and analyses survival data from population-based cancer registries (CRs) in Europe in order to provide data on between-country differences in survival and time trends in survival.

METHODS

This study analyses data on liver cancer, gallbladder and extrahepatic biliary tract cancers ("biliary tract cancers"), and pancreatic cancer diagnosed in 2000-2007 from 88 CRs in 29 countries. Relative survival (RS) was estimated overall, by region, sex, age and period of diagnosis using the complete approach. Time trends in 5-year RS over 1999-2007 were also analysed using the period approach.

RESULTS

The prognosis of the studied cancers was poor. Age-standardised 5-year RS was 12% for liver cancer, 17% for biliary tract cancers and 7% for pancreatic cancer. There were some between-country differences in survival. In general, RS was low in Eastern Europe and high in Central and Southern Europe. For all sites, 5-year RS was similar in men and women and decreased with advancing age. No substantial changes in survival were reported for pancreatic cancer over the period 1999-2007. On average, there was a crude increase in 5-year RS of 3 percentage points between the periods 1999-2001 and 2005-2007 for liver cancer and biliary tract cancers.

CONCLUSIONS

The major changes in imaging techniques over the study period for the diagnosis of the three studied cancers did not result in an improvement in the prognosis of these cancers. In the near future, new innovative treatments might be the best way to improve the prognosis in these cancers.

[Pathomimia and plastic surgery, a case report]

Pathomimia is defined as a dummy pathology self-induced deliberately and is neither associated with mental confusion nor disturbance of consciousness. This article reports a case of pathomimia in plastic surgery. One of our patients had intentionally injected physiological saline solution into her breast implants in order to increase their volume. Implants removal was necessary because of severe local inflammatory signs. Psychiatric assessment revealed body dysmorphic disorder (BDD) developed on an hysterical personality, which explained the self-induced injuries. This nosologic entity must be promptly identified because it's diagnosis remains problematic and a multidisciplinary medical management is essential.

Deregulation of miR-183 and KIAA0101 in Aggressive and Malignant Pituitary Tumors

Changes in microRNAs (miRNAs) expression in many types of cancer suggest that they may be involved in crucial steps during tumor progression. Indeed, miRNAs deregulation has been described in pituitary tumorigenesis, but few studies have described their role in pituitary tumor progression toward aggressiveness and malignancy. To assess the role of miRNAs within the hierarchical cascade of events in prolactin (PRL) tumors during progression, we used an integrative genomic approach to associate clinical-pathological features, global miRNA expression, and transcriptomic profiles of the same human tumors. We describe the specific down-regulation of one principal miRNA, miR-183, in the 8 aggressive (A, grade 2b) compared to the 18 non-aggressive (NA, grades 1a, 2a) PRL tumors. We demonstrate that it acts as an anti-proliferative gene by directly targeting KIAA0101, which is involved in cell cycle activation and inhibition of p53-p21-mediated cell cycle arrest. Moreover, we show that miR-183 and KIAA0101 expression significantly correlate with the main markers of pituitary tumors aggressiveness, Ki-67 and p53. These results confirm the activation of proliferation in aggressive and malignant PRL tumors compared to non-aggressive ones. Importantly, these data also demonstrate the ability of such an integrative genomic strategy, applied in the same human tumors, to identify the molecular mechanisms responsible for tumoral progression even from a small cohort of patients.

A role for PPARα in the medial prefrontal cortex in formalin-evoked nociceptive responding in rats

BACKGROUND AND PURPOSE

The nuclear hormone receptor, PPARα, and its endogenous ligands, are involved in pain modulation. PPARα is expressed in the medial prefrontal cortex (mPFC), a key brain region involved in both the cognitive-affective component of pain and in descending modulation of pain. However, the role of PPARα in the mPFC in pain responding has not been investigated. Here, we investigated the effects of pharmacological modulation of PPARα in the rat mPFC on formalin-evoked nociceptive behaviour and the impact of formalin-induced nociception on components of PPARα signalling in the mPFC.

EXPERIMENTAL APPROACH

The effects of intra-mPFC microinjection of a PPARα agonist (GW7647) or a PPARα antagonist (GW6471) on formalin-evoked nociceptive behaviour in rats were studied. Quantitative real-time PCR and LC-MS/MS were used to study the effects of intraplantar injection of formalin on PPARα mRNA expression and levels of endogenous ligands, respectively, in the mPFC.

KEY RESULTS

Intra-mPFC administration of GW6471, but not GW7647, resulted in delayed onset of the early second phase of formalin-evoked nociceptive behaviour. Furthermore, formalin-evoked nociceptive behaviour was associated with significant reductions in mPFC levels of endogenous PPARα ligands (N-palmitoylethanolamide and N-oleoylethanolamide) and a 70% reduction in PPARα mRNA but not protein expression.

CONCLUSIONS AND IMPLICATIONS

These data suggest that endogenous ligands may act at PPARα in the mPFC to play a facilitatory/permissive role in second phase formalin-evoked nociceptive behaviour in rats.

LINKED ARTICLES

This article is part of a themed section on Cannabinoids 2013. To view the other articles in this section visit http://dx.doi.org/10.1111/bph.2014.171.issue-6.

The monoacylglycerol lipase inhibitor JZL184 attenuates LPS-induced increases in cytokine expression in the rat frontal cortex and plasma: differential mechanisms of action

BACKGROUND AND PURPOSE

JZL184 is a selective inhibitor of monoacylglycerol lipase (MAGL), the enzyme that preferentially catabolizes the endocannabinoid 2-arachidonoyl glycerol (2-AG). Here, we have studied the effects of JZL184 on inflammatory cytokines in the brain and plasma following an acute immune challenge and the underlying receptor and molecular mechanisms involved.

EXPERIMENTAL APPROACH

JZL184 and/or the CB₁ receptor antagonist, AM251 or the CB₂ receptor antagonist, AM630 were administered to rats 30 min before lipopolysaccharide (LPS). 2 h later cytokine expression and levels, MAGL activity, 2-AG, arachidonic acid and prostaglandin levels were measured in the frontal cortex, plasma and spleen.

KEY RESULTS

JZL184 attenuated LPS-induced increases in IL-1β, IL-6, TNF-α and IL-10 but not the expression of the inhibitor of NFkB (IκBα) in rat frontal cortex. AM251 attenuated JZL184-induced decreases in frontal cortical IL-1β expression. Although arachidonic acid levels in the frontal cortex were reduced in JZL184-treated rats, MAGL activity, 2-AG, PGE₂ and PGD₂ were unchanged. In comparison, MAGL activity was inhibited and 2-AG levels enhanced in the spleen following JZL184. In plasma, LPS-induced increases in TNF-α and IL-10 levels were attenuated by JZL184, an effect partially blocked by AM251. In addition, AM630 blocked LPS-induced increases in plasma IL-1β in the presence, but not absence, of JZL184.

CONCLUSION AND IMPLICATIONS

Inhibition of peripheral MAGL in rats by JZL184 suppressed LPS-induced circulating cytokines that in turn may modulate central cytokine expression. The data provide further evidence for the endocannabinoid system as a therapeutic target in treatment of central and peripheral inflammatory disorders.