Dataset Information

MPIC: Molecular Prognostic Indicators in Cirrhosis Database for Clinical Context-Specific in Silico Prognostic Biomarker Validation.

ABSTRACT: Prognostic biomarkers are vital in the management of progressive chronic diseases such as liver cirrhosis, affecting 1-2% of the global population and causing over 1 million deaths every year. Despite numerous candidate biomarkers in literature, the costly and lengthy process of validation hampers their clinical translation. Existing omics databases are not suitable for in silico validation due to the ignorance of critical factors, i.e., study design, clinical context of biomarker application, and statistical power. To address the unmet need, we have developed the Molecular Prognostic Indicators in Cirrhosis (MPIC) database as a representative example of an omics database tailored for prognostic biomarker validation. MPIC consists of (i) a molecular and clinical database structured by defined disease context and specific clinical outcome and annotated with employed study design and anticipated statistical power by disease domain experts, (ii) a bioinformatics analysis engine for user-provided gene-signature- or gene-based prognostic prediction, and (iii) a user interface for interactive exploration of relevant clinical cohort/scenario and assessment of significance and reliability of the result for prognostic prediction. MPIC assists cost-effective prognostic biomarker development by facilitating the process of validation, and will transform the care of chronic diseases such as cirrhosis. MPIC is freely available at www.mpic-app.org. The website is implemented in Java, Apache, and MySQL with all major browsers supported.

SUBMITTER: Yip SH

PROVIDER: S-EPMC6759478 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Publications

MPIC: Molecular Prognostic Indicators in Cirrhosis Database for Clinical Context-Specific <i>in Silico</i> Prognostic Biomarker Validation.

Yip Shun H SH Fujiwara Naoto N Burke Jason J Shetler Anand A Peralta Celina C Qian Tongqi T Hoshida Hiroki H Zhu Shijia S Hoshida Yujin Y

Frontiers in genetics 20190918

Prognostic biomarkers are vital in the management of progressive chronic diseases such as liver cirrhosis, affecting 1-2% of the global population and causing over 1 million deaths every year. Despite numerous candidate biomarkers in literature, the costly and lengthy process of validation hampers their clinical translation. Existing omics databases are not suitable for <i>in silico</i> validation due to the ignorance of critical factors, i.e., study design, clinical context of biomarker applica ...[more]

PMID: 31620162

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Project description:Sarcopenia is an increasingly recognized complication of cirrhosis that is associated with morbidity and mortality. Differences in the prevalence and prognosis of sarcopenia between men and women have been reported in other patient groups, but there is insufficient understanding of how sex impacts the prognostic value of sarcopenia in cirrhosis. A search of MEDLINE and Embase was conducted from earliest entries to April 2021. Studies were included if they examined sex-stratified mortality impact of reduced muscle function or mass in outpatient populations with cirrhosis. We identified 700 studies of which 6 were deemed relevant for inclusion in this narrative review. Studies of interest were heterogeneous, precluding pooling of data and making interpretation of the literature challenging. Muscle mass was assessed in five studies (n = 2566, 1730 men, 836 women) and was reduced in 36-50% of men and 24-43% of women. All five studies found that reduced muscle mass determined by computed tomography, dual-energy X-ray absorptiometry, and bioelectrical impedance analysis was associated with increased mortality in men. Of these, two studies identified a corresponding relationship in women; reduced muscle mass defined by computed tomography was associated with increased mortality [hazard ratio (HR) 2.82, P = 0.001], while increasing muscle mass by bioelectrical impedance analysis likewise conferred a survival benefit (HR 0.45, P = 0.0016). Only one study assessed the relationship of muscle function with sex-stratified mortality (n = 1405, 827 men, 578 women), concluding that reduced muscle function predicted mortality in both men and women (HR 1.65, P < 0.001 and HR 1.54, P < 0.001, respectively). Reduced muscle mass in cirrhosis is consistently associated with mortality in men, but lack of sex-stratification of mortality analyses limits the ability to make strong conclusions about the impact of sarcopenia specifically in women, with even fewer data available for analysing muscle function. Improved understanding of the sex-specific impacts of sarcopenia may help address patient deterioration and mortality while awaiting liver transplantation and allow for early intervention to mitigate mortality risk. Large, multicentre studies with adequate female participation and sex-stratified mortality analyses are warranted.

Project description:BACKGROUND: Mosquitoes are the transmissive vectors for several infectious pathogens that affect man. However, the control of mosquitoes through insecticide and pesticide spraying has proved difficult in the past. We hypothesized that, by virtue of their reported vertical inheritance among mosquitoes, group II introns - a class of small coding ribonucleic acids (scRNAs) - may form a potential species-specific biomarker. Structurally, introns are a six-moiety complex. Depending on the function of the protein encoded within the IV moiety, the highly mobile class of group II introns or retroposons is sub-divided into two: Restriction Endonuclease (REase)-like and Apurinic aPyramydinic Endonuclease (APE)-like. REase-like retroposons are thought to be the ancestors of APE retroposons. Our aim in this study was to find evidence for the highly species-specific conservation of the APE subclass of mosquito retroposons. METHODS AND RESULTS: In silico targeted sequence alignments were conducted across a 1,779-organism genome database (1,518 bacterial, 59 archeal, 201 eukaryotic, and the human), using three mosquito retroposon sequence tags (RST) as BLASTN queries [AJ970181 and AJ90201 of Culex pipien origin and AJ970301 of Anoplese sinensis origin]. At a calibration of E = 10, A & D = 100, default filtration and a homology cut-off of >95% identity, no hits were found on any of the 1,518 bacterial genomes. Eleven (100%) and 15 (100%) hits obtained on the 201-eukaryote genome database were homologs (>95% score) of C.pipien quinquefasciatus JHB retroposons, but none of An. sinensis. Twenty and 221 low score (30-43% identity) spurious hits were found at flanking ends of genes and contigs in the human genome with the C.pipien and An. sinensis RSTs respectively. Functional and positional inference revealed these to be possible relatives of human genomic spliceosomes. We advance two models for the application of mosquito RST: as precursors for developing molecular biomarkers for mosquitoes, and as RST-specific monoclonal antibody (MAb)-DDT immunoconjugates to enhance targeted toxicity. CONCLUSION: We offer evidence to support the species-specific conservation of mosquito retroposons among lower taxa. Our findings suggest that retroposons may therefore constitute a unique biomarker for mosquito species that may be exploited in molecular entomology. Mosquito RST-specific MAbs may possibly permit synthesis of DDT immunoconjugates that could be used to achieve species-tailored toxicity.

Dataset Information

MPIC: Molecular Prognostic Indicators in Cirrhosis Database for Clinical Context-Specific in Silico Prognostic Biomarker Validation.

Publications

MPIC: Molecular Prognostic Indicators in Cirrhosis Database for Clinical Context-Specific <i>in Silico</i> Prognostic Biomarker Validation.

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