Randomized clinical trial to evaluate the efficacy and safety of valganciclovir in a subset of patients with chronic fatigue syndrome

There is no known treatment for chronic fatigue syndrome (CFS). Little is known about its pathogenesis. Human herpesvirus 6 (HHV‐6) and Epstein–Barr virus (EBV) have been proposed as infectious triggers. Thirty CFS patients with elevated IgG antibody titers against HHV‐6 and EBV were randomized 2:1 to receive valganciclovir (VGCV) or placebo for 6 months in a double‐blind, placebo‐controlled trial. Clinical endpoints aimed at measuring physical and mental fatigue included the Multidimensional Fatigue Inventory (MFI‐20) and Fatigue Severity Scale (FSS) scores, self‐reported cognitive function, and physician‐determined responder status. Biological endpoints included monocyte and neutrophil counts and cytokine levels. VGCV patients experienced a greater improvement by MFI‐20 at 9 months from baseline compared to placebo patients but this difference was not statistically significant. However, statistically significant differences in trajectories between groups were observed in MFI‐20 mental fatigue subscore ( P  = 0.039), FSS score ( P  = 0.006), and cognitive function ( P  = 0.025). VGCV patients experienced these improvements within the first 3 months and maintained that benefit over the remaining 9 months. Patients in the VGCV arm were 7.4 times more likely to be classified as responders ( P  = 0.029). In the VGCV arm, monocyte counts decreased ( P  < 0.001), neutrophil counts increased ( P  = 0.037) and cytokines were more likely to evolve towards a Th1‐profile ( P  < 0.001). Viral IgG antibody titers did not differ between arms. VGCV may have clinical benefit in a subset of CFS patients independent of placebo effect, possibly mediated by immunomodulation and/or antiviral effect. Further investigation with longer treatment duration and a larger sample size is warranted. J. Med. Virol. 85:2101–2109, 2013 . © 2013 Wiley Periodicals, Inc.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/100139/1/jmv23713.pd

Addressing statistical biases in nucleotide-derived protein databases for proteogenomic search strategies

[Image: see text] Proteogenomics has the potential to advance genome annotation through high quality peptide identifications derived from mass spectrometry experiments, which demonstrate a given gene or isoform is expressed and translated at the protein level. This can advance our understanding of genome function, discovering novel genes and gene structure that have not yet been identified or validated. Because of the high-throughput shotgun nature of most proteomics experiments, it is essential to carefully control for false positives and prevent any potential misannotation. A number of statistical procedures to deal with this are in wide use in proteomics, calculating false discovery rate (FDR) and posterior error probability (PEP) values for groups and individual peptide spectrum matches (PSMs). These methods control for multiple testing and exploit decoy databases to estimate statistical significance. Here, we show that database choice has a major effect on these confidence estimates leading to significant differences in the number of PSMs reported. We note that standard target:decoy approaches using six-frame translations of nucleotide sequences, such as assembled transcriptome data, apparently underestimate the confidence assigned to the PSMs. The source of this error stems from the inflated and unusual nature of the six-frame database, where for every target sequence there exists five “incorrect” targets that are unlikely to code for protein. The attendant FDR and PEP estimates lead to fewer accepted PSMs at fixed thresholds, and we show that this effect is a product of the database and statistical modeling and not the search engine. A variety of approaches to limit database size and remove noncoding target sequences are examined and discussed in terms of the altered statistical estimates generated and PSMs reported. These results are of importance to groups carrying out proteogenomics, aiming to maximize the validation and discovery of gene structure in sequenced genomes, while still controlling for false positives

Association between expression of the Bone morphogenetic proteins 2 and 7 in the repair of circumscribed cartilage lesions with clinical outcome

<p>Abstract</p> <p>Background</p> <p>Although there is much known about the role of BMPs in cartilage metabolism reliable data about the <it>in vivo </it>regulation in natural and surgically induced cartilage repair are still missing.</p> <p>Methods</p> <p>Lavage fluids of knee joints of 47 patients were collected during surgical therapy. 5 patients had no cartilage lesion and served as a control group, the other 42 patients with circumscribed cartilage defects were treated by microfracturing (19) or by an Autologous Chondrocyte Implantation (23). The concentrations of BMP-2 and BMP-7 were determined by ELISA. The clinical status was evaluated using the IKDC Score prior to and 1 year following the operation.</p> <p>Results</p> <p>High level expression in the control group was found for BMP-2, concentrations of BMP-7 remained below detection levels. No statistical differences could be detected in concentrations of BMP-2 or BMP-7 in the lavage fluids of knees with cartilage lesions compared to the control group. Levels of BMP-7 did not change after surgical cartilage repair, whereas concentrations of BMP-2 statistically significant increased after the intervention (p < 0.001). The clinical outcome following cartilage regenerating surgery increased after 1 year by 29% (p < 0.001). The difference of the IKDC score after 1 year and prior to the operation was used to quantify the degree of improvement following surgery. This difference statistically significant correlated with initial BMP-2 (R = 0.554, p < 0.001) but not BMP-7 (R = 0.031, n.s.) levels in the knee joints.</p> <p>Conclusions</p> <p>BMP-2 seems to play an important role in surgically induced cartilage repair; synovial expression correlates with the clinical outcome.</p

OrthoList: A Compendium of C. elegans Genes with Human Orthologs

C. elegans is an important model for genetic studies relevant to human biology and disease. We sought to assess the orthology between C. elegans and human genes to understand better the relationship between their genomes and to generate a compelling list of candidates to streamline RNAi-based screens in this model.We performed a meta-analysis of results from four orthology prediction programs and generated a compendium, "OrthoList", containing 7,663 C. elegans protein-coding genes. Various assessments indicate that OrthoList has extensive coverage with low false-positive and false-negative rates. Part of this evaluation examined the conservation of components of the receptor tyrosine kinase, Notch, Wnt, TGF-ß and insulin signaling pathways, and led us to update compendia of conserved C. elegans kinases, nuclear hormone receptors, F-box proteins, and transcription factors. Comparison with two published genome-wide RNAi screens indicated that virtually all of the conserved hits would have been obtained had just the OrthoList set (∼38% of the genome) been targeted. We compiled Ortholist by InterPro domains and Gene Ontology annotation, making it easy to identify C. elegans orthologs of human disease genes for potential functional analysis.We anticipate that OrthoList will be of considerable utility to C. elegans researchers for streamlining RNAi screens, by focusing on genes with apparent human orthologs, thus reducing screening effort by ∼60%. Moreover, we find that OrthoList provides a useful basis for annotating orthology and reveals more C. elegans orthologs of human genes in various functional groups, such as transcription factors, than previously described

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

We systematically generated large-scale data sets to improve genome annotation for the nematode Caenorhabditis elegans, a key model organism. These data sets include transcriptome profiling across a developmental time course, genome-wide identification of transcription factor-binding sites, and maps of chromatin organization. From this, we created more complete and accurate gene models, including alternative splice forms and candidate noncoding RNAs. We constructed hierarchical networks of transcription factor-binding and microRNA interactions and discovered chromosomal locations bound by an unusually large number of transcription factors. Different patterns of chromatin composition and histone modification were revealed between chromosome arms and centers, with similarly prominent differences between autosomes and the X chromosome. Integrating data types, we built statistical models relating chromatin, transcription factor binding, and gene expression. Overall, our analyses ascribed putative functions to most of the conserved genome

The C. elegans transcriptome

As part of the modENCODE consortium, we are characterizing the C. elegans transcriptome using tiling arrays, RNA-seq, RT-PCR and mass spectrometry. Our earlier studies on whole animals of various stages and conditions and on specific cells and tissues led to a much improved set of protein coding genes covering greater than 95% of all genes including more than 12,413 trans-spliced leaders, 20,515 different trans-spliced transcript start sites, 28,199 polyA sites, 111,786 confirmed splice junctions, >7,000 inferred non-coding (nc) RNAs, and over 50 new miRNAs (1-5). More recently, we have (1) analyzed biological replicates with RNA-seq for different stages and conditions, validating the observed expression levels; (2) closed gaps in RNA-seq coverage of weakly expressed genes with RT-PCR; (3) characterized the RNA content of more finely staged embryos with RNA-seq; (4) tested methods that deplete rRNA to allow direct analysis by RNA-seq of ncRNAs and smaller samples, such as specific embryonic cells and tissues; (5) analyzed polyA+ RNA from selected stages of C. briggsae, C. remanei, C. brenneri and C. japonica; (6) analyzed miRNAs under additional stresses and conditions; and (7) characterized the proteins present in 12 size fractions from 16 different stages and conditions. All of the data are available through the modENCODE Data Coordinating Center and increasingly through WormBase. Our goal is to provide the community with a comprehensive description of the transcripts of the C. elegans genome, providing information about their specific utilization where possible. References 1. Hillier et al. Genome Research PMID: 19181841 2. Gerstein et al Science PMID: 21177976 3. Lu et al. Genome Reseaarch PMID: 21177971 4. Allen et al. Genome Research PMID: 21177958 5. Spencer et al. Genome Research PMID: 21177967

The C. elegans transcriptome

As part of the modENCODE consortium, we are characterizing the C. elegans transcriptome using tiling arrays, RNA-seq, RT-PCR and mass spectrometry. Our earlier studies on whole animals of various stages and conditions and on specific cells and tissues led to a much improved set of protein coding genes covering greater than 95% of all genes including more than 12,413 trans-spliced leaders, 20,515 different trans-spliced transcript start sites, 28,199 polyA sites, 111,786 confirmed splice junctions, >7,000 inferred non-coding (nc) RNAs, and over 50 new miRNAs (1-5). More recently, we have (1) analyzed biological replicates with RNA-seq for different stages and conditions, validating the observed expression levels; (2) closed gaps in RNA-seq coverage of weakly expressed genes with RT-PCR; (3) characterized the RNA content of more finely staged embryos with RNA-seq; (4) tested methods that deplete rRNA to allow direct analysis by RNA-seq of ncRNAs and smaller samples, such as specific embryonic cells and tissues; (5) analyzed polyA+ RNA from selected stages of C. briggsae, C. remanei, C. brenneri and C. japonica; (6) analyzed miRNAs under additional stresses and conditions; and (7) characterized the proteins present in 12 size fractions from 16 different stages and conditions. All of the data are available through the modENCODE Data Coordinating Center and increasingly through WormBase. Our goal is to provide the community with a comprehensive description of the transcripts of the C. elegans genome, providing information about their specific utilization where possible. References 1. Hillier et al. Genome Research PMID: 19181841 2. Gerstein et al Science PMID: 21177976 3. Lu et al. Genome Reseaarch PMID: 21177971 4. Allen et al. Genome Research PMID: 21177958 5. Spencer et al. Genome Research PMID: 21177967