Genome-Wide Platelet RNA Profiling in Clinical Samples

2009 ◽  
pp. 273-283 ◽  
Author(s):  
Angelika Schedel ◽  
Nina Rolf
Keyword(s):  
Clinical Samples ◽  
Rna Profiling ◽  
Genome Wide

scholarly journals Viral Entry Properties Required for Fitness in Humans Are Lost through Rapid Genomic Change during Viral Isolation

mBio ◽  
2018 ◽  
Vol 9 (4) ◽  
Author(s):  
Sho Iketani ◽  
Ryan C. Shean ◽  
Marion Ferren ◽  
Negar Makhsous ◽  
Dolly B. Aquino ◽  
...  
Keyword(s):  
Primary Culture ◽  
Parainfluenza Virus ◽  
Clinical Samples ◽  
Genomic Change ◽  
Viral Isolation ◽  
Dimer Interface ◽  
Genome Wide ◽  
A Genome ◽  
Immortalized Cells ◽  
Human Parainfluenza Virus

ABSTRACTHuman parainfluenza viruses cause a large burden of human respiratory illness. While much research relies upon viruses grown in cultured immortalized cells, human parainfluenza virus 3 (HPIV-3) evolves in culture. Cultured viruses differ in their properties compared to clinical strains. We present a genome-wide survey of HPIV-3 adaptations to culture using metagenomic next-generation sequencing of matched pairs of clinical samples and primary culture isolates (zero passage virus). Nonsynonymous changes arose during primary viral isolation, almost entirely in the genes encoding the two surface glycoproteins—the receptor binding protein hemagglutinin-neuraminidase (HN) or the fusion protein (F). We recovered genomes from 95 HPIV-3 primary culture isolates and 23 HPIV-3 strains directly from clinical samples. HN mutations arising during primary viral isolation resulted in substitutions at HN’s dimerization/F-interaction site, a site critical for activation of viral fusion. Alterations in HN dimer interface residues known to favor infection in culture occurred within 4 days (H552 and N556). A novel cluster of residues at a different face of the HN dimer interface emerged (P241 and R242) and imply a role in HPIV-3-mediated fusion. Functional characterization of these culture-associated HN mutations in a clinical isolate background revealed acquisition of the fusogenic phenotype associated with cultured HPIV-3; the HN-F complex showed enhanced fusion and decreased receptor-cleaving activity. These results utilize a method for identifying genome-wide changes associated with brief adaptation to culture to highlight the notion that even brief exposure to immortalized cells may affect key viral properties and underscore the balance of features of the HN-F complex required for fitness by circulating viruses.IMPORTANCEHuman parainfluenza virus 3 is an important cause of morbidity and mortality among infants, the immunocompromised, and the elderly. Using deep genomic sequencing of HPIV-3-positive clinical material and its subsequent viral isolate, we discover a number of known and novel coding mutations in the main HPIV-3 attachment protein HN during brief exposure to immortalized cells. These mutations significantly alter function of the fusion complex, increasing fusion promotion by HN as well as generally decreasing neuraminidase activity and increasing HN-receptor engagement. These results show that viruses may evolve rapidly in culture even during primary isolation of the virus and before the first passage and reveal features of fitness for humans that are obscured by rapid adaptation to laboratory conditions.

scholarly journals From raw reads to trees: Whole genome SNP phylogenetics across the tree of life

2015 ◽  
Author(s):  
Sanaa Afroz Ahmed ◽  
Chien-Chi Lo ◽  
Po-E Li ◽  
Karen W Davenport ◽  
Patrick S.G. Chain
Keyword(s):  
Ad Hoc ◽  
Phylogenetic Reconstruction ◽  
Clinical Samples ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Complex Samples ◽  
Phylogenetic Characterization ◽  
Genome Wide ◽  
Genome Assemblies

Next-generation sequencing is increasingly being used to examine closely related organisms. However, while genome-wide single nucleotide polymorphisms (SNPs) provide an excellent resource for phylogenetic reconstruction, to date evolutionary analyses have been performed using different ad hoc methods that are not often widely applicable across different projects. To facilitate the construction of robust phylogenies, we have developed a method for genome-wide identification/characterization of SNPs from sequencing reads and genome assemblies. Our phylogenetic and molecular evolutionary (PhaME) analysis software is unique in its ability to take reads and draft/complete genome(s) as input, derive core genome alignments, identify SNPs, construct phylogenies and perform evolutionary analyses. Several examples using genomes and read datasets for bacterial, eukaryotic and viral linages demonstrate the broad and robust functionality of PhaME. Furthermore, the ability to incorporate raw metagenomic reads from clinical samples with suspected infectious agents shows promise for the rapid phylogenetic characterization of pathogens within complex samples.

scholarly journals Genome-Wide Transcript and Small RNA Profiling Reveals Transcriptomic Responses to Heat Stress

2019 ◽  
Vol 181 (2) ◽  
pp. 609-629 ◽  
Author(s):  
Juan He ◽  
Zengming Jiang ◽  
Lei Gao ◽  
Chenjiang You ◽  
Xuan Ma ◽  
...  
Keyword(s):  
Heat Stress ◽  
Small Rna ◽  
Rna Profiling ◽  
Genome Wide ◽  
Transcriptomic Responses

scholarly journals Genome-wide RNA profiling of long-lasting stem cell-like memory CD8 T cells induced by Yellow Fever vaccination in humans

Genomics Data ◽  
2015 ◽  
Vol 5 ◽  
pp. 297-301 ◽  
Author(s):  
Silvia A. Fuertes Marraco ◽  
Charlotte Soneson ◽  
Mauro Delorenzi ◽  
Daniel E. Speiser
Keyword(s):  
T Cells ◽  
Stem Cell ◽  
Yellow Fever ◽  
Cd8 T Cells ◽  
Memory Cd8 T Cells ◽  
Rna Profiling ◽  
Genome Wide ◽  
Yellow Fever Vaccination

scholarly journals Fusion transcriptome profiling provides insights into alveolar rhabdomyosarcoma

2016 ◽  
Vol 113 (46) ◽  
pp. 13126-13131 ◽  
Author(s):  
Zhongqiu Xie ◽  
Mihaela Babiceanu ◽  
Shailesh Kumar ◽  
Yuemeng Jia ◽  
Fujun Qin ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Fusion Gene ◽  
Transcriptome Profiling ◽  
Alveolar Rhabdomyosarcoma ◽  
Clinical Samples ◽  
Cell Of Origin ◽  
Rna Profiling ◽  
Chimeric Rnas ◽  
Fusion Products ◽  
Time Point

Gene fusions and fusion products were thought to be unique features of neoplasia. However, more and more studies have identified fusion RNAs in normal physiology. Through RNA sequencing of 27 human noncancer tissues, a large number of fusion RNAs were found. By analyzing fusion transcriptome, we observed close clusterings between samples of same or similar tissues, supporting the feasibility of using fusion RNA profiling to reveal connections between biological samples. To put the concept into use, we selected alveolar rhabdomyosarcoma (ARMS), a myogenic pediatric cancer whose exact cell of origin is not clear. PAX3–FOXO1 (paired box gene 3 fused with forkhead box O1) fusion RNA, which is considered a hallmark of ARMS, was recently found during normal muscle cell differentiation. We performed and analyzed RNA sequencing from various time points during myogenesis and uncovered many chimeric fusion RNAs. Interestingly, we found that the fusion RNA profile of RH30, an ARMS cell line, is most similar to the myogenesis time point when PAX3–FOXO1 is expressed. In contrast, full transcriptome clustering analysis failed to uncover this connection. Strikingly, all of the 18 chimeric RNAs in RH30 cells could be detected at the same myogenic time point(s). In addition, the seven chimeric RNAs that follow the exact transient expression pattern as PAX3–FOXO1 are specific to rhabdomyosarcoma cells. Further testing with clinical samples also confirmed their specificity to rhabdomyosarcoma. These results provide further support for the link between at least some ARMSs and the PAX3–FOXO1-expressing myogenic cells and demonstrate that fusion RNA profiling can be used to investigate the etiology of fusion-gene-associated cancers.

scholarly journals Genome-wide Spatial Expression Profiling in FFPE Tissues

2020 ◽  
Author(s):  
Eva Gracia Villacampa ◽  
Ludvig Larsson ◽  
Linda Kvastad ◽  
Alma Andersson ◽  
Joseph Carlson ◽  
...  
Keyword(s):  
Expression Profiling ◽  
Molecular Mechanisms ◽  
Clinical Samples ◽  
Tissue Sections ◽  
Genome Wide ◽  
Formalin Fixed Paraffin ◽  
Spatial Composition ◽  
Ffpe Tissues ◽  
Ovarian Carcinosarcoma ◽  
Using Data

AbstractFormalin-fixed paraffin embedding (FFPE) is the most widespread long-term tissue preservation approach. Here we present a procedure to perform genome-wide spatial analysis of mRNA in FFPE tissue sections. The procedure takes advantage of well-established, commercially available methods for imaging and spatial barcoding using slides spotted with barcoded oligo(dT) probes to capture the 3’ end of mRNA molecules in tissue sections. First, we conducted expression profiling and cell type mapping in coronal sections from the mouse brain to demonstrate the method’s capability to delineate anatomical regions from a molecular perspective. Second, we explored the spatial composition of transcriptomic signatures in ovarian carcinosarcoma samples using data driven analysis methods, exemplifying the method’s potential to elucidate molecular mechanisms in heterogeneous clinical samples.

scholarly journals Genome-wide Small Rna Profiling Reveals Tiller Development in Tall Fescue (Festuca Arundinacea Schreb.)

2020 ◽  
Author(s):  
Tao Hu ◽  
Tao Wang ◽  
Huiying Li ◽  
Misganaw Wassie ◽  
Liang Chen
Keyword(s):  
Production Rate ◽  
Small Rna ◽  
Tall Fescue ◽  
Festuca Arundinacea ◽  
Target Genes ◽  
Cool Season ◽  
Rna Profiling ◽  
Mirna Genes ◽  
Genome Wide ◽  
A Genome

Abstract Background: Tall fescue (Festuca arundinacea Schreb.) is a major cool-season forage and turfgrass species. The low tiller density and size dramatically limits its turf performance and forage yield. MicroRNAs (miRNA)-genes modules play critical roles in tiller development in plants. In this study, a genome-wide small RNA profiling was carried out in two tall fescue genotypes contrasting for tillering production (‘Ch-3’, high tiller production rate and ‘Ch-5’, low tiller production rate) andtwo types of tissue samples at different tillering development stage (Pre-tillering, grass before tillering; Tillering, grass after tillering). ‘Ch-3’, ‘Ch-5’, Pre-tillering, and Tillering samples were analyzed using high-throughput RNA sequencing.Results: A total of 222 million high-quality clean reads were generated and 208 miRNAs were discovered, including 148 known miRNAs belonging to 70 families and 60 novel ones. Furthermore, 18 miRNAs were involved in tall fescue tiller development process. Among them, 14 miRNAs displayed increased abundance in both Ch-3 and Tillering plants compared with that in Ch-5 and Pre-tillering plants and were positive with tillering, while another four miRNAs were negative with tiller development. Out ofthe three miRNAs osa-miR156a, zma-miR528a-3p and osa-miR444b.2, the rest of 15 miRNAs were newfound controllers mediating tiller development in plants. Based on our previous full-length transcriptome analysis in tall fescue, 2 8927 potential target genes were discoveredfor all identified miRNAs. Most of the 212 target genes of the 18 miRNAs were dominantly enriched into “ubiquitin-mediated proteolysis”, “phagosome”, “fatty acid biosynthesis”, “oxidative phosphorylation”, and “biosynthesis of unsaturated fatty acids” KEGG pathways.Conclusions: This is the first genome-wide miRNA profiles analysis to identifyregulators involved in tiller development in cool-season turfgrass. Tillering related 18 miRNAs and their 212 target genes provide novel information for the understanding of the molecular mechanisms of miRNA-genes mediated tiller development in cool-season turfgrass.

scholarly journals Genome-wide small RNA profiling reveals tiller development in tall fescue (Festuca arundinacea Schreb.)

2020 ◽  
Author(s):  
Tao Hu ◽  
Tao Wang ◽  
Huiying Li ◽  
Misganaw Wassie ◽  
Huawei Xu ◽  
...  
Keyword(s):  
Production Rate ◽  
Small Rna ◽  
Tall Fescue ◽  
Festuca Arundinacea ◽  
Target Genes ◽  
Cool Season ◽  
Rna Profiling ◽  
Mirna Genes ◽  
Genome Wide ◽  
A Genome

Abstract Background: Tall fescue (Festuca arundinacea Schreb.) is a major cool-season forage and turfgrass species. The low tiller density and size dramatically limits its turf performance and forage yield. MicroRNAs (miRNA)-genes modules play critical roles in tiller development in plants. In this study, a genome-wide small RNA profiling was carried out in two tall fescue genotypes contrasting for tillering production (‘Ch-3’, high tiller production rate and ‘Ch-5’, low tiller production rate) and two types of tissue samples at different tillering development stage (Pre-tillering, grass before tillering; Tillering, grass after tillering). ‘Ch-3’, ‘Ch-5’, Pre-tillering, and Tillering samples were analyzed using high-throughput RNA sequencing. Results: A total of 222 million high-quality clean reads were generated and 208 miRNAs were discovered, including 148 known miRNAs belonging to 70 families and 60 novel ones. Furthermore, 18 miRNAs were involved in tall fescue tiller development process. Among them, 14 miRNAs displayed increased abundance in both Ch-3 and Tillering plants compared with that in Ch-5 and Pre-tillering plants and were positive with tillering, while another four miRNAs were negative with tiller development. Out of the three miRNAs osa-miR156a, zma-miR528a-3p and osa-miR444b.2, the rest of 15 miRNAs were newfound and associated with tiller development in plants. Based on our previous full-length transcriptome analysis in tall fescue, 2 8927 potential target genes were discovered for all identified miRNAs. Most of the 212 target genes of the 18 miRNAs were dominantly enriched into “ubiquitin-mediated proteolysis”, “phagosome”, “fatty acid biosynthesis”, “oxidative phosphorylation”, and “biosynthesis of unsaturated fatty acids” KEGG pathways. In addition, bdi-miR167e-3p targets two kinase proteins EIF2AK4 and IRAK4, and osa-miR397a targets auxin response factor 5, which may be the significant miRNA-genes controllers in tillering development. Conclusions: This is the first genome-wide miRNA profiles analysis to identify regulators involved in tiller development in cool-season turfgrass. Tillering related 18 miRNAs and their 212 target genes provide novel information for the understanding of the molecular mechanisms of miRNA-genes mediated tiller development in cool-season turfgrass.

scholarly journals The RNA demethylase FTO is required for maintenance of bone mass and functions to protect osteoblasts from genotoxic damage

2019 ◽  
Vol 116 (36) ◽  
pp. 17980-17989 ◽  
Author(s):  
Qian Zhang ◽  
Ryan C. Riddle ◽  
Qian Yang ◽  
Clifford R. Rosen ◽  
Denis C. Guttridge ◽  
...  
Keyword(s):  
Dna Damage ◽  
Association Studies ◽  
Metabolic Stress ◽  
Genome Wide Association Studies ◽  
Mineral Density ◽  
Rna Profiling ◽  
Genotoxic Damage ◽  
Age Related ◽  
Genome Wide ◽  
The Stability

The fat mass and obesity-associated gene (FTO) encodes an m6A RNA demethylase that controls mRNA processing and has been linked to both obesity and bone mineral density in humans by genome-wide association studies. To examine the role of FTO in bone, we characterized the phenotype of mice lacking Fto globally (FtoKO) or selectively in osteoblasts (FtoOcKO). Both mouse models developed age-related reductions in bone volume in both the trabecular and cortical compartments. RNA profiling in osteoblasts following acute disruption of Fto revealed changes in transcripts of Hspa1a and other genes in the DNA repair pathway containing consensus m6A motifs required for demethylation by Fto. Fto KO osteoblasts were more susceptible to genotoxic agents (UV and H2O2) and exhibited increased rates of apoptosis. Importantly, forced expression of Hspa1a or inhibition of NF-κB signaling normalized the DNA damage and apoptotic rates in Fto KO osteoblasts. Furthermore, increased metabolic stress induced in mice by feeding a high-fat diet induced greater DNA damage in osteoblast of FtoOc KO mice compared to controls. These data suggest that FTO functions intrinsically in osteoblasts through Hspa1a–NF-κB signaling to enhance the stability of mRNA of proteins that function to protect cells from genotoxic damage.

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