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Concept: Serial analysis of gene expression

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Because most human stroke victims are elderly, studies of experimental stroke in the aged rather than the young rat model may be optimal for identifying clinically relevant cellular responses, as well for pinpointing beneficial interventions.

Concepts: Gene, Gene expression, Cell, Evolution, Transcription, Serial analysis of gene expression

28

Management of locally advanced rectal cancer (RC) consists of neoadjuvant chemoradiotherapy (CRT) with fluoropyrimidines, followed by total mesorectal excision. We sought to evaluate the expression of selected genes, some of which were derived from a previous undirected SAGE (serial analysis of gene expression)-based approach, before and after CRT, to identify mechanisms of resistance.

Concepts: Gene, Gene expression, Cancer, Transcription, Molecular biology, Colorectal cancer, Total mesorectal excision, Serial analysis of gene expression

7

Analysis of the pattern of proteins or messengerRNAs (mRNAs) in histological tissue sections is a cornerstone in biomedical research and diagnostics. This typically involves the visualization of a few proteins or expressed genes at a time. We have devised a strategy, which we call “spatial transcriptomics,” that allows visualization and quantitative analysis of the transcriptome with spatial resolution in individual tissue sections. By positioning histological sections on arrayed reverse transcription primers with unique positional barcodes, we demonstrate high-quality RNA-sequencing data with maintained two-dimensional positional information from the mouse brain and human breast cancer. Spatial transcriptomics provides quantitative gene expression data and visualization of the distribution of mRNAs within tissue sections and enables novel types of bioinformatics analyses, valuable in research and diagnostics.

Concepts: DNA, Gene, Gene expression, Cancer, Transcription, Molecular biology, RNA, Serial analysis of gene expression

7

The majority of RNA-seq expression studies in plants remain underutilised and inaccessible due to the use of disparate transcriptome references and the lack of skills and resources to analyse and visualise this data. We have developed expVIP, an expression Visualisation and Integration Platform, which allows easy analysis of RNA-seq data combined with an intuitive and interactive interface. Users can analyse public and user-specified datasets with minimal bioinformatics knowledge using the expVIP virtual machine. This generates a custom web browser to visualise, sort and filter the RNA-seq data and provides outputs for differential gene expression analysis. We demonstrate expVIP’s suitability for polyploid crops and evaluate its performance across a range of biologically-relevant scenarios. To exemplify its use in crop research we developed a flexible wheat expression browser (www.wheat-expression.com) which can be expanded with user-generated data in a local virtual machine environment. The open-access expVIP platform will facilitate the analysis of gene expression data from a wide variety of species by enabling the easy integration, visualisation and comparison of RNA-seq data across experiments.

Concepts: DNA, Gene, Gene expression, Molecular biology, Organism, Serial analysis of gene expression, RNA-Seq, Virtual machine

2

The distribution and co-occurrence of species are partly the outcome of their interactions with environmental drivers. Drought is a key driver related to the distribution of plant species. Drought events continue to increase in frequency and severity and identifying those aspects of plant function that are related to drought is critical. Here, we perform a community-level analysis of gene expression in relation to experimental drought and relate the similarity in gene set enrichment across species to their natural co-occurrence. Species with similar gene set enrichment in response to experimental drought tend to non-randomly co-occur in a natural stand. We demonstrate that similarity in the transcriptomic response of species to drought is a significantly better indicator of natural co-occurrence than measures of functional trait similarity and phylogenetic relatedness and that transcriptomics has the capacity to greatly enhance ecological investigations of species distributions and community structure.

Concepts: Gene, Gene expression, Evolution, Biology, Organism, Life, Species, Serial analysis of gene expression

2

This study investigates effects of dipeptide balenine, as a major component of whale meat extract (hereafter, WME), supplementation on senescence-accelerated mouse prone 8 (SAMP8), an Alzheimer’s disease (AD) model at level of learning and memory formation and brain expression profiles genome-wide in brain. Mice fed experimental balenine (+ WME) supplemented diet for 26 weeks were subjected to four behavioral tests - open field, Y-maze, new object recognition, and water-filled multiple T-maze - to examine effects on learning and memory. Brain transcriptome of SAMP8 mice-fed the WME diet over control low-safflower oil (LSO) diet-fed mice was delineated on a 4 × 44 K mouse whole genome DNA microarray chip. Results revealed the WME diet not only induced improvements in the learning and memory formation but also positively modulated changes in the brain of the SAMP8 mouse; the gene inventories are publically available for analysis by the scientific community. Interestingly, the SAMP8 mouse model presented many genetic characteristics of AD, and numerous novel molecules (Slc2a5, Treh, Fbp1, Aldob, Ppp1r1a, DNase1, Agxt2l1, Cyp2e1, Acsm1, Acsm2, and Pah) were revealed over the SAMR1 (senescence-accelerated mouse resistant 1) mouse, to be oppositely regulated/recovered under the balenine (+ WME) supplemented diet regime by DNA microarray and bioinformatics analyses. Our present study demonstrates an experimental strategy to understand the effects of dipeptide balenine, prominetly contained in meat diet, on SAMP8, providing new insight into whole brain transcriptome changes genome-wide. The gene expression data has been deposited into the Gene Expression Omnibus (GEO): GSE76459. The data will be a valuable resource in examining the effects of natural products, and which could also serve as a human model for further functional analysis and investigation.

Concepts: DNA, Psychology, Gene, Genetics, Gene expression, Bioinformatics, DNA microarray, Serial analysis of gene expression

2

Pseudostellaria heterophylla produces both closed (cleistogamous, CL) and open (chasmogamous, CH) flowers on the same individual but in different seasons. The production of CH and CL flowers might be in response to environmental changes. To better understand the molecular mechanisms of CH and CL flowering, we compared the transcriptome of the two types of flowers to examine differential gene expression patterns, and to identify gene regulatory networks that control CH and CL flowering.

Concepts: DNA, Gene, Gene expression, Transcription, Molecular biology, Cellular differentiation, Serial analysis of gene expression, RNA-Seq

2

This article introduces a manually curated data collection for gene expression meta-analysis of patients with ovarian cancer and software for reproducible preparation of similar databases. This resource provides uniformly prepared microarray data for 2970 patients from 23 studies with curated and documented clinical metadata. It allows users to efficiently identify studies and patient subgroups of interest for analysis and to perform meta-analysis immediately without the challenges posed by harmonizing heterogeneous microarray technologies, study designs, expression data processing methods and clinical data formats. We confirm that the recently proposed biomarker CXCL12 is associated with patient survival, independently of stage and optimal surgical debulking, which was possible only through meta-analysis owing to insufficient sample sizes of the individual studies. The database is implemented as the curatedOvarianData Bioconductor package for the R statistical computing language, providing a comprehensive and flexible resource for clinically oriented investigation of the ovarian cancer transcriptome. The package and pipeline for producing it are available from http://bcb.dfci.harvard.edu/ovariancancer. Database URL: http://bcb.dfci.harvard.edu/ovariancancer.

Concepts: Gene, Gene expression, Hereditary nonpolyposis colorectal cancer, BRCA2, RNA splicing, DNA microarray, Serial analysis of gene expression, RNA-Seq

1

Mahafacyclin B is a cyclic peptide isolated from the latex of Jatropha mahafalensis and is an antimalarial agent. However, the physiological effects of mahafacyclin B in mammalian cells are not known. Here, we assessed the growth, morphology, and alterations in the transcriptome of CHO-K1 cells exposed to mahafacyclin B (0-22 μM). Mahafacyclin B at 2.2 μM did not affect the proliferation or death of CHO-K1 cells. Mahafacyclin B was not toxic to mammalian cells at 2.2 μM, which represents a normal physiological concentration at which mahafacyclin B retains its antimalarial properties. Interestingly, mahafacyclin B altered the size and morphology of CHO-K1 cells. Comparative transcriptomics revealed that mahafacyclin B modulated the expression of a specific subset of genes.

Concepts: DNA, Protein, Gene, Gene expression, RNA, Species, Serial analysis of gene expression, RNA-Seq

1

Formalin-fixed paraffin-embedded (FFPE) tissue samples represent a potentially invaluable resource for transcriptomic research. However, use of FFPE samples in genomic studies has been limited by technical challenges resulting from nucleic acid degradation. Here we evaluated gene expression profiles derived from fresh-frozen (FRO) and FFPE mouse liver tissues preserved in formalin for different amounts of time using two DNA microarray protocols and two whole-transcriptome sequencing (RNA-seq) library preparation methodologies. The ribo-depletion protocol outperformed the other methods by having the highest correlations of differentially expressed genes (DEGs), and best overlap of pathways, between FRO and FFPE groups. The effect of sample time in formalin (18 hours or 3 weeks) on gene expression profiles indicated that test article treatment, not preservation method, was the main driver of gene expression profiles. Meta- and pathway analyses indicated that biological responses were generally consistent for 18-hour and 3-week FFPE samples compared to FRO samples. However, clear erosion of signal intensity with time in formalin was evident, and DEG numbers differed by platform and preservation method. Lastly, we investigated the effect of time in paraffin on genomic profiles. Ribo-depletion RNA-seq analysis of 8-, 19-, and 26-year-old control blocks resulted in comparable quality metrics, including expected distributions of mapped reads to exonic, UTR, intronic, and ribosomal fractions of the transcriptome. Overall, our results indicate that FFPE samples are appropriate for use in genomic studies in which frozen samples are not available, and that ribo-depletion RNA-seq is the preferred method for this type of analysis in archival and long-aged FFPE samples.

Concepts: DNA, Gene, Genetics, Gene expression, Molecular biology, RNA, DNA microarray, Serial analysis of gene expression