Recommendations for the analysis of gene expression data to identify intrinsic differences between similar tissues

A transcriptome atlas of leg muscles from healthy human volunteers reveals molecular and cellular signatures associated with muscle location

Skeletal muscles support the stability and mobility of the skeleton but differ in biomechanical properties and physiological functions. The intrinsic factors that regulate muscle-specific characteristics are poorly understood. To study these, we constructed a large atlas of RNA-seq profiles from six leg muscles and two locations from one muscle, using biopsies from 20 healthy young males. We identified differential expression patterns and cellular composition across the seven tissues using three bioinformatics approaches confirmed by large-scale newly developed quantitative immune-histology procedures. With all three procedures, the muscle samples clustered into three groups congruent with their anatomical location. Concomitant with genes marking oxidative metabolism, genes marking fast- or slow-twitch myofibers differed between the three groups. The groups of muscles with higher expression of slow-twitch genes were enriched in endothelial cells and showed higher capillary content. In addition, expression profiles of Homeobox (HOX) transcription factors differed between the three groups and were confirmed by spatial RNA hybridization. We created an open-source graphical interface to explore and visualize the leg muscle atlas (https://tabbassidaloii.shinyapps.io/muscleAtlasShinyApp/). Our study reveals the molecular specialization of human leg muscles, and provides a novel resource to study muscle-specific molecular features, which could be linked with (patho)physiological processes.

Transcriptomic responses of females to consumption of nuptial food gifts as a potential mediator of sexual conflict in decorated crickets

Nuptial food gift provisioning by males to females at mating is a strategy in many insects that is thought to be shaped by sexual conflict or sexual selection, as it affords males access to a female's physiology. While males often attempt to use these gifts to influence female behaviour to their own advantage, females can evolve counter mechanisms. In decorated crickets, the male's nuptial gift comprises part of the spermatophore, the spermatophylax, the feeding on which deters the female from prematurely terminating sperm transfer. However, ingested compounds in the spermatophylax and attachment of the sperm-containing ampulla could further influence female physiology and behaviour. We investigated how mating per se and these two distinct routes of potential male-mediated manipulation influence the female transcriptomic response. We conducted an RNA sequencing experiment on gut and head tissues from females for whom nuptial food gift consumption and receipt of an ejaculation were independently manipulated. In the gut tissue, we found that females not permitted to feed during mating exhibited decreased overall gene expression, possibly caused by a reduced gut function, but this was countered by feeding on the spermatophylax or a sham gift. In the head tissue, we found only low numbers of differentially expressed genes, but a gene co-expression network analysis revealed that ampulla attachment and spermatophylax consumption independently induce distinct gene expression patterns. This study provides evidence that spermatophylax feeding alters the female post-mating transcriptomic response in decorated crickets, highlighting its potential to mediate sexual conflict in this system.

Elucidating genes and gene networks linked to individual susceptibility to milk fat depression in dairy goats

Dietary supplementation with marine lipids modulates ruminant milk composition toward a healthier fatty acid profile for consumers, but it also causes milk fat depression (MFD). Because the dairy goat industry is mainly oriented toward cheese manufacturing, MFD can elicit economic losses. There is large individual variation in animal susceptibility with goats more (RESPO+) or less (RESPO-) responsive to diet-induced MFD. Thus, we used RNA-Seq to examine gene expression profiles in mammary cells to elucidate mechanisms underlying MFD in goats and individual variation in the extent of diet-induced MFD. Differentially expression analyses (DEA) and weighted gene co-expression network analysis (WGCNA) of RNA-Seq data were used to study milk somatic cell transcriptome changes in goats consuming a diet supplemented with marine lipids. There were 45 differentially expressed genes (DEGs) between control (no-MFD, before diet-induced MFD) and MFD, and 18 between RESPO+ and RESPO-. Biological processes and pathways such as "RNA transcription" and "Chromatin modifying enzymes" were downregulated in MFD compared with controls. Regarding susceptibility to diet-induced MFD, we identified the "Triglyceride Biosynthesis" pathway upregulated in RESPO- goats. The WGCNA approach identified 9 significant functional modules related to milk fat production and one module to the fat yield decrease in diet-induced MFD. The onset of MFD in dairy goats is influenced by the downregulation of SREBF1, other transcription factors and chromatin-modifying enzymes. A list of DEGs between RESPO+ and RESPO- goats (e.g., DBI and GPD1), and a co-related gene network linked to the decrease in milk fat (ABCD3, FABP3, and PLIN2) was uncovered. Results suggest that alterations in fatty acid transport may play an important role in determining individual variation. These candidate genes should be further investigated.

Comparative transcriptome profiling and weighted gene co-expression network analysis to identify core genes in maize (Zea mays L.) silks infected by multiple fungi

Maize (Zea mays L.) is the third most popular Poaceae crop after wheat and rice and used in feed and pharmaceutical sectors. The maize silk contains bioactive components explored by traditional Chinese herbal medicine for various pharmacological activities. However, Fusarium graminearum, Fusarium verticillioides, Trichoderma atroviride, and Ustilago maydis can infect the maize, produce mycotoxins, hamper the quantity and quality of silk production, and further harm the primary consumer's health. However, the defense mechanism is not fully understood in multiple fungal infections in the silk of Z. mays. In this study, we applied bioinformatics approaches to use the publicly available transcriptome data of Z. mays silk affected by multiple fungal flora to identify core genes involved in combatting disease response. Differentially expressed genes (DEGs) were identified among intra- and inter-transcriptome data sets of control versus infected Z. mays silks. Upon further comparison between up- and downregulated genes within the control of datasets, 4,519 upregulated and 5,125 downregulated genes were found. The DEGs have been compared with genes in the modules of weighted gene co-expression network analysis to relevant specific traits towards identifying core genes. The expression pattern of transcription factors, carbohydrate-active enzymes (CAZyme), and resistance genes was analyzed. The present investigation is supportive of our findings that the gene ontology, immunity stimulus, and resistance genes are upregulated, but physical and metabolic processes such as cell wall organizations and pectin synthesis were downregulated respectively. Our results are indicative that terpene synthase TPS6 and TPS11 are involved in the defense mechanism against fungal infections in maize silk.

Weighted Co-Expression Network Analysis Identifies RNF181 as a Causal Gene of Coronary Artery Disease

Background: Coronary artery disease (CAD) exerts a global challenge to public health. Genetic heritability is one of the most vital contributing factors in the pathophysiology of CAD. Co-expression network analysis is an applicable and robust method for the interpretation of biological interaction from microarray data. Previous CAD studies have focused on peripheral blood samples since the processes of CAD may vary from tissue to blood. It is therefore necessary to find biomarkers for CAD in heart tissues; their association also requires further illustration.

Materials and Methods: To filter for causal genes, an analysis of microarray expression profiles, GSE12504 and GSE22253, was performed with weighted gene co-expression network analysis (WGCNA). Co-expression modules were constructed after batch effect removal and data normalization. The results showed that 7 co-expression modules with 8,525 genes and 1,210 differentially expressed genes (DEGs) were identified. Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted. Four major pathways in CAD tissue and hub genes were addressed in the Hybrid Mouse Diversity Panel (HMDP) and Human Protein Atlas (HPA), and isoproterenol (ISO)/doxycycline (DOX)-induced heart toxicity models were used to validate the hub genes. Lastly, the hub genes and risk variants were verified in the CAD cohort and in genome-wide association studies (GWAS).

Results: The results showed that RNF181 and eight other hub genes are perturbed during CAD in heart tissues. Additionally, the expression of RNF181 was validated using RT-PCR and immunohistochemistry (IHC) staining in two cardiotoxicity mouse models. The association was further verified in the CAD patient cohort and in GWAS.

Conclusion: Our findings illustrated for the first time that the E3 ubiquitination ligase protein RNF181 may serve as a potential biomarker in CAD, but further in vivo validation is warranted.

In silico-driven analysis of the Glossina morsitans morsitans antennae transcriptome in response to repellent or attractant compounds

BACKGROUND

High-throughput sequencing generates large volumes of biological data that must be interpreted to make meaningful inference on the biological function. Problems arise due to the large number of characteristics p (dimensions) that describe each record [n] in the database. Feature selection using a subset of variables extracted from the large datasets is one of the approaches towards solving this problem.

METHODOLOGY

In this study we analyzed the transcriptome of Glossina morsitans morsitans (Tsetsefly) antennae after exposure to either a repellant (δ-nonalactone) or an attractant (ε-nonalactone). We identified 308 genes that were upregulated or downregulated due to exposure to a repellant (δ-nonalactone) or an attractant (ε-nonalactone) respectively. Weighted gene coexpression network analysis was used to cluster the genes into 12 modules and filter unconnected genes. Discretized and association rule mining was used to find association between genes thereby predicting the putative function of unannotated genes.

RESULTS AND DISCUSSION

Among the significantly expressed chemosensory genes (FDR < 0.05) in response to Ɛ-nonalactone were gustatory receptors (GrIA and Gr28b), ionotrophic receptors (Ir41a and Ir75a), odorant binding proteins (Obp99b, Obp99d, Obp59a and Obp28a) and the odorant receptor (Or67d). Several non-chemosensory genes with no assigned function in the NCBI database were co-expressed with the chemosensory genes. Exposure to a repellent (δ-nonalactone) did not show any significant change between the treatment and control samples. We generated a coexpression network with 276 edges and 130 nodes. Genes CAH3, Ahcy, Ir64a, Or67c, Ir8a and Or67a had node degree values above 11 and therefore could be regarded as the top hub genes in the network. Association rule mining showed a relation between various genes based on their appearance in the same itemsets as consequent and antecedent.

Intrauterine growth restriction followed by oxygen support uniquely interferes with genetic regulators of myelination

Intrauterine growth restriction (IUGR) and oxygen exposure in isolation and combination adversely affect the developing brain, putting infants at risk for neurodevelopmental disability including cerebral palsy. Rodent models of IUGR and postnatal hyperoxia have demonstrated oligodendroglial injury with subsequent white matter injury (WMI) and motor dysfunction. Here we investigate transcriptomic dysregulation in IUGR with and without hyperoxia exposure to account for the abnormal brain structure and function previously documented. We performed RNA sequencing and analysis using a mouse model of IUGR and found that IUGR, hyperoxia, and the combination of IUGR with hyperoxia (IUGR/hyperoxia) produced distinct changes in gene expression. IUGR in isolation demonstrated the fewest differentially expressed genes compared to control. In contrast, we detected several gene alterations in IUGR/hyperoxia; genes involved in myelination were strikingly downregulated. We also identified changes to specific regulators including TCF7L2, BDNF, SOX2, and DGCR8, through Ingenuity Pathway Analysis, that may contribute to impaired myelination in IUGR/hyperoxia. Our findings show that IUGR with hyperoxia induces unique transcriptional changes in the developing brain. These indicate mechanisms for increased risk for WMI in IUGR infants exposed to oxygen and suggest potential therapeutic targets to improve motor outcomes.Significance StatementThis study demonstrates that perinatal exposures of IUGR and/or postnatal hyperoxia result in distinct transcriptomic changes in the developing brain. In particular, we found that genes involved in normal developmental myelination, myelin maintenance, and remyelination were most dysregulated when IUGR was combined with hyperoxia. Understanding how multiple risk factors lead to WMI is the first step in developing future therapeutic interventions. Additionally, because oxygen exposure is often unavoidable after birth, an understanding of gene perturbations in this setting will increase our awareness of the need for tight control of oxygen use to minimize future motor disability.