RNA-Seq analysis of seasonal and individual variation in blood transcriptomes of healthy managed bottlenose dolphins

Morey, Jeanine S.; Neely, Marion G.; Lunardi, Denise; Anderson, Paul E.; Schwacke, Lori H.; Campbell, Michelle R.; Dolah, Frances M. Van

doi:10.1186/s12864-016-3020-8

Cited by 28 publications

(24 citation statements)

References 42 publications

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“…To evaluate the performance of C3, we collected gene expression profiles from four GEO data series (GSE43013 [10], GSE74754 [11], GSE78770 [12], and GSE53393 [13]), which collectively contain data from 13 different species ( B. taurus , C. familiaris , C. porcellus , E. caballus , E. europaeus , F. catus , M. musculus , O. cuniculus , R. norvegicus , S. scrofa , D. rerio , T. truncates , and M. mulatta ) across five different tissue types (brain, kidney, liver, blood, and skeletal muscle). We tested whether C3 could correctly identify the cell type of the samples when compared against a human compendium or a mouse compendium constructed from ENCODE data [7, 8].…”

Section: Resultsmentioning

confidence: 99%

C3: An R package for cross-species compendium-based cell-type identification

Kabir¹,

Djordjevic

O’Connor³

et al. 2018

Preprint

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21Cell type identification from an unknown sample can often be done by comparing its gene 22 expression profile against a gene expression database containing profiles of a large number of 23 cell-types. This type of compendium-based cell-type identification strategy is particularly 24 successful for human and mouse samples because a large volume of data exists for these 25 organisms. However, such rich data repositories often do not exist for most non-model 26 organisms. This makes transcriptome-based sample classification in these species 27 challenging. We propose to overcome this challenge by performing a cross-species 28 compendium comparison. The key is to utilise a recently published cross-species gene set 29 analysis (XGSA) framework to correct for biases that may arise due to potentially complex 30 homologous gene mapping between two species. The framework is implemented as an open 31 source R package called C3. We have evaluated the performance of C3 using a variety of 32 public data in NCBI Gene Expression Omnibus. We also compared the functionality and 33 performance of C3 against some similar gene expression profile matching tools. Our 34 evaluation shows that C3 is a simple and effective method for cell type identification. C3 is 35 available at https://github.com/VCCRI/C3. 36 37 38 set analysis 39 40 41 65from just two species: Homo sapiens (human) and Mus musculus (mouse). In fact, around 66 two thirds of these GSE data sets are derived from human or mouse samples (Figure 1). The 67 other third come from more than 1,300 species, with only 33 species having over 100 GSE 68 (Figure 1). In other words, while it is possible to curate a useful gene expression compendium 69 for human and mouse, it is practically impossible for other species, especially non-model 70 organisms. 72We propose to alleviate this lack of species-specific compendia by performing a cross-73 species cell identification, where a query profile is matched against a database of samples 74 4 which come from different organisms. A key challenge to implementing such a cross-species 75 analysis scheme is that many pairs of species, especially those that are evolutionary distant, 76 can have complex "many-to-many" homologous gene relationships. Failure to properly 77 account for the homology gene mapping can lead to statistical biases [6]. 78 79

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Section: Resultsmentioning

confidence: 99%

C3: An R package for cross-species compendium-based cell-type identification

Kabir¹,

Djordjevic

O’Connor³

et al. 2018

Preprint

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“…In addition to polar bear hemoglobin transcripts, the sgRNAs designed for this study will also target human hemoglobin transcripts making them useful for basic research as well as clinical applications in cancer biology and disease diagnosis ( Fig. S1) (43)(44)(45)(46). Further, the sgRNA sequences used in Long-DASH can be easily adapted to any organisms or gene.…”

Section: Discussionmentioning

confidence: 99%

Depletion of hemoglobin transcripts and long read sequencing improves the transcriptome annotation of the polar bear (Ursus maritimus)

Byrne

Supple

Volden

et al. 2019

Preprint

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Transcriptome studies evaluating whole blood and tissues are often confounded by overrepresentation of highly abundant transcripts. These abundant transcripts are problematic as they compete with and prevent the detection of rare RNA transcripts, obscuring their biological importance. This issue is more pronounced when using long-read sequencing technologies for isoform-level transcriptome analysis, as they have relatively lower throughput compared to short-read sequencers. As a result long-read based transcriptome analysis is prohibitively expensive for non-model organisms. While there are off-the-shelf kits available for select model organisms capable of depleting highly abundant transcripts for alpha (HBA) and beta (HBB) hemoglobin, they are unsuitable for non-model organisms. To address this, we have adapted the recent CRISPR/Cas9 based depletion method (Depletion of Abundant Sequences by Hybridization) for long-read full-length cDNA sequencing approaches that we call Long-DASH. Using a recombinant Cas9 protein with appropriate guide RNAs, full-length hemoglobin transcripts can be depleted in-vitro prior to performing any short-and long-read sequencing library preparations. Using this method, we sequenced depleted full-length cDNA in parallel using both our Oxford Nanopore Technology (ONT) based R2C2 long-read approach, as well as the Illumina short-read based Smart-seq2 approach. To showcase this, we have applied our methods to create an isoform-level transcriptome from whole blood samples derived from three polar bears (Ursus maritimus). Using Long-DASH, we succeeded in depleting hemoglobin transcripts and generated deep Smart-seq2 Illumina datasets and 3.8 million R2C2 full-length cDNA consensus reads. Applying Long-DASH with our isoform identification pipeline, Mandalorion we discovered ~6,000 high-confidence isoforms and a number of novel genes. This indicates there is a high diversity of gene isoforms within Ursus maritimus not yet reported. This reproducible and straightforward approach has not only improved the polar bear transcriptome annotations but will serve as the foundation for future efforts to investigate transcriptional dynamics within the 19 polar bear subpopulations around the Arctic.

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“…In addition to rhythms in hormone production, rhythmic patterns of gene expression may also underlie season and health relationships (18). Studies in humans and other animals have found seasonal patterns of gene expression in tissues such as blood (18)(19)(20) and adipose tissue (18,21), although some of these differences may also reflect seasonal changes in cell populations (22). These rhythms can vary by tissue type and share pathways with the core circadian clock system (23).…”

Section: Introductionmentioning

confidence: 99%

Seasonally Variant Gene Expression in Full-Term Human Placenta

Clarkson-Townsend

Kennedy

Everson

et al. 2020

Preprint

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Seasonal exposures influence human health and development. The placenta, as a mediator of the maternal and fetal systems and a regulator of development, is an ideal tissue to understand the biological pathways underlying relationships between season of birth and later life health outcomes. Here, we conducted a transcriptome-wide association study of season of birth in full-term human placental tissue to evaluate whether the placenta may be influenced by seasonal cues. Of the analyzed transcripts, 583 displayed differential expression between summer and winter births (FDR q<0.05); among these, BHLHE40, MIR210HG, and HILPDA had increased expression among winter births (Bonferroni p<0.05). Enrichment analyses of the seasonally variant genes between summer and winter births indicated over-representation of transcription factors HIF1A, VDR, and CLOCK, among others, and of GO term pathways related to ribosomal activity and infection. Additionally, a cosinor analysis found rhythmic expression for approximately 11.9% of all 17,664 analyzed placental transcripts. These results suggest that the placenta responds to seasonal cues and add to the growing body of evidence that the placenta acts as a peripheral clock, which may provide a molecular explanation for the extensive associations between season of birth and health outcomes.

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RNA-Seq analysis of seasonal and individual variation in blood transcriptomes of healthy managed bottlenose dolphins

Cited by 28 publications

References 42 publications

C3: An R package for cross-species compendium-based cell-type identification

C3: An R package for cross-species compendium-based cell-type identification

Depletion of hemoglobin transcripts and long read sequencing improves the transcriptome annotation of the polar bear (Ursus maritimus)

Seasonally Variant Gene Expression in Full-Term Human Placenta

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