Update: evidence of a broad histamine footprint on the human exercise transcriptome

Update: evidence of a broad histamine footprint on the human exercise transcriptome In the article by Romero et al. (), it was demonstrated that the human response to exercise includes an altered expression of thousands of protein‐coding genes, and much of this response appears to be driven by histamine. More recently, we have been mining this data for additional insight to guide future studies. In so doing, we noted that the mRNA for tissue necrosis factor alpha (TNF) was not present in the dataset of protein‐coding genes originally published in this article. Since the mRNA signal for TNF has been documented previously in human skeletal muscle tissue, we knew this warranted a deeper investigation. We went back to the raw Illumina fastq files, and found evidence that the TNF sequence was present in that level of the data.In short, we noticed that the reads which aligned to TNF had aligned to multiple locations in the reference. The reference sequence file used for alignment contained several alternate haplotype sequences for the MHC locus, which contains the TNF gene sequence. As the analysis package used in the original report was conservative by design, these hits which mapped to multiple locations were disregarded by the program and not carried forward to the dataset of protein‐coding genes.Therefore, to determine the response of TNF to the combination of exercise and histamine blockade and explore whether additional protein‐coding genes had likewise been impacted by this process, we re‐analysed the raw sequence fastq file with a newer version of STAR aligner (2.5.2a) that was not available at the time of the original report. This new version of STAR does not report alignments found for multiple haplotype sequences in the reference as secondary alignments. An additional 1522 protein coding genes (8% more) were identified in the dataset, but most of the additional genes were not impacted by exercise and histamine blockade. While this does not radically change the results or conclusions of the original report by Romero et al. (), it does provide additional information on a few genes that were previously excluded from analysis (for example, it identified 806 rather than 795 genes which were differentially expressed between the control and blockade condition at 3 h post‐exercise). In this dataset, TNF expression increased in response to exercise, but was unaffected by histamine blockade.As this new analysis may be of use to others, the updated sequence data, counts for protein‐coding genes, and supplemental tables S1 to S6 for this study have been deposited in the NCBI Gene Expression Omnibus website (GEO, http://www.ncbi.nlm.nih.gov/geo) and are accessible through GEO Series accession number GSE71972.ReferenceRomero SA, Hocker AD, Mangum JE, Luttrell MJ, Turnbull DW, Struck AJ, Ely MR, Sieck DC, Dreyer HC & Halliwill JR (2016). Evidence of a broad histamine footprint on the human exercise transcriptome. J Physiol 594, 5009–5023. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png The Journal of Physiology Wiley
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Publisher
Wiley Subscription Services, Inc., A Wiley Company
Copyright
Journal compilation © 2018 The Physiological Society
ISSN
0022-3751
eISSN
1469-7793
D.O.I.
10.1113/JP275834
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Abstract

In the article by Romero et al. (), it was demonstrated that the human response to exercise includes an altered expression of thousands of protein‐coding genes, and much of this response appears to be driven by histamine. More recently, we have been mining this data for additional insight to guide future studies. In so doing, we noted that the mRNA for tissue necrosis factor alpha (TNF) was not present in the dataset of protein‐coding genes originally published in this article. Since the mRNA signal for TNF has been documented previously in human skeletal muscle tissue, we knew this warranted a deeper investigation. We went back to the raw Illumina fastq files, and found evidence that the TNF sequence was present in that level of the data.In short, we noticed that the reads which aligned to TNF had aligned to multiple locations in the reference. The reference sequence file used for alignment contained several alternate haplotype sequences for the MHC locus, which contains the TNF gene sequence. As the analysis package used in the original report was conservative by design, these hits which mapped to multiple locations were disregarded by the program and not carried forward to the dataset of protein‐coding genes.Therefore, to determine the response of TNF to the combination of exercise and histamine blockade and explore whether additional protein‐coding genes had likewise been impacted by this process, we re‐analysed the raw sequence fastq file with a newer version of STAR aligner (2.5.2a) that was not available at the time of the original report. This new version of STAR does not report alignments found for multiple haplotype sequences in the reference as secondary alignments. An additional 1522 protein coding genes (8% more) were identified in the dataset, but most of the additional genes were not impacted by exercise and histamine blockade. While this does not radically change the results or conclusions of the original report by Romero et al. (), it does provide additional information on a few genes that were previously excluded from analysis (for example, it identified 806 rather than 795 genes which were differentially expressed between the control and blockade condition at 3 h post‐exercise). In this dataset, TNF expression increased in response to exercise, but was unaffected by histamine blockade.As this new analysis may be of use to others, the updated sequence data, counts for protein‐coding genes, and supplemental tables S1 to S6 for this study have been deposited in the NCBI Gene Expression Omnibus website (GEO, http://www.ncbi.nlm.nih.gov/geo) and are accessible through GEO Series accession number GSE71972.ReferenceRomero SA, Hocker AD, Mangum JE, Luttrell MJ, Turnbull DW, Struck AJ, Ely MR, Sieck DC, Dreyer HC & Halliwill JR (2016). Evidence of a broad histamine footprint on the human exercise transcriptome. J Physiol 594, 5009–5023.

Journal

The Journal of PhysiologyWiley

Published: Jan 15, 2018

References

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