Full-length-transcriptomic analysis in mice and human heart using Single-Molecule Real-time Sequencing (SMRT) identified 15 novel isoforms and a novel promoter region of PGC1-alpha

Background

Alternative splicing is a process by which exons within a pre-mRNA are joined or skipped, resulting in isoforms being encoded by a single gene. Alternative Splicing affecting transcription factors may have substantial impact on cellular dynamics. The PPARG Coactivator 1 Alpha (PGC1-α), is a major modulator in energy metabolism. Data from murine skeletal muscle revealed distinctive isoform patterns giving rise to different phenotypes, i.e. mitogenesis and hypertrophy. Here, we aimed to establish a complete dataset of isoforms in murine and human heart applying single-molecule real-time (SMRT)-sequencing as novel approach to identify transcripts without need for assembly, resulting in true full-length sequences. Moreover, we aimed to unravel functional relevance of the various isoforms during experimental ischemia reperfusion (I/R).

Methods

RNA-Isolation was performed in murine (C57Bl/6J) or human heart tissue (obtained during LVAD-surgery), followed by library preparation and SMRT-Sequencing. Bioinformatic analysis was done using a modified IsoSeq3-Pipeline and OS-tools. Identification of PGC1-α isoforms was fulfilled by similarity search against exonic sequences within the full-length, non-concatemere (FLNC) reads. Isoforms with Open-Reading-Frame (ORF) were manually curated and validated by PCR and Sanger-Sequencing. I/R was induced by ligature of the LAD for 45 min in mice on standard chow as well as on high-fat-high-sucrose diet. Area At Risk (AAR) and remote tissue were collected three and 16 days after I/R or sham-surgery (n=4 per time point). Promotor patterns were analyzed by qPCR.

Results

Deciphering the full-length transcriptome of murine and human heart resulted in ∼60000 Isoforms with 99% accuracy on mRNA-sequence. Focusing on murine PGC1-α-isoforms we discovered and verified 15 novel transcripts generated by hitherto unknown splicing events. Additionally, we identified a novel Exon 1 originating between the known promoters followed by a valid ORF, suggesting the discovery of a novel promoter. Remarkably, we found a homologous novel Exon1 in human heart, suggesting conservation of the postulated promoter.

In I/R the AAR exhibited a significant lower expression of established and novel promoters compared to remote under standard chow 3d post I/R. 16d post I/R, the difference between AAR & Remote equalized in standard chow while remaining under High-Fat-Diet.

Conclusion

Applying SMRT-technique, we generated the first time a complete full-length-transcriptome of the murine and human heart, identifying 15 novel potentially coding transcripts of PGC1-α and a novel exon 1. These transcripts are differentially regulated in experimental I/R in AAR and remote myocardium, suggesting transcriptional regulation and alternative splicing modulating PGC1-α function in heart. Differences between standard chow and high fat diet suggest impact of impaired glucose metabolism on regulatory processes after myocardial infarction.

Funding Acknowledgement

Type of funding source: Public grant(s) – National budget only. Main funding source(s): Collaborative Research Centre 1116 (German Research Foundation)

Indocyanine green angiography for evaluation of gastric conduit perfusion during esophagectomy--first experience

BACKGROUND

A complication of esophageal surgery is leakage at the anastomosis site and one of the factors involved in this complication is poor blood flow in the distal portion of the tube. The aim of this study was to evaluate the feasibility of indocyanine green fluorescence imaging as a method of determining the perfusion of the gastric conduit after esophagectomy.

METHODS

We analysed 15 consecutive patients who underwent transhiatal esophagectomy (THE) due to cancer. All of the patients had reconstruction of the gastrointestinal tract using the gastric conduit. Before performing the anastomosis, the blood flow in the area of the tube was evaluated using intravenous indocyanine green and observing its vascular flow with a camera equipped with an infrared laser.

RESULTS

In all cases it was possible to visualize the vascular flow of indocyanine green within the region of the gastric tube. The fluorescence imaging system showed vascular insufficiency of the distal gastric conduit in 4 patients--in all of these patients the anastomosis was performed end-to-side and there was no subsequent leak. Leakage at the anastomosis site was observed in 1 patient (6.66%). The leak was observed in the 9th postoperative day, despite visualization of a good vascular supply of the tube.

CONCLUSIONS

Indocyanine green fluorescence imaging of gastric tube allows for intraoperative modifications, but it must be noted that the patient's comorbidities and general health may also increase the risk of anastomosis leakage.