Livia S. Eberlin: Our “DESIUM” preprint is out
Livia S. Eberlin, Professor of Baylor College of Medicine and Co-Founder & Chief Scientific Officer at MS Pen Technologies, shared an article by Trevor M. Godfrey on LinkedIn:
“Our “DESIUM” preprint is OUT!
I am thrilled to share our new method integrating DESI-MS imaging and Visium Spatial Transcriptomics on the same tissue section! The results are beautiful — we were able to identify many spatial RNA-metabolite correlations across human cancer tissues!
Check it out.
Here are some of of our key findings:
- Technical: we show that performing DESI before Visium doesn’t cause significant RNA degradation. As we’ve been saying for years – DESI is a gentle technique, and even though we are extracting metabolites, lipids, and some proteins from tissues, other tissue components remain largely intact. We’ve now shown that doing DESI in the open air, ambient conditions, before Visium does not alter RNA content or distribution. We are pumped!
- Spatial omics: we have often observed different distributions of metabolites and lipids in cancer tissue regions that are histologically identical by pathology – but from our data, molecularly different. Now we have RNA data to confirm and help us understand these patterns! For example, in one lobular breast cancer sample we observed distinct RNA transcript and metabolite localization patterns across three tumor nodules that appeared histologically identical as seen in our NMF component analysis.
- Cancer biology: we found some very interesting correlations between RNA and metabolites in breast and lung cancer tissues. For example, we observed a correlation score of 0.82 between the glycerophosphorylethanolamine (GPEA) and the transcription factor XBP1, known to promote breast cancer and the transcription of genes involved in lipid biosynthesis. In lepidic lung adenocarcinoma, we found a correlation of 0.77 between phosphatidylglycerol PG 22:6_22:5 and the MSLN gene that produces a lipid anchored differentiation antigen present in lung cancers. While these are only spatial correlations, they may point to deeper relationships that can be explored in further studies.
Thanks to all of our amazing collaborators in this study!
Led by my amazing student Trevor Godfrey with contributions from Yasmin Shanneik & Faith Jackobs, in collaboration with Aspect Analytics team Marc Claesen, Alice Ly, Wanqiu Zhang, Thao Tran, Nico Verbeeck and our pathologists Chandandeep Nagi, Maheshwari Ramineni, Baylor College of Medicine.”
Integrating Ambient Mass Spectrometry Imaging and Spatial Transcriptomics on the Same Cancer Tissues to Identify Gene-Metabolite Correlations.
Authors: Trevor M. Godfrey, et al.
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