Spatial Metatranscriptomics - Gene Expression in the Gut Microbiome
Spatial transcriptomics is a groundbreaking research method that allows spatial mapping of gene expression within specific areas of our tissues. Earlier this month, KTH students visited the spatial research unit at SciLifeLab to learn more about how this technology is being used to improve our understanding of gene expression in chronic gut disorder, such as Intestinal Bowel Disease (IBD).
Spatial transcriptomics is a RNA sequencing method that profiles the gene expression of tissues. Tissue samples are placed onto a glass slide that is engineered with barcoded oligonucleotides, binding the RNA sequences in the tissue to generate a complementary DNA library. The gene transcripts are assigned to spatial barcodes and then visualized as a high-quality and color-coded spatial map overlaid on the tissue.
Traditional bulk methods measure gene expression from homogenized biological samples, producing an average signal and therefore cannot map the precise location of gene activity within the tissue. Spatial transcriptomics overcomes this limitation as gene expression is quantified while their spatial location is preserved within tissue sections.
With spatial metatranscriptomics, the host transcriptome and the microbiome is characteracterized simultaneously. This method is applied to study microbiome interactions in host cells and human gut tissue. In their ongoing research, the group investigates how different diets (e.g. fiber-rich and seaweed-rich) change gene expression at specific areas of the gut by using host and microbial models. The goal is to identify which diets may be beneficial for IBD by studying how they reshape the microbiome and whether they reduce intestinal inflammation.
It is also of interest to study how gene expression is influenced by extreme environments. In collaboration with NASA, the SciLifeLab unit has analyzed brain samples from mice flown in NASA’s Rodent Research program on the International Space Station. The results from that study will provide further understanding on how extreme spaceflight environment (e.g microgravity radiation) affects brain tissue, and may support the development of gut resilience for future astronauts.
The visit to SciLifeLab raised awareness on the modern of RNA-sequencing tools and how it is branching out from conventional methods, enabling new insights into complex tissues and disease, including diet-driven changes in the gut microbiome.
Visit the Spatial Transcriptomics unit website here.
Text by: Catherine Shi