Noninvasive, low-cost RNA-sequencing enhances discovery potential of transcriptome studies

Author(s): Molly Martorella,Renee Garcia-Flores,Tuuli Lappalainen

Affiliation(s): New York Genome Center

Social media: https://twitter.com/SubmarineGene

The study of large-scale transcriptomics has great potential in elucidating the effects of genetic variation and has a vital role in achieving the objectives of precision medicine. It can help to identify biomarkers that can indicate disease risk, onset, prognosis, and treatment response, discover new therapies, and assess the effect of environmental or pharmacological exposures. However, integrating transcriptomic data with genetic information is a challenging area of research. Expanding transcriptomic studies to include large, multi-ancestry sample sizes and more comprehensive sampling methodologies, is necessary to capture meaningful biology and mitigate health disparities. However, current limitations include the high cost of processing sufficient sample sizes for discovery and the relatively limited selection of sample collection options. Collecting samples directly from the relevant tissue types provides more biologically relevant data. But, current approaches include surgical extractions and post-mortem donations, resulting in high costs, complicated logistics, and low participant enrollment, which is often biased against vulnerable and minority populations. Noninvasive sample types such as buccal swabs, hair follicles, saliva, and urine cell pellets may offer a solution. In this work we investigated the biological utility of noninvasive sample types and identified sources of technical variance. We explored the possibility of using invasive tissue type proxies and demonstrated their use in transcriptomic and disease-relevant applications. For this presentation at the Bioconductor Conference, I am gonna focus on the possibility of using these samples to identify the microbiome of the tissues we used, and for sex-based differential expression. The results from the microbiome analysis show distinct microbial signatures across the noninvasive tissues that support previously known microbiota of the oral cavity, human skin, and genitourinary tract. These findings support noninvasive samples may bear biological utility in follow-up microbiome studies using microbiome-specific or total RNA library preparations. In the sex-based differential expression as one of the top results we identified estrogen response as greatly enriched in females, among others. Which demonstrates the potential for noninvasive samples to elucidate underlying biology in a variety of potential contexts and assays. Overall, of the four tissues we studied (buccal swabs, hair follicles, saliva, and urine cell pellets), we found hair follicles and urine cell pellets have the highest quality and were most consistently processed. In all, we demonstrated use of noninvasive sample types has potential to greatly augment efforts to understand the regulatory architecture of the human genome. We anticipate future use of noninvasive sampling will facilitate discovery by increasing sample sizes in more diverse populations and in tissues with greater cell type diversity and biological relatedness to disease mechanisms. But, fully scaling the use of noninvasive samples will require further testing with larger sample sizes in clinical settings. In all, we demonstrated use of noninvasive sample types has potential to greatly augment efforts to understand the regulatory architecture of the human genome. I, Renee Garcia-Flores, am a young Mexican scientist. I joined this project in my last year of my undergraduate (2021-2022) and I will present the results of my work there. I’m currently interested in gaining more experience as a bioinformatician and in the last year I have been involved in activities such as helping teach https://lcolladotor.github.io/rnaseq_LCG-UNAM_2023/ as well as other research projects.