Theses Doctoral

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

Martorella, Molly

Transcriptome studies disentangle functional mechanisms of gene expression regulation and may lend key insights into disease mechanisms. However, the cost of RNA-sequencing and types of tissues currently assayed pose major limitations to study expansion and disease-relevant discovery. This thesis develops methods for sampling noninvasive biospecimens for transcriptome studies, investigating their technical and biological characteristics, and assessing the feasibility of using noninvasive samples in transcriptomic and clinical applications.

Chapter 1 explores the technical and biological features of four potential noninvasive sample types (buccal swabs, hair follicles, saliva, and urine cell pellets) in a pilot study of 19 individuals whereby four separate collections of each tissue were performed (i.e. 76 samples/tissue, 304 samples in total). From this data, consistency of library preparation, cell type content, replication of GTEx cis-eQTLs, and disease applications were assessed. In all, hair follicles and urine cell pellets were found to be most promising for future applications.

Chapter 2 investigates the scaling potential of noninvasive sampling in SPIROMICS, a COPD clinical cohort. To do so, 140 hair follicle and 110 buccal swab samples were collected from seven different clinical sites. Consistency of sample quality was observed to be high for hair follicles, and hair cell type abundance estimates were consistent within SPIROMICS and compared to the 19 subject pilot study. Mapping of cis-eQTLs in hair revealed 339 associations not identified in any prior study. These cis-eQTLs show higher replication in GTEx tissues that share cell types with hair follicles, indicating hair follicles may indeed capture gene expression regulatory mechanisms found in more invasive tissue types of the body.

This thesis suggests 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. Moreover, the nature of noninvasive sampling enables complex, longitudinal study designs with greater ability to capture context-dependent mechanisms of genetic regulation not currently able to be interrogated.


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More About This Work

Academic Units
Cellular, Molecular and Biomedical Studies
Thesis Advisors
Lappalainen, Tuuli E.
Przeworski, Molly
Ph.D., Columbia University
Published Here
January 11, 2023