Nasir M. Stovall

Nasir Stovall, a junior at Stony Brook University studying biology, utilized the spatial transcriptomics tool Slide-seq to map gene expression in immune tissue.

Within the past ten years, many sequencing technologies have been created to help better understand gene expression.

My summer at the Broad was more fruitful than I had ever imagined. This experience positioned me to build on and benefit from new networks I've been able to develop through my research mentor. Additionally, working at the Broad for my first research experience set the bar high for my next scientific research experience, as well as raising the standards I set for myself throughout life.These past sequencing technologies lack spatial information on where genes are expressed, especially at the cellular level. Slide-seq, however, allows for high-resolution spatial mapping of the whole transcriptome. Slide-seq captures transcriptome-wide expression information from intact tissue sections at cellular resolution. Emerging long-read sequencing (LRS) technologies are being integrated with Slide-seq. Applications of LRS with Slide-seq include the field of immunology, targeting specifically B-cell antibodies. The necessity of LRS comes from the need to sequence the whole B-cell antibody transcript, in order to create antibodies in-vitro for both HIV and cancer treatments. Traditional Slide-seq utilizes short-read sequencing (SRS) limited to sequencing only a few hundred bases of DNA. However, B-cell antibody transcripts can be thousands of bases long. LRS is able to sequence several thousands of bases. Sequence information of the whole transcript is necessary to distinguish between regions intended to be reconstructed, from regions intended to remain constant. Both the spatial information obtained from Slide-seq and the sequencing information produced from LRS offer spatial maps of tissues for entire antibody sequences, as well as more insight into the sequences of target antigens near neighboring immune cells. Generally, any form of research with the purpose of sequencing an entire transcript and understanding the spatial significance of the transcript will benefit from the use of Slide-Seq and LRS.

Project: Applications of emerging sequencing technologies to map gene expression in intact immune tissue

Mentors: Robert Stickels and Dylan Cable, Macosko Lab, Stanley Center for Psychiatric Research