STORM-seq Reveals Differentiation Trajectories of Primary Human Fallopian Tube Epithelium

• Published in: bioRxiv
• Main Authors: Johnson, Benjamin K, Rhodes, Mary, Wegener, Marc, Himadewi, Pamela, Foy, Kelly, Schipper, Joshua L, Siwicki, Rebecca A, Rossell, Larissa L, Siegwald, Emily J, Chesla, Dave W, Sheridan, Rachael Tc, Adams, Marie, Triche, Timothy J, Shen, Hui
• Format: Paper
• Language: English
• Published: Cold Spring Harbor Cold Spring Harbor Laboratory Press 05.09.2022
• Subjects: Carcinogenesis; Epithelium; Fallopian tube; Fallopian tubes; Non-coding RNA; Progenitor cells; Stem cells; Transcription; Transcriptomes
• ISSN: 2692-8205; 2692-8205
• DOI: 10.1101/2022.03.14.484332

We present Single-cell TOtal RNA Miniaturized sequencing (STORM-seq), a full-length single-cell ribo-reduced RNA sequencing protocol, optimized to profile thousands of cells per run. Using off-the-shelf reagents and random hexamer priming, STORM-seq recovers comprehensive RNA profiles from single cells with library complexity approaching that of bulk RNA-seq. STORM-seq identifies thousands of additional coding and non-coding transcripts not detected by existing methods, and recovers clinically relevant structural variants at the single-cell level. We apply STORM-seq to primary human Fallopian tube epithelium (FTE), a complex solid tissue, key to both human reproductive biology and ovarian carcinogenesis. In differentiation trajectory analyses, the improved resolution from STORM-seq reveals intermediate/transitional cell states, and a putative progenitor cell population. The results support a trajectory from a bipotent progenitor population to ciliated and secretory cell types in normal FTE. These findings are consistent across human subjects, sequencing depths, and platforms. Long intergenic non-coding RNAs (lincRNAs) appear as key driver genes in both ciliated and secretory lineage trajectories, underscoring the importance of both coding and non-coding RNA in this tissue. By capturing essentially complete individual cellular transcriptomes, STORM-seq sheds new light on the transcriptional programs that establish cellular state and fate in complex tissues. Competing Interest Statement The authors have declared no competing interest. Footnotes * Figure 1 revised