Small-RNA Sequencing of Single Cells

Next-generation sequencing has moved beyond the confines of genomic samples obtained from heterogeneous tissues and begun to disseminate information at the single-cell level. The information gathered from these single-cell genomic methods is becoming increasingly important as researchers dive deeper into various genetic disorders and cancers. Now, investigators at the Karolinska Institute have just published data describing a new method that can measure the absolute numbers of short, noncoding RNA sequences in individual embryonic stem cells. This new approach could improve the understanding of how our genes are regulated and different cell types develop.

As a cornerstone of molecular biology, information in our genes is first translated to messenger RNA (mRNA), which functions as a blueprint for proteins. However, our cells also contain noncoding, short RNA sequences that do not contribute to the formation of proteins and whose functions are partly unknown. The best known of these is microRNA (miRNA), which can interact with mRNA and thereby regulate genes and cell function.

“Our knowledge of the function of short RNA molecules is quite general. We have a picture of the general mechanisms, but it is less clear what specific role these molecules play in different types of cells or diseases,” explained senior study investigator Rickard Sandberg, Ph.D., associate professor in the department of cell and molecular biology at the Karolinska Institute and an affiliated member of the Ludwig Cancer Research in Stockholm.

The Karolinska researchers were able to perform their analysis using single-cell transcriptomics, a technique that makes it possible to measure the absolute numbers of short RNA molecules in a cell. Two types of embryonic stem cells were used, intended to mimic the early embryo before and after it has attached to the uterine lining.

“We [discovered] a single-cell method for small-RNA sequencing and apply it to naive and primed human embryonic stem cells and cancer cells,” the authors wrote. “Analysis of microRNAs and fragments of tRNAs [transfer RNAs] and small nucleolar RNAs (snoRNAs) reveals the potential of microRNAs as markers for different cell types and states.”

The findings from this study were published recently in Nature Biotechnology in an article entitled “Single-Cell Sequencing of the Small-RNA Transcriptome.”

The investigators detected scores of small RNAs in both cell states, including miRNA as well as shorter RNA fragments (tRNA and snoRNA) whose function is largely unknown. The researchers also found that large numbers of miRNAs are expressed differently in the two cell states.

“This is basic research and a demonstration that the method works, giving suggestions for further research,” noted lead study author Omid Faridani, Ph.D., a postdoctoral researcher at the Karolinska Institute. “To map the levels of short RNA molecules in a cell is a first step in identifying the particular function of these molecules.”

The researchers were excited by their findings and are optimistic about the clinical applications of their new method.

“We are interested in the role short RNA molecules play during embryonic development. We hope that, with more knowledge, this method could be used to identify which embryos have the best chance to develop, which would then be used to improve current in vitro fertilization (IVF) treatments,” Dr. Sandberg concluded.