'Nature' Paper About Blood Cell Formation Stirs Scientific Pot
by Nick Miller
Scientists call it “impact factor”—defined by the National Institutes of Health as the average frequency that articles in a given journal are cited by other publications in a particular year.
What this rather dry definition doesn’t necessarily reflect is the degree of spirited debate, newly nurtured collaboration or groundbreaking knowledge produced by a specific study or article. Using any of these standards, a paper about blood cell formation published in Nature last year by Cincinnati Children’s researchers is having significant impact.
“The data we have are a bit controversial and the paper has been viewed over 30,000 times,” explains H. Leighton Grimes, PhD, one of the study’s investigators and a member of the Division of Immunobiology. “The study is making a contribution and people still discuss it at scientific meetings. Some say they don’t believe our data.”
The paper has an Altmetric score of 566, which is in the 99th percentile of all research outputs rated by the organization. To gauge how much online buzz a study generates, Altmetric includes factors such as social media, online media coverage, etc.
Genetic Tug of War
Published Aug. 31, 2016, in Nature (impact factor 38.138) the paper shows blood cells in mice appear to reach their final states following competitions between opposing gene regulatory networks.
From left to right: Nathan Salomonis, PhD, research assistant Andre Olsson (with back to camera), H. Leighton Grimes, PhD, and Harinder Singh, PhD.
As blood cells develop, they experience genetic turbulence that can be observed by turning on alternate lineage genes in individual cells. These are termed multi-lineage states and authors of the study describe the condition as “dynamic instability.” The data show that before becoming a neutrophil or a monocyte, a cell not only goes through a readily observable multi-lineage state but also flits through a rarer bi-stable state.
What cues blood cells to their final types remains unknown, but this research points to the competing gene networks. Although firmly grounded in the realm of basic research, the study could lead to insights about developmental miscues that cause blood or immune system disorders. The production of neutrophils or monocytes, for example, has to be precisely balanced. Having too many or too few of either can be deadly.
The paper was a collaboration between Grimes, Harinder Singh, PhD, Director of Immunobiology, and Nathan Salomonis, PhD, Biomedical Informatics. The study infers that within these genetic tugs of war that determine the fates of blood cells there are still other as yet undiscovered multi-lineage intermediates.
Deep vs. Wide Debate
As Cincinnati Children’s researchers work to provide more evidence for understanding the necessity of multi-lineage cells as key developmental intermediates, and as the mechanism of dynamic instability, they have learned that other research groups either support the paper’s conclusions or reject them.
Key to the Nature paper was use of emerging single-cell RNA sequencing technology, which can identify different genes and regulatory networks within individual cells. Because the technology is fairly new, scientists have not yet established gold standards for how to use it in varying research contexts, according to Grimes.
Some researchers favor sequencing and analyzing thousands of cells without diving as deeply into the different genes that are switching on and off. In this approach, Singh, Salomonis and Grimes sequenced only about 500 cells, and then probed much more deeply into the gene expression patterns and regulatory networks involved in pulling blood cells in one direction or the other.
“Single-cell RNA sequencing is still a relatively new tool, so you can imagine that there will be a lot of back and forth around its use,” Singh says. “This is a major conversation around sequencing thousands of cells at low depth versus fewer cells at deeper depth.”
What makes the Cincinnati Children’s paper in Nature even more compelling—and valid the researchers say—is that it relies on more than single-cell RNA sequencing to draw its conclusions.
“Predictions from single-cell RNA sequencing were tested using different kinds of genetic and molecular experiments,” Singh explains.
More to the Nature Story
A notable feature of the article is a new bioinformatics pipeline developed by Salomonis called ICGS (Iterative Clustering and Guide-Gene Selection).
ICGS gives researchers an automated platform to process and analyze all of the single-cell RNA sequencing data to identify the transitioning or shifting genomic states of cells.
"A number of other researchers are using bioinformatics tools that we developed to test new hypotheses,” says Salomonis. “We also are in touch with other research groups who are using data we generated in the Nature paper to test different hypotheses for the exact cell populations we describe.”