New technology has allowed scientists to create the most comprehensive map of B-cell development to date, according to a paper published in Cell.
The team combined emerging technologies for studying single cells with an advanced computational algorithm to map human B-cell development.
They believe their approach could improve researchers’ ability to investigate development in all cells and make it possible to identify rare aberrations that lead to disease.
“There are so many diseases that result from malfunctions in the molecular programs that control the development of our cell repertoire and so many rare, yet important, regulatory cell types that we have yet to discover,” said study author Dana Pe’er, PhD, of Columbia University in New York.
“We can only truly understand what goes wrong in these diseases if we have a complete map of the progression in normal development.”
Combining technologies
Dr Pe’er and her colleagues used mass cytology to observe cells in a bone marrow sample. In a single experiment, mass cytology can measure 44 molecular markers simultaneously in millions of individual cells. This provides data that can be used to compare, categorize, and order cells, as well as identify the molecular systems responsible for development.
Taking advantage of this data required the researchers to develop new mathematical and computational methods for interpreting it. Just as one can represent a physical object in 3 dimensions, the Pe’er lab’s approach involved thinking of the 44 measurements as a 44-dimensional geometric object.
So they created a new computational algorithm called Wanderlust, which uses mathematical concepts from a field called graph theory to reduce this high-dimensional data into a simple form that is easier to interpret. Wanderlust converts the developmental marker measurements in each cell into a single, 1-dimensional value that corresponds to the cell’s place within the chronology of development.
“Our body has trillions of cells of countless different types, each type bearing different molecular features and behavior,” Dr Pe’er noted. “This complexity expands from a single cell in a carefully regulated process called development.”
“This regulation creates patterns and shapes in the high-dimensional data we measure. By using Wanderlust to analyze these data, we can find the pattern and trace the trajectory that cellular development follows.”
Mapping B-cell development
To test their approach, the researchers studied development in human B cells. The team used mass cytometry to profile 44 markers in a cohort of approximately 200,000 healthy immune cells that were gathered from a single bone marrow sample.
In each cell, they measured surface markers that help identify cell type, as well as markers inside the cell that can reveal what the cell is doing, including markers for signaling, the cell cycle, apoptosis, and genome rearrangement.
Using Wanderlust to analyze the high-dimensional data provided by mass cytometry, the researchers accurately ordered the entire trajectory of 200,000 cells according to their developmental chronology. Wanderlust captured and correctly ordered all of the primary molecular landmarks known to be present in human B-cell development.
The algorithm also pinpointed a number of previously unknown regulatory signaling checkpoints that are required for human B-cell development, as well as uncharacterized subtypes of B-cell progenitors that correspond to developmental stages.
The researchers identified rare, previously unknown signaling events involving STAT5 that occurred in just 7 out of 10,000 cells. The team found that disrupting these signaling events using kinase inhibitors fully stalled the development of B cells.
Identifying and characterizing the regulatory checkpoints that control and monitor cell fate can have many practical applications, the researchers said, including the development of new diagnostics and therapeutics.
Furthermore, the team’s mapping process can be applied to any type of cell. They believe their method offers the possibility of studying normal development as well as the processes responsible for any kind of developmental disease.
“This current project is a landmark, both in the study of development and in single-cell research, and has completely changed the way I think about science,” Dr Pe’er said. “A fire has been lit, and these findings are just the tip of the iceberg of what is now possible.”
