08:36pm Monday 06 July 2020

Research Finds 'Encyclopedia' of Genes That Regulate Blood Cell Development

The discovery emerged from so-called “junk” DNA, sequences in the genome thought to have no real purpose.

The scientists have completed the functional analysis of one of the DNA segments identified, which they know now to be required for blood cell precursors — the cells that give rise to the different types of blood cells — to function properly.

“Identifying new mechanisms that reveal potential therapeutic targets to control the production or function of precursor cells is so important. Everyone is trying to find ways to expand blood stem cells,” said Emery Bresnick, Kellett Professor of Cell and Regenerative Biology at the UW School of Medicine and Public Health. “Cord blood and bone-marrow stem cells have immediate therapeutic relevance; we need to find new ways to expand them, because the existing approaches are less than satisfactory.”

When the Human Genome Project pulled the veil away from the 3 billion base pairs that form our genetic makeup, they found more than 20,000 genes, known as coding DNA, that encode the proteins we need to perform the vast assortment of biological functions: responding to stimuli, speeding chemical reactions, replicating DNA, moving molecules from point A to point B.

But that was followed by the disheartening notion that only two percent of our genome directly produces all those vital proteins. At the outset, it seemed the remaining 98 percent was a genetic junkyard, responsible for seemingly nothing.

But within the last decade, researchers are removing the “junk” from that hasty labeling. The instructions embedded in noncoding DNA are essential for controlling the remaining coding DNA. If the coding DNA defines how a car navigates a corner, the noncoding DNA regulates how far and in what direction the steering wheel turns.

When noncoding DNA doesn’t regulate coding DNA properly, the car doesn’t make the turn as needed — perhaps the steering wheel is turned too far or not far enough to the left, or it’s turned to the right — and serious consequences can occur.

“We’re undertaking the broad challenge of assigning function to parts of the genome previously considered junk,” said Kyle Hewitt, an American Heart Association-funded postdoctoral fellow in the Bresnick group at the UW Blood Research Program and UW Carbone Cancer Center. “Our aim was to develop an encyclopedia of non-coding DNA segments that control blood cell formation and function.”

Hewitt and Bresnick aren’t probing through the undefined 98 percent blindly. Bresnick’s group has extensively studied how GATA-2 — one member of the GATA family of proteins implicated in cell growth, differentiation and cancer — is important for hematopoiesis, the formation of blood cell components derived from blood stem cells. And while GATA factors bind to millions of sequences in the genome, Bresnick’s group had previously identified a single site that binds GATA-2 and regulates blood stem cell genesis.

So armed with the unique expertise of Sunduz Keles, professor of biostatistics and medical informatics at the UW School of Medicine and Public Health, with interests in genome science, Hewitt was able to identify similar DNA segments across the genome. Because the Bresnick group has already determined that the GATA-2-binding DNA element is required to create blood stem cells, the team used that site as a guide to narrow the search.

The hunt yielded just under 800 similar sites, and the Keles’ group created profiles of the types of proteins that bind to each site to compare against the original GATA-2-binding site.

To show whether any of these sites have a vital role in blood cell precursors, the team prioritized a small subset of noncoding sequences using sophisticated computational and experimental analysis.

“We removed several prioritized sites in a cell line using CRISPR-Cas9 and TALEN gene editing techniques with the help of Jin-Soo Kim, a collaborator from Seoul National University and an expert in gene editing technologies,” said Hewitt. “For one particular site, when I reduced its expression in blood cell precursors, their ability to produce blood cell progeny was impaired.”

The results suggest that Samd14 is required for blood precursors to function properly.

“The analysis of this gene was a proof of principle that our strategy has identified new regulators of blood cell development, and it is likely that our non-coding DNA encyclopedia will yield many more important discoveries,” said Hewitt.

The gene encodes a protein that stimulates the Stem Cell Factor/c-Kit signalling pathway, which promotes cell growth and survival.

“We have every reason to believe that a causal relationship exists; Samd14 regulates the progenitors by controlling Stem Cell Factor/c-Kit signalling,” said Bresnick.

c-Kit receptor dysfunction and mutation is often a cause of leukemias and other blood cell disorders, including mastocytosis. Like many other receptors, c-Kit requires a molecule to turn it ‘on’ and initiate crucial cell functions. Many leukemias have mutations that cause the receptor to be stuck in the ‘on’ position, that underlie disease progression. Mastocytosis disorders (involving deregulation of mast cells involved with allergy and anaphylaxis) have a similar dysfunction.

Now knowing that the protein product of Samd14 enhances c-Kit signalling, Bresnick predicts that this mechanism may provide a new approach to treat disorders resulting from uncontrolled c-Kit signaling.

The study was released online this week, published by the journal Molecular Cell.

University of Wisconsin School of Medicine and Public Health

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