Research From the Lewis Katz School of Medicine at Temple University and Fox Chase Cancer Center Reveals New Insights Into Protein Phosphatases That Could Assist in Hunt for New Cancer Therapies

Xavier Graña, PhD

A new study published in the prestigious journal Nature Communications by researchers from the Lewis Katz School of Medicine at Temple University and the Fox Chase Cancer Center sheds light on how protein phosphatases target proteins and help regulate cell cycle progression, work that could help lay the groundwork for potential new targets for cancer therapies. 

Researchers found that protein phosphatase 2A, or PP2A, an enzyme known to play a role in activating a family of tumor suppressors found in retinoblastoma, binds to a previously unknown helix-shaped motif on an inhibitor called FAM122A. This helix-shaped motif binds a subunit of PP2A named B55α. They also found a second adjacent short helix that “docks” directly into the active site of PP2A, inhibiting the enzyme.

“While it is early, identifying the key substrates of PP2A in checkpoint pathways and the mode of recruitment and regulation of the FAM122A, PP2A, and B55α could illuminate novel targets for treatment of certain cancers and help us to better understand the effects of the current drugs that target these pathways,” said lead author Xavier Graña, PhD, a professor at the Fels Cancer Institute for Personalized Medicine at the Lewis Katz School of Medicine. He is also a professor in the Cancer Signaling and Microenvironment Research Program at Fox Chase. 

Protein kinases have been widely studied and are the targets of many cancer therapies. These enzymes attach phosphate groups to proteins called substrates, playing a key role in cell growth and signaling. Protein phosphatases are an essential counterpart to this process, removing phosphate groups from substrates to help regulate the cell cycle. However, these enzymes are far less studied and understood.

In a previous study of PP2A, the researchers identified a protein sequence pattern, or motif, found on PP2A/B55 substrates and the surface area of B55, where this motif binds to reach the PP2A enzyme. They proposed that this motif, which they thought was linear, was likely present in other PP2A/B55 substrates. This work was done with Roland L. Dunbrack Jr., PhD, a professor in the Cancer Signaling and Microenvironment Research Program, and other collaborators at Fox Chase.

For the new study, which Graña also conducted with Dunbrack and colleagues at Fox Chase, Temple, and other institutions, the team first searched for other proteins that had similar sequence motifs. They zeroed in on a protein called FAM122A, which had previously been found to act as an inhibitor for PP2A.

Researchers then used a modeling tool called AlphaFold2, which uses artificial intelligence to predict how proteins fold into their final shape, to learn more about the protein’s structure. This resulted in a surprising finding — that the motif they believed was a linear pattern actually had the shape of a short helix that contacted B55. AlphaFold2 revealed another surprise: a second adjacent helix forming an L shape that was positioned where it would contact the active site of PP2A.

Researchers then conducted experiments in cells and confirmed that the FAM122A inhibitor helps regulate cell cycle progression during the early stages of the cell cycle. They also showed that it is involved in key checkpoints that monitor DNA integrity during the DNA synthesis phase of the cell cycle.

“Our data suggest that FAM122A may control the activity of checkpoint kinases activated as a result of DNA damage, supporting additional functions for PP2A/B55α in these critical pathways, which are the target of intense investigation as anticancer agents,” Graña said.

Researchers also found evidence that FAM122A may be recruited to the sites of DNA damage, suggesting a mechanism for localized control of PP2A/B55α.

The team plans to continue its work to discover other substrates of PP2A and B55α, and better understand the mechanism by which the phospho-group is presented to the enzyme’s active site. They also plan to study how FAM122A is recruited to the locations of DNA damage and which substrates are involved in DNA damage checkpoints.

The paper, “FAM122A Ensures Cell Cycle Interphase Progression and Checkpoint Control by Inhibiting B55α/PP2A Through Helical Motifs,” was published in Nature Communications.