The obesity rate has more than doubled in the last 30 years, affecting more than one billion people worldwide. This prevalent condition is also linked to other metabolic disorders, including type 2 diabetes, cardiovascular diseases, chronic kidney disease, and cancers. Current treatment options include lifestyle interventions, bariatric surgery, and GLP-1 drugs like Ozempic or Wegovy, but many patients struggle to access or complete these treatments or to maintain their weight loss afterwards. Salk Institute scientists are looking for a new treatment strategy in microproteins, an understudied class of molecules found throughout the body that play roles in both health and disease. In a new study, the researchers screened thousands of fat cell genes using CRISPR gene editing to find dozens of genes that likely code for microproteins -- one of which they confirmed -- that regulate either fat cell proliferation or lipid accumulation. The findings, published in Proceedings of the National Academy of Sciences on August 7, 2025, identify new microproteins that could potentially serve as drug targets to treat obesity and other metabolic disorders. The study also showcases the value of CRISPR screening in future microprotein discovery.  "CRISPR screening is extremely effective at finding important factors in obesity and metabolism that could become therapeutic targets," says senior author Alan Saghatelian, a professor and holder of the Dr. Frederik Paulsen Chair at Salk. "These new screening technologies are allowing us to reveal a whole new level of biological regulation driven by microproteins. The more we screen, the more disease-associated microproteins we find, and the more potential targets we have for future drug development."
When our energy consumption exceeds our energy expenditure, fat cells can grow in both size and number. Fat cells store the excess energy in the form of fatty molecules called lipids. But while some excess storage is manageable, too much can cause fat deposits to accumulate around the body -- leading to whole-body inflammation and organ dysfunction. Many factors regulate this complex energy storage system. The problem is, how do we find them all, and how do we filter for factors that may make good therapeutic candidates?
This has been a longstanding question for Salk scientists. In fact, Salk Professor Ronald Evans has been working on it for decades. Evans is an expert on PPAR gamma, a key regulator of fat cell development and a potent target for treating diabetes. Several drugs have been developed to target PPAR gamma to treat obesity, but they resulted in side effects like weight gain and bone loss. An ideal PPAR gamma-based obesity therapeutic has yet to hit the market. When PPAR gamma drugs fell short, GLP-1 drugs entered the scene. GLP-1 is a peptide small enough to be considered a microprotein, and it serves as a blood sugar and appetite regulator. But, like PPAR gamma, GLP-1 drugs have their own shortcomings, such as muscle loss and nausea. Nonetheless, the popularity of GLP-1 drugs demonstrates a promising future for microprotein drugs in the obesity therapeutic space.
Saghatelian's team is now searching for the next microprotein therapeutic with new genetic tools that bring microproteins out of the "dark." For many years, long stretches of the genome have been considered "junk" and thus left unexplored. But recent technological advances have allowed scientists to look at these dark sections and find a hidden world of microproteins -- in turn, expanding protein libraries by 10 to 30 percent. In particular, the Salk team is using innovative CRISPR screening to scour the "dark" for possible microproteins. This approach is enabling the simultaneous discovery of thousands of potential microproteins involved in lipid storage and fat cell biology, accelerating the search for the next PPAR gamma or GLP-1 drug.
CRISPR screens work by cutting out genes of interest in cells and observing whether the cell thrives or dies without them. From these results, scientists can determine the importance and function of specific genes. In this case, the Salk team was interested in genes that may code for microproteins involved in fat cell differentiation or proliferation.
"We wanted to know if there was anything we had been missing in all these years of research into the body's metabolic processes," says first author Victor Pai, a postdoctoral researcher in Saghatelian's lab. "And CRISPR allows us to pick out interesting and functional genes that specifically impact lipid accumulation and fat cell development."
This latest research follows up on a prior study from Saghatelian's lab. The previous study identified thousands of potential microproteins by analyzing microprotein-coding RNA strands derived from mouse fat tissues. These microprotein-coding RNA strands were filed away to await investigation into their functions.