A research team from the Johns Hopkins Kimmel Cancer Center reports it has discovered a metabolic vulnerability in multiple types of cancer cells that bear a common genetic mutation affecting cellular machines called spliceosomes. In test tube and mouse experiments, the researchers learned that the resulting spliceosome malfunction cripples the cells’ chemical process for generating the amino acid serine, making the cancer cells dependent on external (dietary) sources of the amino acid. Among foods high in serine are soybeans, nuts, eggs, lentils, meat and shellfish. Previous studies showed that serine deprivation could limit the growth of cancer in lab-grown cells and in mice with tumors, but what cancers would likely respond to this treatment was unknown. When mice were fed a serine-restricted diet, their tumors (myeloid sarcomas, the solid tumor version of acute myeloid leukemia) shrank, suggesting that a similar dietary intervention might be helpful for patients bearing the mutation. Scientists, led by W. Brian Dalton, MD, PhD, assistant professor of Oncology at the Johns Hopkins University School of Medicine, discovered that culprits are mutations in a protein called SF3B1. SF3B1 makes a protein that forms part of spliceosomes, cellular machines in the nuclei that are essential for the correct translation of the genetic code. Previous studies revealed that mutations in the SF3B1 gene cause the spliceosome to malfunction.
Normally, when a gene’s DNA is read in the nucleus, a copy is made in the form of messenger RNA (mRNA). These strands of genetic code initially contain segments called introns that need to be removed to create more succinct messages. In normal circumstances, the unprocessed mRNA is exported to the cytoplasm, and it encounters spliceosomes, which splice — or cut out — the introns, leaving a clean strand of genetic code to be “translated” into amino acids to form proteins. Mutated spliceosomes, however, don’t follow the splicing cues contained in the mRNA, Dalton says, resulting in garbled RNA messages that are often caught by a proofreading mechanism that destroys the faulty mRNA. The result is a decrease in the protein produced from hundreds of genes. SF3B1 mutations occur with relatively high frequency in blood cancers, including at least 30% of patients with myelodysplastic syndrome, 15% with chronic lymphocytic leukemia and 5% with acute myeloid leukemia. It’s found at lower levels in solid tumors such as breast, lung and prostate cancers, but the higher incidence of these cancers contributes to an overall incidence of the mutation in about 100,000 patients in the USA. Dalton and colleagues wanted to know how that decrease affects cellular function. For the new study, they genetically introduced the most common SF3B1 mutation into noncancerous human breast cells (MCF-10A) grown in the laboratory.
An analysis of the mRNA produced by the cells showed that hundreds of genes were misspliced, and dozens of those had decreased total mRNA expression. A look at the abundance of more than 5,700 newly produced proteins showed increases, decreases and missplicing. When the protein changes were assessed overall, the researchers found that many of the protein levels enhanced by the mutation were involved in mRNA processing, while those with diminished levels were often involved in energy metabolism. Metabolism is simply how nutrients are used to create the molecular building blocks cells need to function and replicate, so it’s super important for cancer cells that want to replicate frequently. One metabolic gene with severely affected activity was phosphoglycerate dehydrogenase (PHGDH), an enzyme critical to the creation of the building block serine. Because mammalian cells are equipped with enzymes that can make serine from other molecules, it is usually considered a nonessential amino acid, meaning it does not need to be consumed regularly in the human diet. But Dr. Dalton wondered if the suppression of PHGDH had changed that. To test the cells’ ability to thrive without serine, the researchers grew mutated cells in a nutritional broth in the lab. This broth lacked serine and glycine, a precursor to serine. The cells grew more slowly under those conditions and produced little serine and glycine of their own.
When the researchers introduced the SF3B1 mutation into human breast cancer cells (T47D), they found that the PHGDH mRNA was misspliced, and its protein levels had decreased. Furthermore, the tumorlike spheres normally formed by the cells were 30% to 40% smaller when grown in nutrient “media” lacking serine and glycine. Partial growth suppression without serine and glycine was also found when the researchers introduced SF3B1 mutations into multiple types of leukemia cells, and the suppression was relieved when they compensated for the loss of PHGDH either genetically or chemically. Finally, the researchers tested their observations in mice implanted with two types of human leukemias (HNT-34, MUTZ-3). As expected, the tumors grew more slowly in mice receiving a serine/glycine-free diet. According to Dr. Dalton, the reliance of these SF3B1 cancers on external serine is a promising trait to exploit because healthy cells maintain their ability to create serine, so they can tolerate its dietary removal. Dalton is a clinical expert in myelodysplastic syndromes (MDS) and acute myeloid leukemia. With his colleague, Amy DeZern, MD, MHS., associate professor of oncology at Johns Hopkins, is designing a feasibility study to see if serine levels can be safely lowered in MDS patients with the SF3B1 mutation. They also plan to see if the number of cells with the mutation decreases in time.
He conculdes; “Early in MDS, disease progression is slow, so there’s a good test window for this dietary intervention. If it works, we would ultimately think about integrating the diet with other standard therapies”. The whole research was published online in the Sept. 30 issue of The Journal of Clinical Investigation.
- Edited by Dr. Gianfrancesco Cormaci, PhD, specialist in Clinical Biochemistry.
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