A mutation in a newly discovered small protein is connected to a significant increase in the risk for Alzheimer’s disease (AD), according to the results of a study, carried out in humans and in animal models, and headed by researchers at the University of Southern California (USC), Los Angeles. The findings expand the number of known gene targets for AD, and present a potential new avenue for treatment. The protein, called SHMOOSE, is a tiny microprotein encoded by a newly discovered gene within the cell’s energy-producing mitochondria.

The study showed that a mutation within the gene partially inactivates the SHMOOSE microprotein and that this was associated with a 20–50% higher risk for AD across four different cohorts. They suggest that nearly a quarter of people of European ancestry have the mutated version of the protein. They also noted that both the high prevalence of the previously unidentified SHMOOSE mutation, and the substantial risk associated with it, differentiate this microprotein from other proteins involved in AD. Apart from APOE4—the most potent known genetic risk factor for the disease—only a limited number of other gene mutations have been identified, and these only mildly increased risk by less than 10%. in addition, the SHMOOSE microprotein is approximately the size of the insulin peptide, so it could, potentially, be easily administered, which increases its therapeutic potential.

“This discovery opens exciting new directions for developing precision medicine-based therapies for Alzheimer’s disease, focusing on SHMOOSE as a target area,” said Pinchas Cohen, MD, professor of gerontology, medicine, and biological sciences, and senior author of the team’s study, which is published in Molecular Psychiatry. “Administration of SHMOOSE analogs in individuals who carry the mutation and produce the mutant protein may prove to have benefit in neurodegenerative and other diseases of aging.” Cohen and colleagues reported their findings in a paper titled, “Mitochondrial DNA variation in Alzheimer’s disease reveals a unique microprotein called SHMOOSE,” in which they concluded, “Altogether, SHMOOSE has vast implications for the fields of neurobiology, Alzheimer’s disease, and microproteins.”

For decades, scientists have studied biology mostly by considering a set of 20,000 large protein-coding genes. However, new technology has highlighted hundreds of thousands of potential genes that encode smaller microproteins. These are biologically active peptides, encoded by small open reading frames (sORFs), of around 100 codons or fewer. So while most microproteins have been missed by past genomic and proteomic studies, as the authors noted, “… now thousands have been identified due to refined techniques … Mitochondrial-encoded microproteins are a potential part of AD that have not been heavily studied.”

The USC Leonard Davis School of Gerontology say they are leaders in the study of microproteins, especially those coded within the mitochondrial genome. In 2003, Cohen and his colleagues were one of the three research teams to independently discover the protein humanin, which appears to have protective health effects in Alzheimer’s, atherosclerosis, and diabetes.  In the past few years, the Cohen laboratory discovered several other mitochondrial microproteins, including, small humanin-like peptides, or SHLPs, and a microprotein called MOTS-c, an exercise-mimetic peptide that has entered clinical trials for obesity and fatty liver.

Brendan Miller, PhD, first author of the newly reported study, used big data techniques to identify genetic variations in mitochondrial DNA associated with disease risk. After analyses revealed that a gene mutation increased Alzheimer’s disease risk, brain atrophy, and energy metabolism, Miller and his colleagues discovered that the mutated gene (which they subsequently designated SHMOOSE.D47N) coded for a mutated SHMOOSE microprotein. The researchers stated that SHMOOSE is the first mitochondrial-DNA-encoded microprotein to have been detected using both antibodies and mass spectrometry. “We identified SHMOOSE as the first biologically active mitochondrial-encoded microprotein detected by mass spectrometry, immunoblot, and ELISA,” they wrote. “… we detected two unique SHMOOSE-derived peptide fragments in mitochondria by using mass spectrometry—the first unique mass spectrometry-based detection of a mitochondrial encoded microprotein to date.”

The team’s further study of the mutated and default forms of SHMOOSE indicated that the microprotein appears to modify energy signaling and metabolism in the central nervous system. It was found in mitochondria of neurons and its levels in cerebrospinal fluid correlated with biomarkers of Alzheimer’s disease. “… cerebrospinal fluid (CSF) SHMOOSE levels in humans correlated with age, CSF tau, and brain white matter volume,” they continued. A variety of cell culture and animal experiments showed that SHMOOSE alters energy metabolism in the brain in part by inhibiting a crucial part of the mitochondria, the inner mitochondrial membrane. “… SHMOOSE acted on the brain following intracerebroventricular administration, differentiated mitochondrial gene expression in multiple models, localized to mitochondria, bound the inner mitochondrial membrane protein mitofilin, and boosted mitochondrial oxygen consumption.”

Miller said the findings highlight the importance of the relatively new field of microproteins. “The field of microproteins is still so new,” Miller said. “We don’t yet know how many microprotein genes are even functional, and the cost to study a potential microprotein one by one from a list of thousands is just too expensive and inefficient. The approach my colleagues and I used to detect SHMOOSE shows the power of integrating big genetics data with molecular and biochemical techniques to discover functional microproteins.”

The results also demonstrated that mitochondrial DNA variants can associate with several neurobiological phenotypes, and that mitochondrial DNA variants can be mapped to sORFs that encode biologically functional microproteins. “We identified SHMOOSE as the first biologically active mitochondrial encoded microprotein detected by mass spectrometry, immunoblot, and ELISA,” they noted. The correlation among CSF levels of SHMOOSE, CSF AD-related biomarkers (e.g., tau), and brain white matter, also suggests that SHMOOSE has potential as a biomarker, the authors commented. “Finally, SHMOOSE is yet another microprotein of a growing number that modify mitochondrial biology.”

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