Just as genetic variants can be tied to altered gene expression, they can also be pegged to protein changes. Researchers led by Carlos Cruchaga and Oscar Harari, both at Washington University School of Medicine, St. Louis, linked Alzheimer's disease-associated loci to altered protein amounts in brain tissue, cerebrospinal fluid, and plasma from people with AD. Using these protein quantitative trait loci (pQTLs), they identified risk genes from GWAS hits—and, while they were at it, perhaps even some candidate drugs.
- Loci pegged to protein changes in AD brain, CSF, plasma.
- More than 70 percent of brain loci also turned up in the fluids.
- Could some of 25 drugs known to target the altered proteins be repurposed?
Alzforum previously covered a medRxiv preprint of this work (Feb 2021 news). Now published in the July 8 Nature Neuroscience, the study includes more data about how pQTLs overlap in the brain, CSF, and plasma, and how they relate to other QTLs or disease risk genes. The researchers also earmarked some altered proteins as potential targets for repurposing FDA-approved drugs.
As reported in their preprint, first author Chengran Yang and colleagues searched for pQTLs by correlating more than 14 million SNPs with protein levels in parietal lobe tissue, CSF, and plasma from 428, 971, and 636 older donors, respectively. Of those, 297, 249, and 230 participants had AD; the rest were cognitively normal. The researchers found 32 pQTLs in brain tissue, 274 in the CSF, and 127 in the plasma.
In the peer-reviewed paper, the researchers reported how many loci overlapped between the tissue types. More than 70 percent of all brain tissue loci also popped up in the fluids, once again confirming these fluids as proxies for what is happening in the brain. The CSF shared more pQTLs with the brain than did the plasma. Some loci tweaked levels of more than one protein, with the most extreme being an APOE variant that altered 13 different CSF proteins (see image below).
One Locus, Many Proteins. An APOE-TOMM40 locus altered the concentration of 13 CSF proteins (left), while an ABO variant affected seven plasma proteins (middle) and an SPCS3-VEGFC variant, five brain proteins (right). Thicker lines reflect a stronger effect size. Red indicates higher, blue lower protein concentration in the respective tissue. [Courtesy of Yang et al., Nature Neuroscience, 2021.]
To better understand exactly how these pQTLs might control protein levels, Yang and colleagues determined whether they overlapped with expression, splicing, or epigenetic QTLs. The assumption is that if two QTLs co-localize, then that variant alters protein levels through that mechanism. Within the three sample types, 16 to 28 percent of pQTLs altered gene expression, 3 to 17 percent changed splicing, 1 to 10 percent altered DNA methylation, and less than 2 percent modified histone acetylation. On the other hand, 48 to 77 percent of all pQTLs did not overlap with any of the other QTLs, indicating that those variants alter protein levels in other ways. “They may modify protein secretion, cleavage, or receptor expression,” Cruchaga told Alzforum.
How did these variants relate to known risk alleles? Using Mendelian randomization to link GWAS data to the pQTLs, the geneticists identified which protein-altering variants also increase risk of Parkinson’s disease, frontotemporal dementia, amyotrophic lateral sclerosis, and stroke, from within respective GWAS loci found for these diseases. These included the plasma myeloid cell receptor CD33 for AD, the plasma lysosomal hydrolase IDUA for PD, CSF carbonic anhydrase IV for ALS, and CSF or plasma E-selectin for stroke. The scientists confirmed these findings with co-localization, showing that 42.5 percent of the loci flagged as pQTLs were also GWAS risk loci.
Last but not least, the authors searched for drugs known to interact with these disease-associated proteins. Of the 25 they found, one is AVE9633, an anti-CD33 antibody that was discontinued after a Phase 1 trial for acute myeloid leukemia (Maakaron et al., 2021). Another CD33 antibody, AL003, is currently in Phase 1 for AD (May 2019 conference news). When expressed on microglia, CD33 hampers TREM2 signaling (Jul 2019 news; Apr 2019 conference news). These new proteomic data validate the premise of therapeutically suppressing CD33, Rudy Tanzi, Massachusetts General Hospital, Boston, wrote to Alzforum (full comment below).
Another candidate drug is chondroitin sulfate, a glycosaminoglycan and component of cartilage that is sold as a supplement. The authors place chondroitin sulfate into the α-L-iduronidase (IDUA) pathway, which degrades glycosaminoglycans in the lysosome. IDUA deficiency causes the recessive lysosomal storage disorder mucopolysaccharidosis type I, and as such is a target of experimental enzyme replacement gene therapy (Maccarana et al., 2021; Hordeaux, 2019).
Two FDA-approved drugs are acetazolamide, a diuretic sold as Diamox, and the beta-blocker carvedilol; they inhibit carbonic anhydrase and E-selectin, respectively. “We are considering what compounds to move into clinical trials,” Cruchaga said.
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