With the help of more than 100 clinical collaborators around the world, Friedhelm Hildebrandt, MD has received thousands of blood samples from patients with nephrotic syndrome. They have helped Hildebrandt’s lab determine several underlying causes of this serious kidney disorder, in which high levels of protein are expelled in the urine.
“Nephrotic syndrome is not one disease; in fact, we already know that it is 55 different diseases,” says Hildebrandt, chief of the Division of Nephrology at Boston Children’s Hospital.
Over the course of time, Hildebrandt’s lab has discovered 35 of the more than 55 genes that can cause nephrotic syndrome. Identifying the different genetic pieces of the puzzle can help tailor a precision medicine approach to treating patients.
The latest piece, published earlier this month in Nature Genetics, is a set of four single-gene mutations that cause Galloway-Mowat syndrome (GAMOS) a rare disorder causing early-onset nephrotic syndrome and, often, microcephaly (abnormally small head size). Until now, the genetic changes underlying GAMOS and why they affect two disparate organs — the brain and kidney — have not been well understood.
Identifying the culprits
Using whole-exome sequencing, the researchers examined exons – the portions of DNA that contain the recipe for the body’s proteins. They screened samples from more than 900 people with nephrotic syndrome, including 91 with GAMOS. They narrowed this group down to 37 individuals from 32 families with GAMOS who all shared mutations in the same four genes. These genes coded for proteins — LAGE3, OSGEP, TP53RK and TPRKB — which form the KEOPS complex (Kinase, Endopeptidase and Other Proteins of small Size).
The KEOPS complex has many functions, including one of utmost importance. It chemically modifies a transfer RNA molecule, the link between the genetic sequence and protein synthesis. If the KEOPS complex is disrupted, it can trigger the body to produce large numbers of abnormal proteins.
Many mechanisms, many problems
Having zoomed in on this four-gene complex, Hildebrandt’s lab proceeded to investigate the specific role of each gene in zebrafish, mice and yeast. By using CRISPR-Cas9 to delete or alter the four genes one by one, they could observe what happened when each corresponding protein was missing or impaired.
Genetic alterations to one or more of the four genes caused the KEOPS complex to malfunction, leading to a progressive breakdown of cellular processes, the researchers found. With KEOPS unable to correctly modify transfer RNA, faulty proteins quickly begin to build up and cause cell death.
“The cellular machinery that creates the proteins that every cell needs for survival is overwhelmed with these faulty proteins,” says Daniela Braun, MD, first author on the paper. “On the one hand, the cell is lacking a ‘good protein’ to actually execute its function, on the other hand it has to deal with all these faulty proteins that need to be removed from the body.”
Could neurons and kidney cells be similar?
Hildebrandt’s team also found that the four genetic mutations were associated with a dysfunctional DNA damage response (DDR). DNA routinely becomes damaged, and if cells cannot repair it, genetic mutations accumulate and lead to cell death. DDR and increased cellular death in individuals are well-known underlying mechanisms that can cause microcephaly.
Parallels in the appearance of microcephaly and early-onset nephrotic syndrome in GAMOS patients suggests that neurons and the kidney’s podocyte cells are disrupted by the same mechanisms.
Hildebrandt’s group speculates that podocytes, like neurons, are permanent cells that do not regenerate, possibly explaining why mutations in the KEOPS complex cause such drastic effects in both cell types. Once damaged, these cells cannot be resurrected.
Braun believes that whatever we learn from podocytes may help in our understanding of neurons and vice versa.
Avenues for treatment?
In the future, Hildebrandt’s team hopes to evaluate existing therapies and find new classes of drugs that might treat patients with impaired KEOPS complexes. While these candidate drugs likely will not cure these GAMOS patients, cranking down the “bad proteins” might at least alleviate some symptoms, Braun says.
“Rather than hoping for one drug that will be a cure-all, we may have to keep going and find drugs for groups of patients,” says Hildebrandt.