Ly shows that one function this serves is to send versions of a protein to different parts of the cell. Many proteins contain ZIP code-like sequences that tell the cell’s machinery where to deliver them so the proteins can do their jobs. Ly found many examples in which longer and shorter versions of the same protein contained different ZIP codes and ended up in different places within the cell.
In particular, Ly found many cases in which one version of a protein ended up in mitochondria, structures that provide energy to cells, while another version ended up elsewhere. Because of the mitochondria’s role in the essential process of energy production, mutations to mitochondrial genes are often implicated in disease.
Ly wondered what would happen when a disease-causing mutation eliminates one version of a protein but leaves the other intact, causing the protein to only reach one of its two intended destinations. He looked through a database containing genetic information from people with rare diseases to see if such cases existed, and found that they did. In fact, there may be tens of thousands of such cases. However, without access to the people, Ly had no way of knowing what the consequences of this were in terms of symptoms and severity of disease.
Meanwhile, Cheeseman, who is also a professor of biology at MIT, had begun working with Boston Children’s Hospital to foster collaborations between Whitehead Institute and the hospital’s researchers and clinicians to accelerate the pathway from research discovery to clinical application. Through these efforts, Cheeseman and Ly met Fleming.
One group of Fleming’s patients have a type of anemia called SIFD — sideroblastic anemia with B-cell immunodeficiency, periodic fevers, and developmental delay — that is caused by mutations to the TRNT1 gene. TRNT1 is one of the genes Ly had identified as producing a mitochondrial version of its protein and another version that ends up elsewhere: in the nucleus.
Fleming shared anonymized patient data with Ly, and Ly found two cases of interest in the genetic data. Most of the patients had mutations that impaired both versions of the protein, but one patient had a mutation that eliminated only the mitochondrial version of the protein, while another patient had a mutation that eliminated only the nuclear version.
When Ly shared his results, Fleming revealed that both of those patients had very atypical presentations of SIFD, supporting Ly’s hypothesis that mutations affecting different versions of a protein would have different consequences. The patient who only had the mitochondrial version was anemic, but developmentally normal. The patient missing the mitochondrial version of the protein did not have developmental delays or chronic anemia, but did have other immune symptoms, and was not correctly diagnosed until his 50s. There are likely other factors contributing to each patient’s exact presentation of the disease, but Ly’s work begins to unravel the mystery of their atypical symptoms.
Cheeseman and Ly want to make more clinicians aware of the prevalence of genes coding for more than one protein, so they know to check for mutations affecting any of the protein versions that could contribute to disease. For example, several TRNT1 mutations that only eliminate the shorter version of the protein are not flagged as disease-causing by current assessment tools. Cheeseman lab researchers, including Ly and graduate student Matteo Di Bernardo, are now developing a new assessment tool for clinicians, called SwissIsoform, that will identify relevant mutations that affect specific protein versions, including mutations that would otherwise be missed.
“Jimmy and Iain’s work will globally support genetic disease variant interpretation and help with connecting genetic differences to variation in disease symptoms,” Fleming says. “In fact, we have recently identified two other patients with mutations affecting only the mitochondrial versions of two other proteins, who similarly have milder symptoms than patients with mutations that affect both versions.”
Long term, the researchers hope that their discoveries could aid in understanding the molecular basis of disease and in developing new gene therapies: Once researchers understand what has gone wrong within a cell to cause disease, they are better equipped to devise a solution. More immediately, the researchers hope that their work will make a difference by providing better information to clinicians and people with rare diseases.
“As a basic researcher who doesn’t typically interact with patients, there’s something very satisfying about knowing that the work you are doing is helping specific people,” Cheeseman says. “As my lab transitions to this new focus, I’ve heard many stories from people trying to navigate a rare disease and just get answers, and that has been really motivating to us, as we work to provide new insights into the disease biology.”