NEW YORK – A research team at the Children's Hospital of Philadelphia (CHOP) is looking for clues in mitochondrial DNA (mtDNA) as to why the severity of COVID-19 symptoms vary so widely between patients.
This research, investigators hope, will lay the groundwork for new diagnostics and therapeutics for the viral infection.
In the first roughly year and a half of the COVID-19 pandemic, an estimated 146.6 million people were infected with SARS-CoV-2. However, patients varied widely in how they responded to infection. Of the 124 million patients who experienced disease symptoms, 7.5 million had symptoms severe enough to warrant hospitalization, according to the US Centers for Disease Control and Prevention.
Yet, after more than three years, it's still unknown why some people have a worse reaction to the virus than others.
Researchers at CHOP's Center for Mitochondrial and Epigenomic Medicine (CMEM) think a major factor may be genetic variations in mitochondrial DNA. They will explore this hypothesis with a $2.3 million award from the Bill & Melinda Gates Foundation in the hopes of generating data that leads to diagnostics for identifying individuals most likely to suffer from severe COVID-19 symptoms.
"The plan, if we can find the right [variations] to test for, is a very direct clinical application," said Douglas Wallace, a geneticist and the director and founder of CMEM.
Since the early days of the pandemic, Wallace and colleagues have been investigating the effect of SARS-CoV-2 on the mitochondria and mitochondrial energy production and were part of a consortium that found evidence that the virus produces viral polypeptides that bind to proteins in the mitochondria, blocking their function and ability to produce energy. The virus also inhibits transcription, they found, so that the host's cells can't produce more mitochondria, setting off a chain reaction that redirects energy to the virus to replicate.
But while earlier investigations had found that COVID-19 has an adverse effect on mitochondrial gene expression and function, it's unclear the extent to which that contributes to illness severity.
Now, with the Gates Foundation grant, the team is studying whether different mtDNA haplogroups — populations with different mtDNA makeups — have varying sensitivity and resistance to viral infection. If that's true, researchers would be able to predict who's more prone to severe COVID-19 infection, Wallace said.
In 1988, Wallace and colleagues published the first paper showing that mutations in mtDNA could cause disease. They showed specifically that a mutation in the MT-ND4 gene at the nucleotide position 11778 caused a type of blindness called Leber hereditary optic neuropathy. Then, in 1990, Wallace founded a center at Emory University, which he relocated to the University of California, Irvine, in 2002, and to CHOP in 2010, to study mtDNA variation and mitochondrial energy deficiency and their links to metabolic and degenerative diseases such as diabetes, obesity, Parkinson's disease, and blindness.
Today, there are about 1,000 known pathogenic mtDNA mutations, nearly 100 of which are clinically diagnostic, said Wallace, citing data from an mtDNA variation database that his team developed, called MITOMAP. "In the last 50 years, we have created a new field," by proving that mtDNA variants can cause disease, he reflected.
The fundamental concept underlying Wallace's research is that if mitochondria have DNA, that mtDNA too can mutate — and with enough damage, cells won't be able to produce enough energy to function well. This can lead to failure in organs that need a lot of energy for normal functioning, such as the brain, heart, and kidneys.
For the COVID-19 study, researchers at CHOP are working with collaborators at the North-West University in South Africa and the University of Hyderabad in India to collect representative samples of mtDNA in their respective regions. They have hypothesized that populations that appear to have mtDNA that generate energy more efficiently, such as individuals from sub-Saharan Africa, may be more resistant to severe COVID-19 symptoms.
"Being part of this study is an excellent opportunity to also include African populations, which are notoriously understudied in large-scale research despite the unique genetic diversity seen in Africa," Marianne Venter, a senior lecturer and researcher at North-West University and a collaborator on the research project, said in an email.
Investigators will use a technique in which they swap the mtDNAs within a cell — without changing other traits, such as the nuclear genome — to create cell lines called transmitochondrial cybrids. These cybrids are infected with the virus in a Biosafety Level 3 lab where researchers will assess the influence of mtDNA on the cell's function.
"We can take the same cell and substitute mitochondria from all different regions," Wallace said. "Then, see if, in fact, the viral propagation is modulated by the virus."
His team already has created some cybrids, but over the next two years will create many more for this research.
Wallace envisions a future in which clinicians could sequence patients' mtDNA to identify those most at-risk for severe COVID-19. That process could involve collecting cells from a patient's blood or tissue sample, amplifying the mtDNA using long-extension PCR followed by next-generation sequencing.
Doctors, armed with information on whether or not patients carry mtDNA variants associated with worse COVID-19 illness, could personalize their treatment based on whether they're likely to have severe symptoms. Down the line, Wallace said the team will also look to develop therapeutic approaches that increase mtDNA expression.
Since researchers aim to investigate mtDNA haplogroups common in different regions, it's possible they may also find various COVID-19 infection susceptibilities. "This can lead to completely new therapeutic targets that are also tailored to be population specific," Venter wrote in an email. "Because mitochondrial (dys)function is also thought to be in so many other complex diseases, these insights could even contribute to a better understanding of diseases beyond COVID-19."