When Ruslan Afasizhev and Inna Afasizheva were studying at Moscow State University in the early 1990s, research in genetics was buzzing with possibilities. Scientists across the globe were on the cusp of sequencing the entirety of the human genome, busting open a new door for molecular science, medicine, and biology. And researchers were eager to learn more about how the genome, our DNA, provides instructions for cells in the body through RNA (ribonucleic acid) that's present in all living cells.
Afasizhev and Afasizheva, who were freshmen when they met, couldn't wait to be part of this exciting new world. As molecular biologists, they wanted to explore the complexity of living cells, dive into the latest research, and learn as much as possible.
And then, in 1991, the Soviet Union collapsed. The Russian economy staggered into a new era-and investment in research tumbled. The newly married couple's scientific dreams were shattered by uncertainty.
"We went from a very well-funded research lab at the Russian Academy of Sciences to nothing," says Afasizhev, a BU Henry M. Goldman School of Dental Medicine professor of molecular and cell biology. "There was no way to do any work in the lab. There was no money or research. And that's how I started graduate school, the two of us with a little baby."
Their commitment to science and to each other eventually pushed them to a tough decision: leaving their home country. Despite the challenges of moving their family from Russia, sometimes forcing them to spend months and years apart, they've remained steadfast in their passion for science, publishing dozens of papers on the mechanics of mitochondrial DNA and RNA in a single-celled, disease-causing parasite called Trypanosoma brucei. Decades of breakthroughs have led to their latest paper published in Science, which provides a detailed look at a mystifying process called RNA editing and could potentially help treat a deadly disease.
"Now we can start more broader research," says Afasizheva, an SDM associate professor of molecular and cell biology. "Since now we know exactly how proteins interact with RNA."
A Jaw-Dropping Discovery
Afasizheva was earning her degree in biophysics when she met Afasizhev, a student in the molecular biology program. Despite being from different regions of Russia-Afasizheva from Moscow, and Afasizhev from a small university town in southern Russia-it was love.
"We fell in love first, and then we fell in love with the same science," says Afasizheva.
That science is small RNA biology-the study of small RNA strands that serve specific functions in a cell. Their relationship just so happened to coincide with the nascency of the field. Without RNA, our cells couldn't perform fundamental tasks, like construct other cells, carry amino acids from one part of the cell to the other, or mount immune responses to viruses and diseases. We also wouldn't have certain types of cancer treatments, immune therapies, or vaccines that use RNA as the guiding mechanism, such as the COVID-19 vaccines.
RNA comes in different forms, including messenger RNA (mRNA), which translates DNA so it can be read by the rest of the cell. It was long believed that DNA tells the cellular machinery the exact sequence of mRNA-meaning that mRNA is a copy of DNA. But, in 1986, an exception to this rule was discovered in Trypanosoma. Scientists saw nucleotide insertions in the mRNA strand that were not present in the gene, and found that those insertions served an important purpose: fixing a broken gene.
When Afasizhev first learned about this phenomenon during a college lecture, his jaw dropped.
"That blew the existing dogmas out of the water," Afasizhev says. In Trypanosoma, those nucleotide insertions resulted from a process called RNA editing, which is when genetic mutations passed on from DNA are fixed in the transcribed mRNA. Mutations in DNA are very common in the parasite, so even though the genetic code is unreadable, the edited mRNA version becomes a functional part of the cell.
The lecture stuck with him, even as a freshman in college. In the years following the discovery of RNA editing in 1986, scientists at the University of California, Los Angeles (UCLA) found the answer to a central question: How does the cell know where and how to make corrections in mRNA, if the gene is broken? Researchers described how the changes are directed by guide RNA (gRNA), a small RNA strand that pairs with the mRNA region that needs fixing.
That study led to even more questions: How does gRNA work? What are the proteins that enable its function? From there, the search was on for the specific molecules that interact with gRNA. And that's when Afasizhev and Afasizheva jumped in. They've been studying how information flows from DNA to RNA in Trypanosoma for nearly three decades. In that time, they've gotten closer and closer to cracking the code.
In their newest paper, Afasizhev and Afasizheva-along with collaborators at UCLA, University of California, Irvine (UCI), and ShanghaiTech University-are the first to determine the architecture of the molecular machines that harbor gRNA strands and allow those strands to engage mRNA. Identifying these cellular mechanisms could give scientists essential information for treating African sleeping sickness, the disease caused by Trypanosoma. Spread by tsetse flies that harbor the parasite, African sleeping sickness is usually fatal, and many of the available treatments have safety concerns, making molecular studies particularly important for drug development.
"If we find a way to inhibit the editing process, we can kill the parasite without harming human cells," says Afasizhev, who is also a professor of biochemistry at the BU Chobanian & Avedisian School of Medicine and corresponding author on the paper.
It's Not Just Work, It's Life
When the Soviet Union collapsed in December 1991-just months before their daughter was born-and the path the couple had envisioned from student to independent investigator blurred, they'd been forced to reassess their next steps.
Afasizhev first worked with a team in Strasbourg, France, where his PhD mentor had strong research connections. He finished his PhD-while Afasizheva pushed forward with her own in molecular biology-and contacted Larry Simpson, the professor at UCLA who discovered gRNA in Trypanosoma. Simpson offered him a postdoctoral fellowship in his lab at the Howard Hughes Medical Institute at UCLA, and the couple decided Afasizhev's opportunity in the United States was worth being apart long distance for a short while. By the time she finished her PhD in 1998, Afasizheva had accepted a postdoctoral position in Simpson's lab, too, reuniting the family in Los Angeles. They later moved to the UCI School of Medicine, where Afasizhev was appointed as a tenure-track assistant professor, and Afasizheva worked in his lab as a staff scientist. In 2013, BU offered them two independent faculty positions to continue their work.
"It helps to be together and work in the same area because science is not work, it's a style of life," says Afasizheva. "We'll discuss something exciting over dinner, and we don't feel bad or like we're discussing work. It's not work. It's just life."
It helps to be together and work in the same area because science is not work, it's a style of life. We'll discuss something exciting over dinner, and we don't feel bad or like we're discussing work. It's not work. It's just life.
Since that initial jaw-dropping lecture Afasizhev heard, RNA research has evolved and advanced tremendously-and so has the technology to study the inside of cells. Today, the couple's team uses cryo-electron microscopy and molecular approaches to provide a detailed understanding of RNA editing. Using this technology, their latest study found that a protein complex called the editosome is responsible for orchestrating changes guided by gRNA, which happen as a cascade of insertions and deletions of uridine, a chemical component of RNA.
RNA editing regulates many cellular processes in nearly all organisms that have cells with a nucleus and mitochondria. But, Afasizhev says, the RNA editing mechanisms in different organisms have nothing in common, meaning those mechanisms evolved for different purposes specific to different species. This is what makes the RNA editing mechanisms of Trypanosomes an attractive therapeutic target for stopping the parasite from causing disease, since it won't interfere with human cells. Now that they know the protein structures unique to RNA editing in Trypanosomes, the next phase of their research is identifying the enzymes that ignite the reactions in the cell.
"The next question is how these reactions happen, how these enzymes come to the substrate, and how they create the magnificent work to change the RNA sequence," Afasizheva says.
In addition to working on RNA editing, they recently received funding from the Howard Hughes Medical Institute's Emerging Pathogens Initiative, along with seven other BU researchers, to decipher complete repertoires of mitochondrial proteins in single-cell pathogenic parasites.
"Ruslan has the ability to see important questions and paths to approach these questions, however distant they may seem at times," Afasizheva says.
She and Afasizhev hope to bring in more students to their lab who can embrace the technological advances in their field, and continue to solve this complicated puzzle, just as they have.
"Inna's enduring enthusiasm for science is most remarkable," Afasizhev says. "She has always been absolutely unintimidated by the complexity of problems we work on. If she feels that the 'juice is worth the squeeze,' then the barriers fall, and discoveries happen."
This study was funded by the National Institutes of Health and National Science Foundation.
