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Newly Discovered Gene Linked to Hepatitis C Virus Clearance, Treatment Response

Human liver cells treated to mimic infection with hepatitis C, showing the cell cytoplasm (green), nucleus (blue), and IFNL4 protein (red). The image shows cells from carriers of the favorable genetic variant (left) and the unfavorable variant (right). INFL4 is expressed only in carriers of the unfavorable variant.

Researchers have identified a genetic variant that is strongly associated with the ability to spontaneously clear infection with the hepatitis C virus (HCV) and with the response to treatment for chronic HCV infection, the leading cause of liver cancer in the United States.
And, in a surprising finding, the discovery of the variant led to the first identification of a previously unknown gene, IFNL4. The variant in this gene is directly responsible for the creation of a newly identified protein, called interferon lambda 4 (IFLN4), from the interferon lambda family of proteins.
Results from the study, led by NCI investigators, were published online January 6 in Nature Genetics.
Compared with a previously identified single nucleotide polymorphism (SNP) that is already being used in the clinic to guide treatment decisions, the new variant (called ss469415590) was found to be a stronger predictor of spontaneous infection clearance and treatment response in people of African ancestry. In people of Asian and European ancestry, the new variant provided the same predictive accuracy as the previously identified SNP (called rs12979860).
In the United States, nearly one-quarter of all chronic HCV infections are in African Americans. Overall, 80 percent of people infected with the virus will develop a chronic infection, and approximately 5 percent of those infections will develop into liver cancer.
The finding could quickly be translated into a new genetic test to help guide treatment, and it might eventually be the basis for new treatments for HCV, according to the study's co-lead investigator, Dr. Ludmila Prokunina-Olsson of the Laboratory of Translational Genomics in NCI's Division of Cancer Epidemiology and Genetics (DCEG).
And the finding could also lead to other discoveries. "It's a big deal to find a new interferon gene," Dr. Prokunina-Olsson said. "It raises the question of whether [the gene] might be important in other diseases as well."
No Variant, No Gene or Protein
The newly discovered gene is related to the interferon lambda family of genes, which contains three other members. These genes, which themselves were discovered just a decade ago, encode proteins that play a role in helping cells ward off some viruses.

It's a big deal to find a new interferon gene. It raises the question of whether [the gene] might be important in other diseases as well.

—Dr. Ludmila Prokunina-Olsson

The new variant has two forms, one in which a single nucleotide has been deleted and another in which this nucleotide is present. Only the deletion variant produces the IFNL4 protein, which appears to somehow hamper HCV clearance and response to standard HCV treatments, Dr. Prokunina-Olsson explained.
"If there is no genetic variant, there is no protein," she said. "It's a yes or no question."
Building on Prior Research
The study follows earlier genome-wide association studies (GWAS) that identified SNPs in a region of chromosome 19 near the IFNL3 gene (previously known as IL28B). These SNPs were strongly associated with HCV infection clearance and the response to treatment, which typically involves a combination of pegylated-interferon alfa and ribavirin, and, more recently, the addition of protease inhibitors.
For this new study, the research team wanted to examine more closely what was happening in this chromosomal region during an HCV assault, explained the study's other lead investigator, Dr. Thomas O'Brien of DCEG's Infections and Immunoepidemiology Branch.
"The original studies and follow-up studies didn't point to a specific functional variant or mechanism, which is not uncommon in GWAS," Dr. O'Brien noted.
Using RNA sequencing, the team analyzed the expression of all genes in fresh human liver cells that had been treated with synthetic RNA to mimic hepatitis C infection. Unlike other genome analysis techniques, RNA sequencing is not constrained by having to work from a known set of genes, Dr. Prokunina-Olsson said. "RNA sequencing shows you whatever is there, whether anybody knows about it or not," she explained.
The RNA sequencing analysis turned up expected activity among genes known to reside in this region of chromosome 19.
"Then we saw something that was not expected," Dr. Prokunina-Olsson continued. What they found were transcripts—RNA molecules—located near IFNL3 and in the area which was not known to contain any known or predicted genes.
"It took about 9 months to get from RNA sequencing to cloning and characterization of the new gene," she said. "It's very unusual to identify a totally new gene that was not even predicted to exist."
Using samples from two clinical trials involving patients with chronic HCV infection, the researchers found that, in African American patients, the deletion variant was much more strongly associated with poor treatment response than the previously identified SNP. They saw a similar pattern for spontaneous HCV clearance when they analyzed samples from two other studies. They also found that the deletion variant is far more common in individuals of African ancestry than in Europeans or Asians.
The finding presents a paradox, Dr. O'Brien continued. Interferons are so named because they interfere with infections. "But, in HCV infection, the IFNL4 protein appears to interfere with viral clearance," he said.
Implications for Patients and Researchers
The impact of this finding could be far-reaching, noted Dr. Charles Rice, a leading HCV researcher at Rockefeller University in New York.
"Especially in terms of understanding more of the biology, more of the mechanisms, [the finding] has great promise," Dr. Rice said. The previous GWAS studies highlighted the importance of this chromosomal region to HCV clearance and treatment response. This new gene, Dr. Rice said, "looks like it may be a large part of the story …. It opens up a whole new series of investigations to figure out exactly what it's doing. It's really quite a breakthrough."
From a clinical perspective, developing a test to help predict the likelihood of treatment response could be a distinct possibility.
"If we want to use just one genetic test irrespective of a person's racial background, this new variant could be a universal clinical predictor for all patients because it appears to be more accurate than the current test in African American patients," Dr. O'Brien said.
The IFNL4 protein might also be a good target for therapy, the research team wrote. Because many individuals do not generate the IFNL4 protein at all, Dr. O'Brien noted, it does not appear to be essential and could potentially be inhibited therapeutically without adverse consequences.
Drs. O'Brien and Prokunina-Olsson are already studying whether the variant affects the response to an interferon-based treatment for advanced melanoma. They are also working with researchers at the National Institute of Allergy and Infectious Diseases to study whether the variant affects the response to new treatments that directly attack HCV.
Treatment for chronic HCV infection is rapidly shifting away from interferon-based therapies—which, although effective, can have particularly bad side effects—to newer antiviral treatments, Dr. Rice explained, so assessing how this new variant and the other SNPs affect response to these new therapies will be important.
—Carmen Phillips