A few weeks ago, Srilatha Raghuram, the journals publishing manager of Journal of Interferon and Cytokine Research at Mary Ann Liebert, sat down with Adolfo Garcia-Sastre, virologist at the Icahn School of Medicine at Mt. Sinai University, New York, in the first interview series called “Experts Speak” to talk about his involvement in SARS-CoV-2 research.
Journal of Interferon & Cytokine Research: You recently published a review on coronaviruses in JICR? Refer: Kehrer et al., 2021, JICR Vol. 41 (6)
Adolfo Garcia-Sastre: Yes. That was a review that basically was discussing the different ways how SARS-CoV-2, the virus that causes COVID-19, has for inhibiting interferon pathways, including interferon induction, interferon signaling, and the activity of interferon stimulated genes. These viruses are large RNA viruses. They code more proteins than most of the other RNA viruses. Many of these proteins that are encoded interact with host factors to try to inhibit antiviral host responses, most of them related to interferon. They have multiple ways how to prevent interferon induction and interferon signaling.
My laboratory has been concentrated at this moment in the activity of 2 of the SARS-CoV-2 proteins. The first one is ORF6, which is a protein that we and others identified as able to inhibit interferon signaling, the JAK-STAT pathway. That was described already for the first SARS-CoV. ORF6 of SARS-CoV-2 is related in sequence to the first SARS virus. What we found is that the mechanism was a new mechanism not described before how to inhibit interferon signaling, and that is by interacting with components of the nuclear pore, specifically with the nuclear pore NUP96. That competes out karyopherins involved in the STAT translocation from the cytoplasm to the nucleus, which is required to initiate the stimulation of transcription of interferon-stimulated genes. That was one of the proteins that we have been working with.
Also, we are working with another nonstructural protein of the virus. This is mainly in collaboration with a colleague of mine, Beatrriz Fontoura, who was also involved in the ORF6 studies. It involves the Nsp1 protein. The Nsp1 is a protein that is known to inhibit host responses due to cellular RNA degradation. That is one of the things that Nsp1 is promoting. We also identified a previously not described function for this protein, which is its ability of interacting with components involved in the nuclear cytoplasmic transport of messenger RNAs. This protein is able to inhibit the export of polyadenylated messenger RNA and, therefore, prevents host gene expression including expression of interferon-inducible genes.
This activity of Nsp1 is quite reminiscent of the activity of another protein of a virus, which is NS1 of influenza. The NS1 of influenza virus is also able to inhibit the same pathway through interaction with the same factor. An interesting thing is that the Nsp1 of SARS-CoV-2 and the NS1 of influenza virus interact with different domains on the same factor that is inhibited. We do not understand what peculiarities they confer with respect to perhaps specific inhibition of export of some RNAs versus some other RNAs. That is something that we are very interested to determine. This research is mainly driven in my group by a senior person, Lisa Miorin, who is working with a couple of her students to understand in more detail the activities of Orf6 and NSP1, using now mutant SARS-CoV-2 in collaboration with another investigator, Luis Martinez-Sobrido.
JICR: Do the Nsp1 and NS1 inhibit the same signaling cascades? Is there any correlation there?
Adolfo Garcia-Sastre: The SARS-CoV-2 Nsp1 interacts with the same host factor as the NS1 of influenza virus, a factor that this is involved in export of messenger RNA. But they interact with different domains of this factor. We are trying to understand whether this has different implications with respect to the specificity of inhibition of messenger RNA export. We do not know. But they achieve the same thing, inhibition of host expression. It is slightly different, but they target the same factor. That is the interesting thing.
JICR: What experimental approaches have you been using in your laboratory for all these studies?
Adolfo Garcia-Sastre: In general, we use biochemical approaches as well as cell biology approaches. These may involve, in the beginning, overexpression of the factors to find out the impacts in signaling, what host factors are interacting with these factors. As soon as we have candidates and specific findings, then we try to prove that these interactions occur also during viral infection. We attempt to find the connection mechanistically between a particular inhibitory function, for example, inhibition of interferon signaling, with specific interactions that we identify by biochemistry. We identify mutations that would prevent interactions. The next steps are generating mutant viruses to block the ability to interact to find the phenotype of these viruses.
JICR: What are the major findings so far from the studies that you have had? Also, if you could tell me, what future do you see from these studies?
Adolfo Garcia-Sastre: I think that some interesting things are that the virus seems to come with multiple ways how to inhibit interferon. Some may be redundant, or some may be more important as unique mechanisms that are completely required for the virus to be able to survive. There are also implications about how these mechanisms play in induction of immunity. The innate immune system is very well known to contribute also to adaptive immunity. So, we are interested on how these different mechanisms contribute to potentially promote virus transmission, pathogenesis, or contribute to the wrong immune response, facilitating viral replication or disease.
Adolfo Garcia-Sastre: Also, as these mechanisms are being conducted mainly by protein–protein interactions and SARS-CoV-2 is a bat virus but now has a new host, which is humans, this might impact the fitness of the virus. The fact is that the virus has evolved to interact with bat proteins, which is where it comes from. Human proteins might not have exactly the same sequence as the bat proteins. Then, how the virus manages to be interacted with the human proteins? The viral proteins interact optimally already with the human factors. These are some of the questions that we are interested in, as well as many other researchers who are working on pathogenesis of SARS.
JICR: You also talked about therapeutic intervention. When you say that, do you mean antivirals or anti-inflammatory?
Adolfo Garcia-Sastre: It would be both antivirals and anti-inflammatories. It is too early to know whether some of these early host–virus interactions contribute or not to some of the later immunopathology in COVID-19. Once the immunopathology has been established, perhaps targeting the viral factors is too late. Probably, we need to target more of the environment and not the factors that contributed to this environment that is already established.
JICR: Last question for you. We read in the literature about how micro-organisms, bacteria and viruses in general, are changing, that they are mutating so much. There are new viruses emerging. With the existing viruses, let us say the influenza viruses, are these mutations occurring faster? Are there more virulent mutations occurring right now? What is really going on?
Adolfo Garcia-Sastre: Well, as we increase the number of interactions that are between humans and rare viruses that are found in unique niches that before humans did not have too much access to, then the types of infection possibilities increase. We know that most of the biggest and latest viral outbreaks that humans have been through are from zoonotic infections. HIV clearly came from primates. HIV-1 jumped to humans most likely through interactions of humans with chimpanzees. If this interaction would have not taken place, perhaps it would not have been able to enter humans. The same thing happened with pandemic influenza. The same thing happened with these SARS coronaviruses. There are some other viruses that get adapted to other hosts and then this allows more infections in humans. An example is the mosquito-borne viruses. They infect mosquitoes and if they adapt to a new mosquito that is more abundant and is more involved in biting humans, then you also get outbreaks of mosquito-borne viruses. Many of these zoonotic viruses come because of these increased interactions between humans and our environment. Specifically, humans and viruses. Ebola outbreaks probably also occurs the same way.
Adolfo Garcia-Sastre: The more humans there are, the most likely that these interactions will happen. That is a challenge of being successful as humans in this world, that you encounter now, more and more of these viruses. Before, it was more difficult for a human to interact with them.
JICR: Thank you for taking the time to speak with me.
