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Research Overview


The long-term research goals in Dr. Li’s laboratory are to understand, in mechanistic detail, how RNA viruses enter, replicate, and express genetic information in order to understand viral pathogenesis, and to facilitate the rational design and development of new vaccines and anti-viral drugs. Currently, we are studying RNA viruses that causes respiratory infection including human respiratory syncytial virus (RSV), human metapneumovirus (hMPV), and SARS-CoV-2; and RNA viruses that cause enteric infection including porcine epidemic diarrhea virus (PEDV), porcine deltacoronavirus (PDCoV), and human norovirus.

The Li lab is one of only a few laboratories studying RNA processing and RNA modifications in viruses. During 2004-2008, he characterized mRNA capping enzyme and mRNA cap methyltransferases in non-segmented negative-sense RNA viruses. During 2008-2016, he characterized the roles of mRNA cap methylation in viral replication, pathogenesis, innate and adaptive immunity. Since 2016, the Li laboratory has been focused on characterization of viral and host internal RNA methylation and understand their roles in viral replication, gene expression, and pathogenesis.

Research interest I: Human metapneumovirus (hMPV) and human respiratory syncytial virus (RSV).

Pneumoviridae is a new virus family in the order Mononegavirales. It was created in 2016 by elevating the paramyxoviral subfamily Pneumovirinae to family status. The Pneumoviridae family includes two medically important pathogens, human respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) which are the no.1 and 2 causative agents of acute viral respiratory tract infections in infants, young children, the elderly, and immunocompromised individuals. Despite the enormous economic loss and emotional burden these viruses cause, no vaccines or anti-viral drugs are currently available. Development of such agents requires a better understanding of all aspects of their life cycle.

  1. Understand mechanisms by which viral RNA epigenetic modifications modulate pneumovirus replication, gene expression, and pathogenesis. RNA methylation is a reversible post-translational modification to RNA that epigenetically impacts numerous biological processes. Among over 170 RNA modifications, the most prevalent and abundant RNA modifications include N6-methyladenosine (m6A), C5-methylcytosine (m5C), pseudouridine (Ψ), 2’-O-methylation (Nm), and N1-methyladenosine (m1A). These internal RNA modifications are catalyzed by host RNA methyltransferases. Currently, the roles of these RNA modifications in virus replication, gene expression, and pathogenesis are poorly understood. We recently found that hMPV and RSV genome, antigenome, and mRNA contains major internal RNA methylations including m6A, m5C, Ψ, Nm, and m1A. We have found that the internal m6A methylation in viral RNAs promotes pneumovirus replication and gene expression (Xue et al., Nature Communications, 2019; Lu et al., Nature Microbiology, 2020). Our goals are to understand the roles of internal RNA methylation in pneumovirus replication and pathogenesis in vivo; and to define mechanism(s) by which RNA methylation modulate pneumovirus life cycle.
  2. Define the roles of viral and host RNA modifications in innate and adaptive immunity. The innate immune system is the first line of defense against invading pathogens and must discriminate cellular (self) and viral (non-self) nucleic acids to mount a protective immune response. Viruses are “smart” microorganisms and they must hide or modify their nucleic acids to evade innate immune recognition. Using hMPV and RSV as models, we have provided the first evidence that m6A methylation serves as a molecular marker for host innate immunity to discriminate self RNA from non-self RNAs (Lu et al., Nature Microbiology, 2020; Lu et al., Journal of Virology, 2021., Xue et al., PloS Pathogens, 2021). Specifically, m6A-deficient hMPV RNAs are more efficiently detected by host pattern recognition receptors (PRRs), which leads to enhanced activation of type I interferon responses. Also, we recently found that knockout of NSUN2, a m5C RNA methyltransferase, strongly inhibits viral replication and gene expression and that RNA m5C methylation modulates host innate immunity (Zhang et al., PNAS, 2022). Our goals are to understand signaling pathways and mechanisms how RNA modifications involved in discrimination of self and non-self RNAs by innate immunity and to determine how RNA internal methylation modulates viral pathogenesis, innate immunity, and adaptive immunity.
  3. Develop new live attenuated vaccine candidates for hMPV and RSV. A live attenuated vaccine is one of the most promising vaccines for hMPV and RSV. Our laboratory is interested in developing novel, more immunogenic live attenuated vaccine candidates for hMPV and RSV by targeting viral mRNA cap methylation and/or internal RNA methylation. Messenger RNAs (mRNAs) of pneumoviruses typically possess guanine-N-7 (G-N-7) and ribose 2′-O (2′-O) methylation. G-N-7 methylation is essential for mRNA stability as well as efficient translation whereas ribose 2′-O methylation provides a molecular signature for the discrimination of self and nonself mRNA by innate immunity. In addition, viral genome, antigenome, and mRNAs of hMPV and RSV are heavily modified by host RNA methyltransferases. These internal RNA modifications modulate viral replication, gene expression, and innate and adaptive immunity. We will generate recombinant hMPVs and RSVs lacking mRNA cap methylation and/or internal RNA methylation, and test hypothesis whether an enhanced innate immunity can enhance the immunogenicity of live attenuated vaccines. These vaccine candidates will be tested in in primary well differentiated human airway epithelial (HAE) cultures, mice, cotton rats, and nonhuman primates.

Research interest II: SARS-CoV-2 and porcine coronaviruses.

Dr. Li’s laboratory is one of the research groups in the US who first isolated and characterized two pig coronaviruses (porcine epidemic diarrhea virus, PEDV; porcine deltacoronavirus, PDCoV) during the 2013-2016 outbreaks (Ma et al., mBio, 2015; Lu et al., J. Virol., 2020). In response to the SARS-CoV-2 pandemic, we quickly generated serval recombinant measles virus-based SARS-CoV-2 vaccine candidates (Lu et al., PNAS, 2021, featured by NIH Research Matters), recombinant mumps virus-based SARS-CoV-2 vaccine candidates (Zhang et al., PNAS, 2022), and found that prefusion spike with 6 prolines is more immunogenic than prefusion spike with 2 prolines (Lu et al., PNAS, 2022). Several vaccine candidates have been licensed to a major vaccine company. We also found that RNA of several coronaviruses (such as SARS-CoV-2, PEDV, and PDCoV) contains numerous internal RNA modifications including N6-methyladenosine (m6A), C5-methylcytosine (m5C), pseudouridine (Ψ), and 2’-O-methylation (Nm). We will characterize these internal RNA methylations; identify host RNA methyltransferases that modify SARS-CoV-2 RNA; determine the roles of these RNA methylations in SARS-CoV-2 replication, gene expression, pathogenesis and immune evasion; and screen drugs that can inhibit viral and host RNA methylation and test their therapeutic effects in animal models.

Research interest III: Vaccine development

Our laboratory has extensive experience in developing reverse genetic system for RNA viruses. We recently developed a highly efficient yeast-based recombinant system to rapid construction of infectious cDNA clones (Lu et al., PNAS, 2021). We are particularly interested in utilizing non-segmented negative-sense RNA viruses (vesicular stomatitis virus, VSV; measles virus, MeV; and mumps, MuV) as a vector to deliver vaccines for highly pathogenic viruses (such as SARS-CoV-2, Zika virus, Nipah virus, Hendra virus, human norovirus, and other emerging viruses). We recently developed a MeV-based SARS-CoV-2 vaccine candidate (Lu et al., PNAS, 2021, featured by NIH Research Matter, 2021 March), a MuV-based SARS-CoV-2 vaccine candidate (Zhang et al., PNAS, 2022), a VSV-based SARS-CoV-2 vaccine candidate (Lu et al., PNAS, 2022), a VSV-based Zika virus vaccine candidate (Li et al., Nature Communications, 2018), and many other vectored vaccine candidates. Several of vaccine candidates have been licensed to major pharmaceutical companies. Currently, we are using these vectors to develop pan-coronavirus vaccine candidates and to develop vaccines for other emerging viruses such as Nipah virus and Hendra virus.