About
Nicholas Scott Heaton is a Professor of Molecular Genetics and Microbiology at Duke University. He also holds positions as a Professor in Cell Biology and in Integrative Immunobiology. Heaton is a member of the Duke Cancer Institute and the Duke Human Vaccine Institute. His research focuses on molecular genetics, microbiology, and immunobiology, contributing to the understanding of host-microbial interactions and immune responses. Heaton's work is integral to advancing knowledge in these fields, supporting the development of novel therapeutic strategies and enhancing scientific understanding of microbial and immune system functions.
Research topics
- Virology
- Medicine
- Biology
- Immunology
- Pharmacology
- Internal medicine
- Computational biology
- Genetics
- Pathology
- Biochemistry
- Political Science
- Biotechnology
- Chemistry
- Cancer research
- Bioinformatics
- Cell biology
Selected publications
CGRP reception potentiates anxiety in an influenza A derived immune engram
bioRxiv (Cold Spring Harbor Laboratory) · 2026-05-22
articleOpen accessAn immune engram is a recently described phenomenon in which neuronal populations encode functional aspects of an immune challenge. Here we investigate an immune engram arising from respiratory infection with influenza A virus, demonstrating a molecular mechanism with differential influence over behavioral and immunological aspects of the engram. We first define a cellular response to acute non-neurotropic influenza A/Puerto Rico/8/1934 (PR8) infection by mapping cFos+ cells and microglia morphology across brain regions. In the posterior insula, this response has an early peak at 3 days post infection. Using a cre-dependent excitatory chemogenetic system in TRAP2 mice, we capture an engram at this same region and infection timepoint. Activation of this PR8 engram results in anxiety behavior and increased transcriptional expression of cytokines in lung tissue but not spleen tissue. We further explore how pulmonary signals contribute to this PR8 engram. Using tissue-specific, cre-dependent expression of diphtheria toxin fragment in Calca-cre mice, we ablate Calca-expressing cells including pulmonary neuroendocrine cells in respiratory tissue. Loss of Calca-expressing cells prevents changes in synaptic engulfment by microglia in the insula during PR8 infection without altering the cellular response to infection in pulmonary tissue. Signaling of calcitonin gene related peptide (CGRP), a peptide encoded by Calca, can be blocked with the small molecule CGRP receptor antagonist rimegepant. Using rimegepant during acute PR8 infection we again demonstrate that loss of Calca signaling prevents the cellular response to PR8 infection in the insula. Finally, applying rimegepant alongside the chemogenetic system in TRAP2 mice we show that CGRP receptor antagonism during engram formation prevents anxiety behavior but not peripheral gene expression changes resulting from PR8 engram activation.
mBio · 2026-05-06
articleOpen accessABSTRACT Coronaviruses (CoVs) replicate their RNA genomes with a higher degree of fidelity than other RNA viruses, a mechanism mediated by the proofreading and recombination activities of the exoribonuclease domain of replicase nonstructural protein 14 (nsp14-ExoN). Both murine hepatitis virus (MHV) and SARS-CoV tolerate nsp14-ExoN loss-of-function mutations (ExoN−) (D90A and E92A), but have impaired replication fidelity and pathogenesis; yet identical substitutions in MERS-CoV and SARS-CoV-2 have been reported to be lethal. Here, we report a saturation mutagenesis approach facilitating the recovery and analysis of several constellations of SARS-CoV-2 nsp14 ExoN-inactivating, loss-of-function substitutions, including the canonical D90A and E92A. Biochemical assays with purified WT or ExoN-nsp10-14 fusion proteins confirmed that active site substitutions abolished ExoN activity (ExoN−). SARS-CoV-2 ExoN− viruses exhibited impaired replication, RNA synthesis, and recombination, as well as decreased replication fidelity and loss of fitness in vitro . ExoN− viruses were significantly attenuated for replication in human primary airway epithelial cells and were attenuated for replication and pathogenesis in WT mice, as well as the highly susceptible K18 transgenic mice. In the absence of interferon signaling in vivo , SARS-CoV and SARS-CoV-2 ExoN− viral replication could be partially restored. These results demonstrate that SARS-CoV-2 ExoN− viruses are viable but highly impaired for replication, fitness, and fidelity in vitro, as well as innate immune antagonism and pathogenesis in vivo . Collectively, our results solidify the multiple critical roles of nsp14-ExoN across CoV genera and establish new approaches for rescuing and analyzing loss-of-function substitutions in studies of CoV replication, pathogenesis, and evolution. IMPORTANCE Coronaviruses (CoV) are important human pathogens causing hundreds of millions of infections and millions of deaths over the past 20 years. The study of how these viruses multiply and cause disease identifies points of attack for therapeutics. Using a high-throughput genetic approach, we systematically inactivated an essential enzyme CoV needs for replication called ExoN. We show that without ExoN, CoV replication fidelity and fitness are reduced in cell culture. Replication without ExoN in mice was diminished but could be partially restored in mice that lack key components of the immune response. Altogether, we reveal new insights into the complexities of CoV replication and virus and host interactions, which could be leveraged for the development of novel multifaceted therapeutics that attack the ever-expanding functions of the CoV replication complex in replication and pathogenesis
Proceedings of the National Academy of Sciences · 2026-03-03
articleOpen accessSenior authorCorrespondingSialic acid is an abundant terminal glycan found on the surface of almost all mammalian cells and is utilized by many viruses as an attachment factor and/or bona fide receptor. Altering canonical cellular glycosylation can affect the ability of viruses to initiate infections; however, no systematic analysis of the effects of altering expression of glycan "capping" enzymes on viral infection rates has been previously performed. We therefore designed an arrayed CRISPR activation screen that targeted 54 glycosyltransferases known to perform terminal glycan modifications and then examined the susceptibility of 12 different viruses that rely on sialic acid receptors on the resultant cell lines. We identified two glycosyltransferases, fucosyltransferase 1 (FUT1) and galactose-3-O-sulfotransferase 2 (GAL3ST2), as capable of inhibiting a broad range of viruses when upregulated, including influenza viruses, respiroviruses, paramyxoviruses, enteroviruses, and coronaviruses. Lectin and viral particle binding assays revealed that the fucosylation and sulfation mediated by FUT1 and GAL3ST2 reduced availability of cell surface expressed α2-3 and α2-6 sialylation and impaired viral attachment during the initial entry process. Furthermore, through adeno-associated virus delivery, we confirmed the inhibitory effects of FUT1 and GAL3ST2 on influenza viruses in various cell models, including primary differentiated human airway cells. Together, our findings identify FUT1 and GAL3ST2 as host restriction factors and suggest that their therapeutic dysregulation may represent a broad-spectrum antiviral strategy.
bioRxiv (Cold Spring Harbor Laboratory) · 2026-01-13
articleOpen accessAbstract Coronaviruses (CoVs) replicate their RNA genomes with increased fidelity than other RNA viruses, a mechanism mediated by the proofreading and recombination activities of the exoribonuclease domain of replicase nonstructural protein 14 (nsp14-ExoN). Both murine hepatitis virus (MHV) and SARS-CoV tolerate nsp14-ExoN loss-of-function mutations (ExoN-) (D90A and E92A) but have impaired replication fidelity and pathogenesis yet identical substitutions in MERS-CoV and SARS-CoV-2 have been reported to be lethal. Here, we report a saturation mutagenesis approach facilitating the recovery and analysis of several constellations of SARS-CoV-2 nsp14 ExoN-inactivating, loss-of-function substitutions, including the canonical D90A and E92A. Biochemical assays with purified WT or ExoN- nsp10-14 fusion proteins confirmed that active site substitutions abolished ExoN activity (ExoN-). SARS-CoV-2 ExoN- viruses had impaired replication, RNA synthesis, and recombination, as well as decreased replication fidelity and loss of fitness in vitro . ExoN- viruses were significantly attenuated for replication in human primary airway epithelial cells and were attenuated for replication and pathogenesis in WT mice as well as the highly susceptible K18 transgenic mice. In the absence of interferon signaling in vivo , SARS-CoV and SARS-CoV-2 ExoN- viral replication could be nearly fully restored. These results demonstrate that SARS-CoV-2 ExoN- are viable but highly impaired for replication, fitness, and fidelity in vitro as well as innate immune antagonism and pathogenesis in vivo . Collectively, our results solidify the multiple critical roles for nsp14-ExoN across CoV genera and establish new approaches for rescue and analysis of loss-of-function substitutions for studies of CoV replication, pathogenesis, and evolution.
Species-specific chromatin architecture and neurogenesis mediated by a human enhancer
Cell stem cell · 2026-03-19
articlemBio · 2026-05-05
articleOpen accessABSTRACT Antiviral defenses at mucosal barriers are essential for preventing viral entry and systemic infection. Interferon epsilon (IFNε) is a unique type I IFN that, unlike other family members, is not induced by infection but is constitutively expressed in epithelial tissues. IFNε was initially characterized in the female reproductive tract (FRT), where it provides broad antiviral protection, but its roles outside the FRT remain poorly defined. Here, we used Ifnε −/− mice and single-cell RNA sequencing to delineate IFNε function across distinct mucosal surfaces. In the FRT, Ifnε expression was restricted to specific epithelial subsets, was independent of estrous stage, and maintained basal ISG expression. IFNε was also retained intracellularly in primary human FRT-derived cells. Extending these analyses to the intestine, we found that IFNε is highly expressed in villous-tip enterocytes of the small intestine in vivo , where it sustains inflammatory enterocyte subsets and maintains type III IFN expression. Loss of Ifnε depleted these subsets and rendered mice more susceptible to enteric viral infection. Together, these findings establish IFNε as a constitutively expressed, spatially restricted IFN that coordinates mucosal antiviral defenses across both reproductive and gastrointestinal epithelial tissues. IMPORTANCE Interferon epsilon (IFNε) is a unique type I IFN that, unlike other family members, is not induced by infection but is constitutively expressed in epithelial tissues. In this manuscript, we define the epithelial cell types that constitutively express IFNε in the uterus and small intestine at a single-cell resolution. We show that mice lacking IFNε lose key antiviral defenses in a tissue-dependent manner; uterine epithelial cells have diminished basal ISG expression, and key populations of cytokine-expressing enterocytes are absent from the small intestine. In the intestine, this correlates with increased susceptibility to infection with an enteric virus in mice. These findings establish IFNε as a key contributor to mucosal immunity, sustaining antiviral defenses within tissue-specific epithelial cells of both the female reproductive tract and intestine, and broaden our understanding of its role beyond traditional pathogen-induced interferon responses.
UNC Libraries · 2026-05-21
articleOpen accessCoronaviruses (CoVs) replicate their RNA genomes with a higher degree of fidelity than other RNA viruses, a mechanism mediated by the proofreading and recombination activities of the exoribonuclease domain of replicase nonstructural protein 14 (nsp14-ExoN). Both murine hepatitis virus (MHV) and SARS-CoV tolerate nsp14-ExoN loss-of-function mutations (ExoN-) (D90A and E92A), but have impaired replication fidelity and pathogenesis; yet identical substitutions in MERS-CoV and SARS-CoV-2 have been reported to be lethal. Here, we report a saturation mutagenesis approach facilitating the recovery and analysis of several constellations of SARS-CoV-2 nsp14 ExoN-inactivating, loss-of-function substitutions, including the canonical D90A and E92A. Biochemical assays with purified WT or ExoN-nsp10-14 fusion proteins confirmed that active site substitutions abolished ExoN activity (ExoN-). SARS-CoV-2 ExoN- viruses exhibited impaired replication, RNA synthesis, and recombination, as well as decreased replication fidelity and loss of fitness <em>in vitro</em>. ExoN- viruses were significantly attenuated for replication in human primary airway epithelial cells and were attenuated for replication and pathogenesis in WT mice, as well as the highly susceptible K18 transgenic mice. In the absence of interferon signaling <em>in vivo</em>, SARS-CoV and SARS-CoV-2 ExoN- viral replication could be partially restored. These results demonstrate that SARS-CoV-2 ExoN- viruses are viable but highly impaired for replication, fitness, and fidelity <em>in vitro,</em> as well as innate immune antagonism and pathogenesis <em>in vivo</em>. Collectively, our results solidify the multiple critical roles of nsp14-ExoN across CoV genera and establish new approaches for rescuing and analyzing loss-of-function substitutions in studies of CoV replication, pathogenesis, and evolution. IMPORTANCE: Coronaviruses (CoV) are important human pathogens causing hundreds of millions of infections and millions of deaths over the past 20 years. The study of how these viruses multiply and cause disease identifies points of attack for therapeutics. Using a high-throughput genetic approach, we systematically inactivated an essential enzyme CoV needs for replication called ExoN. We show that without ExoN, CoV replication fidelity and fitness are reduced in cell culture. Replication without ExoN in mice was diminished but could be partially restored in mice that lack key components of the immune response. Altogether, we reveal new insights into the complexities of CoV replication and virus and host interactions, which could be leveraged for the development of novel multifaceted therapeutics that attack the ever-expanding functions of the CoV replication complex in replication and pathogenesis.
Research Square · 2026-01-06
preprintOpen access2025-11-28
peer-reviewOpen accessThe enteric bacterial Shigella secretes a virulence factor that degrades the pivotal human defense protein RNF213, thereby protecting cytosolic bacteria from interferon-driven ubiquitylation and associated innate immunity.
eLife · 2025-10-03
articleOpen accessAbstract A central signal that marshals host defense against many infections is the lymphocyte-derived cytokine interferon-gamma (IFNγ). The IFNγ receptor is expressed on most human cells, and its activation leads to the expression of antimicrobial proteins that execute diverse cell-autonomous immune programs. One such immune program consists of the sequential detection, ubiquitylation, and destruction of intracellular pathogens. Recently, the IFNγ-inducible ubiquitin E3 ligase RNF213 was identified as a pivotal mediator of such a defense axis. RNF213 provides host protection against viral, bacterial, and protozoan pathogens. To establish infections, potentially susceptible intracellular pathogens must have evolved mechanisms that subdue RNF213-controlled cell-autonomous immunity. In support of this hypothesis, we demonstrate here that a causative agent of bacillary dysentery, Shigella flexneri, uses the type III secretion system (T3SS) effector IpaH1.4 to induce the degradation of RNF213. S. flexneri mutants lacking IpaH1.4 expression are bound and ubiquitylated by RNF213 in the cytosol of IFNγ-primed host cells. Linear (M1-) and lysine-linked ubiquitylation of S. flexneri requires RNF213 but is independent of the linear ubiquitin chain assembly complex (LUBAC). We find that ubiquitylation of S. flexneri is insufficient to kill intracellular bacteria, suggesting that S. flexneri employs additional virulence factors to escape from host defenses that operate downstream from RNF213-driven ubiquitylation. In brief, this study identified the bacterial IpaH1.4 protein as an inhibitor of mammalian RNF213 and highlights evasion of RNF213-driven immunity as a characteristic of the human-tropic pathogen Shigella.
Recent grants
The effects of cells that survive direct influenza A virus infection on lung repair
NIH · $431k · 2017–2019
Loss of cellular identity after influenza virus infection and effects on pulmonary function
NIH · $2.8M · 2018–2024
Survival of influenza A virus infected cells and effects on pathogenesis
NIH · $267k · 2015–2017
NIH · $4.5M · 2019–2028
Frequent coauthors
- 40 shared
Allison J. Greaney
Fred Hutch Cancer Center
- 40 shared
Jesse D. Bloom
Cape Town HVTN Immunology Laboratory / Hutchinson Centre Research Institute of South Africa
- 40 shared
David J. Bacsik
Cape Town HVTN Immunology Laboratory / Hutchinson Centre Research Institute of South Africa
- 37 shared
Andrew Butler
Cambridge University Hospitals NHS Foundation Trust
- 37 shared
Bernadeta Dadonaite
- 20 shared
Alfred T. Harding
Massachusetts Institute of Technology
- 19 shared
Brook E. Heaton
- 18 shared
Rebekah E. Dumm
Washington University in St. Louis
Labs
- Resume-aware match score
- Save to shortlist
- AI-drafted outreach
See your match with Nicholas Scott Heaton
PhdFit ranks faculty by your research interests, methods, and publications — grounded in their actual work, not templates.
- Free to start
- No credit card
- 30-second signup