Madison Strine | Yale University School of Medicine (original) (raw)

Papers by Madison Strine

Science immunology, Mar 22, 2024

Viruses

Bacteriophages (phages) are the most numerous entities on Earth, but we have only scratched the s... more Bacteriophages (phages) are the most numerous entities on Earth, but we have only scratched the surface of describing phage diversity. We isolated seven Bacillus subtilis phages from desert soil in the southwest United States and then sequenced and characterized their genomes. Comparative analyses revealed high nucleotide and amino acid similarity between these seven phages, which constitute a novel subcluster. Interestingly, the tail fiber and lysin genes of these phages seem to come from different origins and carry out slightly different functions. These genes were likely acquired by this subcluster of phages via horizontal gene transfer. In conjunction with host range assays, our data suggest that these phages are adapting to hosts with different cell walls.

Molecular Cell, Feb 1, 2021

Highlights d The SARS-CoV-2 genome is probed at single-nucleotide resolution in infected cells d ... more Highlights d The SARS-CoV-2 genome is probed at single-nucleotide resolution in infected cells d RNA structure prediction reveals an elaborate SARS-CoV-2 genome architecture d Networks of well-folded secondary structure are conserved across b-coronaviruses d Disruption of conserved secondary structures with LNAs inhibits viral growth

Journal of Virology, Jan 13, 2021

Noroviruses are a leading cause of gastrointestinal infection in humans and mice. Understanding h... more Noroviruses are a leading cause of gastrointestinal infection in humans and mice. Understanding human norovirus (HuNoV) cell tropism has important implications for our understanding of viral pathogenesis. Murine norovirus (MNoV) is extensively used as a surrogate model for HuNoV. We previously identified CD300lf as the receptor for MNoV. Here, we generated a Cd300lf conditional knockout (CD300lf F/F) mouse to elucidate the cell tropism of persistent and nonpersistent strains of murine norovirus. Using this mouse model, we demonstrated that CD300lf expression on intestinal epithelial cells (IECs), and on tuft cells in particular, is essential for transmission of the persistent MNoV strain CR6 (MNoV CR6) in vivo. In contrast, the nonpersistent MNoV strain CW3 (MNoV CW3) does not require CD300lf expression on IECs for infection. However, deletion of CD300lf in myelomonocytic cells (LysM Cre1) partially reduces CW3 viral load in lymphoid and intestinal tissues. Disruption of CD300lf expression on B cells (CD19 Cre), neutrophils (Mrp8 Cre), and dendritic cells (CD11c Cre) did not affect MNoV CW3 viral RNA levels. Finally, we show that the transcription factor STAT1, which is critical for the innate immune response, partially restricts the cell tropism of MNoV CW3 to LysM1 cells. Taken together, these data demonstrate that CD300lf expression on tuft cells is essential for MNoV CR6 ; that myelomonocytic cells are a major, but not exclusive, target cell of MNoV CW3 ; and that STAT1 signaling restricts the cellular tropism of MNoV CW3. This study provides the first genetic system for studying the cell type-specific role of CD300lf in norovirus pathogenesis. IMPORTANCE Human noroviruses (HuNoVs) are a leading cause of gastroenteritis resulting in up to 200,000 deaths each year. The receptor and cell tropism of HuNoV in immunocompetent humans are unclear. We use murine norovirus (MNoV) as a model for HuNoV. We recently identified CD300lf as the sole physiologic receptor for MNoV. Here, we leverage this finding to generate a Cd300lf conditional knockout mouse to decipher the contributions of specific cell types to MNoV infection. We demonstrate that persistent MNoV CR6 requires CD300lf expression on tuft cells. In contrast, multiple CD300lf1 cell types, dominated by myelomonocytic cells, are sufficient for nonpersistent MNoV CW3 infection. CD300lf expression on epithelial cells, B cells, neutrophils, and dendritic cells is not critical for MNoV CW3 infection. Mortality associated with the MNoV CW3 strain in Stat1 2/2 mice does not require CD300lf expression on LysM1 cells, highlighting that both CD300lf receptor expression and innate immunity regulate MNoV cell tropism in vivo.

Nature Genetics, Jul 25, 2022

PLOS Pathogens, Apr 6, 2020

bioRxiv (Cold Spring Harbor Laboratory), Sep 14, 2022

Identifying host genes essential for severe acute respiratory syndrome coronavirus (SARS-CoV-2) h... more Identifying host genes essential for severe acute respiratory syndrome coronavirus (SARS-CoV-2) has the potential to reveal novel drug targets and further our understanding of coronavirus disease 2019 (COVID-19). We previously performed a genome-wide CRISPR/Cas9 screen to identify pro-viral host factors for highly pathogenic human coronaviruses. Very few host factors were required by diverse coronaviruses across multiple cell types, but DYRK1A was one such exception. Although its role in coronavirus infection was completely unknown, DYRK1A encodes Dual Specificity Tyrosine Phosphorylation Regulated Kinase 1A and regulates cell proliferation, and neuronal development, among other cellular processes. Interestingly, individuals with Down syndrome overexpress DYRK1A 1.5-fold and exhibit 5-10x higher hospitalization and mortality rates from COVID-19 infection. Here, we demonstrate that DYRK1A regulates ACE2 and DPP4 transcription independent of its catalytic kinase function to support SARS-CoV, SARS-CoV-2, and MERS-CoV entry. We show that DYRK1A promotes DNA accessibility at the ACE2 promoter and a putative distal enhancer, facilitating transcription and gene expression. Finally, we validate that the pro-viral activity of DYRK1A is conserved across species using cells of monkey and human origin and an in vivo mouse model. In summary, we report that DYRK1A is a novel regulator of ACE2 and DPP4 expression that may dictate susceptibility to multiple highly pathogenic human coronaviruses. Whether DYRK1A overexpression contributes to heightened COVID-19 severity in individuals with Down syndrome through ACE2 regulation warrants further future investigation. .

Nature Genetics, Mar 1, 2023

Extended Data Fig. 8 | Small molecule targeting of mSWI/SNF complexes in primary cells downregula... more Extended Data Fig. 8 | Small molecule targeting of mSWI/SNF complexes in primary cells downregulates ACE2 expression. (a) Cell viability of HBECs after 4 days treatment of Comp12 at 2.5 and 5 μM. (b) HBECs were pre-treated with Comp12 for the indicated times, ACE2 expression was measured by RT-qPCR. HBECs were pre-treated with Comp12 for the indicated times and then infected with SARS-CoV-2 at an MOI of 0.5. Virus titer in the apical supernatant was measured by plaque assay. Dashed line, limit of detection. (c) HBECs were pre-treated with Comp12 at 2.5 μM for the indicated times, HNF1A and SLC4A4 expression was measured by RT-qPCR. (d) Volcano plots reflecting gene expression changes (RNA-seq) in HBECs after 4 days treatment of Comp12 at 2.5 μM. (e) Pathway analysis (Metascape) in Comp12 treated HBECs (n = 2 RNA-Seq biological replicates). P-values calculated using a hypergeometric test by Metascape. (f) HBECs were pretreated with the indicated inhibitors at 2.5 μM for 4 days, HNF1A and SLC4A4 expression were measured by RT-qPCR. Data in (a-c, f) were analyzed by one-way ANOVA with Tukey's multiple comparison test. Shown are mean ± SEM. *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001, n = 3 biological replicates.

The Journal of Immunology

Human norovirus (HNV) is a leading cause of viral gastroenteritis. Infection fails to elicit dura... more Human norovirus (HNV) is a leading cause of viral gastroenteritis. Infection fails to elicit durable immunity and can cause chronic asymptomatic shedding. It is not known how norovirus escapes the adaptive immune response, and rigorous studies of the host and viral determinants underlying immune evasion are impeded by the lack of scalable cell culture systems and reverse genetic tools. Murine norovirus (MNV) recapitulates many aspects of HNV and enables studying norovirus biology in vitro and in vivo. MNV CW3causes non-persistent infection with long-lasting immune memory, whereas MNV CR6causes persistent infection despite inducing functional MNV-specific CD8+ T cells. We recently identified that MNV CR6and other persistent MNV strains require tuft cells for chronic enteric infection. Tuft cells are rare, chemosensory epithelial cells with roles in pathogen surveillance, epithelial repair, and tumorigenesis. To interrogate tuft cell interactions with CD8+ T cells, we adoptively trans...

Current Protocols

Murine norovirus (MNV) is a positive‐sense, plus‐stranded RNA virus in the Caliciviridae family. ... more Murine norovirus (MNV) is a positive‐sense, plus‐stranded RNA virus in the Caliciviridae family. Viruses in this family replicate in the intestine and are transmitted by the fecal‐oral route. MNV is related to the human noroviruses, which cause the majority of nonbacterial gastroenteritis worldwide. Given the technical challenges in studying human norovirus, MNV is often used to study mechanisms in norovirus biology since it combines the availability of a cell culture and reverse genetics system with the ability to study infection in the native host. Adding to our previous protocol collection, here we describe additional techniques that have since been developed to study MNV biology. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC.Basic Protocol 1: Indirect method for measuring cell cytotoxicity and antiviral activityBasic Protocol 2: Measuring murine norovirus genome titers by RT‐qPCRSupport Protocol 1: Preparation of standardBasic Protocol 3: Generation of...

PLOS Pathogens

Identification of host determinants of coronavirus infection informs mechanisms of pathogenesis a... more Identification of host determinants of coronavirus infection informs mechanisms of pathogenesis and may provide novel therapeutic targets. Here, we demonstrate that the histone demethylase KDM6A promotes infection of diverse coronaviruses, including SARS-CoV, SARS-CoV-2, MERS-CoV and mouse hepatitis virus (MHV) in a demethylase activity-independent manner. Mechanistic studies reveal that KDM6A promotes viral entry by regulating expression of multiple coronavirus receptors, including ACE2, DPP4 and Ceacam1. Importantly, the TPR domain of KDM6A is required for recruitment of the histone methyltransferase KMT2D and histone deacetylase p300. Together this KDM6A-KMT2D-p300 complex localizes to the proximal and distal enhancers of ACE2 and regulates receptor expression. Notably, small molecule inhibition of p300 catalytic activity abrogates ACE2 and DPP4 expression and confers resistance to all major SARS-CoV-2 variants and MERS-CoV in primary human airway and intestinal epithelial cells....

PLOS Biology

Identifying host genes essential for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)... more Identifying host genes essential for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has the potential to reveal novel drug targets and further our understanding of Coronavirus Disease 2019 (COVID-19). We previously performed a genome-wide CRISPR/Cas9 screen to identify proviral host factors for highly pathogenic human coronaviruses. Few host factors were required by diverse coronaviruses across multiple cell types, but DYRK1A was one such exception. Although its role in coronavirus infection was previously undescribed, DYRK1A encodes Dual Specificity Tyrosine Phosphorylation Regulated Kinase 1A and is known to regulate cell proliferation and neuronal development. Here, we demonstrate that DYRK1A regulates ACE2 and DPP4 transcription independent of its catalytic kinase function to support SARS-CoV, SARS-CoV-2, and Middle East Respiratory Syndrome Coronavirus (MERS-CoV) entry. We show that DYRK1A promotes DNA accessibility at the ACE2 promoter and a putative distal enhan...

Nature Communications

Compact RNA structural motifs control many aspects of gene expression, but we lack methods for fi... more Compact RNA structural motifs control many aspects of gene expression, but we lack methods for finding these structures in the vast expanse of multi-kilobase RNAs. To adopt specific 3-D shapes, many RNA modules must compress their RNA backbones together, bringing negatively charged phosphates into close proximity. This is often accomplished by recruiting multivalent cations (usually Mg2+), which stabilize these sites and neutralize regions of local negative charge. Coordinated lanthanide ions, such as terbium (III) (Tb3+), can also be recruited to these sites, where they induce efficient RNA cleavage, thereby revealing compact RNA 3-D modules. Until now, Tb3+ cleavage sites were monitored via low-throughput biochemical methods only applicable to small RNAs. Here we present Tb-seq, a high-throughput sequencing method for detecting compact tertiary structures in large RNAs. Tb-seq detects sharp backbone turns found in RNA tertiary structures and RNP interfaces, providing a way to scan...

Science Immunology

Passive immunization with nirsevimab protects infants from severe RSV disease without impairing t... more Passive immunization with nirsevimab protects infants from severe RSV disease without impairing the immune response to natural infection.

Scientific Reports

Sero-surveillance can monitor and project disease burden and risk. However, SARS-CoV-2 antibody t... more Sero-surveillance can monitor and project disease burden and risk. However, SARS-CoV-2 antibody test results can produce false positive results, limiting their efficacy as a sero-surveillance tool. False positive SARS-CoV-2 antibody results are associated with malaria exposure, and understanding this association is essential to interpret sero-surveillance results from malaria-endemic countries. Here, pre-pandemic samples from eight malaria endemic and non-endemic countries and four continents were tested by ELISA to measure SARS-CoV-2 Spike S1 subunit reactivity. Individuals with acute malaria infection generated substantial SARS-CoV-2 reactivity. Cross-reactivity was not associated with reactivity to other human coronaviruses or other SARS-CoV-2 proteins, as measured by peptide and protein arrays. ELISAs with deglycosylated and desialated Spike S1 subunits revealed that cross-reactive antibodies target sialic acid on N-linked glycans of the Spike protein. The functional activity of...