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Principal Investigator: MANUEL R AMIEVA
Organization: STANFORD UNIVERSITY
Fiscal Year: 2024
Award: $1,484,612
Funding agency: National Institute of Allergy and Infectious Diseases
Stanford/UNC Biomimetic U19 Research Center
PROJECT SUMMARY/ABSTRACT – CENTER OVERVIEW
Infectious diseases continue to pervasively afflict global health and socioeconomic stability despite substantial
prevention and treatment initiatives. Respiratory and gastrointestinal pathogens rank amongst the most
intractable infectious diseases, particularly notable for recurrent waves of zoonotic coronaviruses and the recent
COVID-19 pandemic, engendered by SARS-CoV-2. Overall, an urgent need exists for improved in vitro
experimental models of human disease to study pathogenesis and to validate therapeutics. The central mission
of the Stanford/UNC Biomimetic U19 Research Center is thus to deploy novel 3-dimensional organoid culture
models to elucidate the biology and therapy of respiratory and gastrointestinal infectious pathogens.
Our application is a renewal of our prior Stanford NAMSED U19 Research Center and is comprised of
two Cores and three research Projects, leveraging complementary and synergistic expertise of our investigators
at Stanford University and the University of North Carolina. The Center continues to be led by the Multi-PIs,
Calvin Kuo and Manuel Amieva, who also co-lead Core A (Administrative Core). Core B (Organoid Core) is led
by Calvin Kuo and provides novel capabilities for lung and GI organoid culture, gene editing and multiplexed
screening. The three Projects extensively utilize organoid biomimetics for exploration of GI and respiratory
pathogens. Project 1, (PI, Manuel Amieva) investigates H. pylori and Salmonella colonization, competition and
invasion in the GI tract, while Project 2 (PI, Harry Greenberg) investigates rotavirus host range, neutralization,
and M cell interactions in enteric biomimetics. Project 3 (PI, Ralph Baric) is a new addition and extensively uses
organoids to model SARS-CoV-2, other closely related epidemic and pre-epidemic emerging coronaviruses and
1918 H1N1 influenza to reveal common and unique host networks associated with severe pulmonary outcomes.
The activities of the Stanford/UNC Biomimetic U19 Research Center reside within three overarching
Aims. In Aim 1, our Center performs organoid modeling of the epithelium-pathogen interface to investigate
pathogenesis, susceptibility and host range restriction. This employs robust reverse genetics and CRISPR
screens to systematically manipulate host versus viral/bacterial compartments, within novel apical-basal polarity
modulated distal lung/alveolar, nasal sinus, stomach and intestinal organoid systems. Aim 2 defines how SARS-
CoV-2, pre-epidemic coronaviruses, rotavirus and Salmonella can perturb reciprocal cross-talk between tissue
epithelium and resident immune cells. This exploits a unique 3D air-liquid interface organoid method preserving
GI and lung epithelium en bloc with diverse endogenous infiltrating immune cell types without artificial
reconstitution. Lastly, Aim 3 performs organoid-based evaluation of therapeutic candidates against SARS-CoV-
2, pre-epidemic coronaviruses and rotavirus in medium- to high-throughput formats including epithelium and/or
immune cells. Overall, the explorations of the Stanford/UNC Biomimetic U19 Research Center directly apply
advanced organoid systems to the investigation and therapy of recalcitrant infectious pathogens.
Terms: <1918 H1N1><1918 influenza A virus><1918 influenza H1N1 virus><1918 influenza virus><2019 novel corona virus><2019 novel coronavirus><2019-nCoV><2019-nCoV S protein><2019-nCoV spike glycoprotein><2019-nCoV spike protein><3-D><3-Dimensional><3D><3D cell culture><3D culture><ARDS><Accessory Sinuses><Acute><Acute Respiratory Distress><Acute Respiratory Distress Syndrome><Adult ARDS><Adult RDS><Adult Respiratory Distress Syndrome><Air><Airway failure><Airway infections><Airway mucosa><Alimentary Canal><Alveolar><Alveolus><Antigenic Determinants><Apical><Bacteria><Bacterial Infections><Basic Research><Basic Science><Bats><Binding><Binding Determinants><Biological Mimetics><Biology><Biomimetics><Body Tissues><Bronchial Alveolus><C pylori><C. pylori><COVID crisis><COVID epidemic><COVID pandemic><COVID test><COVID tests><COVID-19><COVID-19 S protein><COVID-19 crisis><COVID-19 epidemic><COVID-19 era><COVID-19 global health crisis><COVID-19 global pandemic><COVID-19 health crisis><COVID-19 pandemic><COVID-19 period><COVID-19 public health crisis><COVID-19 spike><COVID-19 spike glycoprotein><COVID-19 spike protein><COVID-19 test><COVID-19 tests><COVID-19 virus><COVID-19 years><COVID19 test><COVID19 tests><COVID19 virus><CRISPR><CRISPR activation><CRISPR activator><CRISPR based activation><CRISPR editing screen><CRISPR gene activation><CRISPR interference><CRISPR screen><CRISPR transcription activation><CRISPR transcriptional activation><CRISPR-Cas-9-mediated gene activation><CRISPR-based gene activation><CRISPR-based screen><CRISPR-dCAS9 Activator><CRISPR-dCas9-mediated repression><CRISPR-mediated transcriptional activation><CRISPR/CAS9 activation><CRISPR/CAS9 gene activation><CRISPR/Cas system><CRISPR/Cas9 screen><CRISPR/dCas9 activation><CRISPR/dCas9 interference><CRISPR/dCas9-based transcriptional activation><CRISPR/dCas9-mediated transcriptional inhibition><CRISPRa><CRISPRi><CV-19><Campylobacter pylori><Causality><Cell Body><Cell Communication><Cell Interaction><Cell-to-Cell Interaction><Cells><Chiroptera><Chronic><Clinical Treatment Moab><Clustered Regularly Interspaced Short Palindromic Repeats><Clustered Regularly Interspaced Short Palindromic Repeats interference><Co-culture><CoV emergence><CoV-2><CoV2><Cocultivation><Coculture><Coculture Techniques><Communicable Diseases><Coronaviridae><Coronavirus><Coronavirus Infectious Disease 2019><Da Nang Lung><Digestion><Digestive Tract><Disease><Disorder><Distal><Dysfunction><E coli><E. coli><Enteral><Enteric><Epidemic><Epithelium><Epitopes><Escherichia coli><Etiology><Exhibits><Experimental Models><Functional disorder><GI Tract><Gastrointestinal Diseases><Gastrointestinal Tract><Gastrointestinal tract structure><Generalized Growth><Genes><Genetic Screening><Glycoproteins><Goals><Grippe><Growth><Gut Epithelium><H pylori><H pylory><H. pylori><H. pylory><HCoV><Helicobacter pylori><Human><Immune><Immune infiltrates><Immune response><Immunes><Immunity><Immunological response><In Vitro><Incubators><Infection><Infectious Disease Pathway><Infectious Diseases><Infectious Disorder><Influenza><Innate Immune Response><Intestinal><Intestines><Invaded><Investigation><Investigators><Lead><Liquid substance><Lung><Lung Respiratory System><Lung infections><M cell><MERS><MERS corona virus><MERS coronavirus><MERS coronavirus disease><MERS virus><MERS-CoV><MERS-CoV disease><Mediating><Methods><Middle East Respiratory Syndrome><Middle East Respiratory Syndrome CoV disease><Middle East Respiratory Syndrome Corona Virus><Middle East Respiratory Syndrome Coronavirus><Middle East Respiratory Syndrome Virus><Middle East Respiratory Syndrome coronavirus disease><Middle East Respiratory Syndrome-CoV><Middle East Respiratory Virus><Middle East Respiratory coronavirus><Middle Eastern Respiratory Syndrome><Middle Eastern Respiratory Syndrome CoV disease><Middle Eastern Respiratory Syndrome Corona virus><Middle Eastern Respiratory Syndrome Coronavirus><Middle Eastern Respiratory Syndrome Virus><Middle Eastern Respiratory Syndrome coronavirus disease><Middle Eastern Respiratory Syndrome-CoV><Mission><Modeling><Modern Man><Molecular Interaction><Monoclonal Antibodies><Morbidity><Morbidity - disease rate><Myelogenous><Myeloid><NIAID><Nasal Sinuses><Nasal cavity/Paranasal><Nasal cavity/Paranasal sinuses><National Institute of Allergy and Infectious Disease><Norovirus><North Carolina><Norwalk-like Viruses><Organoids><Outcome><Paranasal Sinuses><Pathogenesis><Pathogenicity><Pb element><Physiopathology><Play><Pneumonia><Population><Predisposition><Prevention><R-Series Research Projects><R01 Mechanism><R01 Program><Recurrence><Recurrent><Research><Research Grants><Research Personnel><Research Project Grants><Research Projects><Researchers><Resistance><Respiratory Epithelium><Respiratory Failure><Respiratory Infections><Respiratory Mucosa><Respiratory Therapy><Respiratory Tract Infections><Role><Rotavirus><Route><S enterica serovar Typhi><S enterica serovar Typhimurium><S typhi><S typhimurium><S typhosa><S. enterica Typhimurium><S. enterica serovar Typhi><S. enterica serovar Typhimurium><S. typhi><S. typhimurium><S. typhosa><SARS><SARS Virus><SARS corona virus><SARS corona virus 2><SARS coronavirus><SARS coronavirus disease><SARS-Associated Coronavirus><SARS-CO-V2><SARS-COVID-2><SARS-CoV><SARS-CoV disease><SARS-CoV-1><SARS-CoV-2><SARS-CoV-2 S><SARS-CoV-2 S protein><SARS-CoV-2 epidemic><SARS-CoV-2 global health crisis><SARS-CoV-2 global pandemic><SARS-CoV-2 inhibitor><SARS-CoV-2 pandemic><SARS-CoV-2 spike><SARS-CoV-2 spike glycoprotein><SARS-CoV-2 spike protein><SARS-CoV-2 test><SARS-CoV-2 tests><SARS-CoV2><SARS-Related Coronavirus><SARS-associated corona virus 2><SARS-associated coronavirus 2><SARS-coronavirus-2><SARS-coronavirus-2 epidemic><SARS-coronavirus-2 pandemic><SARS-related corona virus 2><SARS-related coronavirus 2><SARSCoV2><Salmonella><Salmonella enterica Typhimurium><Salmonella enterica serovar Typhi><Salmonella enterica serovar Typhimurium><Salmonella typhi><Salmonella typhimurium><Salmonella typhosa><Severe Acute Respiratory Coronavirus><Severe Acute Respiratory Coronavirus 2><Severe Acute Respiratory Distress Syndrome CoV 2><Severe Acute Respiratory Distress Syndrome Corona Virus 2><Severe Acute Respiratory Distress Syndrome Coronavirus 2><Severe Acute Respiratory Syndrome><Severe Acute Respiratory Syndrome CoV 2><Severe Acute Respiratory Syndrome CoV 2 epidemic><Severe Acute Respiratory Syndrome CoV 2 pandemic><Severe Acute Respiratory Syndrome CoV disease><Severe Acute Respiratory Syndrome Virus><Severe Acute Respiratory Syndrome corona virus><Severe Acute Respiratory Syndrome coronavirus><Severe Acute Respiratory Syndrome coronavirus disease><Severe Acute Respiratory Syndrome-associated coronavirus 2><Severe Acute Respiratory Syndrome-related coronavirus 2><Severe acute respiratory syndrome associated corona virus 2><Severe acute respiratory syndrome coronavirus 2><Severe acute respiratory syndrome coronavirus 2 S protein><Severe acute respiratory syndrome coronavirus 2 epidemic><Severe acute respiratory syndrome coronavirus 2 inhibitor><Severe acute respiratory syndrome coronavirus 2 pandemic><Severe acute respiratory syndrome coronavirus 2 spike glycoprotein><Severe acute respiratory syndrome coronavirus 2 spike protein><Severe acute respiratory syndrome related corona virus 2><Shock Lung><Sinus><Spanish flu><Spanish influenza><Stiff lung><Stomach><Structure of respiratory epithelium><Surface><Susceptibility><System><Terminal Bronchiole><Testing><Therapeutic><Time><Tissue Engineering><Tissue Growth><Tissues><Universities><Viral><Viral Diseases><Virulence><Virus><Virus Diseases><Wuhan coronavirus><Zoonoses><Zoonotic><Zoonotic Infection><absorption><activating CRISPR technology><adaptive immune response><airway epithelium><alimentary tract><bacteria infection><bacterial disease><bioengineered tissue><block SARS-CoV-2><block severe acute respiratory syndrome coronavirus 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