Selected Grantee Publications
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- Microbiome
- Somatic Cell Genome Editing
Targeted Suppression of Human IBD-Associated Gut Microbiota Commensals by Phage Consortia for Treatment of Intestinal Inflammation
Federici et al., Cell. 2022.
https://www.doi.org/10.1016/j.cell.2022.07.003
Human gut commensals increasingly are suggested to affect noncommunicable diseases, such as inflammatory bowel disease (IBD), yet their targeted suppression remains an unmet challenge. In this report, investigators identified a clade of Klebsiella pneumoniae (Kp) strains—featuring a unique antibiotic resistance and mobilome signature—that is associated strongly with disease exacerbation and severity. Transfer of clinical IBD-associated Kp strains into colitis-prone, germ-free, and colonized mice of both sexes enhances intestinal inflammation. An orally administered combination phage therapy targeting sensitive and resistant IBD-associated Kp clade members enables effective Kp suppression, suggesting the feasibility of avoiding antibiotic resistance while effectively inhibiting noncommunicable disease–contributing pathobionts. Supported by ORIP (P40OD010995) and NIDDK.
Large Comparative Analyses of Primate Body Site Microbiomes Indicate That the Oral Microbiome Is Unique Among All Body Sites and Conserved Among Nonhuman Primates
Asangba et al., Microbiology Spectrum. 2022.
https://www.doi.org/10.1128/spectrum.01643-21
Microbiomes are critical to host health and disease, but large gaps remain in the understanding of the determinants, coevolution, and variation of microbiomes across body sites and host species. Thus, researchers conducted the largest comparative study of primate microbiomes to date by investigating microbiome community composition at eight distinct body sites in 17 host species. They found that the oral microbiome is unique in exhibiting notable similarity across primate species while being distinct from the microbiomes of all other body sites and host species. This finding suggests conserved oral microbial niche specialization, despite substantial dietary and phylogenetic differences among primates. Supported by ORIP (P51OD010425, P51OD011107, P40OD010965, R01OD010980), NIA, NIAID, and NICHD.
The Early Life Microbiota Mediates Maternal Effects on Offspring Growth in a Nonhuman Primate
Petrullo et al., iScience. 2022.
https://www.doi.org/10.1016/j.isci.2022.103948
Mammalian mothers influence offspring development by providing nutrients and other bioactive compounds through the placenta or milk. A relatively unexplored mechanism for maternal effects is vertical transmission of bacteria through milk to the infant gut. Infants that receive more glycan-utilizing bacteria from milk might better exploit oligosaccharides, which could improve nutrition and accelerate growth. Researchers found that first-time vervet mothers harbored a milk bacterial community that was less diverse due to the dominance of Bacteroides fragilis, a glycan-utilizing bacteria. These low-parity females had infants that grew faster, suggesting that vertical transmission of bacteria via milk can mediate maternal effects on growth. These results indicate non-nutritive milk constituents play important roles in development. Commercial milk formula might need to be improved or supplemented to better support infant health. Supported by ORIP (P40OD010965) and NCATS.
AAV5 Delivery of CRISPR-Cas9 Supports Effective Genome Editing in Mouse Lung Airway
Liang et al., Molecular Therapy. 2022.
https://www.cell.com/molecular-therapy-family/molecular-therapy/fulltext/S1525-0016(21)00530-X
Genome editing in the lung has the potential to provide long-term expression of therapeutic protein to treat lung genetic diseases. The authors illustrated that AAV5 can efficiently deliver CRISPR-Cas9 to mouse lung airways and was the first to achieve ∼20% editing efficiency in those airways. Results were confirmed through independent experiments at two different institutes. This highly efficient dual AAV platform will facilitate the study of genome editing in the lung and other tissue types. Supported by ORIP (U42OD026645).
Cannabinoid Control of Gingival Immune Activation in Chronically SIV-Infected Rhesus Macaques Involves Modulation of the Indoleamine-2,3-Dioxygenase-1 Pathway and Salivary Microbiome
McDew-White et al., EBioMedicine. 2021.
https://pubmed.ncbi.nlm.nih.gov/34954656/
HIV-associated periodontal disease (PD) affects people living with HIV (PLWH) on combination anti-retroviral therapy (cART). Researchers used a systems biology approach to investigate the molecular, metabolome, and microbiome changes underlying PD and its modulation by phytocannabinoids (Δ9-THC) in rhesus macaques. Δ9-THC reduced IDO1 protein expression. The findings suggest that phytocannabinoids may help reduce gingival/systemic inflammation, salivary dysbiosis, and potentially metabolic disease in PLWH on cART. Supported by ORIP (P51OD011104, P51OD011133, U42OD010442), NIAID, NIDA, NIDDK, NIDCR, and NIMH.
AAV Capsid Variants with Brain-Wide Transgene Expression and Decreased Liver Targeting After Intravenous Delivery in Mouse and Marmoset
Goertsen et al., Nature Neuroscience. 2021.
https://www.nature.com/articles/s41593-021-00969-4
Genetic intervention is increasingly being explored as a therapeutic option for debilitating disorders of the central nervous system (CNS). This project focused on organ-specific targeting of adeno-associated virus (AAV) capsids after intravenous delivery. These results constitute an important step forward toward achieving the goal of engineered AAV vectors that can be used to broadly deliver gene therapies to the CNS in humans. Supported by ORIP (U24OD026638), NIMH, and NINDS.
Deciphering the Role of Mucosal Immune Responses and the Cervicovaginal Microbiome in Resistance to HIV Infection in HIV-Exposed Seronegative Women
Ponnan et al., Microbiology Spectrum. 2021.
https://journals.asm.org/doi/10.1128/Spectrum.00470-21
Identifying correlates of protection in HIV-exposed seronegative (HESN) individuals requires identification of HIV-specific local immune responses. Researchers performed a comprehensive investigation of the vaginal mucosa and cervicovaginal microbiome in HESN women. They found elevated antiviral cytokines, soluble immunoglobulins, activated NK cells, CXCR5+ CD8+ T cells, and T follicular helper cells in HESN women compared to HIV-unexposed healthy women. They also found greater bacterial diversity and increased abundance of Gardnerella species in the mucosa of HESN women. These findings suggest that the genital tract of HESN women contains innate immune factors, antiviral mediators, and T cell subsets that protect against HIV. Supported by ORIP (P51OD011132) and NIAID.
IL-21 and IFNα Therapy Rescues Terminally Differentiated NK Cells and Limits SIV Reservoir in ART-Treated Macaques
Harper et al., Nature Communications. 2021.
https://doi.org/10.1038/s41467-021-23189-7
Nonpathogenic simian immunodeficiency virus (SIV) infections in natural hosts, such as vervet monkeys, are characterized by a lack of gut microbial translocation, robust secondary lymphoid natural killer cell responses, and limited SIV dissemination in lymph node B-cell follicles. Using antiretroviral therapy-treated, SIV-infected rhesus monkeys—a pathogenic model—researchers showed that interleukin-21 and interferon alpha therapy generate terminally differentiated blood natural killer cells with potent human leukocyte antigen-E-restricted activity in response to SIV envelope peptides. The correlated reduction of replication-competent SIV in lymph node demonstrates that vervet-like natural killer cell differentiation can be rescued in rhesus monkeys to promote viral clearance. Supported by ORIP (P51OD011132, R24OD010947), NIAID, and NCI.
Tract Pathogen-Mediated Inflammation Through Development of Multimodal Treatment Regimen and Its Impact on SIV Acquisition in Rhesus Macaques
Bochart et al., PLOS Pathogens. 2021.
https://doi.org/10.1371/journal.ppat.1009565
In addition to being premier HIV models, rhesus macaques are models for other infectious diseases and colitis, where background colon health and inflammation may confound results. Starting with the standard specific-pathogen-free (SPF) model, researchers established a gastrointestinal pathogen-free (GPF) colony via multimodal therapy (enrofloxacin, azithromycin, fenbendazole, and paromomycin) to eliminate common endemic pathogens (EPs). This treatment combined with continued pathogen exclusion eliminated common EPs, improved mucosal barriers, and reduced mucosal and systemic inflammation without microbiota disruption. GPF animals challenged with SIV intrarectally demonstrated a more controlled and consistent rate of SIV acquisition, suggesting the value of this model for HIV studies. Supported by ORIP (U42OD023038, P51OD011092), NCI, and NIAID.