Selected Grantee Publications
- Clear All
- 34 results found
- Genetics
- Spectrometry
- 2022
Two Neuronal Peptides Encoded from a Single Transcript Regulate Mitochondrial Complex III in Drosophila
Bosch et al., eLife. 2022.
https://www.doi.org/10.7554/eLife.82709
Transcripts with small open-reading frames (smORFs) are underrepresented in genome annotations. Functions of peptides encoded by smORFs are poorly understood. The investigators systematically characterized human-conserved smORF genes in Drosophila and found two peptides, Sloth1 and Sloth2, that are highly expressed in neurons. They showed that Sloth1 and Sloth2 are paralogs with high sequence similarity but are not functionally redundant. Loss of either peptide resulted in lethality, impaired mitochondrial function, and neurodegeneration. This work suggests the value of phenotypic analysis of smORFs using Drosophila as a model. Supported by ORIP (R24OD019847), NHGRI, and NIGMS.
Cell-Specific Regulation of Gene Expression Using Splicing-Dependent Frameshifting
Ling et al., Nature Communications. 2022.
https://www.doi.org/10.1038/s41467-022-33523-2
Precise and reliable cell-specific gene delivery remains technically challenging. Investigators report a splicing-based approach for controlling gene expression whereby separate translational reading frames are coupled to the inclusion or exclusion of mutated, frameshifting cell-specific alternative exons. Candidate exons are identified by analyzing thousands of publicly available RNA sequencing datasets and filtering by cell specificity, conservation, and local intron length. This method, which they denote as splicing-linked expression design (SLED), can be combined in a Boolean manner with such existing techniques as minipromoters and viral capsids. SLED can use strong constitutive promoters, without sacrificing precision, by decoupling the tradeoff between promoter strength and selectivity. AAV-packaged SLED vectors can selectively deliver fluorescent reporters and calcium indicators to various neuronal subtypes in vivo. The authors also demonstrate gene therapy utility by creating SLED vectors that can target PRPH2 and SF3B1 mutations. The flexibility of SLED technology enables creative avenues for basic and translational research. Supported by ORIP (T32OD011089, S10OD026859), NEI, and NIMH.
Long-Term Evolutionary Adaptation of SIVcpz toward HIV-1 Using a Humanized Mouse Model
Schmitt et al., Journal of Medical Primatology. 2022.
https://www.doi.org/10.1111/jmp.12616
Chimpanzee-derived simian immunodeficiency viruses (SIVcpz) are thought to have evolved into the highly pathogenic HIV-1 Group M, but the genetic adaptations required for SIV progenitor viruses to become pathogenic and established as HIVs in the human population have remained unclear. Using humanized mice of both sexes, researchers mimicked the evolution of SIVcpz into HIV-1 Group M through serial passaging. After four generations, the researchers observed increased initial viral load, increased CD4+ T cell decline, and nonsynonymous substitutions. Overall, these data indicate increased viral fitness and pathogenicity. This work also demonstrates the utility of humanized mice in recreating the adaptive pressures necessary for the evolution of SIVcpz into HIV-1. Supported by ORIP (P51OD011104, P51OD011106), NCATS, and NIAID.
System-Wide Identification of Myeloid Markers of TB Disease and HIV-Induced Reactivation in the Macaque Model of Mtb Infection and Mtb/SIV Co-Infection
Gough et al., Frontiers in Immunology. 2022.
https://www.doi.org/10.3389/fimmu.2022.777733
HIV is known to catalyze the reactivation of latent tuberculosis (TB) infection. The investigators characterized Mycobacterium tuberculosis (Mtb) and simian immunodeficiency virus (SIV) coinfection using a rhesus macaque model of both sexes, with a focus on pathways relevant to myeloid origin cells (e.g., macrophages). They identified gene signatures of host disease state and progression, as well as clustering algorithms for differentiation between host disease states and relationships among genes. The gene signatures were associated with pathways relevant to apoptosis, adenosine triphosphate production, phagocytosis, cell migration, and type I interferon, which are related to macrophage function. Collectively, these findings suggest that novel macrophage functions influence Mtb infection both with and without SIV coinfection. Supported by ORIP (P51OD011104, P51OD011103, U42OD010442) and NIAID.
Mendelian Gene Identification through Mouse Embryo Viability Screening
Cacheiro et al., Genome Medicine. 2022.
https://www.doi.org/10.1186/s13073-022-01118-7
The investigators dissected phenotypic similarities between patients and model organisms by assessing the embryonic stage at which homozygous loss of function results in lethality in mice of both sexes obtained from the International Mouse Phenotyping Consortium. Information on knockout mouse embryo lethality can be used to prioritize candidate genes associated with certain disorders. Access to unsolved cases from rare-disease genome sequencing programs allows for the screening of those genes for potentially pathogenic variants, which could lead to a diagnosis and new potential treatment options to inform the management of human disease. Supported by ORIP (UM1OD023221, UM1OD023222, U42OD011174) and NHGRI.
Canine Reference Genome Accuracy Impacts Variant Calling: Lessons Learned from Investigating Embryonic Lethal Variant
Kinsey et al., Animal Genetics. 2022.
https://www.doi.org/10.1111/age.13241
With increasingly affordable whole-genome sequencing, hundreds of canine genomes now can be analyzed for embryonic lethal mutations. Investigators examined whole-genome sequence data from 675 dogs of both sexes to investigate for variants with missing homozygosity and high predicted impact. They identified 45 likely embryonic lethal mutations in 32 genes but found that all but one of those were labeled incorrectly and were artifacts associated with a widely utilized canine reference genome. This effect is a major obstacle to studies focusing on loci with high heterozygosity. The investigators propose that by using newer, multiple reference genomes, researchers could reduce artifacts and identify variants more accurately. Supported by ORIP (K01OD027051, K01OD019912).
De Novo Variants in EMC1 Lead to Neurodevelopmental Delay and Cerebellar Degeneration and Affect Glial Function in Drosophila
Chung et al., Human Molecular Genetics. 2022.
https://www.doi.org/10.1093/hmg/ddac053
Variants in EMC1, which encodes a subunit of the endoplasmic reticulum (ER)–membrane protein complex (EMC), are associated with developmental delay in children. Functional consequences of these variants are poorly understood. The investigators identified de novo variants in EMC1 in three children affected by global developmental delay, hypotonia, seizures, visual impairment, and cerebellar atrophy. They demonstrated in Drosophila that these variants are loss-of-function alleles and lead to lethality when expressed in glia but not in neurons. This work suggests the causality of EMC variants in disease. Supported by ORIP (R24OD022005, R24OD031447), NINDS, and NICHD.
Molecular Insights Into Antibody-Mediated Protection Against the Prototypic Simian Immunodeficiency Virus
Zhao et al., Nature Communications. 2022.
https://www.doi.org/10.1038/s41467-022-32783-2
Most simian immunodeficiency virus (SIV) vaccines have focused on inducing T cell responses alone or in combination with non-neutralizing antibody responses. To date, studies investigating neutralizing antibody (nAb) responses to protect against SIV have been limited. In this study, researchers isolated 12 potent monoclonal nAbs from chronically infected rhesus macaques of both sexes and mapped their binding specificities on the envelope trimer structure. They further characterized the structures using cryogenic electron microscopy, mass spectrometry, and computational modeling. Their findings indicate that, in the case of humoral immunity, nAb activity is necessary and sufficient for protection against SIV challenge. This work provides structural insights for future vaccine design. Supported by ORIP (P51OD011106), NIAID, and NCI.
Pharmacogenetic Gene–Drug Associations in Pediatric Burn and Surgery Patients
Grimsrud et al., Journal of Burn Care & Research. 2022.
https://www.doi.org/10.1093/jbcr/irac062
Simultaneous administration of many medications is common in management of critically ill patients. The researchers investigated drug–drug interactions in these treatments during hospitalization, which might decrease drug efficacy or increase adverse reactions. Genetic and medication data from 30 pediatric burn and surgery patients were analyzed to identify pharmacogene–drug associations. Nineteen patients were identified with predicted altered gene functions. Approximately one-third of the patients tested had functionally impactful genotypes in each of the primary drug metabolizing pathways. This study suggests that the vast variability in drug efficacy is partly due to genetic variants and that pharmacogenetic analysis may help optimize dosing regimens. Supported by ORIP (K01OD026608) and NCI.
Lesion Environments Direct Transplanted Neural Progenitors Towards a Wound Repair Astroglial Phenotype in Mice
O’Shea et al., Nature Communications. 2022.
https://www.doi.org/10.1038/s41467-022-33382-x
Neural progenitor cells (NPCs) are potential cell transplantation therapies for central nervous system (CNS) injuries. Investigators derived NPCs expressing a ribosomal protein-hemagglutinin tag (RiboTag) for transcriptional profiling. Their findings reveal similarities between the transcriptional profiles, cellular morphologies, and functional features of cells transplanted into subacute CNS lesions and host astroglia. The astroglia are stimulated by injuries to proliferate and adopt a naturally occurring, border-forming wound repair phenotype in mice of both sexes. Understanding the autonomous cues instructing NPCs transplanted in CNS host tissue will be fundamental to therapeutic NPC transplantation. Supported by ORIP (U42OD010921,U42OD011174, UM1OD023222) and NINDS.