Selected Grantee Publications
- 701 results found
EpicTope: Predicting and Validating Non-disruptive Epitope Tagging Sites
Zinski et al., Development. 2026.
https://pubmed.ncbi.nlm.nih.gov/41816951
Epitope (a specific part of the molecule that an antibody recognizes) tagging is an in vivo (done within an organism) technique used to label, track, and purify proteins of interest. In this study, researchers develop a computation modeling tool—EpicTope—to identify the amino acid (building blocks of a protein) positions that are ideal for epitope insertion. The tool scores suitability based on many factors—including secondary (an intermediate form before a protein takes on its 3D structure) and tertiary (3D-folded) protein structure—to identify locations on the protein where adding an epitope would minimize disruptions to the protein’s function. Using zebrafish, researchers validated EpicTope-identified epitope tag insertion sites for two proteins, Smad5 and Hdac1. mRNA encoding Smad5- and Hdac1-tagged proteins rescued expression levels when injected into mutant zebrafish embryos. Results also showed that these tagged proteins are readily accessible and detectable using antibodies with different laboratory techniques. These findings support EpicTope as an effective tool for identifying sites for epitope tags. Supported by ORIP (R24OD020166, R24OD036201), NICHD, and NIGMS.
MIC-Drop-seq: Scalable Single-Cell Phenotyping of Mutant Vertebrate Embryos
Carey et al., Nature Communications. 2026.
https://pubmed.ncbi.nlm.nih.gov/41922342
Pooled perturbation screens (altering many genes at once with a gene-editing technique) can uncover regulatory networks, but it is difficult to scale this technique for large screens in animal models. In this study, researchers show the utility of MIC-Drop-seq to address the challenges with large-scale screens. MIC-Drop-seq is a technique that combines gene disruption, using CRISPR (a type of gene-editing technique), with single-cell RNA sequencing (a method to identify all the RNA molecules in a cell). Using MIC-Drop-seq with zebrafish embryos, researchers showed that loss of function mutations in 50 transcription factors (proteins that control the activity of genes) cause gene expression and cell number changes across 74 cell types. These results uncover several new roles for transcription factors in controlling embryonic development. This study emphasizes the importance of large-scale screens to understand how changes to one cell type influence the development of other cell types. MIC-Drop-seq will be useful for exploring gene networks that guide animal development. Supported by ORIP (R24OD035409), NHGRI, NHLBI, and NIGMS.
Adjuvant IL-15 Blockade Significantly Improves Survival in a CD28-Based Immunosuppression Protocol of Pig-to–Nonhuman Primate Renal Xenotransplantation
Keiler et al., Transplantation. 2026.
https://pubmed.ncbi.nlm.nih.gov/41489976
End-stage organ disease requires organ transplantation, but organ shortage remains the critical barrier for patients. Xenotransplantation (organ transfer from one organism to another) is a promising solution for this shortage. In a previous study, researchers identified a specific immune cell—natural killer (NK) cells—in rejected xenografts. Using a swine-to–nonhuman primate model for xenotransplantation (sex not stated), researchers showed that adding adjuvant αIL-15—an agent that reduces NK cells—to the immunosuppressive routine (drugs that decrease the immune response and chance of organ rejection) significantly increased xenograft survival and function. Results also showed that adjuvant αIL-15 shifted NK cells to a phenotype (physical characteristics) that lacked CD16 and CD56 expression. These findings support the use of an NK cell-targeted therapy to improve xenograft outcomes. Supported by ORIP (P51OD011132, U42OD011140) and NIAID.
Environmental and Developmental Factors Shape Anti-AAV Immunity in Pigs
Iroanya et al., Gene Therapy. 2026.
https://pubmed.ncbi.nlm.nih.gov/42215798
Adeno-associated viruses (AAVs) show promise for delivering gene therapies to treat monogenic (caused by changes in a single gene) diseases. Researchers evaluated the utility of pigs (sex not stated) as models for testing AAV-based therapies. Consistent with previous studies, they showed that pigs naturally produce antibodies (protective proteins made by the immune system) that can block AAV vectors. These antibodies appeared by 2 weeks of age and increased over time. Immune responses also varied by environment, with pigs in standard housing showing stronger and more diverse responses than those in highly controlled settings. Removing IgG (a type of antibody found in blood and extracellular fluid) restored AAV activity in laboratory tests. This study suggests that pigs can help researchers test ways to overcome immune barriers associated with gene therapies. Supported by ORIP (U42OD027090, U42OD035738).
Genome-Wide Association Mapping and Targeted Loss of Function Studies Identify Shroom3 as a Driver of Hyperpolyploidy and Ventricular Dilation
Purdy et al., PNAS. 2026.
https://pubmed.ncbi.nlm.nih.gov/42189988
Cardiomyocyte polyploidy (a condition where heart muscle cells replicate their DNA but fail to divide) is associated with responses to cardiac injury, but researchers do not fully understand the mechanisms explaining this effect. Researchers studied heart muscle cells in rats (both sexes used) and found that cells with extra chromosome copies were linked to weaker heart pumping and enlarged heart chambers. By scanning rat genomes, they identified the gene Shroom3 as an important driver of this process. When Shroom3 was disrupted in heart cells, polyploidy increased and heart function worsened. The findings suggest Shroom3 helps control heart cell structure and may offer clues for understanding heart disease. Supported by ORIP (R24OD024617), NHLBI, and NIGMS.
Development of a Spatially Defined 3D In Vitro Coculture Construct Modeling Pancreatic Cancer–Associated Cachexia
Kuss et al., Biofabrication. 2026.
https://pubmed.ncbi.nlm.nih.gov/41985529
Up to 85% of pancreatic cancer patients experience cachexia, a debilitating metabolic wasting syndrome. Researchers developed a 3D organoid platform that mimics in vivo interfaces, allowing them to better understand the interactions between cancer cells and adipocytes (fat cells). The system precisely compartmentalizes adipocytes and cancer cells within a hydrogel while reproducing key processes seen in the body, including fat breakdown, changes in fat cells that increase energy use, and the spread of pancreatic cancer cells into surrounding fatty tissue. The model provides a controlled, physiologically relevant environment for understanding the mechanisms of cancer-associated cachexia and for testing potential treatments. Supported by ORIP (S10OD030486), NCI, and NIGMS.
Construction of Saturated Tn-Seq Libraries of Brucella abortus S19 for Transposon Insertion and Effective Density Analysis Across Stress Conditions
Knebel et al., Microbiology Resource Announcements. 2026.
https://pubmed.ncbi.nlm.nih.gov/41984032
Brucella abortus is a bacterial pathogen that can spread between animals and humans. It is highly resilient and can survive in harsh conditions, including acidic environments, exposure to harmful oxygen-containing molecules, and the body’s natural antimicrobial defenses. To better understand how B. abortus survives and causes infection, researchers created large sequencing libraries using the weakened S19 strain of the bacteria with different genetic disruptions. Using this tool, they identified genes that are important for the pathogen’s survival. This rich dataset can be used to explore the genetic fitness of the pathogen B. abortus across multiple environments. Supported by ORIP (T32OD011126).
Impact of Sample Processing Method and Volume on 16 S rRNA Profiling of the Urobiome
Ramirez et al., BMC Microbiology. 2026.
https://pubmed.ncbi.nlm.nih.gov/42251288
The urinary microbiome (urobiome) plays an important role in the health of the urinary and reproductive systems in both humans and animals. Studying these microbial communities can be challenging because urine contains very small numbers of microbes. Researchers compared two methods for processing urine samples from dogs of both sexes—vacuum filtration and pelleting—as well as different sample volumes. They evaluated how these approaches affected bacterial DNA recovery, contamination levels, and the diversity of microbes detected. The results showed that both methods produced similar microbial profiles, even when using smaller urine samples. Overall, the findings suggest that differences in urinary microbiomes are driven mainly by biology rather than sample-processing methods, provided that careful steps are taken to control contamination. Supported by ORIP (T35OD011118), NCATS, and NIEHS.
Triphenyl Phosphate Promotes Lipid Accumulation in Human Mesenchymal Stem Cells Through Metabolic Stress Pathways
Gronske et al., Archives of Toxicology. 2026.
https://pubmed.ncbi.nlm.nih.gov/42228132
Organophosphate esters (OPEs) are chemicals commonly added to plastics and other products to improve flexibility and reduce fire risk. Growing evidence suggests that OPEs can interfere with normal cell functions and place stress on cells, potentially affecting metabolism and other important biological processes. In this in vitro laboratory study, researchers analyzed the effects of an OPE—triphenyl phosphate (TPhP)—on the development and function of human mesenchymal stem cells (which can develop into bone, cartilage, and fat cells). They found that TPhP may disrupt the balance between bone formation and fat metabolism, potentially promoting fat accumulation within bone-forming tissues. Ultimately, TPhP may affect the biological pathways involved in various health conditions, including obesity, type 2 diabetes, and osteoporosis. Supported by ORIP (T35OD011070) and NIEHS.
Impact of Tongue Exercise on Hypoglossal Axis Survival, Structure, and Output in a Rodent Model of Hypoglossal Motor Neuron Degeneration
Keilholz et al., Journal of Neurophysiology. 2026.
https://pubmed.ncbi.nlm.nih.gov/42012472
Motor neuron diseases (MNDs) are a group of neuromuscular (communication between nerves and muscles) disorders caused by the progressive loss of motor neurons. Motor neurons are nerve cells that control such important activities as breathing and swallowing. Obstructive sleep apnea (OSA) is common in patients with MNDs, and OSA may aid the progression of MNDs. Using a 3- to 4-month-old male rat model for MND—and CTB-SAP injections to mimic motor neuron loss in OSA—researchers studied whether high-repetition, low-resistance tongue exercises protected against motor neuron degeneration. Results showed that the tongue exercises increased microglia (an immune cell of the nervous system) density and reduced deficits in nerve outputs. These findings highlight the potential use of tongue exercises to improve functional outcomes in patients with OSA and MND. Supported by ORIP (T32OD011126) and NHLBI.