Selected Grantee Publications
- Clear All
- 12 results found
- CRISPR
- Spectrometry
- 2021
Deep Learning Is Widely Applicable to Phenotyping Embryonic Development and Disease
Naert et al., Development. 2021.
https://pubmed.ncbi.nlm.nih.gov/34739029/
Genome editing simplifies the generation of new animal models for congenital disorders. The authors illustrate how deep learning (U-Net) automates segmentation tasks in various imaging modalities. They demonstrate this approach in embryos with polycystic kidneys (pkd1 and pkd2) and craniofacial dysmorphia (six1). They provide a library of pre-trained networks and detailed instructions for applying deep learning to datasets and demonstrate the versatility, precision, and scalability of deep neural network phenotyping on embryonic disease models. Supported by ORIP (P40OD010997, R24OD030008), NICHD, NIDDK, and NIMH.
MIC-Drop: A Platform for Large-scale In Vivo CRISPR Screens
Parvez et al., Science. 2021.
https://pubmed.ncbi.nlm.nih.gov/34413171/
CRISPR screens in animals are challenging because generating, validating, and keeping track of large numbers of mutant animals is prohibitive. These authors introduce Multiplexed Intermixed CRISPR Droplets (MIC-Drop), a platform combining droplet microfluidics, single-needle en masse CRISPR ribonucleoprotein injections, and DNA barcoding to enable large-scale functional genetic screens in zebrafish. In one application, they showed that MIC-Drop could identify small-molecule targets. Furthermore, in a MIC-Drop screen of 188 poorly characterized genes, they discovered several genes important for cardiac development and function. With the potential to scale to thousands of genes, MIC-Drop enables genome-scale reverse genetic screens in model organisms. Supported by ORIP (R24OD017870), NIGMS, and NHLBI.
TGF-β1 Signaling Is Essential for Tissue Regeneration in the Xenopus Tadpole Tail
Nakamura et al., Biochemical and Biophysical Research Communications. 2021.
https://www.sciencedirect.com/science/article/pii/S0006291X21008731
Amphibians, such as Xenopus tropicalis, exhibit a remarkable capacity for tissue regeneration after traumatic injury. Nakamura et al. show that inhibition of TGF-β1 function prevents tail regeneration in Xenopus tropicalis tadpoles. CRISPR-mediated knock-out (KO) of tgfb1 retards tail regeneration; the phenotype of tgfb1 KO tadpoles can be rescued by injection of tgfb1 mRNA. Cell proliferation, critical for tissue regeneration, is downregulated in tgfb1 KO tadpoles; tgfb1 KO reduces the expression of phosphorylated Smad2/3 (pSmad2/3). These results show that TGF-β1 regulates cell proliferation through the activation of Smad2/3. They propose that TGF-β1 plays a critical role in TGF-β receptor-dependent tadpole tail regeneration in Xenopus. Supported by ORIP (P40OD010997, R24OD030008).
Phase Separation Drives Aberrant Chromatin Looping and Cancer Development
Ahn et al., Nature. 2021.
https://doi.org/10.1038/s41586-021-03662-5
How unstructured intrinsically disordered regions (IDRs) contribute to oncogenesis is elusive. Using an Orbitrap fusion tribrid mass spectrometer, investigators show that IDRs contained within NUP98–HOXA9, a homeodomain-containing transcription factor chimera recurrently detected in leukaemias, are essential for establishing liquid–liquid phase separation (LLPS) puncta of chimera and for inducing leukaemic transformation. LLPS of NUP98–HOXA9 not only promotes chromatin occupancy of chimera transcription factors, but also is required for the formation of a broad “super-enhancer”-like binding pattern typically seen at leukaemogenic genes, which potentiates transcriptional activation. An artificial HOX chimera, created by replacing the phenylalanine and glycine repeats of NUP98 with an unrelated LLPS-forming IDR of the FUS protein, had similar enhancing effects on the genome-wide binding and target gene activation of the chimera. This report describes a proof-of-principle example in which cancer acquires mutation to establish oncogenic transcription factor condensates via phase separation, which simultaneously enhances their genomic targeting and induces organization of aberrant three-dimensional chromatin structure during tumor transformation. Supported by ORIP (S10OD018445).
Nonhuman Primate Models for SARS-CoV-2 Research: Cryopreservation as a Means to Maintain Critical Models and Enhance the Genetic Diversity of Colonies
Arnegard and Hild et al., Lab Animal. 2021.
https://doi.org/10.1038/s41684-021-00792-1
This commentary, written by ORIP staff, addresses the need for improved cryopreservation methods and resources for nonhuman primate (NHP) gametes and embryos to safeguard newly developed NHP models and enhance the genetic diversity of NHP colonies without reliance on animal importations. Cryopreservation also plays critical roles in medical approaches to preserve the fertility of patients who must undergo potentially gonadotoxic treatments, as well as nascent genome editing efforts to develop new NHP models for human diseases. Given these diverse benefits to research progress, ORIP continues to fund the development of cryopreservation tools and approaches for NHPs and other animal models.
Identification of Basp1 as a Novel Angiogenesis-regulating Gene by Multi-Model System Studies
Khajavi et al., FASEB Journal. 2021.
https://pubmed.ncbi.nlm.nih.gov/33899275/
The authors previously used genetic diversity in inbred mouse strains to identify quantitative trait loci (QTLs) responsible for differences in angiogenic response. Employing a mouse genome-wide association study (GWAS) approach, the region on chromosome 15 containing Basp1 was identified as being significantly associated with angiogenesis in inbred strains. To investigate its role in vivo, they knocked out basp1 in transgenic kdrl:zsGreen zebrafish embryos using a widely adopted CRISPR-Cas9 system. They further showed that basp1 promotes angiogenesis by upregulating β-catenin gene and the Dll4/Notch1 signaling pathway. These results provide the first in vivo evidence to indicate the role of basp1 as an angiogenesis-regulating gene. Supported by ORIP (R24OD017870) and NEI.
Establishing an Immunocompromised Porcine Model of Human Cancer for Novel Therapy Development with Pancreatic Adenocarcinoma and Irreversible Electroporation
Hendricks-Wenger et al., Scientific Reports. 2021.
https://pubmed.ncbi.nlm.nih.gov/33828203/
Efficacious interventions to treat pancreatic cancer lack a preclinical model to recapitulate patients' anatomy and physiology. The authors developed RAG2/IL2RG deficient pigs using CRISPR/Cas9 with the novel application of cancer xenograft studies of human pancreatic adenocarcinoma. These pigs were successfully generated using on-demand genetic modifications in embryos. Human Panc01 cells injected into the ears of RAG2/IL2RG deficient pigs demonstrated 100% engraftment. The electrical properties and response to irreversible electroporation of the tumor tissue were found to be similar to excised human pancreatic cancer tumors. This model will be useful to bridge the gap of translating therapies from the bench to clinical application. Supported by ORIP (R21OD027062), NIBIB, and NCI.
Sensitive Tracking of Circulating Viral RNA Through All Stages of SARS-CoV-2 Infection
Huang et al., Journal of Clinical Investigation. 2021.
https://www.jci.org/articles/view/146031
Circulating SARS-CoV-2 RNA could represent a more reliable indicator of infection than nasal RNA, but quantitative reverse transcription PCR (RT-qPCR) lacks diagnostic sensitivity for blood samples. Researchers developed a CRISPR-amplified, blood-based COVID-19 (CRISPR-ABC) assay to detect SARS-CoV-2 in plasma. They evaluated the assay using samples from SARS-CoV-2-infected African green monkeys and rhesus macaques, as well as from COVID-19 patients. CRISPR-ABC consistently detected viral RNA in the plasma of the experimentally infected primates from 1 to 28 days after infection. The increases in plasma SARS-CoV-2 RNA in the monkeys preceded rectal swab viral RNA increases. In the patient cohort, the new assay demonstrated 91.2% sensitivity and 99.2% specificity versus RT-qPCR nasopharyngeal testing, and it also detected COVID-19 cases with transient or negative nasal swab RT-qPCR results. These findings suggest that detection of SARS-CoV-2 RNA in blood by CRISPR-augmented RT-PCR could improve COVID-19 diagnosis, facilitate the evaluation of SARS-CoV-2 infection clearance, and help predict the severity of infection. Supported by ORIP (P51OD011104).
Metabolomics Analysis of Follicular Fluid Coupled With Oocyte Aspiration Reveals Importance of Glucocorticoids in Primate Periovulatory Follicle Competency
Ravisankar et al., Scientific Reports. 2021.
https://www.nature.com/articles/s41598-021-85704-6
Assisted reproductive therapy in primates requires ovarian stimulation protocols, which result in multiple heterogeneous oocytes with variable capacity for fertilization, cleavage, and blastocyst formation. Recovered oocytes from rhesus macaque follicles (n=74 follicles) were fertilized in vitro and classified as failed to cleave, cleaved but arrested, or able to form blastocysts. Metabolomics analysis of the follicular fluid identified 60 metabolites that were different among embryo classifications; key was an increase in the intrafollicular ratio of cortisol to cortisone in the blastocyst group, which was associated with translocation of the glucocorticoid receptor, NR3C1. The data suggest a role for NR3C1 in the regulation of follicular processes, such as expansion of cumulus granulosa cells, via paracrine signaling. Supported by ORIP (P51OD011092) and NICHD.
Endogenous Zebrafish Neural Cre Drivers Generated by CRISPR/Cas9 Short Homology Directed Targeted Integration
Almeida et al., Scientific Reports. 2021.
https://pubmed.ncbi.nlm.nih.gov/33462297/
Almeida et al. previously reported precision targeted integration of reporter DNA in zebrafish using CRISPR/Cas9. Here, they isolated zebrafish Cre recombinase drivers. A 2A-Cre recombinase transgene with 48 bp homology arms was targeted into proneural genes ascl1b, olig2 and neurod1. They observed high rates of germline transmission from 10 to 100% (10% olig2; 20% neurod1; 100% ascl1b). The lines Tg(ascl1b-2A-Cre)is75, Tg(olig2-2A-Cre)is76, and Tg(neurod1-2A-Cre)is77 expressed functional Cre recombinase in the cell populations. Results demonstrate Cre recombinase expression is driven by the native promoter and regulatory elements of targeted genes. This approach is a cost-effective method to generate cell type specific zebrafish Cre and CreERT2 drivers. Supported by ORIP (R24OD020166).