A5003140042- CRISPR and Genetic Engineering
- Cholangiocarcinoma and Gallbladder Cancer Studies
- Advanced biosensing and bioanalysis techniques
- RNA regulation and disease
- Transgenic Plants and Applications
- Plant Virus Research Studies
- Cancer Genomics and Diagnostics
- Epigenetics and DNA Methylation
- RNA Interference and Gene Delivery
- Renal and related cancers
- Virus-based gene therapy research
- Animal Genetics and Reproduction
- Gut microbiota and health
- Genetics, Aging, and Longevity in Model Organisms
- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- IL-33, ST2, and ILC Pathways
- Ferroptosis and cancer prognosis
- Machine Learning in Bioinformatics
- Histone Deacetylase Inhibitors Research
- Cancer-related gene regulation
- Immune Cell Function and Interaction
- Innovation and Socioeconomic Development
- Advanced Proteomics Techniques and Applications
- Pancreatic and Hepatic Oncology Research
University of Copenhagen
2021-2023
Aarhus University
2022-2023
Dalian University of Technology
2018
Abstract The design of CRISPR gRNAs requires accurate on-target efficiency predictions, which demand high-quality gRNA activity data and efficient modeling. To advance, we here report on the generation for 10,592 SpCas9 gRNAs. Integrating these with complementary published data, train a deep learning model, CRISPRon, 23,902 Compared to existing tools, CRISPRon exhibits significantly higher prediction performances four test datasets not overlapping training used development tools....
Abstract A major challenge of CRISPR/Cas9-mediated genome engineering is that not all guide RNAs (gRNAs) cleave the DNA efficiently. Although heterogeneity gRNA activity well recognized, current understanding how CRISPR/Cas9 regulated remains incomplete. Here, we identify a sweet spot range binding free energy change for optimal efficiency which largely explains why gRNAs display changes in at on- and off-target sites, including can an with higher than on-target. Using energy-based model,...
Sulforaphene (LFS-01) is a natural compound derived from traditional herbal medicine. Here we show that oral administration of LFS-01 able to dramatically alter the skewed gut microbiota and reverse colitis in model mice associated with an increase intestinal gamma delta T cells. Through 16S rDNA sequencing, showed can selectively suppress enteric pathogens such as Escherichia-Shigellaand Helicobacterwhereasthe protective strains includingLactobacillusand Lachnospiraceae were significantly...
Methods for sensitive and high-throughput evaluation of CRISPR RNA-guided nucleases (RGNs) off-targets (OTs) are essential advancing RGN-based gene therapies. Here we report SURRO-seq simultaneously evaluating thousands therapeutic RGN OTs in cells. captures RGN-induced indels cells by pooled lentiviral libraries deep sequencing, an approach comparable complementary to detection T7 endonuclease 1, GUIDE-seq, CIRCLE-seq. Application 8150 from 110 RGNs identifies significantly detectable 783...
Abstract The transcription factor cyclic-AMP response element-binding protein 1 (CREB1) responds to cAMP level and controls the expression of target genes, which regulates nutrition partitioning. promoters CREB1-targeted genes responsive have been extensively investigated characterized with presence both element TATA box. Compelling evidence demonstrates that CREB1 also plays an essential role in promoting tumor development. However, only very few required for cell survival, proliferation...
Recent progress in CRISPR gene editing tools has substantially increased the opportunities for curing devastating genetic diseases. Here we compare in-frame deletion by CRISPR-based non-homologous blunt end joining (NHBEJ), homology-directed repair (HDR), and prime (PE, PE2, PE3)-based correction of two Duchenne Muscular Dystrophy (DMD) loss-of-function mutations (c.5533G>T c.7893delC). To enable accurate rapid evaluation efficiency, generated a genomically integrated synthetic reporter...
Allele-specific protospacer adjacent motif (asPAM)-positioning SNPs and CRISPRs are valuable resources for gene therapy of dominant disorders. However, one technical hurdle is to identify the haplotype comprising disease-causing allele distal asPAM SNPs. Here, we describe a novel CRISPR-based method (CRISPR-hapC) haplotyping. Based on generation (with pair CRISPRs) extrachromosomal circular DNA in cells, CRISPR-hapC can map haplotypes from few hundred bases over 200 Mb. To streamline...
Abstract The CRISPR RNA-guided endonucleases Cas9, and Cas9-derived adenine/cytosine base editors (ABE/CBE), have been used in both research therapeutic applications. However, broader use of this gene editing toolbox is hampered by the great variability efficiency among different target sites. Here we present TRAP-seq, a versatile scalable approach which gRNA expression cassette corresponding surrogate site are captured T argeted R eporter A nchored P ositional Seq uencing cells. TRAP-seq...
Summary The elucidation of protein function and its exploitation in bioengineering have greatly contributed to the development life sciences. Existing mining efforts generally rely on amino acid sequences rather than structures due technical difficulties structural elucidation. We describe here for use AlphaFold2 predict subsequently cluster an entire family based predicted structure similarities. selected deaminase proteins analyze through this approach identified many previously unknown...
Abstract Sensitive and high-throughput evaluation of CRISPR RNA-guided nucleases (RGNs) off-targets (OTs) in cells are essential for safety assessment advancing RGN-based gene therapies. Here we apply a modified library approach, SURRO-seq, simultaneously evaluating thousands off-target sites therapeutic RGNs cells. The SURRO-seq captures RGN-induced indels barcoded surrogate by pool lentiviral vectors targeted deep sequencing. We first evaluate 170 previously investigated OTs from 11 with...
Abstract Cell free extrachromosomal circular DNA (eccDNA) is evolving as a potential biomarker in liquid biopsies for disease diagnosis. In this study, an optimized next generation sequencing-based Circle-Seq method was developed to investigate urinary cell eccDNA (ucf-eccDNA) from 28 adult healthy volunteers (mean age = 28, 19 males/ 9 females). The genomic distributions and sequence compositions of ucf-eccDNAs were comprehensively characterized. Approximately 1.2 million unique are...