Browsing by Author "Park, So Hyun"

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    Comprehensive analysis and accurate quantification of unintended large gene modifications induced by CRISPR-Cas9 gene editing
    (AAAS, 2022) Park, So Hyun; Cao, Mingming; Pan, Yidan; Davis, Timothy H.; Saxena, Lavanya; Deshmukh, Harshavardhan; Fu, Yilei; Treangen, Todd; Sheehan, Vivien A.; Bao, Gang
    Most genome editing analyses to date are based on quantifying small insertions and deletions. Here, we show that CRISPR-Cas9 genome editing can induce large gene modifications, such as deletions, insertions, and complex local rearrangements in different primary cells and cell lines. We analyzed large deletion events in hematopoietic stem and progenitor cells (HSPCs) using different methods, including clonal genotyping, droplet digital polymerase chain reaction, single-molecule real-time sequencing with unique molecular identifier, and long-amplicon sequencing assay. Our results show that large deletions of up to several thousand bases occur with high frequencies at the Cas9 on-target cut sites on the HBB (11.7 to 35.4%), HBG (14.3%), and BCL11A (13.2%) genes in HSPCs and the PD-1 (15.2%) gene in T cells. Our findings have important implications to advancing genome editing technologies for treating human diseases, because unintended large gene modifications may persist, thus altering the biological functions and reducing the available therapeutic alleles.
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    Genome editing strategies for treating β-hemoglobinopathies
    (2020-04-23) Park, So Hyun; Bao, Gang
    β-hemoglobinopathies including sickle cell disease (SCD) and β-thalassemia are debilitating, painful diseases and a major cause of global mortality and health disparities. Currently, there is no cure for the majority of patients with β-hemoglobinopathies and therapeutic options are limited. We have developed novel approaches to curing β-hemoglobinopathies using CRISPR/Cas9 based ex vivo genome editing of β-globin (HBB) gene in patients’ hematopoietic stem and progenitor cells (HSPCs). Although gene-editing strategies, including correction of the sickle mutation, targeted insertion of the β-globin gene and induction of fetal hemoglobin are very promising in curing β-hemoglobinopathies, significant safety concerns exist, including off-target effects, large deletions and insertions in HBB, and chromosomal rearrangements. In Aim 1, we optimized the design of CRISPR gRNA and short single-strand oligonucleotide donor template to correct the sickle mutation, and demonstrated high rates of gene correction in SCD HSPCs. Erythrocytes derived from gene-edited cells showed high levels of normal hemoglobin expression and a marked reduction of sickle cells. We found that gene-corrected HSPCs retained the ability to engraft in mouse models, and the off-target effects could be significantly reduced by using HiFi-Cas9. In Aim 2, we developed and validated two next-generation sequencing-based assays, LongAmp-seq (long-range PCR amplification based sequencing) and NEW-seq (nuclease-activity identified by gEnome-wide sequencing), to comprehensively investigate the gene-editing outcomes and the potential consequences of unexpected mutations. We performed a thorough analysis of gene-editing outcomes, including large deletions and insertions at the HBB cut site not previously reported. The LongAmp-seq and NEW-seq also have the potential to detect and quantify chromosomal rearrangements including inversions, translocations and large chromosomal deletions. To aid the development of new therapies for β-hemoglobinopathies, in Aim 3, we applied genome editing to establish erythroid cell models for SCD and β-thalassemia that exhibit disease phenotypes. These cell models are reliable, reproducible and low-cost in performing disease studies, including validation of genome editing based therapies and screening of pharmacological drugs. The systematic studies of the efficiency and safety of the gene-editing approaches, and the cell models developed for discovery of therapeutic agents may significantly facilitate the clinical translation of gene editing based therapies for β-hemoglobinopathies.
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    Highly efficient editing of the β-globin gene in patient-derived hematopoietic stem and progenitor cells to treat sickle cell disease
    (Oxford University Press, 2019) Park, So Hyun; Lee, Ciaran M.; Dever, Daniel P.; Davis, Timothy H.; Camarena, Joab; Srifa, Waracharee; Zhang, Yankai; Paikari, Alireza; Chang, Alicia K.; Porteus, Matthew H.; Sheehan, Vivien A.; Bao, Gang; Bioengineering
    Sickle cell disease (SCD) is a monogenic disorder that affects millions worldwide. Allogeneic hematopoietic stem cell transplantation is the only available cure. Here, we demonstrate the use of CRISPR/Cas9 and a short single-stranded oligonucleotide template to correct the sickle mutation in the β-globin gene in hematopoietic stem and progenitor cells (HSPCs) from peripheral blood or bone marrow of patients with SCD, with 24.5 ± 7.6% efficiency without selection. Erythrocytes derived from gene-edited cells showed a marked reduction of sickle cells, with the level of normal hemoglobin (HbA) increased to 25.3 ± 13.9%. Gene-corrected SCD HSPCs retained the ability to engraft when transplanted into non-obese diabetic (NOD)-SCID-gamma (NSG) mice with detectable levels of gene correction 16–19 weeks post-transplantation. We show that, by using a high-fidelity SpyCas9 that maintained the same level of on-target gene modification, the off-target effects including chromosomal rearrangements were significantly reduced. Taken together, our results demonstrate efficient gene correction of the sickle mutation in both peripheral blood and bone marrow-derived SCD HSPCs, a significant reduction in sickling of red blood cells, engraftment of gene-edited SCD HSPCs in vivo and the importance of reducing off-target effects; all are essential for moving genome editing based SCD treatment into clinical practice.
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    In Vivo Ryr2 Editing Corrects Catecholaminergic Polymorphic Ventricular Tachycardia
    (American Heart Association, 2018) Pan, Xiaolu; Philippen, Leonne; Lahiri, Satadru K.; Lee, Ciaran; Park, So Hyun; Word, Tarah A.; Li, Na; Jarrett, Kelsey E.; Gupta, Rajat; Reynolds, Julia O.; Lin, Jean; Bao, Gang; Lagor, William R.; Wehrens, Xander H.T.; Bioengineering
    Rationale:Autosomal-dominant mutations in ryanodine receptor type 2 (RYR2) are responsible for ≈60% of all catecholaminergic polymorphic ventricular tachycardia. Dysfunctional RyR2 subunits trigger inappropriate calcium leak from the tetrameric channel resulting in potentially lethal ventricular tachycardia. In vivo CRISPR/Cas9-mediated gene editing is a promising strategy that could be used to eliminate the disease-causing Ryr2 allele and hence rescue catecholaminergic polymorphic ventricular tachycardia.Objective:To determine if somatic in vivo genome editing using the CRISPR/Cas9 system delivered by adeno-associated viral (AAV) vectors could correct catecholaminergic polymorphic ventricular tachycardia arrhythmias in mice heterozygous for RyR2 mutation R176Q (R176Q/+).Methods and Results:Guide RNAs were designed to specifically disrupt the R176Q allele in the R176Q/+ mice using the SaCas9 (Staphylococcus aureus Cas9) genome editing system. AAV serotype 9 was used to deliver Cas9 and guide RNA to neonatal mice by single subcutaneous injection at postnatal day 10. Strikingly, none of the R176Q/+ mice treated with AAV-CRISPR developed arrhythmias, compared with 71% of R176Q/+ mice receiving control AAV serotype 9. Total Ryr2 mRNA and protein levels were significantly reduced in R176Q/+ mice, but not in wild-type littermates. Targeted deep sequencing confirmed successful and highly specific editing of the disease-causing R176Q allele. No detectable off-target mutagenesis was observed in the wild-type Ryr2 allele or the predicted putative off-target site, confirming high specificity for SaCas9 in vivo. In addition, confocal imaging revealed that gene editing normalized the enhanced Ca2+ spark frequency observed in untreated R176Q/+ mice without affecting systolic Ca2+ transients.Conclusions:AAV serotype 9–based delivery of the SaCas9 system can efficiently disrupt a disease-causing allele in cardiomyocytes in vivo. This work highlights the potential of somatic genome editing approaches for the treatment of lethal autosomal-dominant inherited cardiac disorders, such as catecholaminergic polymorphic ventricular tachycardia.
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    LPA disruption with AAV-CRISPR potently lowers plasma apo(a) in transgenic mouse model: A proof-of-concept study
    (Elsevier, 2022) Doerfler, Alexandria M.; Park, So Hyun; Assini, Julia M.; Youssef, Amer; Saxena, Lavanya; Yaseen, Adam B.; De Giorgi, Marco; Chuecos, Marcel; Hurley, Ayrea E.; Li, Ang; Marcovina, Santica M.; Bao, Gang; Boffa, Michael B.; Koschinsky, Marlys L.; Lagor, William R.; Bioengineering
    Lipoprotein(a) (Lp(a)) represents a unique subclass of circulating lipoprotein particles and consists of an apolipoprotein(a) (apo(a)) molecule covalently bound to apolipoprotein B-100. The metabolism of Lp(a) particles is distinct from that of low-density lipoprotein (LDL) cholesterol, and currently approved lipid-lowering drugs do not provide substantial reductions in Lp(a), a causal risk factor for cardiovascular disease. Somatic genome editing has the potential to be a one-time therapy for individuals with extremely high Lp(a). We generated an LPA transgenic mouse model expressing apo(a) of physiologically relevant size. Adeno-associated virus (AAV) vector delivery of CRISPR-Cas9 was used to disrupt the LPA transgene in the liver. AAV-CRISPR nearly completely eliminated apo(a) from the circulation within a week. We performed genome-wide off-target assays to determine the specificity of CRISPR-Cas9 editing within the context of the human genome. Interestingly, we identified intrachromosomal rearrangements within the LPA cDNA in the transgenic mice as well as in the LPA gene in HEK293T cells, due to the repetitive sequences within LPA itself and neighboring pseudogenes. This proof-of-concept study establishes the feasibility of using CRISPR-Cas9 to disrupt LPA in vivo, and highlights the importance of examining the diverse consequences of CRISPR cutting within repetitive loci and in the genome globally.
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    Multiplexed high-throughput localized electroporation workflow with deep learning–based analysis for cell engineering
    (AAAS, 2022) Patino, Cesar A.; Pathak, Nibir; Mukherjee, Prithvijit; Park, So Hyun; Bao, Gang; Espinosa, Horacio D.; Bioengineering
    Manipulation of cells for applications such as biomanufacturing and cell-based therapeutics involves introducing biomolecular cargoes into cells. However, successful delivery is a function of multiple experimental factors requiring several rounds of optimization. Here, we present a high-throughput multiwell-format localized electroporation device (LEPD) assisted by deep learning image analysis that enables quick optimization of experimental factors for efficient delivery. We showcase the versatility of the LEPD platform by successfully delivering biomolecules into different types of adherent and suspension cells. We also demonstrate multicargo delivery with tight dosage distribution and precise ratiometric control. Furthermore, we used the platform to achieve functional gene knockdown in human induced pluripotent stem cells and used the deep learning framework to analyze protein expression along with changes in cell morphology. Overall, we present a workflow that enables combinatorial experiments and rapid analysis for the optimization of intracellular delivery protocols required for genetic manipulation.