Jessica Paige Hampton

All Publications

• Comparative analysis of CRISPR off-target discovery tools following ex vivo editing of CD34+ hematopoietic stem and progenitor cells. Molecular therapy : the journal of the American Society of Gene Therapy Cromer, M. K., Majeti, K. R., Rettig, G. R., Murugan, K., Kurgan, G. L., Bode, N. M., Hampton, J. P., Vakulskas, C. A., Behlke, M. A., Porteus, M. H. 2023

  Abstract

  While a number of methods exist to investigate CRISPR off-target (OT) editing, few have been compared head-to-head in primary cells following clinically relevant editing processes. Therefore, we compared in silico tools (COSMID, CCTop, and Cas-OFFinder) and empirical methods (CHANGE-Seq, CIRCLE-Seq, DISCOVER-Seq, GUIDE-Seq, and SITE-Seq) following ex vivo hematopoietic stem and progenitor cell (HSPC) editing. We performed editing using 11 different gRNAs complexed with Cas9 protein (high-fidelity (HiFi) or wild-type versions), then performed targeted next-generation sequencing of nominated OT sites identified by in silico and empirical methods. We identified an average of <1 OT site per gRNA and all OT sites generated using HiFi Cas9 and a 20nt gRNA were identified by all OT detection methods with the exception of SITE-seq. This resulted in high sensitivity for the majority of OT nomination tools and COSMID, DISCOVER-Seq, and GUIDE-Seq attained the highest positive predictive value. We found that empirical methods did not identify off-target sites that were not also identified by bioinformatic methods. This study supports that refined bioinformatic algorithms could be developed that maintain both high sensitivity and positive predictive value, thereby enabling more efficient identification of potential OT sites without compromising a thorough examination for any given gRNA.

  View details for DOI 10.1016/j.ymthe.2023.02.011

  View details for PubMedID 36793210

• Ultra-deep sequencing validates safety of CRISPR/Cas9 genome editing in human hematopoietic stem and progenitor cells. Nature communications Cromer, M. K., Barsan, V. V., Jaeger, E., Wang, M., Hampton, J. P., Chen, F., Kennedy, D., Xiao, J., Khrebtukova, I., Granat, A., Truong, T., Porteus, M. H. 2022; 13 (1): 4724

  Abstract

  As CRISPR-based therapies enter the clinic, evaluation of safety remains a critical and active area of study. Here, we employ a clinical next generation sequencing (NGS) workflow to achieve high sequencing depth and detect ultra-low frequency variants across exons of genes associated with cancer, all exons, and genome wide. In three separate primary human hematopoietic stem and progenitor cell (HSPC) donors assessed in technical triplicates, we electroporated high-fidelity Cas9 protein targeted to three loci (AAVS1, HBB, and ZFPM2) and harvested genomic DNA at days 4 and 10. Our results demonstrate that clinically relevant delivery of high-fidelity Cas9 to primary HSPCs and ex vivo culture up to 10 days does not introduce or enrich for tumorigenic variants and that even a single SNP in a gRNA spacer sequence is sufficient to eliminate Cas9 off-target activity in primary, repair-competent human HSPCs.

  View details for DOI 10.1038/s41467-022-32233-z

  View details for PubMedID 35953477

• A Universal Correction Strategy for alpha-Thalassemia Using CRISPR/AAV-Mediated Genome Editing Cromer, M., Wienert, B., Hampton, J. P., Majeti, K. R., Conklin, B. R., Porteus, M. H., MacKenzie, T. C. CELL PRESS. 2022: 328

  View details for Web of Science ID 000794043701298

• Compliance to an enhanced recovery pathway among patients with a high frailty index after major gastrointestinal surgery results in improved 30-day outcomes. Surgery Hampton, J. P., Owodunni, O. P., Bettick, D. n., Chen, S. Y., Sateri, S. n., Magnuson, T. n., Gearhart, S. L. 2019; 166 (1): 75–81

  Abstract

  Enhanced recovery pathways have been shown to improve clinical outcomes after surgery. Concerns exist about the feasibility of implementing enhanced recovery pathways in frail patients, who are at a greater risk for adverse postoperative outcomes. This study evaluated compliance and outcomes after enhanced recovery pathway implementation in high-risk, abdominal surgery patients.Patients entered into the American College of Surgeons National Surgical Quality Improvement Program database who underwent abdominal surgery after enhanced recovery pathway implementation at two Johns Hopkins Medical Institutions were included. Risk was assessed using the American College of Surgeons National Surgical Quality Improvement Program validated, modified 5-item frailty index. Primary outcomes included compliance with 14 enhanced recovery pathway standards and postoperative length of stay, major complications (Clavien-Dindo score II-IV), and 30-day readmission.This study included 646 patients who participated in our enhanced recovery pathway program and 65 patients with modified 5-item frailty index ≥ 2 before enhanced recovery pathway implementation. Overall, 325 patients (50.3%) were high compliers (>75% compliance) with enhanced recovery pathway standards, with similar proportions of patients with a modified 5-item frailty index ≥ 2 or < 2 achieving high compliance (51.6% vs 50.2%, P = .89, respectively). Examining causality for "low compliers" among patients with a high frailty score (modified 5-item frailty index ≥2) demonstrated significant less use of goal-directed therapy when compared with "high compliers" (43% vs 75%, P = .01). Low compliers were also less likely than high compliers to experience mobilization the day of surgery (43% vs 78%, P = .01), postoperative day 1 (43% vs 88%, P < .01), and postoperative day 2 (60% vs 100%, P < .01). In addition, low compliers were less likely than high compliers to have their diet advanced to solids on postoperative day 1 (17% vs 59%, P < .01) and have their Foley catheter removed on postoperative day 1 (45% vs 97%, P < .01). Comparing our pre-enhanced recovery pathway patients with our enhanced recovery pathway cohort with a high frailty score, enhanced recovery pathway patients had a significantly shorter length of stay (4.5 vs 6 days, P = .04). However, adjusted analysis demonstrated that high compliance, and not just the enhanced recovery pathway intervention among patients with a high frailty score, was independently associated with a decrease in length of stay (odds ratio 0.72, 95% confidence interval 0.63-0.82, P < .01) and a significant reduction in major complications (odds ratio 0.30, 95% confidence interval 0.14-0.65, P < .01.This study demonstrates that frail patients comply well with a robust enhanced recovery pathway protocol and subsequently experience improved outcomes. Targeted interventions that seek to maximize compliance with specific enhanced recovery pathway standards may further improve outcomes in this population.

  View details for DOI 10.1016/j.surg.2019.01.027

  View details for PubMedID 30885399

• High Compliance to an Enhanced Recovery Pathway for Patients ≥65 Years Undergoing Major Small and Large Intestinal Surgery Is Associated With Improved Postoperative Outcomes. Annals of surgery Owodunni, O. P., Hampton, J., Bettick, D., Sateri, S., Magnuson, T., Wick, E., Psoter, K. J., Gearhart, S. L. 2018

  Abstract

  This study was performed to evaluate compliance to an Enhanced Recovery Pathway (ERP) among patients ≥65 years and determine the effect of compliance on postoperative outcomes.ERPs improve postoperative outcomes in patients undergoing major surgery. Given the inherent decline of the older surgical patient, the benefit of an ERP in this population has been questioned.Patients undergoing major small and large intestinal surgery prior to and following ERP implementation at the Johns Hopkins Medical Institutions were entered into the ACS-NSQIP database. Outcomes included ERP compliance rates, complications, length of stay (LOS), and 30-day readmission rates were determined for older patients.Nine hundred seventy-four patients (693 < 65 yrs and 281 ≥ 65 yrs) were included. Of those ≥ 65 years, 142 (51%) were entered prior to and 139 (49%) were entered following ERP implementation. More ERP than pre-ERP patients underwent laparoscopic procedures (45.3% vs. 32.4%, P = 0.02), had disseminated malignancies (9.4% vs. 2.8%, P = 0.03), and smoked (14.4% vs. 4.9%, P = 0.01). Overall compliance was 74.5%, and 47% of older ERP patients achieved high compliance (≥75% compliance with ERP variables). High compliance was associated with a 30% decrease LOS (IRR: 0.7 P = 0.001) and 60% decrease in major (CD ≥ II) complications (OR: 0.4 P = 0.05).LOS and complication rates following implementation of an ERP were significantly improved in highly compliant elderly patients. Interventions to further improve outcomes should target decreasing variability by increasing individual compliance with an effective clinical pathway.

  View details for DOI 10.1097/SLA.0000000000002872

  View details for PubMedID 29923874

• A Nigro-Vagal Pathway Controls Gastric Motility and Is Affected in a Rat Model of Parkinsonism GASTROENTEROLOGY Anselmi, L., Toti, L., Bove, C., Hampton, J., Travagli, R. 2017; 153 (6): 1581–93

  Abstract

  In most patients with Parkinson's disease, gastrointestinal (GI) dysfunctions, such as gastroparesis and constipation, are prodromal to the cardinal motor symptoms of the disease. Sporadic Parkinson's disease has been proposed to develop after ingestion of neurotoxicants that affect the brain-gut axis via the vagus nerve, and then travel to higher centers, compromising the substantia nigra pars compacta (SNpc) and, later, the cerebral cortex. We aimed to identify the pathway that connects the brainstem vagal nuclei and the SNpc, and to determine whether this pathway is compromised in a rat model of Parkinsonism.To study this neural pathway in rats, we placed tracers in the dorsal vagal complex or SNpc; brainstem and midbrain were examined for tracer distribution and neuronal neurochemical phenotype. Rats were given injections of paraquat once weekly for 3 weeks to induce features of Parkinsonism, or vehicle (control). Gastric tone and motility were recorded after N-methyl-d-aspartate microinjection in the SNpc and/or optogenetic stimulation of nigro-vagal terminals in the dorsal vagal complex.Stimulation of the SNpc increased gastric tone and motility via activation of dopamine 1 receptors in the dorsal vagal complex. In the paraquat-induced model of Parkinsonism, this nigro-vagal pathway was compromised during the early stages of motor deficit development.We identified and characterized a nigro-vagal monosynaptic pathway in rats that controls gastric tone and motility. This pathway might be involved in the prodromal gastric dysmotility observed in patients with early-stage Parkinson's disease.

  View details for DOI 10.1053/j.gastro.2017.08.069

  View details for Web of Science ID 000416933500028

  View details for PubMedID 28912019

  View details for PubMedCentralID PMC5705565