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Browsing by Author "Hartigan, Kelly"

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    Comparative analysis of nuclei isolation methods for brain single-nucleus RNA sequencing
    (bioRxiv, 2025-03-26) Kersey, Holly N.; Acri, Dominic J.; Dabin, Luke C.; Hartigan, Kelly; Mustaklem, Richard; Park, Jung Hyun; Kim, Jungsu; Medical and Molecular Genetics, School of Medicine
    Single-nucleus RNA sequencing (snRNA-seq) enables resolving cellular heterogeneity in complex tissues. snRNA-seq overcomes limitations of traditional single-cell RNA-seq by using nuclei instead of cells, allowing to utilize frozen tissues and difficult-to-isolate cell types. Although various nuclei isolation methods have been developed, systematic evaluations of their effects on nuclear integrity and subsequent data quality remain lacking, a critical gap with profound implications for the rigor and reproducibility. To address this, we compared three mechanistically distinct nuclei isolation strategies with brain tissues: a sucrose gradient centrifugation-based method, a spin column-based method, and a machine-assisted platform. All methods successfully captured diverse cell types but revealed considerable protocol-dependent differences in cell type proportions, transcriptional homogeneity, and the preservation of cell-type-specific and cell-state-specific markers. Moreover, isolation workflows differentially influenced contamination levels from ambient, mitochondrial, and ribosomal RNAs. Our findings establish nuclei isolation methodology as a critical experimental variable shaping snRNA-seq data quality and biological interpretation. Motivation: Single-nucleus RNA sequencing (snRNA-seq) has become an essential tool for transcriptomic analysis of complex tissues. However, the quality and efficiency of data generation depend heavily on the method used for nuclear isolation. The existing isolation techniques vary in their ability to preserve nuclear integrity, minimize ambient RNA contamination, and optimize recovery rates. Despite these differences in quality, a systematic comparison of these methods, specifically for brain tissue, is lacking. This gap poses a challenge for researchers in choosing the most suitable approach for their particular experimental requirements. To address this critical issue, our study directly compared three nuclei isolation methods and evaluated their performance in terms of yield, purity, and downstream sequencing quality. By providing a comprehensive assessment, we aim to guide researchers in selecting the most appropriate isolation protocol for their snRNA-seq experiments, ensuring optimal results and advancing the study of complex brain tissues at the single-nucleus level.
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    Efficacy of supplemental oxygen in reducing the need for laser or intravitreal bevacizumab in preterm infants with stage 2 retinopathy of prematurity
    (Springer Nature, 2024-05-24) Minturn, Robert; Hartigan, Kelly; Vegunta, Sravanthi; Boente, Charline; Golzarri-Arroyo, Lilian; Hynes, Elizabeth; Laughlin, Elleen; Haider, Kathryn; Kua, Kok Lim; Ophthalmology, School of Medicine
    Background: Retinopathy of prematurity (ROP) is a disease that affects preterm infants born younger than 30 weeks of gestation. The pathophysiology of ROP involves an initial vaso-obliterative phase followed by vaso-proliferative phase that leads to disease progression. The use of supplemental oxygen during the vaso-proliferative phase of ROP has been associated with reduced disease progression, but how this impacts the need for ROP treatment is unclear. The goal of this study was to compare the rate of laser or intravitreal bevacizumab after implementation of a new supplemental oxygen therapy protocol in preterm infants with stage 2 ROP. Methods: This is a retrospective chart review of preterm infants diagnosed with stage 2 ROP at Riley Hospital for Children between 1/2017 and 12/2022. Patients diagnosed between 1/2017 and 6/2020 were classified as Cohort A, preprotocol implementation. Patients diagnosed from 8/2020 to 12/2022 were classified as Cohort B, postprotocol implementation. In Cohort A, oxygen saturation was kept at 91-95% through the entire hospitalization. In Cohort B, oxygen saturation was increased to 97-99% as soon as Stage 2 ROP was diagnosed. Statistical analyses were performed using chi-square and Student's T test, followed by multivariate analyses to determine the impact of the oxygen protocol on the need for ROP treatment. Results: A total of 211 patients were diagnosed with stage 2 ROP between 1/2017 and 12/2022. Of those patients, 122 were before protocol implementation therapy (Cohort A), and 89 were after implementation of supplemental oxygen protocol (Cohort B). Gestational age was slightly higher in Cohort B (Cohort A 25.3 ± 1.9, Cohort B 25.8 ± 1.84, p = 0.04). There was no difference in birth weight, NEC, BPD, or survival. Cohort B had lesser need for invasive mechanical ventilation and higher days on CPAP during hospitalization. Notably, Cohort A had 67 (55%) patients treated with laser photocoagulation or intravitreal bevacizumab versus 20 (22%) patients in Cohort B (OR 0.19, 0.08-0.40). Conclusion: The need for laser photocoagulation or intravitreal bevacizumab was significantly decreased in high-risk patients treated with the supplemental oxygen protocol. This result supports the idea that targeted supplemental oxygen therapy to keep saturations between 97 and 99% can reduce disease progression in infants with stage 2 ROP and potentially decrease the burden of additional procedures.
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