1
|
Santiago CP, Gimmen MY, Lu Y, McNally MM, Duncan LH, Creamer TJ, Orzolek LD, Blackshaw S, Singh MS. Comparative Analysis of Single-cell and Single-nucleus RNA-sequencing in a Rabbit Model of Retinal Detachment-related Proliferative Vitreoretinopathy. Ophthalmol Sci 2023; 3:100335. [PMID: 37496518 PMCID: PMC10365955 DOI: 10.1016/j.xops.2023.100335] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 07/28/2023]
Abstract
Purpose Proliferative vitreoretinopathy (PVR) is the most common cause of failure of retinal reattachment surgery, and the molecular changes leading to this aberrant wound healing process are currently unknown. Our ultimate goal is to study PVR pathogenesis by employing single-cell transcriptomics to dissect cellular heterogeneity. Design Here we aimed to compare single-cell RNA sequencing (scRNA-seq) and single-nucleus RNA-sequencing (snRNA-seq) of retinal PVR samples in the rabbit model. Participants Unilateral induction of PVR lesions in rabbit eyes with contralateral eyes serving as controls. Methods Proliferative vitreoretinopathy was induced unilaterally in Dutch Belted rabbits. At different timepoints after PVR induction, retinas were dissociated into either cells or nuclei suspension and processed for scRNA-seq or snRNA-seq. Main Outcome Measures Single cell and nuclei transcriptomic profiles of retinas after PVR induction. Results Single-cell RNA sequencing and snRNA-seq were conducted on retinas at 4 hours and 14 days after disease induction. Although the capture rate of unique molecular identifiers and genes were greater in scRNA-seq samples, overall gene expression profiles of individual cell types were highly correlated between scRNA-seq and snRNA-seq. A major disparity between the 2 sequencing modalities was the cell type capture rate, however, with glial cell types overrepresented in scRNA-seq, and inner retinal neurons were enriched by snRNA-seq. Furthermore, fibrotic Müller glia were overrepresented in snRNA-seq samples, whereas reactive Müller glia were overrepresented in scRNA-seq samples. Trajectory analyses were similar between the 2 methods, allowing for the combined analysis of the scRNA-seq and snRNA-seq data sets. Conclusions These findings highlight limitations of both scRNA-seq and snRNA-seq analysis and imply that use of both techniques together can more accurately identify transcriptional networks critical for aberrant fibrogenesis in PVR than using either in isolation. Financial Disclosures Proprietary or commercial disclosure may be found after the references.
Collapse
Affiliation(s)
- Clayton P. Santiago
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, Maryland
| | - Megan Y. Gimmen
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, Maryland
| | - Yuchen Lu
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Minda M. McNally
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Leighton H. Duncan
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, Maryland
| | - Tyler J. Creamer
- Institute for Basic Biomedical Sciences, Johns Hopkins University, Baltimore, Maryland
| | - Linda D. Orzolek
- Institute for Basic Biomedical Sciences, Johns Hopkins University, Baltimore, Maryland
| | - Seth Blackshaw
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, Maryland
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Institute for Cell Engineering, Johns Hopkins University, Baltimore, Maryland
- Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, Maryland
| | - Mandeep S. Singh
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| |
Collapse
|
3
|
Taparra K, Ing BI, Ewongwo A, Vo JB, Shing JZ, Gimmen MY, Keli'i KMK, Uilelea J, Pollom E, Kidd E. Racial Disparities in Brachytherapy Treatment among Women with Cervical and Endometrial Cancer in the United States. Cancers (Basel) 2023; 15:cancers15092571. [PMID: 37174037 PMCID: PMC10177217 DOI: 10.3390/cancers15092571] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
Brachytherapy improves clinical outcomes among women diagnosed with cervical and endometrial cancers. Recent evidence demonstrates that declining brachytherapy boosts for women with cervical cancer were associated with higher mortality. In this retrospective cohort study, women diagnosed with endometrial or cervical cancer in the United States between 2004 and 2017 were selected from the National Cancer Database for evaluation. Women ≥18 years of age were included for high intermediate risk (PORTEC-2 and GOG-99 definition) or FIGO Stage II-IVA endometrial cancers and FIGO Stage IA-IVA-non-surgically treated cervical cancers. The aims were to (1) evaluate brachytherapy treatment practice patterns for cervical and endometrial cancers in the United States; (2) calculate rates of brachytherapy treatment by race; and (3) determine factors associated with not receiving brachytherapy. Treatment practice patterns were evaluated over time and by race. Multivariable logistic regression assessed predictors of brachytherapy. The data show increasing rates of brachytherapy for endometrial cancers. Compared to non-Hispanic White women; Native Hawaiian and other Pacific Islander (NHPI) women with endometrial cancer and Black women with cervical cancer were significantly less likely to receive brachytherapy. For both NHPI and Black women, treatment at community cancer centers was associated with a decreased likelihood of brachytherapy. The data suggest racial disparities among Black women with cervical cancer and NHPI women with endometrial cancer and emphasize an unmet need for brachytherapy access within community hospitals.
Collapse
Affiliation(s)
- Kekoa Taparra
- Department of Radiation Oncology, Stanford Health Care, Stanford, CA 94305, USA
| | - Brandon I Ing
- Department of Obstetrics and Gynecology, Kaiser Permanente, Los Angeles, CA 90027, USA
| | - Agnes Ewongwo
- Department of Radiation Oncology, Stanford Health Care, Stanford, CA 94305, USA
| | - Jacqueline B Vo
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, USA
| | - Jaimie Z Shing
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, USA
| | | | | | | | - Erqi Pollom
- Department of Radiation Oncology, Stanford Health Care, Stanford, CA 94305, USA
| | - Elizabeth Kidd
- Department of Radiation Oncology, Stanford Health Care, Stanford, CA 94305, USA
| |
Collapse
|
4
|
Ling JP, Bygrave AM, Santiago CP, Carmen-Orozco RP, Trinh VT, Yu M, Li Y, Liu Y, Bowden KD, Duncan LH, Han J, Taneja K, Dongmo R, Babola TA, Parker P, Jiang L, Leavey PJ, Smith JJ, Vistein R, Gimmen MY, Dubner B, Helmenstine E, Teodorescu P, Karantanos T, Ghiaur G, Kanold PO, Bergles D, Langmead B, Sun S, Nielsen KJ, Peachey N, Singh MS, Dalton WB, Rajaii F, Huganir RL, Blackshaw S. Cell-specific regulation of gene expression using splicing-dependent frameshifting. Nat Commun 2022; 13:5773. [PMID: 36182931 PMCID: PMC9526712 DOI: 10.1038/s41467-022-33523-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 09/21/2022] [Indexed: 01/29/2023] Open
Abstract
Precise and reliable cell-specific gene delivery remains technically challenging. Here we report a splicing-based approach for controlling gene expression whereby separate translational reading frames are coupled to the inclusion or exclusion of mutated, frameshifting cell-specific alternative exons. Candidate exons are identified by analyzing thousands of publicly available RNA sequencing datasets and filtering by cell specificity, conservation, and local intron length. This method, which we denote splicing-linked expression design (SLED), can be combined in a Boolean manner with existing techniques such as minipromoters and viral capsids. SLED can use strong constitutive promoters, without sacrificing precision, by decoupling the tradeoff between promoter strength and selectivity. AAV-packaged SLED vectors can selectively deliver fluorescent reporters and calcium indicators to various neuronal subtypes in vivo. We also demonstrate gene therapy utility by creating SLED vectors that can target PRPH2 and SF3B1 mutations. The flexibility of SLED technology enables creative avenues for basic and translational research.
Collapse
Affiliation(s)
- Jonathan P Ling
- Departments of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD, 21218, USA.
| | - Alexei M Bygrave
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Clayton P Santiago
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Rogger P Carmen-Orozco
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Vickie T Trinh
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Minzhong Yu
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
- Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, 44195, USA
| | - Yini Li
- Departments of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Ying Liu
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Kyra D Bowden
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Leighton H Duncan
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Jeong Han
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Kamil Taneja
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Rochinelle Dongmo
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Travis A Babola
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Patrick Parker
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Lizhi Jiang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Patrick J Leavey
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Jennifer J Smith
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Zanvyl Krieger Mind/Brain Institute, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Rachel Vistein
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Zanvyl Krieger Mind/Brain Institute, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Megan Y Gimmen
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Benjamin Dubner
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Eric Helmenstine
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Patric Teodorescu
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Theodoros Karantanos
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Gabriel Ghiaur
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Patrick O Kanold
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD, 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Dwight Bergles
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Ben Langmead
- Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD, 21218, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Shuying Sun
- Departments of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Kristina J Nielsen
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD, 21218, USA
- Zanvyl Krieger Mind/Brain Institute, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Neal Peachey
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
- Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, 44195, USA
- Research Service, Louis Stokes Cleveland VA Medical Center, Cleveland, OH, 44106, USA
| | - Mandeep S Singh
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - W Brian Dalton
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Fatemeh Rajaii
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Richard L Huganir
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Seth Blackshaw
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Zanvyl Krieger Mind/Brain Institute, Johns Hopkins University, Baltimore, MD, 21218, USA.
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| |
Collapse
|