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Qing KX, Lo ACY, Lu S, Zhou Y, Yang D, Yang D. Integrated bioinformatics analysis of retinal ischemia/reperfusion injury in rats with potential key genes. BMC Genomics 2024; 25:367. [PMID: 38622534 PMCID: PMC11017533 DOI: 10.1186/s12864-024-10288-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 04/07/2024] [Indexed: 04/17/2024] Open
Abstract
The tissue damage caused by transient ischemic injury is an essential component of the pathogenesis of retinal ischemia, which mainly hinges on the degree and duration of interruption of the blood supply and the subsequent damage caused by tissue reperfusion. Some research indicated that the retinal injury induced by ischemia-reperfusion (I/R) was related to reperfusion time.In this study, we screened the differentially expressed circRNAs, lncRNAs, and mRNAs between the control and model group and at different reperfusion time (24h, 72h, and 7d) with the aid of whole transcriptome sequencing technology, and the trend changes in time-varying mRNA, lncRNA, circRNA were obtained by chronological analysis. Then, candidate circRNAs, lncRNAs, and mRNAs were obtained as the intersection of differentially expression genes and trend change genes. Importance scores of the genes selected the key genes whose expression changed with the increase of reperfusion time. Also, the characteristic differentially expressed genes specific to the reperfusion time were analyzed, key genes specific to reperfusion time were selected to show the change in biological process with the increase of reperfusion time.As a result, 316 candidate mRNAs, 137 candidate lncRNAs, and 31 candidate circRNAs were obtained by the intersection of differentially expressed mRNAs, lncRNAs, and circRNAs with trend mRNAs, trend lncRNAs and trend circRNAs, 5 key genes (Cd74, RT1-Da, RT1-CE5, RT1-Bb, RT1-DOa) were selected by importance scores of the genes. The result of GSEA showed that key genes were found to play vital roles in antigen processing and presentation, regulation of the actin cytoskeleton, and the ribosome. A network included 4 key genes (Cd74, RT1-Da, RT1-Bb, RT1-DOa), 34 miRNAs and 48 lncRNAs, and 81 regulatory relationship axes, and a network included 4 key genes (Cd74, RT1-Da, RT1-Bb, RT1-DOa), 9 miRNAs and 3 circRNAs (circRNA_10572, circRNA_03219, circRNA_11359) and 12 regulatory relationship axes were constructed, the subcellular location, transcription factors, signaling network, targeted drugs and relationship to eye diseases of key genes were predicted. 1370 characteristic differentially expressed mRNAs (spec_24h mRNA), 558 characteristic differentially expressed mRNAs (spec_72h mRNA), and 92 characteristic differentially expressed mRNAs (spec_7d mRNA) were found, and their key genes and regulation networks were analyzed.In summary, we screened the differentially expressed circRNAs, lncRNAs, and mRNAs between the control and model groups and at different reperfusion time (24h, 72h, and 7d). 5 key genes, Cd74, RT1-Da, RT1-CE5, RT1-Bb, RT1-DOa, were selected. Key genes specific to reperfusion time were selected to show the change in biological process with the increased reperfusion time. These results provided theoretical support and a reference basis for the clinical treatment.
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Affiliation(s)
- Kai-Xiong Qing
- Department of Cardiac & Vascular Surgery, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, Yunnan Province, China
| | - Amy C Y Lo
- Department of Ophthalmology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Siduo Lu
- Department of Ophthalmology, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, Yunnan Province, China
| | - You Zhou
- Department of Ophthalmology, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, Yunnan Province, China
| | - Dan Yang
- Department of Ophthalmology, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, Yunnan Province, China
| | - Di Yang
- Department of Ophthalmology, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, Yunnan Province, China.
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Hao S, Amaral MM, Zhou C. High dynamic range 3D motion tracking using circular scans with optical coherence tomography. BIOMEDICAL OPTICS EXPRESS 2023; 14:3881-3898. [PMID: 37799687 PMCID: PMC10549755 DOI: 10.1364/boe.493725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/21/2023] [Accepted: 06/21/2023] [Indexed: 10/07/2023]
Abstract
Motion artifacts, from such sources as heartbeats, respiration, or peristalsis, often degrade microscopic images or videos of live subjects. We have developed a method using circular optical coherence tomography (OCT) scans to track the transverse and axial motion of biological samples at speeds ranging from several micrometers per second to several centimeters per second. We achieve fast and high-precision measurements of the magnitude and direction of the sample's motion by adaptively controlling the circular scan pattern settings and applying interframe and intraframe analyses. These measurements are the basis of active motion compensation via feedback control for future in vivo microscopic and macroscopic imaging applications.
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Affiliation(s)
- Senyue Hao
- Department of Electrical & Systems Engineering,
Washington University in Saint Louis, USA
| | - Marcello Magri Amaral
- Department of Biomedical Engineering, Washington University in Saint Louis, USA
- Biomedical Engineering, Universidade Brasil, Brazil
| | - Chao Zhou
- Department of Electrical & Systems Engineering,
Washington University in Saint Louis, USA
- Department of Biomedical Engineering, Washington University in Saint Louis, USA
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Tan B, McNabb RP, Zheng F, Sim YC, Yao X, Chua J, Ang M, Hoang QV, Kuo AN, Schmetterer L. Ultrawide field, distortion-corrected ocular shape estimation with MHz optical coherence tomography (OCT). BIOMEDICAL OPTICS EXPRESS 2021; 12:5770-5781. [PMID: 34692214 PMCID: PMC8515957 DOI: 10.1364/boe.428430] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 07/08/2021] [Accepted: 07/08/2021] [Indexed: 05/06/2023]
Abstract
Ocular deformation may be associated with biomechanical alterations in the structures of the eye, especially the cornea and sclera in conditions such as keratoconus, congenital glaucoma, and pathological myopia. Here, we propose a method to estimate ocular shape using an ultra-wide field MHz swept-source optical coherence tomography (SS-OCT) with a Fourier Domain Mode-Locked (FDML) laser and distortion correction of the images. The ocular biometrics for distortion correction was collected by an IOLMaster 700, and localized Gaussian curvature was proposed to quantify the ocular curvature covering a field-of-view up to 65°×62°. We achieved repeatable curvature shape measurements (intraclass coefficient = 0.88 ± 0.06) and demonstrated its applicability in a pilot study with individuals (N = 11) with various degrees of myopia.
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Affiliation(s)
- Bingyao Tan
- SERI-NTU Advanced Ocular Engineering (STANCE), Singapore, Singapore
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
- Authors contributed equally to the study
| | - Ryan P McNabb
- Duke University Medical Center, Durham, NC 27607, USA
- Authors contributed equally to the study
| | - Feihui Zheng
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Yin Ci Sim
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Xinwen Yao
- SERI-NTU Advanced Ocular Engineering (STANCE), Singapore, Singapore
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
| | - Jacqueline Chua
- SERI-NTU Advanced Ocular Engineering (STANCE), Singapore, Singapore
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Department of Ophthalmology, Duke-NUS Medical School, Singapore
| | - Marcus Ang
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Department of Ophthalmology, Duke-NUS Medical School, Singapore
| | - Quan V Hoang
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Department of Ophthalmology, Duke-NUS Medical School, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Department of Ophthalmology, Edward S. Harkness Eye Institute, Columbia College of Physicians and Surgeons, New York, NY 10032, USA
| | - Anthony N Kuo
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Duke University Medical Center, Durham, NC 27607, USA
| | - Leopold Schmetterer
- SERI-NTU Advanced Ocular Engineering (STANCE), Singapore, Singapore
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
- Department of Ophthalmology, Duke-NUS Medical School, Singapore
- Department of Clinical Pharmacology, Medical University of Vienna, Vienna, Austria
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
- Institute of Molecular and Clinical Ophthalmology, Basel, Switzerland
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Gong P, Heiss C, Sampson DM, Wang Q, Yuan Z, Sampson DD. Detection of localized pulsatile motion in cutaneous microcirculation by speckle decorrelation optical coherence tomography angiography. JOURNAL OF BIOMEDICAL OPTICS 2020; 25:JBO-200112R. [PMID: 32935499 PMCID: PMC7490763 DOI: 10.1117/1.jbo.25.9.095004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 08/18/2020] [Indexed: 05/21/2023]
Abstract
SIGNIFICANCE Pulsatility is a vital characteristic of the cardiovascular system. Characterization of the pulsatility pattern locally in the peripheral microvasculature is currently not readily available and would provide an additional source of information, which may prove important in understanding the pathophysiology of arterial stiffening, vascular ageing, and their linkage with cardiovascular disease development. AIM We aim to confirm the suitability of speckle decorrelation optical coherence tomography angiography (OCTA) under various noncontact/contact scanning protocols for the visualization of pulsatility patterns in vessel-free tissue and in the microvasculature of peripheral human skin. RESULTS Results from five healthy subjects show distinct pulsatile patterns both in vessel-free tissue with either noncontact or contact imaging and in individual microvessels with contact imaging. Respectively, these patterns are likely caused by the pulsatile pressure and pulsatile blood flow. The pulse rates show good agreement with those from pulse oximetry, confirming that the pulsatile signatures reflect pulsatile hemodynamics. CONCLUSIONS This study demonstrates the potential of speckle decorrelation OCTA for measuring localized peripheral cutaneous pulsatility and defines scanning protocols necessary to undertake such measurements. Noncontact imaging should be used for the study of pulsatility in vessel-free tissue and contact imaging with strong mechanical coupling in individual microvessels. Further studies of microcirculation based upon this method and protocols are warranted.
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Affiliation(s)
- Peijun Gong
- The University of Western Australia, Optical+Biomedical Engineering Laboratory, Department of Electrical, Electronic, and Computer Engineering, Perth, Western Australia, Australia
- Address all correspondence to Peijun Gong, E-mail:
| | - Christian Heiss
- The University of Surrey, Department of Clinical and Experimental Medicine, Faculty of Health and Medical Sciences, Guildford, Surrey, United Kingdom
- Surrey and Sussex Healthcare NHS Trust, Redhill, United Kingdom
| | - Danuta M. Sampson
- The University of Surrey, Centre for Vision, Speech, and Signal Processing, Surrey Biophotonics, Guildford, Surrey, United Kingdom
- The University of Surrey, School of Biosciences and Medicine, Surrey Biophotonics, Guildford, Surrey, United Kingdom
| | - Qiang Wang
- The University of Western Australia, Optical+Biomedical Engineering Laboratory, Department of Electrical, Electronic, and Computer Engineering, Perth, Western Australia, Australia
| | - Zhihong Yuan
- The University of Western Australia, Optical+Biomedical Engineering Laboratory, Department of Electrical, Electronic, and Computer Engineering, Perth, Western Australia, Australia
| | - David D. Sampson
- The University of Surrey, School of Biosciences and Medicine, Surrey Biophotonics, Guildford, Surrey, United Kingdom
- The University of Surrey, Advanced Technology Institute, School of Physics, Surrey Biophotonics, Guildford, Surrey, United Kingdom
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