scholarly journals Profiles of microRNA in aqueous humor of normal tension glaucoma patients using RNA sequencing

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hyemin Seong ◽  
Hyun-kyung Cho ◽  
Changwon Kee ◽  
Dae Hyun Song ◽  
Min-Chul Cho ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Aqueous Humor ◽  
Bioinformatics Analysis ◽  
Final Analysis ◽  
Normal Tension Glaucoma ◽  
Receptor Interaction ◽  
Biological Processes ◽  
Differentially Expressed Mirna ◽  
Novel Targets ◽  
Normal Controls

AbstractWe aimed to identify and compare microRNAs (miRNAs) from individual aqueous humor samples between normal-tension glaucoma (NTG) patients and normal controls. Aqueous humor (80 to 120 µl) was collected before cataract surgery. Six stable NTG patients and seven age-matched controls were included in the final analysis. RNA sequencing was conducted for RNA samples extracted from the 13 aqueous humor samples, and bioinformatics analysis was employed for the miRNA targets and related pathways. Two hundred and twenty-eight discrete miRNAs were detected in the aqueous humor and consistently expressed in all samples. Eight significantly upregulated miRNAs were found in the NTG patients compared to the controls (fold-change > 2, p < 0.05). They were hsa-let-7a-5p, hsa-let-7c-5p, hsa-let-7f-5p, hsa-miR-192-5p, hsa-miR-10a-5p, hsa-miR-10b-5p, hsa-miR-375, and hsa-miR-143-3p. These miRNAs were predicted to be associated with the biological processes of apoptosis, autophagy, neurogenesis, and aging in the gene ontology categories. The related Kyoto encyclopedia of genes and genomes pathways were extracellular matrix-receptor interaction, mucin-type O-glycan biosynthesis, biotin metabolism, and signaling pathways regulating the pluripotency of stem cells. The differentially expressed miRNA in the NTG samples compared to the controls suggest the possible roles of miRNA in the pathogenesis of NTG. The underlying miRNA-associated pathways further imply novel targets for the pathogenesis of NTG.

scholarly journals RNA Sequencing Analysis Between Ruptured and Un-Ruptured Brain AVM

2022 ◽  
Author(s):  
Hao Li ◽  
Zihan Yan ◽  
Ran Huo ◽  
Xiaolong Ya ◽  
Hongyuan Xu ◽  
...  
Keyword(s):  
Extracellular Matrix ◽  
Cell Adhesion ◽  
Rna Sequencing ◽  
Bioinformatics Analysis ◽  
Nervous System Development ◽  
Sequencing Analysis ◽  
Biological Processes ◽  
Cox Regression Analysis ◽  
Inflammatory Processes ◽  
Matrix Organization

Abstract BackgroundBrain arteriovenous malformation (BAVM) arises as congenital vascular abnormalities with a significant risk for intracerebral hemorrhage (ICH). RNA sequencing technology has been recently used to investigate the mechanism of diseases owing to its ability to identify the gene changes on a transcriptome-wide level. In this study, we aimed to gain insights into the potential mechanism involved in BAVM rupture. MethodsSixty-five BAVM nidus samples were collected among which 28 were ruptured and 37 were un-ruptured. Then next-generation RNA sequencing were performed on all of them to obtain differential expressed genes (DEGs) between these two groups. In addition, bioinformatics analysis was performed to evaluate the involved biological processes and pathways by GO and KEGG analysis. Finally, univariate Cox regression analysis was utilized to obtain the early rupture-prone DEGs. Results: A total of 951 genes were differentially expressed between ruptured and un-ruptured BAVM group, of which 740 genes were up-regulated and 211 genes were down-regulated in ruptured BAVMs. Then bioinformatics analysis showed the biological processes and pathways related to the inflammatory processes and extracellular matrix organization were significantly enriched. Meanwhile, some of down-regulated genes are involved in cell adhesion and genes participating in response to muscle activity, as well as the terms about nervous system development. Finally, one hundred and twenty-five genes, a large number of which were involved in inflammation, were correlated with the early rupture of BAVMs. Conclusions: The up-regulated genes in ruptured BAVM group were involved in inflammatory processes and extracellular matrix organization while some of the down-regulated genes were participating in cell adhesion and myofibril assembly, indicating the role of enhanced inflammation and reduced vessel strength in BAVMs rupture.

scholarly journals POS0458 IDENTIFICATION OF HUB GENES AND MOLECULAR PATHWAYS IN PATIENTS WITH RHEUMATOID ARTHRITIS BY BIOINFORMATICS ANALYSIS

2021 ◽  
Vol 80 (Suppl 1) ◽  
pp. 460.1-460
Author(s):  
L. Cheng ◽  
S. X. Zhang ◽  
S. Song ◽  
C. Zheng ◽  
X. Sun ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Signaling Pathway ◽  
Synovial Tissue ◽  
Bioinformatics Analysis ◽  
Metabolic Process ◽  
Shanxi Province ◽  
Molecular Pathways ◽  
Biological Processes ◽  
Hub Genes ◽  
Tissue Samples

Background:Rheumatoid arthritis (RA) is a chronic, inflammatory synovitis based systemic disease of unknown etiology1. The genes and pathways in the inflamed synovium of RA patients are poorly understood.Objectives:This study aims to identify differentially expressed genes (DEGs) associated with the progression of synovitis in RA using bioinformatics analysis and explore its pathogenesis2.Methods:RA expression profile microarray data GSE89408 were acquired from the public gene chip database (GEO), including 152 synovial tissue samples from RA and 28 healthy synovial tissue samples. The DEGs of RA synovial tissues were screened by adopting the R software. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed. Protein-protein interaction (PPI) networks were assembled with Cytoscape software.Results:A total of 654 DEGs (268 up-regulated genes and 386 down-regulated genes) were obtained by the differential analysis. The GO enrichment results showed that the up-regulated genes were significantly enriched in the biological processes of myeloid leukocyte activation, cellular response to interferon-gamma and immune response-regulating signaling pathway, and the down-regulated genes were significantly enriched in the biological processes of extracellular matrix, retinoid metabolic process and regulation of lipid metabolic process. The KEGG annotation showed the up-regulated genes mainly participated in the staphylococcus aureus infection, chemokine signaling pathway, lysosome signaling pathway and the down-regulated genes mainly participated in the PPAR signaling pathway, AMPK signaling pathway, ECM-receptor interaction and so on. The 9 hub genes (PTPRC, TLR2, tyrobp, CTSS, CCL2, CCR5, B2M, fcgr1a and PPBP) were obtained based on the String database model by using the Cytoscape software and cytoHubba plugin3.Conclusion:The findings identified the molecular mechanisms and the key hub genes of pathogenesis and progression of RA.References:[1]Xiong Y, Mi BB, Liu MF, et al. Bioinformatics Analysis and Identification of Genes and Molecular Pathways Involved in Synovial Inflammation in Rheumatoid Arthritis. Med Sci Monit 2019;25:2246-56. doi: 10.12659/MSM.915451 [published Online First: 2019/03/28][2]Mun S, Lee J, Park A, et al. Proteomics Approach for the Discovery of Rheumatoid Arthritis Biomarkers Using Mass Spectrometry. Int J Mol Sci 2019;20(18) doi: 10.3390/ijms20184368 [published Online First: 2019/09/08][3]Zhu N, Hou J, Wu Y, et al. Identification of key genes in rheumatoid arthritis and osteoarthritis based on bioinformatics analysis. Medicine (Baltimore) 2018;97(22):e10997. doi: 10.1097/MD.0000000000010997 [published Online First: 2018/06/01]Acknowledgements:This project was supported by National Science Foundation of China (82001740), Open Fund from the Key Laboratory of Cellular Physiology (Shanxi Medical University) (KLCP2019) and Innovation Plan for Postgraduate Education in Shanxi Province (2020BY078).Disclosure of Interests:None declared

scholarly journals Upregulation of LINC01426 promotes the progression and stemness in lung adenocarcinoma by enhancing the level of SHH protein to activate the hedgehog pathway

2021 ◽  
Vol 12 (2) ◽  
Author(s):  
Xiaoli Liu ◽  
Zuwei Yin ◽  
Linping Xu ◽  
Huaimin Liu ◽  
Lifeng Jiang ◽  
...  
Keyword(s):  
Lung Adenocarcinoma ◽  
Bioinformatics Analysis ◽  
Epithelial Mesenchymal Transition ◽  
Mrna Level ◽  
Hedgehog Pathway ◽  
Biological Processes ◽  
Protein Coding ◽  
Mesenchymal Transition ◽  
Functional Roles ◽  
Rip Assay

AbstractLong noncoding RNAs (lncRNAs) play crucial roles in regulating a variety of biological processes in lung adenocarcinoma (LUAD). In our study, we mainly explored the functional roles of a novel lncRNA long intergenic non-protein coding RNA 1426 (LINC01426) in LUAD. We applied bioinformatics analysis to find the expression of LINC01426 was upregulated in LUAD tissue. Functionally, silencing of LINC01426 obviously suppressed the proliferation, migration, epithelial–mesenchymal transition (EMT), and stemness of LUAD cells. Then, we observed that LINC01426 functioned through the hedgehog pathway in LUAD. The effect of LINC01426 knockdown could be fully reversed by adding hedgehog pathway activator SAG. In addition, we proved that LINC01426 could not affect SHH transcription and its mRNA level. Pull-down sliver staining and RIP assay revealed that LINC01426 could interact with USP22. Ubiquitination assays manifested that LINC01426 and USP22 modulated SHH ubiquitination levels. Rescue assays verified that SHH overexpression rescued the cell growth, migration, and stemness suppressed by LINC01426 silencing. In conclusion, LINC01426 promotes LUAD progression by recruiting USP22 to stabilize SHH protein and thus activate the hedgehog pathway.

scholarly journals The Different Characteristics of Cirrus Optical Coherence Tomography between Superior Segmental Optic Hypoplasia and Normal Tension Glaucoma with Superior Retinal Nerve Fiber Defect

2015 ◽  
Vol 2015 ◽  
pp. 1-7 ◽  
Author(s):  
Jong Chul Han ◽  
Da Ye Choi ◽  
Changwon Kee
Keyword(s):  
Optical Coherence Tomography ◽  
Nerve Fiber ◽  
Normal Tension Glaucoma ◽  
Optical Coherence ◽  
Fiber Layer ◽  
Nerve Fiber Layer ◽  
Superior Segmental Optic Hypoplasia ◽  
Different Characteristics ◽  
Normal Controls ◽  
Retinal Nerve Fiber

Purpose. To evaluate the different characteristics in superior segmental optic hypoplasia (SSOH) and normal tension glaucoma (NTG) with superior retinal nerve fiber layer (RNFL) defect (NTG-SRD) compared to normal control using cirrus optical coherence tomography (OCT).Methods. SSOH eyes and NTG-SRD eyes were reviewed. The peripapillary RNFL (pRNFL) and ganglion cell inner plexiform layer (GCIPL) of the two groups were compared to age-matched normal controls using cirrus OCT.Results. Included in this study were 31 SSOH eyes, 33 NTG patients, and 49 healthy normal controls. Compared to normal controls, pRNFL thickness in SSOH eyes was thinner except in the inferotemporal to the temporal segment. NTG-SRD eyes had thinner pRNFL except in the nasal to inferonasal segment. Meanwhile, GCIPL thickness in SSOH eyes was thinner in the global and sectoral segment, but not in the superonasal and inferonasal sectors compared to normal controls. NTG-SRD eyes showed thinner GCIPL in all sectors compared to normal controls. In case of comparison between SSOH and NTG-SRD, superonasal sector was thinner in NTG-SRD than in SSOH (P=0.03).Conclusions. The different distributions of nerve fiber layer were shown in pRNFL and GCIPL between SSOH eyes and NTG-SRD eyes.

scholarly journals DEBKS: A Tool to Detect Differentially Expressed Circular RNA

2020 ◽  
Author(s):  
Zelin Liu ◽  
Huiru Ding ◽  
Jianqi She ◽  
Chunhua Chen ◽  
Weiguang Zhang ◽  
...  
Keyword(s):  
Open Source ◽  
Rna Sequencing ◽  
Open Source Software ◽  
Simulated Data ◽  
Circular Rna ◽  
Host Gene ◽  
Circular Rnas ◽  
Biological Processes ◽  
Rna Seq ◽  
Disease Pathogenesis

AbstractCircular RNAs (circRNAs) are involved in various biological processes and in disease pathogenesis. However, only a small number of functional circRNAs have been identified among hundreds of thousands of circRNA species, partly because most current methods are based on circular junction counts and overlook the fact that circRNA is formed from the host gene by back-splicing (BS). To distinguish between expression originating from BS and that from the host gene, we present DEBKS, a software program to streamline the discovery of differential BS between two rRNA-depleted RNA sequencing (RNA-seq) sample groups. By applying real and simulated data and employing RT-qPCR for validation, we demonstrate that DEBKS is efficient and accurate in detecting circRNAs with differential BS events between paired and unpaired sample groups. DEBKS is available at https://github.com/yangence/DEBKS as open-source software.

scholarly journals Smoc1 and Smoc2 regulate bone formation as downstream molecules of Runx2

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Yoshifumi Takahata ◽  
Hiromasa Hagino ◽  
Ayaka Kimura ◽  
Mitsuki Urushizaki ◽  
Sachi Kobayashi ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Bone Formation ◽  
Rna Sequencing ◽  
Late Stage ◽  
Bone Sialoprotein ◽  
Endochondral Bone Formation ◽  
Endochondral Bone ◽  
Novel Targets ◽  
Essential Transcription Factor

AbstractRunx2 is an essential transcription factor for bone formation. Although osteocalcin, osteopontin, and bone sialoprotein are well-known Runx2-regulated bone-specific genes, the skeletal phenotypes of knockout (KO) mice for these genes are marginal compared with those of Runx2 KO mice. These inconsistencies suggest that unknown Runx2-regulated genes play important roles in bone formation. To address this, we attempted to identify the Runx2 targets by performing RNA-sequencing and found Smoc1 and Smoc2 upregulation by Runx2. Smoc1 or Smoc2 knockdown inhibited osteoblastogenesis. Smoc1 KO mice displayed no fibula formation, while Smoc2 KO mice had mild craniofacial phenotypes. Surprisingly, Smoc1 and Smoc2 double KO (DKO) mice manifested no skull, shortened tibiae, and no fibulae. Endochondral bone formation was also impaired at the late stage in the DKO mice. Collectively, these results suggest that Smoc1 and Smoc2 function as novel targets for Runx2, and play important roles in intramembranous and endochondral bone formation.

Retinal vascular bed area on ultra-wide field fluorescein angiography indicates the severity of diabetic retinopathy

2021 ◽  
pp. bjophthalmol-2020-317488
Author(s):  
Wenying Fan ◽  
Akihito Uji ◽  
Muneeswar Nittala ◽  
Charles Clifton Wykoff ◽  
David Brown ◽  
...  
Keyword(s):  
Diabetic Retinopathy ◽  
Fluorescein Angiography ◽  
Final Analysis ◽  
Retinal Vasculature ◽  
Wide Field ◽  
Link Type ◽  
Vascular Bed ◽  
Retinal Ischaemia ◽  
Reading Center ◽  
Normal Controls

AimsTo quantify retinal vascular bed area (RVBA) in square millimetres on stereographically projected ultra-wide field (UWF) fluorescein angiography (FA) in eyes with diabetic retinopathy (DR).MethodsA prospective, observational study. Baseline Optos 200Tx UWF FA images of 80 eyes with DR from the DAVE (NCT01552408) and RECOVERY (NCT02863354) studies were stereographically projected at the Doheny Image Reading Center to adjust for peripheral distortion. The early-phase FA frame was used to extract the retinal vasculature as a mask for calculating RVBA. The pixels of the retinal vasculature were automatically computed in square millimetres using manufacturer-provided software.ResultsEighteen of 80 diabetic eyes were excluded because image quality and contrast were insufficient for automatic extraction of the retinal vasculature from the background fluorescence. The remaining 62 eyes were included in the final analysis. In comparison with age-matched and sex-matched normal controls, eyes with DR had a higher global RVBA for the entire retina (p<0.001), and RVBA correlated with DR severity (p<0.001), with a higher RVBA in eyes with proliferative DR (66.1±16.2 mm2) than in those with non-proliferative DR (56.2±16.6 mm2) or in normal controls (37.2±9.9 mm2). This tendency was also present in the posterior retina and mid-periphery but absent in the far-periphery. RVBA did not correlate with retinal ischaemia (p>0.05).ConclusionsEyes with DR harboured a larger global RVBA for the entire retina than normal controls, and RVBA appeared to indicate DR severity. However, this biomarker was not observed to be a good indicator of retinal ischaemia.

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