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Khan M, Shah S, Lv B, Lv Z, Ji N, Song Z, Wu P, Wang X, Mehmood A. Molecular Mechanisms of Alu and LINE-1 Interspersed Repetitive Sequences Reveal Diseases of Visual System Dysfunction. Ocul Immunol Inflamm 2023; 31:1848-1858. [PMID: 36040959 DOI: 10.1080/09273948.2022.2112238] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 08/05/2022] [Indexed: 10/14/2022]
Abstract
BACKGROUND Short interspersed nuclear elements (SINEs) and long interspersed nuclear elements (LINE-1s) are the abundant and well-characterized repetitive elements in the human genome. METHODS For this review, all relevant original research studies were assessed by searching electronic databases, including PubMed, Google Scholar, and Web of Science, by using relevant keywords. Accumulating evidence indicates that the disorder of gene expression regulated by these repetitive sequences is one of the causes of the diseases of visual system dysfunction, including retinal degenerations, glaucoma, retinitis punctata albescens, retinitis pigmentosa, geographic atrophy, and age-related macular degeneration, suggesting that SINEs and LINE-1s may have great potential implications in ophthalmology. RESULTS Alu elements belonging to the SINEs are present in more than one million copies, comprising 10% of the human genome. CONCLUSION This study offers recent advances in Alu and LINE-1 mechanisms in the development of eye diseases. The current study could advance our knowledge of the roles of SINEs and LINE-1s in the developing process of eye diseases, suggesting new diagnostic biomarkers, therapeutic strategies, and significant points for future studies.
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Affiliation(s)
- Murad Khan
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China
| | - Suleman Shah
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China
| | - Baixue Lv
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
- Hubei Province Key Laboratory of Molecular Imaging, Wuhan, Hubei Province, China
| | - Zhanjun Lv
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China
| | - Ning Ji
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China
| | - Zhixue Song
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China
| | - Peiyuan Wu
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China
| | - Xiufang Wang
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China
| | - Arshad Mehmood
- Department of Neurology, the Second Hospital of Hebei Medical University, City Shijiazhuang, P.R. China
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Khan AA, Jain SK, Rai M, Panda S. Exploring SARS-CoV2 host-pathogen interactions and associated fungal infections cross-talk: Screening of targets and understanding pathogenesis. Comput Struct Biotechnol J 2022; 20:4351-4359. [PMID: 35965662 PMCID: PMC9364728 DOI: 10.1016/j.csbj.2022.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 07/29/2022] [Accepted: 08/07/2022] [Indexed: 11/15/2022] Open
Abstract
The COVID-19 associated opportunistic fungal infections have posed major challenges in recent times. Global scientific efforts have identified several SARS-CoV2 host-pathogen interactions in a very short time span. However, information about the molecular basis of COVID-19 associated opportunistic fungal infections is not readily available. Previous studies have identified a number of host targets involved in these opportunistic fungal infections showing association with COVID-19 patients. We screened host targets involved in COVID-19-associated opportunistic fungal infections, in addition to host-pathogen interaction data of SARS-CoV2 from well-known and widely used biological databases. Venn diagram was prepared to screen common host targets involved in studied COVID-19-associated fungal infections. Moreover, an interaction network of studied disease targets was prepared with STRING to identify important targets on the basis of network biological parameters. The host-pathogen interaction (HPI) map of SARS-CoV2 was also prepared and screened to identify interactions of the virus with targets involved in studied fungal infections. Pathway enrichment analysis of host targets involved in studied opportunistic fungal infections and the subset of those involved in SARS-CoV2 HPI were performed separately. This data-based analysis screened six common targets involved in all studied fungal infections, among which CARD9 and CYP51A1 were involved in host-pathogen interactions with SARS-CoV2. Moreover, several signaling pathways such as integrin signaling were screened, which were associated with disease targets involved in SARS-CoV2 HPI. The results of this study indicate several host targets deserving detailed investigation to develop strategies for the management of SARS-CoV2-associated fungal infections.
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Affiliation(s)
- Abdul Arif Khan
- Division of Microbiology, ICMR-National AIDS Research Institute, Pune, Maharashtra, India
| | - Sudhir K Jain
- School of Studies in Microbiology, Vikram University, Ujjain (MP), India
| | - Mahendra Rai
- Department of Microbiology, Nicolaus Copernicus University, Torun, Poland.,Department of Biotechnology, Sant Gadge Baba Amravati University, Amravati, Maharashtra, India
| | - Samiran Panda
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, P.O. Box No. 4911, Ansari Nagar, New Delhi Pin-110029, India
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Sun M, Qiu J, Zhai H, Wang Y, Ma P, Li M, Chen B. Prognostic Implications of Novel Gene Signatures in Gastric Cancer Microenvironment. Med Sci Monit 2020; 26:e924604. [PMID: 32740646 PMCID: PMC7418782 DOI: 10.12659/msm.924604] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background Increasing studies have shown the important clinical role of immune and stromal cells in gastric cancer microenvironment. Based on information of immune and stromal cells in The Cancer Genome Atlas, this study aimed to construct a prognostic risk assessment model for gastric cancer. Material/Methods Based on the immune/structural scores, differentially expressed genes (DEGs) were filtered and analyzed. Afterwards, DEGs associated with prognosis were screened and the risk assessment model was constructed in the training set. Moreover, the validity of the model was verified both in the testing set and the overall sample. Results In this study, patients were divided into high-score and low-score groups based on immune/stromal score, and 919 DEGs were identified. By applying least absolute shrinkage and selection operator (LASSO) and Cox analysis, 10 mRNAs were selected to form a prognostic risk assessment model, risk score=(0.294*SLC17A9) + (−0.477*FERMT3) + (0.866*NRP1) + (0.350*MMRN1) + (0.381*RNASE1) + (0.189*TRIB3) + (0.230*PGAP3) + (0.087*MAGEA3) + (0.182*TACR2) + (0.368*CYP51A1). In the training set, the low-risk group divided by the model was found to have better overall survival, and the prediction efficiency of the model was demonstrated to be good. Multivariate Cox analysis indicated that the model could work as a prognostic factor independently. Similar results were shown in the testing group and overall patients cohort group. Finally, the risk assessment model and other clinical variables were integrated to construct a nomogram. Conclusions In general, this study constructs a prognostic risk assessment model for gastric cancer, which could improve the prognosis stratification of patients combined with other clinical indicators.
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Affiliation(s)
- Mengyu Sun
- Department of Clinical Medicine, Anhui Medical University, Hefei, Anhui, China (mainland)
| | - Jieping Qiu
- Department of Clinical Medicine, Anhui Medical University, Hefei, Anhui, China (mainland)
| | - Huazheng Zhai
- Department of Clinical Medicine, Anhui Medical University, Hefei, Anhui, China (mainland)
| | - Yaoqun Wang
- Department of Clinical Medicine, Anhui Medical University, Hefei, Anhui, China (mainland)
| | - Panpan Ma
- Department of Clinical Medicine, Anhui Medical University, Hefei, Anhui, China (mainland)
| | - Mengyin Li
- Department of Clinical Medicine, Anhui Medical University, Hefei, Anhui, China (mainland)
| | - Bo Chen
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China (mainland)
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Schiff L, Boles NC, Fernandes M, Nachmani B, Gentile R, Blenkinsop TA. P38 inhibition reverses TGFβ1 and TNFα-induced contraction in a model of proliferative vitreoretinopathy. Commun Biol 2019; 2:162. [PMID: 31069271 PMCID: PMC6499805 DOI: 10.1038/s42003-019-0406-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 03/21/2019] [Indexed: 12/20/2022] Open
Abstract
Proliferative vitreoretinopathy (PVR) is a metaplasia in the vitreous of the eye manifested by the transformation of retinal pigment epithelial (RPE) cells and the development of contracting epiretinal membranes (ERM), which lead to retinal detachment and vision loss. While TGFβ1 and TNFα have been associated with PVR, here we show that these cytokines act synergistically to induce an aggressive contraction phenotype on adult human (ah)RPE. Connected RPE detach upon contraction and form motile membranes that recruit more cells. TGFβ1 and TNFα (TNT)-induced contracting membranes uniquely express muscle and extracellular rearrangement genes. Whole transcriptome RNA sequencing of patient-dissected PVR membranes showed activation of the p38-MAPK signaling pathway. Inhibition of p38 during TNT treatment blocks ahRPE transformation and membrane contraction. Furthermore, TNT-induced membrane contractility can be reversed by p38 inhibition after induction. Therefore, targeting the p38-MAPK pathway may have therapeutic benefits for patients with PVR even after the onset of contracting ERMs.
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Affiliation(s)
- Lauren Schiff
- Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- Black Family Stem Cell Institute, New York, NY 10029 USA
| | | | - Marie Fernandes
- Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Bar Nachmani
- Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- Black Family Stem Cell Institute, New York, NY 10029 USA
| | - Ronald Gentile
- Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Timothy A. Blenkinsop
- Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- Black Family Stem Cell Institute, New York, NY 10029 USA
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Strategies to identify natural antisense transcripts. Biochimie 2017; 132:131-151. [DOI: 10.1016/j.biochi.2016.11.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 11/24/2016] [Indexed: 12/15/2022]
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Fronk AH, Vargis E. Methods for culturing retinal pigment epithelial cells: a review of current protocols and future recommendations. J Tissue Eng 2016; 7:2041731416650838. [PMID: 27493715 PMCID: PMC4959307 DOI: 10.1177/2041731416650838] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 04/23/2016] [Indexed: 12/17/2022] Open
Abstract
The retinal pigment epithelium is an important part of the vertebrate eye, particularly in studying the causes and possible treatment of age-related macular degeneration. The retinal pigment epithelium is difficult to access in vivo due to its location at the back of the eye, making experimentation with age-related macular degeneration treatments problematic. An alternative to in vivo experimentation is cultivating the retinal pigment epithelium in vitro, a practice that has been going on since the 1970s, providing a wide range of retinal pigment epithelial culture protocols, each producing cells and tissue of varying degrees of similarity to natural retinal pigment epithelium. The purpose of this review is to provide researchers with a ready list of retinal pigment epithelial protocols, their effects on cultured tissue, and their specific possible applications. Protocols using human and animal retinal pigment epithelium cells, derived from tissue or cell lines, are discussed, and recommendations for future researchers included.
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Affiliation(s)
- Aaron H Fronk
- Department of Biological Engineering, Utah State University, Logan, UT, USA
| | - Elizabeth Vargis
- Department of Biological Engineering, Utah State University, Logan, UT, USA
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