Differential host circRNA expression profiles in human lung epithelial cells infected with SARS-CoV-2

Yang, Meng; Qi, Mengdi; Xu, Liangzi; Huang, Pu; Wang, Xu; Sun, Jing; Shi, Jiandong; Hu, Yunzhang

doi:10.1016/j.meegid.2021.104923

Cited by 24 publications

(22 citation statements)

References 57 publications

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“…After being triggered by clustering of Fc gamma R at sites where leukocytes are bound to the opsonized particles, neutrophils and macrophages engulf IgG-coated particles, which is an essential part of the innate immune response [ 35 ]. Recently, it was found to be significantly enriched in human lung epithelial cells infected with SARS-CoV-2 [ 36 ]. These findings indicate that RBBP7 may exert its effect in BKVN through this pathway, which needs further experimental verification.…”

Section: Discussionmentioning

confidence: 99%

Identifying RBBP7 as a Promising Diagnostic Biomarker for BK Virus-Associated Nephropathy

Wang

Zhang

et al. 2022

Journal of Immunology Research

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BK virus-associated nephropathy (BKVN) remains a major infectious complication due to powerful immunosuppression in kidney transplant recipients, and its histologic appearance can mimic rejection, leading to diagnostic and treatment dilemmas thus molecular diagnostic methods would be beneficial. We collected gene expression profiles of 169 kidney biopsies taken from BKVN, rejection, and stable functioning allografts, based on single sample gene set enrichment analysis and random forest algorithm, and three hallmark activities associated with DNA damage and proliferation were found to be relatively specific in BKVN. Subsequently, weighted gene co-expression network analysis and support vector machines (SVM) algorithm identified RBBP7 as a robust and promising biomarker with high accuracy in both training and validation cohorts (AUC =0.938, 0.977, respectively). Besides, potential drugs for BKVN treatment such as mepacrine were discovered, which may contribute to targeted antiviral therapy and effective patient management rather than simply reducing the doses of immunosuppressive agents in clinical practice. RBBP7 (retinoblastoma binding protein 7) serves as component of serval complexes that regulate chromatin metabolism and functions in affecting DNA replication and controlling cell proliferation. In this research, upregulation of RBBP7 was found to be associated with the higher infiltration of CD8 naïve T, iTreg, and neutrophil cells and the lower amounts of Th1, central memory T, NKT, CD8 T, and dendritic cells. Moreover, the infiltration of Th1, Th17, and NKT cells was steadily different between BKVN and rejection allografts through immune cell assessment. In conclusion, we identified and verified RBBP7 as a molecular biomarker for BKVN diagnosis, which demonstrated great distinguishing ability with allograft rejection and would support clinical decision-making.

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Section: Discussionmentioning

confidence: 99%

Identifying RBBP7 as a Promising Diagnostic Biomarker for BK Virus-Associated Nephropathy

Wang

Zhang

et al. 2022

Journal of Immunology Research

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“…The differential expression of circRNAs was gradually increased with progression of infection. The dysregulated circRNAs could regulate mRNA stability, immunity, and cell death by binding specific proteins [ 134 ].…”

Section: Circular Rnasmentioning

confidence: 99%

Context-Dependent Regulation of Gene Expression by Non-Canonical Small RNAs

Plawgo

Raczyńska

2022

ncRNA

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In recent functional genomics studies, a large number of non-coding RNAs have been identified. It has become increasingly apparent that noncoding RNAs are crucial players in a wide range of cellular and physiological functions. They have been shown to modulate gene expression on different levels, including transcription, post-transcriptional processing, and translation. This review aims to highlight the diverse mechanisms of the regulation of gene expression by small noncoding RNAs in different conditions and different types of human cells. For this purpose, various cellular functions of microRNAs (miRNAs), circular RNAs (circRNAs), snoRNA-derived small RNAs (sdRNAs) and tRNA-derived fragments (tRFs) will be exemplified, with particular emphasis on the diversity of their occurrence and on the effects on gene expression in different stress conditions and diseased cell types. The synthesis and effect on gene expression of these noncoding RNAs varies in different cell types and may depend on environmental conditions such as different stresses. Moreover, noncoding RNAs play important roles in many diseases, including cancer, neurodegenerative disorders, and viral infections.

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“…CircRNAs, molecules closely associated with viral infection, is one option. A differential host circRNA expression profile analysis in human lung epithelial cells infected with SARS-CoV-2 was completed ( 64 ), and two circRNA profile analyses revealed abundant and diverse information regarding the identification and characterization of the circRNAs encoded by SARS-CoV-1, SARS-CoV-2 and MERS-CoV ( 65 , 66 ), facilitating future studies concerning on COVID-19 infection and pathogenesis. Arora et al.…”

Section: Roles Of Circrnas In Immune-related Diseasesmentioning

confidence: 99%

Past, Present and Future: The Relationship Between Circular RNA and Immunity

Huang

et al. 2022

Front. Immunol.

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The immune system has evolved since the birth of humans. However, immune-related diseases have not yet been overcome due to the lack of expected indicators and targeting specificity of current medical technology, subjecting patients to very uncomfortable physical and mental experiences and high medical costs. Therefore, the requirements for treatments with higher specificity and indicative ability are raised. Fortunately, the discovery of and continuous research investigating circular RNAs (circRNAs) represent a promising method among numerous methods. Although circRNAs wear regarded as metabolic wastes when discovered, as a type of noncoding RNA (ncRNA) with a ring structure and wide distribution range in the human body, circRNAs shine brilliantly in medical research by virtue of their special nature and structure-determined functions, such as high stability, wide distribution, high detection sensitivity, acceptable reproducibility and individual differences. Based on research investigating the role of circRNAs in immunity, we systematically discuss the hotspots of the roles of circRNAs in immune-related diseases, including expression profile analyses, potential biomarker research, ncRNA axis/network construction, impacts on phenotypes, therapeutic target seeking, maintenance of nucleic acid stability and protein binding research. In addition, we summarize the current situation of and problems associated with circRNAs in immune research, highlight the applications and prospects of circRNAs in the treatment of immune-related diseases, and provide new insight into future directions and new strategies for laboratory research and clinical applications.

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Differential host circRNA expression profiles in human lung epithelial cells infected with SARS-CoV-2

Cited by 24 publications

References 57 publications

Identifying RBBP7 as a Promising Diagnostic Biomarker for BK Virus-Associated Nephropathy

Identifying RBBP7 as a Promising Diagnostic Biomarker for BK Virus-Associated Nephropathy

Context-Dependent Regulation of Gene Expression by Non-Canonical Small RNAs

Past, Present and Future: The Relationship Between Circular RNA and Immunity

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