Transcriptomics Analysis Identifies the Presence of Upregulated Ribosomal Housekeeping Genes in the Alveolar Macrophages of Patients with Smoking-Induced Chronic Obstructive Pulmonary Disease

Han, Li; Wang, Jing; Ji, Xiangyu; Wang, Zai-Yan; Wang, Yi; Zhang, Liyue; Liu, Hongpeng; Zhang, Zeming; Li, Qingyun

doi:10.2147/copd.s313252

Cited by 13 publications

(6 citation statements)

References 26 publications

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“…For COVID-19-associated genes, we referred the PubChem ( https://pubchem.ncbi.nlm.nih.gov/#query=covid-19 ), CTD ( http://ctdbase.org/ ), DisGeNET ( https://www.disgenet.org/covid/diseases/summary/ ), baillielab net ( https://baillielab.net/maic/covid19 ) and KEGG DISEASE ( https://www.genome.jp/kegg/disease/ ) databases and data sets of ( Grant et al, 2021 ; Blanco-Melo et al, 2020 ; Mahmud et al, 2021 ; Singh et al, 2021 ; Overmyer et al, 2021 ; Mo et al, 2021 ). Regarding COPD-related genes, we considered DisGeNET ( https://www.disgenet.org/ ), CTD ( http://ctdbase.org/ ) and GeneCards ( https://www.genecards.org/ ) databases and data sets of ( O'Beirne et al, 2020 ; Han et al, 2021 ; Morrow et al, 2017 ; Hu et al, 2018 ; Raman et al, 2009 ; Huang et al, 2019 ; Morrow et al, 2019 ; Shen et al, 2021 ). These selected data sets above represent different clinical samples of COVID-19/COPD, specifically including alveolar lavage fluid, lung tissue, airway and peripheral blood.…”

Section: Methodsmentioning

confidence: 99%

Host Factor Interaction Networks Identified by Integrative Bioinformatics Analysis Reveals Therapeutic Implications in COPD Patients With COVID-19

Zheng

Wang

et al. 2021

Front. Pharmacol.

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Background: The COVID-19 pandemic poses an imminent threat to humanity, especially for those who have comorbidities. Evidence of COVID-19 and COPD comorbidities is accumulating. However, data revealing the molecular mechanism of COVID-19 and COPD comorbid diseases is limited.Methods: We got COVID-19/COPD -related genes from different databases by restricted screening conditions (top500), respectively, and then supplemented with COVID-19/COPD-associated genes (FDR<0.05, |LogFC|≥1) from clinical sample data sets. By taking the intersection, 42 co-morbid host factors for COVID-19 and COPD were finally obtained. On the basis of shared host factors, we conducted a series of bioinformatics analysis, including protein-protein interaction analysis, gene ontology and pathway enrichment analysis, transcription factor-gene interaction network analysis, gene-microRNA co-regulatory network analysis, tissue-specific enrichment analysis and candidate drug prediction.Results: We revealed the comorbidity mechanism of COVID-19 and COPD from the perspective of host factor interaction, obtained the top ten gene and 3 modules with different biological functions. Furthermore, we have obtained the signaling pathways and concluded that dexamethasone, estradiol, progesterone, and nitric oxide shows effective interventions.Conclusion: This study revealed host factor interaction networks for COVID-19 and COPD, which could confirm the potential drugs for treating the comorbidity, ultimately, enhancing the management of the respiratory disease.

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Section: Methodsmentioning

confidence: 99%

Host Factor Interaction Networks Identified by Integrative Bioinformatics Analysis Reveals Therapeutic Implications in COPD Patients With COVID-19

Zheng

Wang

et al. 2021

Front. Pharmacol.

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“…In addition, previous studies have shown that housekeeping genes can be involved in multicellular organogenesis, neurogenesis, developmental processes, and affected by disease. 104 - 113 Therefore, the identified plausible housekeeping genes among the UHEGs were not automatically ruled out as being involved in the development of hippocampal functions during the postnatal period.…”

Section: Discussionmentioning

confidence: 99%

The Vulnerability of the Developing Brain: Analysis of Highly Expressed Genes in Infant C57BL/6 Mouse Hippocampus in Relation to Phenotypic Annotation Derived From Mutational Studies

Lindlöf

2022

Bioinform Biol Insights

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The hippocampus has been shown to have a major role in learning and memory, but also to participate in the regulation of emotions. However, its specific role(s) in memory is still unclear. Hippocampal damage or dysfunction mainly results in memory issues, especially in the declarative memory but, in animal studies, has also shown to lead to hyperactivity and difficulty in inhibiting responses previously taught. The brain structure is affected in neuropathological disorders, such as Alzheimer’s, epilepsy, and schizophrenia, and also by depression and stress. The hippocampus structure is far from mature at birth and undergoes substantial development throughout infant and juvenile life. The aim of this study was to survey genes highly expressed throughout the postnatal period in mouse hippocampus and which have also been linked to an abnormal phenotype through mutational studies to achieve a greater understanding about hippocampal functions during postnatal development. Publicly available gene expression data from C57BL/6 mouse hippocampus was analyzed; from a total of 5 time points (at postnatal day 1, 10, 15, 21, and 30), 547 genes highly expressed in all of these time points were selected for analysis. Highly expressed genes are considered to be of potential biological importance and appear to be multifunctional, and hence any dysfunction in such a gene will most likely have a large impact on the development of abilities during the postnatal and juvenile period. Phenotypic annotation data downloaded from Mouse Genomic Informatics database were analyzed for these genes, and the results showed that many of them are important for proper embryo development and infant survival, proper growth, and increase in body size, as well as for voluntary movement functions, motor coordination, and balance. The results also indicated an association with seizures that have primarily been characterized by uncontrolled motor activity and the development of proper grooming abilities. The complete list of genes and their phenotypic annotation data have been compiled in a file for easy access.

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“…The threshold for differential expression was set as adj.p.val < 0.05 and |logFC|> 0.585. After identifying differentially expressed genes, a volcano plot was generated, and expression distribution heatmaps between normal and disease groups were separately illustrated [ 21 – 23 ]. After identifying differentially expressed genes, a volcano plot was generated, and expression distribution heatmaps between normal and disease groups were separately illustrated.…”

Section: Methodsmentioning

confidence: 99%

Analysis of complement system and its related factors in Alzheimer’s disease

Zhu,

Tang,

Zhu

et al. 2023

BMC Neurol

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Alzheimer’s disease (AD) is a primary cause of dementia. The complement system is closely related to AD pathology and may be a potential target for the prevention and treatment of AD. In our study, we conducted a bioinformatics analysis to analyze the role of the complement system and its related factors in AD using Gene Expression Omnibus (GEO) data. We also conducted a functional analysis. Our study verified that 23 genes were closely related to differentially expressed complement system genes in diseases after intersecting the disease-related complement system module genes and differentially expressed genes. The STRING database was used to predict the interactions between the modular gene proteins of the differential complement system. A total of 21 gene proteins and 44 interaction pairs showed close interactions. We screened key genes and created a diagnostic model. The predictive effect of the model was constructed using GSE5281 and our study indicated that the predictive effect of the model was good. Our study also showed enriched negative regulation of Notch signaling, cytokine secretion involved in the immune response pathway, and cytokine secretion involved in immune response hormone-mediated apoptotic signaling pathway. We hope that our study provides a promising target to prevent and delay the onset, diagnosis, and treatment of AD.

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Transcriptomics Analysis Identifies the Presence of Upregulated Ribosomal Housekeeping Genes in the Alveolar Macrophages of Patients with Smoking-Induced Chronic Obstructive Pulmonary Disease

Cited by 13 publications

References 26 publications

Host Factor Interaction Networks Identified by Integrative Bioinformatics Analysis Reveals Therapeutic Implications in COPD Patients With COVID-19

Host Factor Interaction Networks Identified by Integrative Bioinformatics Analysis Reveals Therapeutic Implications in COPD Patients With COVID-19

The Vulnerability of the Developing Brain: Analysis of Highly Expressed Genes in Infant C57BL/6 Mouse Hippocampus in Relation to Phenotypic Annotation Derived From Mutational Studies

Analysis of complement system and its related factors in Alzheimer’s disease

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