Integrated Multiomics Analysis Identifies a Novel Biomarker Associated with Prognosis in Intracerebral Hemorrhage

Existing treatments for intracerebral hemorrhage (ICH) are unable to satisfactorily prevent development of secondary brain injury after ICH and multiple pathological mechanisms are involved in the development of the injury. In this study, we aimed to identify novel genes and proteins and integrated their molecular alternations to reveal key network modules involved in ICH pathology. A total of 30 C57BL/6 male mice were used for this study. The collagenase model of ICH was employed, 3 days after ICH animals were tested neurological. After it, animals were euthanized and perihematomal brain tissues were collected for transcriptome and TMT labeling-based quantitative proteome analyses. Protein-protein interaction (PPI) network, Gene Set Enrichment Analysis (GSEA), and regularized Canonical Correlation Analysis (rCCA) were performed to integrated multiomics data. For validation of hub genes and proteins, qRT-PCR and Western blot were carried out. The candidate biomarkers were further measured by ELISA in the plasma of ICH patients and the controls. A total of 2218 differentially expressed genes (DEGs) and 353 differentially expressed proteins (DEPs) between the ICH model group and control group were identified. GSEA revealed that immune-related gene sets were prominently upregulated and significantly enriched in pathways of inflammasome complex, negative regulation of interleukin-12 production, and pyroptosis during the ICH process. The rCCA network presented two highly connective clusters which were involved in the sphingolipid catabolic process and inflammatory response. Among ten hub genes screened out by integrative analysis, significantly upregulated Itgb2, Serpina3n, and Ctss were validated in the ICH group by qRT-PCR and Western blot. Plasma levels of human SERPINA3 (homologue of murine Serpina3n) were elevated in ICH patients compared with the healthy controls (SERPINA3: 13.3 ng/mL vs. 11.2 ng/mL, p = 0.015 ). Within the ICH group, higher plasma SERPINA3 levels with a predictive threshold of 14.31 ng/mL ( sensitivity = 64.3 % ; specificity = 80.8 % ; AUC = 0.742 , 95% CI: 0.567-0.916) were highly associated with poor outcome (mRS scores 4-6). Taken together, the results of our study exhibited molecular changes related to ICH-induced brain injury by multidimensional analysis and effectively identified three biomarker candidates in a mouse ICH model, as well as pointed out that Serpina3n/SERPINA3 was a potential biomarker associated with poor functional outcome in ICH patients.

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AKNA Is a Potential Prognostic Biomarker in Gastric Cancer and Function as a Tumor Suppressor by Modulating EMT-Related Pathways

BioMed Research International ◽

10.1155/2020/6726759 ◽

2020 ◽

Vol 2020 ◽

pp. 1-10

Author(s):

Gang Wang ◽

Dan Sun ◽

Wenhui Li ◽

Yan Xin

Keyword(s):

Gastric Cancer ◽

Cell Adhesion ◽

Tumor Suppressor ◽

Western Blot ◽

Signaling Pathway ◽

Gene Set Enrichment Analysis ◽

Mesenchymal Transition ◽

Qrt Pcr ◽

Potential Biomarker ◽

Cell To Cell Adhesion

The AT-hook transcription factor, AKNA, is a nuclear protein that affects a few physiological and pathological processes including cancer. Here, we investigated the role of AKNA in gastric cancer (GC). By using quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot assays, AKNA was found deregulated in both GC cell lines and 32 paired GC tissues. Subsequently, Kaplan-Meier analysis and clinicopathological analysis were conducted using both 32 GC cases’ data above and RNA-Seq data of AKNA in 354 GC patients and the corresponding clinical-pathological data obtained from The Cancer Genome Atlas (TCGA), and AKNA expression was found closely related to location, metastasis, and TNM staging of GC. Then, the potential molecular mechanisms of AKNA in GC were explored by gene set enrichment analysis (GSEA), qRT-PCR, and Western blot assays. AKNA was found to be a hub gene related to homotypic cell to cell adhesion, regulation of cell to cell adhesion, leukocyte cell to cell adhesion, and regulation of T cell proliferation in GC. GO analysis revealed that AKNA involved in the regulation of epithelial-mesenchymal transition (EMT)-related pathways including chemokine signaling pathway, cytokine to cytokine receptor interaction, cell adhesion molecules, and jak-stat signaling pathway in GC. To explore the regulation of AKNA expression, Targetscan and TargetMiner were used to predict the possible miRNA which targeted AKNA and found the expression of AKNA was negatively correlated to miR-762 which could be sponged by circTRNC18. In conclusion, AKNA could function as a tumor suppressor by modulating EMT-related pathways in GC. The expression of AKNA might be regulated by circTRNC18/miR-762 axis. AKNA could serve as a potential biomarker and an effective target for GC diagnosis and therapy.

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Mitochondria: Novel Mechanisms and Therapeutic Targets for Secondary Brain Injury After Intracerebral Hemorrhage

Frontiers in Aging Neuroscience ◽

10.3389/fnagi.2020.615451 ◽

2021 ◽

Vol 12 ◽

Author(s):

Weixiang Chen ◽

Chao Guo ◽

Hua Feng ◽

Yujie Chen

Keyword(s):

Brain Injury ◽

Intracerebral Hemorrhage ◽

Hemorrhagic Stroke ◽

Secondary Brain Injury ◽

Valuable Insight ◽

Potential Therapeutic Target ◽

Pathological Mechanism ◽

Clinical Strategies ◽

Inflammatory Activation ◽

Insight Into

Intracerebral hemorrhage (ICH) is a destructive form of stroke that often results in death or disability. However, the survivors usually experience sequelae of neurological impairments and psychiatric disorders, which affect their daily functionality and working capacity. The recent MISTIE III and STICH II trials have confirmed that early surgical clearance of hematomas does not improve the prognosis of survivors of ICH, so it is vital to find the intervention target of secondary brain injury (SBI) after ICH. Mitochondrial dysfunction, which may be induced by oxidative stress, neuroinflammation, and autophagy, among others, is considered to be a novel pathological mechanism of ICH. Moreover, mitochondria play an important role in promoting neuronal survival and improving neurological function after a hemorrhagic stroke. This review summarizes the mitochondrial mechanism involved in cell death, reactive oxygen species (ROS) production, inflammatory activation, blood–brain barrier (BBB) disruption, and brain edema underlying ICH. We emphasize the potential of mitochondrial protection as a potential therapeutic target for SBI after stroke and provide valuable insight into clinical strategies.

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CircRNA-miRNA-mRNA Regulatory Network in Colorectal Cancer

10.21203/rs.3.rs-829473/v1 ◽

2021 ◽

Author(s):

Liyuan Liu ◽

Shan Wu ◽

Dan Jiang ◽

Yuliang Qu ◽

Hongxia Wang ◽

...

Keyword(s):

Colorectal Cancer ◽

Regulatory Network ◽

Research Direction ◽

Differentially Expressed ◽

Circular Rnas ◽

Hub Genes ◽

Protein Protein Interaction ◽

Qrt Pcr ◽

Cancer Tissues ◽

Chip Analysis

Abstract Background: Abnormal expression of Circular RNAs (circRNAs) occurs in the occurrence and progression of colorectal cancer (CRC) and plays an important role in the pathogenesis of tumors. We combined bioinformatics and laboratory-validated methods to search for key circRNAs and possible potential mechanisms. Methods: Colorectal cancer tissues and normal paracancerous tissues were detected by microarray analysis and qRT-PCR validation, and differentially expressed circRNAs were screened and identified. The circRNA-miRNA-mRNA regulatory network (cirReNET) was constructed, Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were used to ascertain the functions of circRNAs in CRCs. In addition, a protein-protein interaction (PPI) network of hub genes which acquired by string and plugin app CytoHubba in cytoscape was established. Validation of expression of hub genes was identified by GEPIA database. Results: 564 differentially expressed circRNAs which include 207 up-regulated and 357 down-regulated circRNAs were detected. The top 3 up-regulated circRNAs (hsa_circRNA_100833, hsa_circRNA_103828, hsa_circRNA_103831) and the top 3 down-regulated circRNAs (hsa_circRNA_103752, hsa_circRNA_071106, hsa_circRNA_102293) in chip analysis were chosen to be verified in 33 pairs of CRCs by qRT-PCR. The cirReNET include of 6 circRNAs, 19 miRNAs and 210 mRNA. And the targeted mRNAs were associated with cellular metabolic process, cell cycle and glandular epithelial cell differentiation and so on. 12 and 10 target hub genes were shown separately in upregulated circRNA-downregulated miRNA-upregulated mRNA (UcDiUm-RNA) group and downregulated circRNA-upregulated miRNA-downregulated mRNA (DcUiDm-RNA) group. Finally, we may have predicted and discovered several critical circRNA-miRNA-mRNA regulatory axes (cirReAXEs) which may play important roles in colorectal cancer. Conclusion: We constructed a cirReNET including 6 candidate circRNAs, which were crucial in CRCs, may become potential diagnostic markers and predictive indicators of CRCs, and we may provide a research direction for the pathogenesis of colorectal cancer.

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Gamma-interferon inducible lysosomal thiolreductase (GILT) effect on breast tumor microenvironment through regulating CXCR6/CXCL16 axis.

Journal of Clinical Oncology ◽

10.1200/jco.2021.39.15_suppl.e15081 ◽

2021 ◽

Vol 39 (15_suppl) ◽

pp. e15081-e15081

Author(s):

YinJiao Fei ◽

MingXing Liang ◽

Lei Li ◽

Yuxin Song ◽

Zhen Liu ◽

...

Keyword(s):

Breast Cancer ◽

Tumor Microenvironment ◽

Immune Responses ◽

Western Blot ◽

Cell Line ◽

Gamma Interferon ◽

Gene Set Enrichment Analysis ◽

High Expression ◽

Axillary Lymph ◽

Potential Biomarker

e15081 Background: Gamma-interferon Inducible Lysosomal Thiolreductase (GILT) is constitutively expressed in most antigens endocytosed by antigen presenting cells (APCs), and its function is to catalyze the reduction of disulfide (S-S) bonds in protein substrates. The cytokine CXCL16 is one of the only two known plasma membrane chemokines which induces chemotaxis of activated T cells and bone marrow plasma cells in tumor microenvironment. It contains a free end folded by two sulfur bonds and therefore could also be a zymolyte of GILT. Previous studies found that specific receptor of CXCL16, CXCR6, was significantly overexpressed in breast cancer tissues and metastatic axillary lymph nodes. We suppose whether CXCR6/CXCL16 axis is regulated by GILT and affect tumor microenvironment, thereby eliciting specific anti-tumor immune responses in breast cancer (BC). Methods: GILT expression in BC was evaluated using publicly available data from The Cancer Genome Atlas (TCGA). GILT gene was analyzed in UALCAN ( http://ualcan.path.uab.edu/analysis-prot.html ) . In vitro, Immunohistochemistry (IHC) was conducted to examine the location and relation of GILT and CXCR6. Gene Set Enrichment Analysis (GSEA) was performed to mine the biological pathways involved in BC related GILT regulatory network. The expression of GILT at protein and RNA levels were detected by Western Blot and RT-PCR assay. Overexpression and knockdown of GILT in BC cell lines was carried out to further analyzed the correlation between GILT and CXCL16/CXCR6. Results: TCGA database showed that GILT expression was increased in the stroma of BC compared with normal, and was correlated to shorter BC overall survival. GSEA suggested that the expression of GILT was associated with chemotactic factors. Pearson analysis and IHC showed GILT had a strong correlation with CXCL16/CXCR6 axis in the aspect of angiogenesis and immunity. qRT-PCR and Western Blot assay also revealed that GILT had high expression in BC. Besides, patients with high expression of GILT in IHC simultaneously showed high immunoreactive to macrophage markers, which was related to neovascularization and anti-tumor immune responses. Compared with the normal breast cell line MCF-10A, GILT protein had high expression in Hs578T and low expression in MDA-MB-231 cell line. GILT was overexpressed in MDA-MB-231 and knockdown in Hs578T. Result showed that high level GILT promoted the production of CXCL16/CXCR6,while GILT siRNA knockdown inhibited the production of CXCL16/CXCR6. Conclusions: GILT could catalyze CXCL16 in BC, function as a key mechanism to affect tumor microenvironment through CXCR6/CXCL16 pathway. GILT-activated CXCL16 levels showed a strong connection with unfavorable outcomes in BC, which could be a potential biomarker of prognosis and a novel therapeutic target.

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RAB7L1 Participates in Secondary Brain Injury Induced by Experimental Intracerebral Hemorrhage in Rats

Journal of Molecular Neuroscience ◽

10.1007/s12031-020-01619-3 ◽

2020 ◽

Vol 71 (1) ◽

pp. 9-18

Author(s):

Xiaoxing Tan ◽

Yuchong Wei ◽

Jie Cao ◽

Degang Wu ◽

Niansheng Lai ◽

...

Keyword(s):

Brain Injury ◽

Intracerebral Hemorrhage ◽

Secondary Brain Injury

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AdipoRon Protects Against Secondary Brain Injury After Intracerebral Hemorrhage via Alleviating Mitochondrial Dysfunction: Possible Involvement of AdipoR1–AMPK–PGC1α Pathway

Neurochemical Research ◽

10.1007/s11064-019-02794-5 ◽

2019 ◽

Vol 44 (7) ◽

pp. 1678-1689 ◽

Cited By ~ 1

Author(s):

Jun Yu ◽

Jingwei Zheng ◽

Jianan Lu ◽

Zeyu Sun ◽

Zefeng Wang ◽

...

Keyword(s):

Brain Injury ◽

Intracerebral Hemorrhage ◽

Mitochondrial Dysfunction ◽

Secondary Brain Injury

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Rbfox-1 contributes to CaMKIIα expression and intracerebral hemorrhage-induced secondary brain injury via blocking micro-RNA-124

Journal of Cerebral Blood Flow & Metabolism ◽

10.1177/0271678x20916860 ◽

2020 ◽

pp. 0271678X2091686 ◽

Cited By ~ 4

Author(s):

Fang Shen ◽

Xiang Xu ◽

Zhengquan Yu ◽

Haiying Li ◽

Haitao Shen ◽

...

Keyword(s):

Brain Injury ◽

Intracerebral Hemorrhage ◽

Protein Level ◽

Rna Binding ◽

Neuronal Degeneration ◽

Binding Protein ◽

Neurological Diseases ◽

Rna Binding Protein ◽

Micro Rna ◽

Secondary Brain Injury

RNA-binding protein fox-1 homolog 1 (Rbfox-1), an RNA-binding protein in neurons, is thought to be associated with many neurological diseases. To date, the mechanism on which Rbfox-1 worsens secondary cell death in ICH remains poorly understood. In this study, we aimed to explore the role of Rbfox-1 in intracerebral hemorrhage (ICH)-induced secondary brain injury (SBI) and to identify its underlying mechanisms. We found that the expression of Rbfox-1 in neurons was significantly increased after ICH, which was accompanied by increases in the binding of Rbfox-1 to Ca2+/calmodulin-dependent protein kinase II (CaMKIIα) mRNA and the protein level of CaMKIIα. In addition, when exposed to exogenous upregulation or downregulation of Rbfox-1, the protein level of CaMKIIα showed a concomitant trend in brain tissue, which further suggested that CaMKIIα is a downstream-target protein of Rbfox-1. The upregulation of both proteins caused intracellular-Ca2+ overload and neuronal degeneration, which exacerbated brain damage. Furthermore, we found that Rbfox-1 promoted the expression of CaMKIIα via blocking the binding of micro-RNA-124 to CaMKIIα mRNA. Thus, Rbfox-1 is expected to be a promising therapeutic target for SBI after ICH.

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Effect of miR-27b-5p on apoptosis of human vascular endothelial cells induced by simulated microgravity

APOPTOSIS ◽

10.1007/s10495-019-01580-6 ◽

2019 ◽

Vol 25 (1-2) ◽

pp. 73-91 ◽

Cited By ~ 1

Author(s):

Yi-Kai Pan ◽

Cheng-Fei Li ◽

Yuan Gao ◽

Yong-Chun Wang ◽

Xi-Qing Sun

Keyword(s):

Endothelial Cells ◽

Western Blot ◽

Target Gene ◽

Simulated Microgravity ◽

Target Genes ◽

Expression Profiles ◽

Differentially Expressed ◽

Luciferase Assay ◽

Qrt Pcr ◽

Differentially Expressed Mirnas

AbstractWeightlessness-induced cardiovascular dysfunction can lead to physiological and pathological consequences. It has been shown that spaceflight or simulated microgravity can alter expression profiles of some microRNAs (miRNAs). Here, we attempt to identify the role of miRNAs in human umbilical vein endothelial cells (HUVECs) apoptosis under simulated microgravity. RNA-sequencing and quantitative real-time PCR (qRT-PCR) assays were used to identify differentially expressed miRNAs in HUVECs under simulated microgravity. Then we obtained the target genes of these miRNAs through target analysis software. Moreover, GO and KEGG enrichment analysis were performed. The effects of these miRNAs on HUVECs apoptosis were evaluated by flow cytometry, Western blot and Hoechst staining. Furthermore, we obtained the target gene of miR-27b-5p by luciferase assay, qRT-PCR and Western blot. Finally, we investigated the relationship between this target gene and miR-27b-5p in HUVECs apoptosis under normal gravity or simulated microgravity. We found 29 differentially expressed miRNAs in HUVECs under simulated microgravity. Of them, the expressions of 3 miRNAs were validated by qRT-PCR. We demonstrated that miR-27b-5p affected HUVECs apoptosis by inhibiting zinc fingers and homeoboxes 1 (ZHX1). Our results reported here demonstrate for the first time that simulated microgravity can alter the expression of some miRNAs in HUVECs and miR-27b-5p may protect HUVECs from apoptosis under simulated microgravity by targeting ZHX1.

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