1
|
Ge P, Yin Z, Tao C, Zeng C, Yu X, Lei S, Li J, Zhai Y, Ma L, He Q, Liu C, Liu W, Zhang B, Zheng Z, Mou S, Zhao Z, Wang S, Sun W, Guo M, Zheng S, Zhang J, Deng X, Liu X, Ye X, Zhang Q, Wang R, Zhang Y, Zhang S, Wang C, Yang Z, Zhang N, Wu M, Sun J, Zhou Y, Shi Z, Ma Y, Zhou J, Yu S, Li J, Lu J, Gao F, Wang W, Chen Y, Zhu X, Zhang D, Zhao J. Multiomics and blood-based biomarkers of moyamoya disease: protocol of Moyamoya Omics Atlas (MOYAOMICS). Chin Neurosurg J 2024; 10:5. [PMID: 38326922 PMCID: PMC10851534 DOI: 10.1186/s41016-024-00358-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/30/2024] [Indexed: 02/09/2024] Open
Abstract
BACKGROUND Moyamoya disease (MMD) is a rare and complex cerebrovascular disorder characterized by the progressive narrowing of the internal carotid arteries and the formation of compensatory collateral vessels. The etiology of MMD remains enigmatic, making diagnosis and management challenging. The MOYAOMICS project was initiated to investigate the molecular underpinnings of MMD and explore potential diagnostic and therapeutic strategies. METHODS The MOYAOMICS project employs a multidisciplinary approach, integrating various omics technologies, including genomics, transcriptomics, proteomics, and metabolomics, to comprehensively examine the molecular signatures associated with MMD pathogenesis. Additionally, we will investigate the potential influence of gut microbiota and brain-gut peptides on MMD development, assessing their suitability as targets for therapeutic strategies and dietary interventions. Radiomics, a specialized field in medical imaging, is utilized to analyze neuroimaging data for early detection and characterization of MMD-related brain changes. Deep learning algorithms are employed to differentiate MMD from other conditions, automating the diagnostic process. We also employ single-cellomics and mass cytometry to precisely study cellular heterogeneity in peripheral blood samples from MMD patients. CONCLUSIONS The MOYAOMICS project represents a significant step toward comprehending MMD's molecular underpinnings. This multidisciplinary approach has the potential to revolutionize early diagnosis, patient stratification, and the development of targeted therapies for MMD. The identification of blood-based biomarkers and the integration of multiple omics data are critical for improving the clinical management of MMD and enhancing patient outcomes for this complex disease.
Collapse
Affiliation(s)
- Peicong Ge
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Zihan Yin
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Chuming Tao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Chaofan Zeng
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Xiaofan Yu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Shixiong Lei
- Department of Neurosurgery, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Junsheng Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Yuanren Zhai
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Long Ma
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Qiheng He
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Chenglong Liu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Wei Liu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Bojian Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Zhiyao Zheng
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Siqi Mou
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Zhikang Zhao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Shuang Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Wei Sun
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Min Guo
- Department of Radiology, Beijing Tiantan Hospital, Beijing, China
| | - Shuai Zheng
- Department of Ultrasound, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jia Zhang
- Department of Neurology, Beijing Tiantan Hospital, Beijing, China
| | - Xiaofeng Deng
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Xingju Liu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Xun Ye
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Qian Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Rong Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Yan Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Shaosen Zhang
- Department of Neurosurgery, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Chengjun Wang
- Department of Neurosurgery, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Ziwen Yang
- Department of Neurosurgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Nijia Zhang
- Department of Neurosurgery, Beijing Childrens Hospital, Capital Medical University, Beijing, China
| | - Mingxing Wu
- Department of Neurosurgery, The Affiliated Children's Hospital, Capital Institute of Pediatrics, Beijing, China
| | - Jian Sun
- Department of Neurosurgery, Beijing Changping District Hospital, Beijing, China
| | - Yujia Zhou
- Department of Neurosurgery, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Zhiyong Shi
- Department of Neurosurgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Yonggang Ma
- Department of NeuroInterventional Surgery, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Jianpo Zhou
- Department of Neurosurgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shaochen Yu
- Department of Neurosurgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiaxi Li
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, Xi'an, China
| | - Junli Lu
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, China
| | - Faliang Gao
- Department of Neurosurgery, Center for Rehabilitation Medicine, Zhejiang Provincial Peoples Hospital, Affiliated Peoples Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Wenjing Wang
- Beijing Institute of Hepatology, Beijing YouAn Hospital, Capital Medical University, Beijing, China
| | - Yanming Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Xingen Zhu
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Dong Zhang
- Department of Neurosurgery, Beijing Hospital, National Center of Gerontology, Beijing, China.
| | - Jizong Zhao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.
- China National Clinical Research Center for Neurological Diseases, Beijing, China.
| |
Collapse
|
2
|
Takayanagi K, Kanamori F, Ishii K, Yokoyama K, Araki Y, Sumitomo M, Maeda S, Goto S, Ota S, Nagata Y, Nishihori M, Maesawa S, Izumi T, Takasu S, Saito R. Higher abundance of Campylobacter in the oral microbiome of Japanese patients with moyamoya disease. Sci Rep 2023; 13:18545. [PMID: 37899472 PMCID: PMC10613609 DOI: 10.1038/s41598-023-45755-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 10/23/2023] [Indexed: 10/31/2023] Open
Abstract
Genetic factors alone cannot explain the pathophysiology of moyamoya disease (MMD), and environmental factors such as an immune response are thought to be involved. Oral and gut microbiomes have attracted attention as environmental factors in the pathophysiology of some vascular and autoimmune diseases. However, the relationship between MMD and these microbiomes is yet to be thoroughly investigated. This prospective case-control study aimed to compare the microbiomes of Japanese patients with MMD with those of healthy individuals to identify the specific bacteria involved in MMD. Saliva and fecal samples were collected from 16 patients with MMD who had not undergone revascularization surgery. Fifteen healthy individuals were matched for age, sex, and body mass index. The microbiomes were determined using 16S rRNA sequencing and analyzed using QIIME2. Differentially abundant microbes were identified using LEfSE and ANCOM-BC. In the oral microbiome, the two analytical methods showed that Campylobacter was more abundant in patients with MMD than in healthy individuals. Differences in the gut microbiome were smaller than those in the oral microbiome. In conclusion, the oral microbiome profiles of patients with MMD significantly differ from those of healthy individuals. Campylobacter spp. could be a substantial environmental factor in the pathophysiology of MMD.
Collapse
Affiliation(s)
- Kai Takayanagi
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Fumiaki Kanamori
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, Nagoya, Aichi, 466-8550, Japan.
| | - Kazuki Ishii
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Kinya Yokoyama
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Yoshio Araki
- Department of Neurosurgery, Japanese Red Cross Aichi Medical Center Nagoya Daini Hospital, Nagoya, Japan
| | - Masaki Sumitomo
- Department of Neurosurgery, Toyota Kosei Hospital, Toyota, Japan
| | - Sachi Maeda
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Shunsaku Goto
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Shinji Ota
- Department of Neurosurgery, Handa City Hospital, Handa, Japan
| | - Yuichi Nagata
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Masahiro Nishihori
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Satoshi Maesawa
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Takashi Izumi
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Syuntaro Takasu
- Department of Neurosurgery, Japan Community Health Care Organization Chukyo Hospital, Nagoya, Japan
| | - Ryuta Saito
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| |
Collapse
|
3
|
Cao L, Ai Y, Dong Y, Li D, Wang H, Sun K, Wang C, Zhang M, Yan D, Li H, Liang G, Yang B. Bioinformatics analysis reveals the landscape of immune cell infiltration and novel immune-related biomarkers in moyamoya disease. Front Genet 2023; 14:1101612. [PMID: 37265961 PMCID: PMC10230076 DOI: 10.3389/fgene.2023.1101612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 04/28/2023] [Indexed: 06/03/2023] Open
Abstract
Objective: This study aimed to identify immune infiltration characteristics and new immunological diagnostic biomarkers in the cerebrovascular tissue of moyamoya disease (MMD) using bioinformatics analysis. Methods: GSE189993 and GSE141022 were downloaded from the GEO database. Differentially expressed gene and PPI analysis were performed. After performing WGCNA, the most significant module associated with MMD was obtained. Next, functional pathways according to GSEA, GO, and KEGG were enriched for the aforementioned core genes obtained from PPI and WGCNA. Additionally, immune infiltration, using the CIBERSORT deconvolution algorithm, immune-related biomarkers, and the relationship between these genes, was further explored. Finally, diagnostic accuracy was verified with ROC curves in the validation dataset GSE157628. Results: A total of 348 DEGs were screened, including 89 downregulated and 259 upregulated genes. The thistlel module was detected as the most significant module associated with MMD. Functional analysis of the core genes was chiefly involved in the immune response, immune system process, protein tyrosine kinase activity, secretory granule, and so on. Among 13 immune-related overlapping genes, 4 genes (BTK, FGR, PTPN11, and SYK) were identified as potential diagnostic biomarkers, where PTPN11 showed the highest specificity and sensitivity. Meanwhile, a higher proportion of eosinophils, not T cells or B cells, was demonstrated in the specific immune infiltration landscape of MMD. Conclusion: Immune activities and immune cells were actively involved in the progression of MMD. BTK, FGR, PTPN11, and SYK were identified as potential immune diagnostic biomarkers. These immune-related genes and cells may provide novel insights for immunotherapy in the future.
Collapse
Affiliation(s)
- Lei Cao
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yunzheng Ai
- Department of Neurosurgery, General Hospital of Northern Theater Command, Shenyang, China
| | - Yang Dong
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Dongpeng Li
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hao Wang
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Kaiwen Sun
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chenchao Wang
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Manxia Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Dongming Yan
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hongwei Li
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Guobiao Liang
- Department of Neurosurgery, General Hospital of Northern Theater Command, Shenyang, China
| | - Bo Yang
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| |
Collapse
|
4
|
Dorschel KB, Wanebo JE. Physiological and pathophysiological mechanisms of the molecular and cellular biology of angiogenesis and inflammation in moyamoya angiopathy and related vascular diseases. Front Neurol 2023; 14:661611. [PMID: 37273690 PMCID: PMC10236939 DOI: 10.3389/fneur.2023.661611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 01/16/2023] [Indexed: 06/06/2023] Open
Abstract
Rationale The etiology and pathophysiological mechanisms of moyamoya angiopathy (MMA) remain largely unknown. MMA is a progressive, occlusive cerebrovascular disorder characterized by recurrent ischemic and hemorrhagic strokes; with compensatory formation of an abnormal network of perforating blood vessels that creates a collateral circulation; and by aberrant angiogenesis at the base of the brain. Imbalance of angiogenic and vasculogenic mechanisms has been proposed as a potential cause of MMA. Moyamoya vessels suggest that aberrant angiogenic, arteriogenic, and vasculogenic processes may be involved in the pathophysiology of MMA. Circulating endothelial progenitor cells have been hypothesized to contribute to vascular remodeling in MMA. MMA is associated with increased expression of angiogenic factors and proinflammatory molecules. Systemic inflammation may be related to MMA pathogenesis. Objective This literature review describes the molecular mechanisms associated with cerebrovascular dysfunction, aberrant angiogenesis, and inflammation in MMA and related cerebrovascular diseases along with treatment strategies and future research perspectives. Methods and results References were identified through a systematic computerized search of the medical literature from January 1, 1983, through July 29, 2022, using the PubMed, EMBASE, BIOSIS Previews, CNKI, ISI web of science, and Medline databases and various combinations of the keywords "moyamoya," "angiogenesis," "anastomotic network," "molecular mechanism," "physiology," "pathophysiology," "pathogenesis," "biomarker," "genetics," "signaling pathway," "blood-brain barrier," "endothelial progenitor cells," "endothelial function," "inflammation," "intracranial hemorrhage," and "stroke." Relevant articles and supplemental basic science articles almost exclusively published in English were included. Review of the reference lists of relevant publications for additional sources resulted in 350 publications which met the study inclusion criteria. Detection of growth factors, chemokines, and cytokines in MMA patients suggests the hypothesis of aberrant angiogenesis being involved in MMA pathogenesis. It remains to be ascertained whether these findings are consequences of MMA or are etiological factors of MMA. Conclusions MMA is a heterogeneous disorder, comprising various genotypes and phenotypes, with a complex pathophysiology. Additional research may advance our understanding of the pathophysiology involved in aberrant angiogenesis, arterial stenosis, and the formation of moyamoya collaterals and anastomotic networks. Future research will benefit from researching molecular pathophysiologic mechanisms and the correlation of clinical and basic research results.
Collapse
Affiliation(s)
- Kirsten B. Dorschel
- Medical Faculty, Heidelberg University Medical School, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
| | - John E. Wanebo
- Department of Neurosurgery, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, AZ, United States
- Department of Neuroscience, HonorHealth Research Institute, Scottsdale, AZ, United States
| |
Collapse
|
5
|
Mamiya T, Kanamori F, Yokoyama K, Ota A, Karnan S, Uda K, Araki Y, Maesawa S, Yoshikawa K, Saito R. Long noncoding RNA profile of the intracranial artery in patients with moyamoya disease. J Neurosurg 2023; 138:709-716. [PMID: 35907193 DOI: 10.3171/2022.5.jns22579] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/25/2022] [Indexed: 11/06/2022]
Abstract
OBJECTIVE Moyamoya disease (MMD) is a rare cerebrovascular disease characterized by progressive stenosis of the internal carotid artery (ICA) and secondary formation of collateral vessels. Revascularization surgery is performed in patients with MMD to prevent stroke; however, the pathogenesis of MMD remains unknown. Recently, long noncoding RNAs (lncRNAs) have been found to play a key role in gene regulation and are implicated in various vascular diseases. However, the lncRNA expression profile in MMD lesions has not been investigated. In this study the authors aimed to determine the characteristics of lncRNA expression in MMD lesions. METHODS The authors collected microsamples of the middle cerebral artery (MCA) from patients with MMD (n = 21) and patients with control conditions (n = 11) who underwent neurosurgical treatment. Using microarray experiments, the authors compared the profiles of lncRNA expression in the MCAs of the MMD and control patient groups and identified differentially expressed lncRNAs (fold change > 2, q < 0.05). In addition, the neighboring coding genes, whose transcription can be regulated in cis by the identified differentially expressed lncRNAs, were investigated and Gene Ontology (GO) analysis was applied to predict associated biological functions. RESULTS The authors detected 308 differentially expressed lncRNAs (fold change > 2, q < 0.05), including 306 upregulated and 2 downregulated lncRNAs in the MCA from patients with MMD. Regarding the prediction of biological function, GO analyses with possible coding genes whose transcription was regulated in cis by the identified differentially expressed lncRNAs suggested involvement in the antibacterial humoral response, T-cell receptor signaling pathway, positive regulation of cytokine production, and branching involved in blood vessel morphogenesis. CONCLUSIONS The profile of lncRNA expression in MMD lesions was different from that in the normal cerebral artery, and differentially expressed lncRNAs were identified. This study provides new insights into the pathophysiology of MMD.
Collapse
Affiliation(s)
- Takashi Mamiya
- 1Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya
| | - Fumiaki Kanamori
- 1Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya
| | - Kinya Yokoyama
- 1Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya
| | - Akinobu Ota
- 2Department of Biochemistry, Aichi Medical University School of Medicine, and
| | - Sivasundaram Karnan
- 2Department of Biochemistry, Aichi Medical University School of Medicine, and
| | - Kenji Uda
- 1Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya
| | - Yoshio Araki
- 1Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya
| | - Satoshi Maesawa
- 1Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya
| | - Kazuhiro Yoshikawa
- 3Division of Research Creation and Biobank, Research Creation Support Center, Aichi Medical University, Nagakute, Japan
| | - Ryuta Saito
- 1Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya
| |
Collapse
|
6
|
Epigenome-Wide Association Study Reveals Differential Methylation Sites and Association of Gene Expression Regulation with Ischemic Moyamoya Disease in Adults. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:7192060. [PMID: 35368875 PMCID: PMC8970806 DOI: 10.1155/2022/7192060] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/28/2022] [Indexed: 12/12/2022]
Abstract
Background The association of DNA methylation with the pathogenesis of adult ischemic moyamoya disease (MMD) is unknown. Here, we investigated the genome-wide DNA methylation profiles in patients with MMD and identified the genes related to the pathogenesis of MMD. Methods Whole blood samples were collected from 20 individuals, including 10 patients with ischemic moyamoya disease without any underlying disease and 10 healthy individuals. Genome-wide DNA methylation analysis was performed using Illumina 850K microarrays. Transcriptional correlation was verified using quantitative reverse transcription-polymerase chain reaction. In vitro experiments were used to analyze the association of functional defects with candidate epigenetic markers. Results The genome-wide methylation level in the whole blood of adults with ischemic MMD was higher than that in the healthy individuals. In total, 759 methylation probes differed significantly between the case and control. The hypermethylated regions were mostly concentrated in the gene spacer regions. Among genes with the highest degree of the differential expression, KCNMA1 and GALNT2 were upregulated, whereas SOX6 and RBM33 were downregulated. Conclusions This is the first study showing that the low expression of genes associated with epigenetic regulation, such as SOX6 and RBM33, may be related to vascular occlusion in MMD, whereas the overexpression of KCNMA1 and GALNT2 may be related to the vascular hyperplasia. The results suggest that DNA methylation was involved in the pathogenesis of MMD, and new pathogenic genes were proposed as biological markers.
Collapse
|
7
|
Identification of immune-infiltrated hub genes as potential biomarkers of Moyamoya disease by bioinformatics analysis. Orphanet J Rare Dis 2022; 17:80. [PMID: 35197088 PMCID: PMC8867641 DOI: 10.1186/s13023-022-02238-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 02/06/2022] [Indexed: 12/21/2022] Open
Abstract
Background Moyamoya disease (MMD) is a rare chronic progressive cerebrovascular disease. Recent studies have shown that autoimmune inflammation may also be an important pathology in MMD but the molecular mechanisms of inflammation in this disease are still large unknown. This study was designed to identify key biomarkers and the immune infiltration in vessel tissue of MMD using bioinformatics analysis. Methods Raw gene expression profiles (GSE157628, GSE141024) were downloaded from the Gene Expression Omnibus (GEO) database, identified differentially expressed genes (DEGs) and performed functional enrichment analysis. The CIBERSORT deconvolution algorithm was used to analyze the proportion of immune cells between MMD and an MMD-negative control group. We screened for neutrophil-associated DEGs, constructed a protein–protein interaction network (PPI) using STRING, and clarified the gene cluster using the Cytoscape plugin MCODE analysis. The receiver operating characteristic (ROC) curve was applied to test and filter the best gene signature. Results A total of 570 DEGs were detected, including 212 downregulated and 358 up-regulated genes. Reactome and KEGG enrichment revealed that DEGs were involved in the cell cycle, molecular transport, and metabolic pathways. The immune infiltration profile demonstrated that MMD cerebrovascular tissues contained a higher proportion of neutrophils, monocytes, and natural killer cells in MMD than in controls. The PPI network and MCODE cluster identified nine DEGs (UNC13D, AZU1, PYCARD, ELANE, SDCBP, CCL11, CCL15, CCL20, and CXCL5) associated with neutrophil infiltration. ROC results showed that UNC13D has good specificity and sensitivity (AUC = 0.7846). Conclusions The characteristics of immune infiltration in the cerebrovascular tissues of MMD patients and abnormal expression of hub genes provide new insights for understanding MMD progression. UNC13D is shows promise as a candidate molecule to determine neutrophil infiltration characteristics in MMD. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-022-02238-4.
Collapse
|
8
|
Jickling GC, Sharp FR. OMICs in Stroke. Stroke 2022. [DOI: 10.1016/b978-0-323-69424-7.00050-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
9
|
Zhao J, Qiu C, Zhang G, Chen L, He S, Ma J. LncRNA-mRNA Co-expression Profiles Relative to Vascular Remodeling in Moyamoya Patients Without RNF213 Mutation. World Neurosurg 2021; 158:e880-e888. [PMID: 34848385 DOI: 10.1016/j.wneu.2021.11.104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/20/2021] [Accepted: 11/22/2021] [Indexed: 11/29/2022]
Abstract
OBJECTIVE Moyamoya disease (MMD) is an idiopathic cerebrovascular disease with unknown etiology. Long noncoding RNA (lncRNA) and messenger RNA (mRNA) profiles in MMD remain unknown. In this current study, we aim to investigate lncRNA-mRNA co-expression pattern and their biological functions in superficial temporal artery (STA) of MMD. METHODS STA of 3 MMD patients without RNF213 mutation and 3 age-matched controls were obtained for transcriptomic RNA sequencing. Bioinformatics analysis was performed to investigate their molecular functions and interactions. Then, differentially expressed genes relative to vascular remodeling were further validated by quantitative real-time polymerase chain reaction and immunofluorescence. WNT5A functions were tested by tube formation assay and wound scratching assay in human microvascular endothelial cells (HMECs). RESULTS We detected 6235 different lncRNAs and 2065 different mRNAs from the RNA-sequencing between MMD patients and controls (P < 0.05; fold change >2.0). Gene ontology showed that altered mRNAs were enriched for endothelial cell morphogenesis and positive regulation of angiogenesis, which were closely related with vascular remodeling. We then searched 76 altered genes related with vascular remodeling and applied Kyoto Encyclopedia of Genes and Genomes analysis. Integrated analysis of lncRNA-TF-mRNA co-expression networks and gene verifications indicated that molecular including WNT5A, TEK, and GATA2 may contribute to the vascular malformation of MMD. Overexpression of WNT5A in HMECs promoted tube formation and cell migration. CONCLUSIONS In MMD patients, genes related to vascular remodeling including WNT5A and their regulators were aberrantly disrupted. These results will help elucidate the complicated pathogenic mechanism of MMD and develop potential therapeutic targets facilitating MMD angiogenesis in the future.
Collapse
Affiliation(s)
- Jinbing Zhao
- Nanjing Comprehensive Stroke Center, Affiliated Nanjing Brain Hospital, Nanjing Medical University, Nanjing, PR China.
| | - Cheng Qiu
- Nanjing Comprehensive Stroke Center, Affiliated Nanjing Brain Hospital, Nanjing Medical University, Nanjing, PR China
| | - Guangxu Zhang
- Nanjing Comprehensive Stroke Center, Affiliated Nanjing Brain Hospital, Nanjing Medical University, Nanjing, PR China
| | - Lijiu Chen
- Nanjing Comprehensive Stroke Center, Affiliated Nanjing Brain Hospital, Nanjing Medical University, Nanjing, PR China
| | - Shengxue He
- Nanjing Comprehensive Stroke Center, Affiliated Nanjing Brain Hospital, Nanjing Medical University, Nanjing, PR China
| | - Jun Ma
- Nanjing Comprehensive Stroke Center, Affiliated Nanjing Brain Hospital, Nanjing Medical University, Nanjing, PR China
| |
Collapse
|
10
|
Han Z, Li L, Liu P, Huang Y, Zhang S, Li G, Li F, Zhao H, Tao Z, Wang R, Ma Q, Luo Y. Metabolic Adjustments by LncRNAs in Peripheral Neutrophils Partly Account for the Complete Compensation of Asymptomatic MMD Patients. CNS & NEUROLOGICAL DISORDERS-DRUG TARGETS 2021; 19:306-317. [PMID: 32552656 DOI: 10.2174/1871527319666200618150827] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 04/29/2020] [Accepted: 05/04/2020] [Indexed: 01/31/2023]
Abstract
BACKGROUND Due to the recent development of non-invasive examinations, more asymptomatic patients with Moyamoya Disease (MMD) have been diagnosed than ever. However, its underlying molecular mechanisms and clinical intervention guidelines are all still obscure. METHODS Microarray was used to explore those differentially expressed mRNAs and lncRNAs in peripheral neutrophils of asymptomatic MMD patients. Then enrichment analyses based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) for those differentially expressed mRNAs and lncRNA associated mRNAs were performed for underlying molecular mechanisms. RESULTS Here, we identified a total of 2824 differentially expressed lncRNAs and 522 differentially expressed mRNAs (fold change > 2 and P<0.05) in peripheral neutrophils of asymptomatic MMD patients, compared with healthy controls. Then enrichment analyses based on GO and KEGG showed that the neighboring protein-coding mRNAs of those up-regulated and down-regulated lncRNAs were mainly involved in distinct metabolic processes respectively, which may act as a complementary response to insufficient blood supplies in MMD. Further enrichment analyses of those differentially expressed mRNAs preferentially listed essential physiological processes such as peptide cross-linking, chromatin assembly among others. Moreover, altered mRNAs also revealed to be enriched in renin secretion, platelet activation, inflammation and others. CONCLUSION We demonstrated for the first time that metabolic adjustments by dysregulated lncRNAs in peripheral neutrophils might partially account for the complete compensation of asymptomatic MMD patients. In addition, more attention should be paid on renin secretion and platelet activation in order to better understand the pathogenesis and guide clinical intervention for asymptomatic MMDs.
Collapse
Affiliation(s)
- Ziping Han
- Institute of Cerebrovascular Diseases Research, Department of Neurology, and Department of Neurosurgery of Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Lingzhi Li
- Institute of Cerebrovascular Diseases Research, Department of Neurology, and Department of Neurosurgery of Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Ping Liu
- Institute of Cerebrovascular Diseases Research, Department of Neurology, and Department of Neurosurgery of Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Yuyou Huang
- Institute of Cerebrovascular Diseases Research, Department of Neurology, and Department of Neurosurgery of Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Sijia Zhang
- Institute of Cerebrovascular Diseases Research, Department of Neurology, and Department of Neurosurgery of Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Guangwen Li
- Institute of Cerebrovascular Diseases Research, Department of Neurology, and Department of Neurosurgery of Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Fangfang Li
- Institute of Cerebrovascular Diseases Research, Department of Neurology, and Department of Neurosurgery of Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Haiping Zhao
- Institute of Cerebrovascular Diseases Research, Department of Neurology, and Department of Neurosurgery of Xuanwu Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Translational Medicine for Cerebrovascular Diseases, Beijing, China
| | - Zhen Tao
- Institute of Cerebrovascular Diseases Research, Department of Neurology, and Department of Neurosurgery of Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Rongliang Wang
- Institute of Cerebrovascular Diseases Research, Department of Neurology, and Department of Neurosurgery of Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Qingfeng Ma
- Institute of Cerebrovascular Diseases Research, Department of Neurology, and Department of Neurosurgery of Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Yumin Luo
- Institute of Cerebrovascular Diseases Research, Department of Neurology, and Department of Neurosurgery of Xuanwu Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Translational Medicine for Cerebrovascular Diseases, Beijing, China.,Beijing Institute for Brain Disorders, Beijing, China
| |
Collapse
|
11
|
Kanamori F, Yokoyama K, Ota A, Yoshikawa K, Karnan S, Maruwaka M, Shimizu K, Ota S, Uda K, Araki Y, Okamoto S, Maesawa S, Wakabayashi T, Natsume A. Transcriptome-wide analysis of intracranial artery in patients with moyamoya disease showing upregulation of immune response, and downregulation of oxidative phosphorylation and DNA repair. Neurosurg Focus 2021; 51:E3. [PMID: 34469870 DOI: 10.3171/2021.6.focus20870] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 06/18/2021] [Indexed: 11/06/2022]
Abstract
OBJECTIVE Moyamoya disease (MMD) is a rare cerebrovascular disease characterized by progressive occlusion of the internal carotid artery and the secondary formation of collateral vessels. Patients with MMD have ischemic attacks or intracranial bleeding, but the disease pathophysiology remains unknown. In this study, the authors aimed to identify a gene expression profile specific to the intracranial artery in MMD. METHODS This was a single-center, prospectively sampled, retrospective cohort study. Microsamples of the middle cerebral artery (MCA) were collected from patients with MMD (n = 11) and from control patients (n = 9). Using microarray techniques, transcriptome-wide analysis was performed. RESULTS Comparison of MCA gene expression between patients with MMD and control patients detected 62 and 26 genes whose expression was significantly (p < 0.001 and fold change > 2) up- or downregulated, respectively, in the MCA of MMD. Gene set enrichment analysis of genes expressed in the MCA of patients with MMD revealed positive correlations with genes involved in antigen processing and presentation, the dendritic cell pathway, cytokine pathway, and interleukin-12 pathway, and negative correlations with genes involved in oxidative phosphorylation and DNA repair. Microarray analysis was validated by quantitative polymerase chain reaction. CONCLUSIONS Transcriptome-wide analysis showed upregulation of genes for immune responses and downregulation of genes for DNA repair and oxidative phosphorylation within the intracranial artery of patients with MMD. These findings may represent clues to the pathophysiology of MMD.
Collapse
Affiliation(s)
- Fumiaki Kanamori
- 1Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya
| | - Kinya Yokoyama
- 1Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya
| | - Akinobu Ota
- 2Department of Biochemistry, Aichi Medical University School of Medicine, Nagakute
| | - Kazuhiro Yoshikawa
- 3Division of Research Creation and Biobank, Research Creation Support Center, Aichi Medical University, Nagakute
| | - Sivasundaram Karnan
- 2Department of Biochemistry, Aichi Medical University School of Medicine, Nagakute
| | - Mikio Maruwaka
- 4Department of Neurosurgery, Toyota Kosei Hospital, Toyota
| | - Kenzo Shimizu
- 5Department of Neurosurgery, Kasugai Municipal Hospital, Kasugai
| | - Shinji Ota
- 6Department of Neurosurgery, Handa City Hospital, Handa; and
| | - Kenji Uda
- 1Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya
| | - Yoshio Araki
- 1Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya
| | - Sho Okamoto
- 7Aichi Rehabilitation Hospital, Nishio, Japan
| | - Satoshi Maesawa
- 1Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya
| | | | - Atsushi Natsume
- 1Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya
| |
Collapse
|
12
|
Li J, Zhang C, Shi Y, Li Q, Li N, Mi Y. Identification of KEY lncRNAs and mRNAs Associated with Oral Squamous Cell Carcinoma Progression. Curr Bioinform 2021. [DOI: 10.2174/1573411016999200729125745] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Oral squamous cell carcinoma (OSCC) has been the sixth most common
cancer worldwide. Emerging studies showed long non-coding RNAs to play a key role in human
cancers. However, the molecular mechanisms underlying the initiation and progression of OSCC
remained to be further explored.
Objective:
The present study aimed to identify differentially expressed lncRNAs and mRNAs in
OSCC.
Methods:
GSE30784 was analyzed to identify differentially expressed lncRNAs and mRNAs in
OSCC. Protein-protein interaction network and co-expression network analyses were performed to
reveal the potential roles of OSCC related mRNAs and lncRNAs.
Results:
In the present study, we identified 21 up-regulated lncRNAs and 54 down-regulated
lncRNAs in OSCC progression. Next, we constructed a lncRNA related co-expression network in
OSCC, which included 692 mRNAs and 2193 edges. Bioinformatics analysis showed that
lncRNAs were widely co-expressed with regulating type I interferon signaling pathway,
extracellular matrix organization, collagen catabolic process, immune response, ECM-receptor
interaction, Focal adhesion, and PI3K-Akt signaling pathway. A key network, including lncRNA
C5orf66-AS1, C21orf15, LOC100506098, PCBP1-AS1, LOC284825, OR7E14P, HCG22, and
FLG-AS1, was found to be involved in the regulation of immune response to tumor cell, Golgi
calcium ion transport, negative regulation of vitamin D receptor signaling pathway, and glycerol-
3-phosphate catabolic process. Moreover, we found higher expressions of CYP4F29P, PCBP1-
AS1, HCG22, and C5orf66-AS1, which were associated with shorter overall survival time in
OSCC samples.
Conclusions:
Our analysis can provide novel insights to explore the potential mechanisms
underlying OSCC progression.
Collapse
Affiliation(s)
- Ju Li
- Jinan Stomatological Hospital, 101 Jingliu Road, Jinan 250001, Shandong,China
| | - Congcong Zhang
- Jinan Stomatological Hospital, 101 Jingliu Road, Jinan 250001, Shandong,China
| | - Yang Shi
- Jinan Stomatological Hospital, 101 Jingliu Road, Jinan 250001, Shandong,China
| | - Qing Li
- Jinan Stomatological Hospital, 101 Jingliu Road, Jinan 250001, Shandong,China
| | - Na Li
- Jinan Stomatological Hospital, 101 Jingliu Road, Jinan 250001, Shandong,China
| | - Yong Mi
- Jinan Stomatological Hospital, 101 Jingliu Road, Jinan 250001, Shandong,China
| |
Collapse
|
13
|
Network of clinically-relevant lncRNAs-mRNAs associated with prognosis of hepatocellular carcinoma patients. Sci Rep 2020; 10:11124. [PMID: 32636408 PMCID: PMC7341759 DOI: 10.1038/s41598-020-67742-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 06/12/2020] [Indexed: 12/16/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are often aberrantly expressed in Hepatocellular Carcinoma (HCC). We hypothesize that lncRNAs modulate HCC prognoses through differential deregulation of key lncRNAs affecting important gene network in key cancer pathways associated with pertinent clinical phenotype. Here, we present a novel approach integrating lncRNA-mRNA expression profiles with clinical characteristics to identify lncRNA signatures in clinically-relevant co-expression lncRNA-mRNA networks residing in pertinent cancer pathways. Notably one network, associated with poorer prognosis, comprises five up-regulated lncRNAs significantly correlated (|Pearson Correlation Coefficient|≥ 0.9) with 91 up-regulated genes in the cell-cycle and Rho-GTPase pathways. All 5 lncRNAs and 85/91 (93.4%) of the correlated genes were significantly associated with higher tumor-grade while 3/5 lncRNAs were also associated with no tumor capsule. Interestingly, 2/5 lncRNAs that are correlated with numerous genes in this oncogenic network were experimentally shown to up-regulate genes involved in cell-cycle and transcriptional regulation. Another network comprising 4 down-regulated lncRNAs and 8 down-regulated metallothionein-family genes are significantly associated with tumor invasion. The identification of these key lncRNAs signatures that deregulate important network of genes in key cancer pathways associated with pertinent clinical phenotype may facilitate the design of novel therapeutic strategies targeting these 'master' regulators for better patient outcome.
Collapse
|
14
|
Multilevel omics for the discovery of biomarkers and therapeutic targets for stroke. Nat Rev Neurol 2020; 16:247-264. [PMID: 32322099 DOI: 10.1038/s41582-020-0350-6] [Citation(s) in RCA: 151] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2020] [Indexed: 02/07/2023]
Abstract
Despite many years of research, no biomarkers for stroke are available to use in clinical practice. Progress in high-throughput technologies has provided new opportunities to understand the pathophysiology of this complex disease, and these studies have generated large amounts of data and information at different molecular levels. The integration of these multi-omics data means that thousands of proteins (proteomics), genes (genomics), RNAs (transcriptomics) and metabolites (metabolomics) can be studied simultaneously, revealing interaction networks between the molecular levels. Integrated analysis of multi-omics data will provide useful insight into stroke pathogenesis, identification of therapeutic targets and biomarker discovery. In this Review, we detail current knowledge on the pathology of stroke and the current status of biomarker research in stroke. We summarize how proteomics, metabolomics, transcriptomics and genomics are all contributing to the identification of new candidate biomarkers that could be developed and used in clinical stroke management.
Collapse
|
15
|
Xiao Q, Luo J, Liang C, Li G, Cai J, Ding P, Liu Y. Identifying lncRNA and mRNA Co-Expression Modules from Matched Expression Data in Ovarian Cancer. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020; 17:623-634. [PMID: 30106686 DOI: 10.1109/tcbb.2018.2864129] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Long non-coding RNAs (lncRNAs) have been shown to be involved in multiple biological processes and play critical roles in tumorigenesis. Numerous lncRNAs have been discovered in diverse species, but the functions of most lncRNAs still remain unclear. Meanwhile, their expression patterns and regulation mechanisms are also far from being fully understood. With the advances of high-throughput technologies, the increasing availability of genomic data creates opportunities for deciphering the molecular mechanism and underlying pathogenesis of human diseases. Here, we develop an integrative framework called JONMF to identify lncRNA-mRNA co-expression modules based on the sample-matched lncRNA and mRNA expression profiles. We formulate the module detection task as an optimization problem with joint orthogonal non-negative matrix factorization that could effectively prevent multicollinearity and produce a good modularity interpretation. The constructed lncRNA-mRNA co-expression network and the gene-gene interaction network are used as the network-regularized constraints to improve the module accuracy, while the sparsity constraints are simultaneously utilized to achieve modular sparse solutions. We applied JONMF to human ovarian cancer dataset and the experiment results demonstrate that the proposed method can effectively discover biologically functional co-expression modules, which may provide insights into the function of lncRNAs and molecular mechanism of human diseases.
Collapse
|
16
|
Corey S, Luo Y. Circular RNAs and neutrophils: Key factors in tackling asymptomatic moyamoya disease. Brain Circ 2019; 5:150-155. [PMID: 31620664 PMCID: PMC6785948 DOI: 10.4103/bc.bc_38_19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 09/01/2019] [Accepted: 09/02/2019] [Indexed: 12/23/2022] Open
Abstract
Moyamoya disease (MMD) represents a rare steno-occlusive disorder affecting the terminal ends of the internal carotid artery and promoting the development of a poor, abnormal vascular network at the brain's base. Primarily affecting East Asian countries over Western populations, MMD can be further divided into symptomatic and asymptomatic subtypes. The current knowledge of the underlying mechanisms and potential management strategies for asymptomatic cases of MMD are largely lacking and thus warrant investigation to elucidate the pathology of this rare disorder. Here, we assess research examining the expression profile of circular RNAs (circRNAs) of neutrophil transcriptome in asymptomatic MMD patients. These findings conclude that 123 differentially expressed circRNAs significantly contributed to metabolism, angiogenesis, and immune response. The hypoxia-inducing factor-1α signaling pathway was also revealed to be crucial in angiogenesis. We also evaluate current therapeutic options demonstrating the potential for MMD patients, such as EC-IC bypass and ischemic pre- and post-conditioning. These approaches combined with recent findings on the circRNA expression profile suggest a crucial role of anti-inflammatory and angiogenic-related mechanisms underlying MMD. Investigating the role of circRNAs and neutrophils in the asymptomatic MMD subtype may provide insight into its elusive pathology and direct future approaches to combat the progression of this rare disease.
Collapse
Affiliation(s)
- Sydney Corey
- Department of Neurosurgery and Brain Repair, College of Medicine, University of South Florida Morsani, Tampa, FL, USA
| | - Yumin Luo
- Department of Neurosurgery and Brain Repair, College of Medicine, University of South Florida Morsani, Tampa, FL, USA.,Institute of Cerebrovascular Diseases Research and Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China
| |
Collapse
|
17
|
Mikami T, Suzuki H, Komatsu K, Mikuni N. Influence of Inflammatory Disease on the Pathophysiology of Moyamoya Disease and Quasi-moyamoya Disease. Neurol Med Chir (Tokyo) 2019; 59:361-370. [PMID: 31281171 PMCID: PMC6796064 DOI: 10.2176/nmc.ra.2019-0059] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Moyamoya disease is a unique cerebrovascular disease that is characterized by progressive bilateral stenotic alteration at the terminal portion of the internal carotid arteries. These changes induce the formation of an abnormal vascular network composed of collateral pathways known as moyamoya vessels. In quasi-moyamoya disease, a similar stenotic vascular abnormality is associated with an underlying disease, which is sometimes an inflammatory disease. Recent advances in moyamoya disease research implicate genetic background and immunological mediators, and postulate an association with inflammatory disease as a cause of, or progressive factor in, quasi-moyamoya disease. Although this disease has well-defined clinical and radiological characteristics, the role of inflammation has not been rigorously explored. Herein, we focused on reviewing two main themes: (1) molecular biology of inflammation in moyamoya disease, and (2) clinical significance of inflammation in quasi-moyamoya disease. We have summarized the findings of the former theme according to the following topics: (1) inflammatory biomarkers, (2) genetic background of inflammatory response, (3) endothelial progenitor cells, and (4) noncoding ribonucleic acids. Under the latter theme, we summarized the findings according to the following topics: (1) influence of inflammatory disease, (2) vascular remodeling, and (3) mechanisms gleaned from clinical cases. This review includes articles published up to February 2019 and provides novel insights for the treatment of the moyamoya disease and quasi-moyamoya disease.
Collapse
Affiliation(s)
| | - Hime Suzuki
- Department of Neurosurgery, Sapporo Medical University
| | | | | |
Collapse
|
18
|
Ma Q, Li L, Yu B, Jiao L, Han Z, Zhao H, Li G, Ma Y, Luo Y. Circular RNA profiling of neutrophil transcriptome provides insights into asymptomatic Moyamoya disease. Brain Res 2019; 1719:104-112. [PMID: 31132337 DOI: 10.1016/j.brainres.2019.05.033] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/21/2019] [Accepted: 05/23/2019] [Indexed: 12/24/2022]
Abstract
Moyamoya disease (MMD) is a rare cerebrovascular disorder with higher incidences in Eastern Asian countries but the natural course remains uncertain. Circular RNAs (circRNAs) have been implicated in brain disorders, but their role in the development of MMD is unclear. Neutrophil depletion has been shown to affect stem cell migration, fate, and therapeutic outcomes. We investigated the circRNAs expression profile of neutrophil transcriptome in patients with asymptomatic MMD. Microarray based circRNAs profiling was determined between neutrophil samples from patients with asymptomatic MMD and healthy subjects. The microarray results were followingly confirmed by quantitative reverse-transcription PCR. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses (KEGG) were adopted for annotation and predicting the functions of differentially expressed circRNAs. From this comparative circRNA microarray analysis of neutrophil samples from patients with asymptomatic MMD and healthy subjects, 123 circRNAs were identified differentially expressed between the two groups. Of these, 54 were upregulated and 69 were downregulated compared to controls (fold change >2.0 and P < 0.05). GO and KEGG analyses revealed that the differentially expressed circRNAs were mainly involved in immune responses, angiogenesis and metabolism in asymptomatic MMD. Besides, the hypoxia inducing factor-1α signaling pathway was found to be the critical pathway involved in the angiogenesis of disease pathogenesis. This is a pilot study on the neutrophils from the asymptomatic MMD and aberrantly expressed circRNAs in the profiling obtained by high-throughput microarray may help provide insights into MMD.
Collapse
Affiliation(s)
- Qingfeng Ma
- Institute of Cerebrovascular Diseases Research, Department of Neurology, and Department of Neurosurgery of Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Lingzhi Li
- Institute of Cerebrovascular Diseases Research, Department of Neurology, and Department of Neurosurgery of Xuanwu Hospital, Capital Medical University, Beijing, China; Beijing Key Laboratory of Translational Medicine for Cerebrovascular Diseases, Beijing, China
| | - Bingxin Yu
- Health Management Center, Xuanwu Hospital of Capital Medical University, China
| | - Liqun Jiao
- Institute of Cerebrovascular Diseases Research, Department of Neurology, and Department of Neurosurgery of Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Ziping Han
- Institute of Cerebrovascular Diseases Research, Department of Neurology, and Department of Neurosurgery of Xuanwu Hospital, Capital Medical University, Beijing, China; Beijing Key Laboratory of Translational Medicine for Cerebrovascular Diseases, Beijing, China
| | - Haiping Zhao
- Institute of Cerebrovascular Diseases Research, Department of Neurology, and Department of Neurosurgery of Xuanwu Hospital, Capital Medical University, Beijing, China; Beijing Key Laboratory of Translational Medicine for Cerebrovascular Diseases, Beijing, China
| | - Guangwen Li
- Institute of Cerebrovascular Diseases Research, Department of Neurology, and Department of Neurosurgery of Xuanwu Hospital, Capital Medical University, Beijing, China; Beijing Key Laboratory of Translational Medicine for Cerebrovascular Diseases, Beijing, China
| | - Yan Ma
- Institute of Cerebrovascular Diseases Research, Department of Neurology, and Department of Neurosurgery of Xuanwu Hospital, Capital Medical University, Beijing, China.
| | - Yumin Luo
- Institute of Cerebrovascular Diseases Research, Department of Neurology, and Department of Neurosurgery of Xuanwu Hospital, Capital Medical University, Beijing, China; Beijing Key Laboratory of Translational Medicine for Cerebrovascular Diseases, Beijing, China; Beijing Institute for Brain Disorders, Beijing, China.
| |
Collapse
|
19
|
Karschnia P, Nishimura S, Louvi A. Cerebrovascular disorders associated with genetic lesions. Cell Mol Life Sci 2019; 76:283-300. [PMID: 30327838 PMCID: PMC6450555 DOI: 10.1007/s00018-018-2934-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 09/30/2018] [Accepted: 10/02/2018] [Indexed: 01/15/2023]
Abstract
Cerebrovascular disorders are underlain by perturbations in cerebral blood flow and abnormalities in blood vessel structure. Here, we provide an overview of the current knowledge of select cerebrovascular disorders that are associated with genetic lesions and connect genomic findings with analyses aiming to elucidate the cellular and molecular mechanisms of disease pathogenesis. We argue that a mechanistic understanding of genetic (familial) forms of cerebrovascular disease is a prerequisite for the development of rational therapeutic approaches, and has wider implications for treatment of sporadic (non-familial) forms, which are usually more common.
Collapse
Affiliation(s)
- Philipp Karschnia
- Departments of Neurosurgery and Neuroscience, Program on Neurogenetics, Yale School of Medicine, P.O. Box 208082, New Haven, CT, 06520-8082, USA
| | - Sayoko Nishimura
- Departments of Neurosurgery and Neuroscience, Program on Neurogenetics, Yale School of Medicine, P.O. Box 208082, New Haven, CT, 06520-8082, USA
| | - Angeliki Louvi
- Departments of Neurosurgery and Neuroscience, Program on Neurogenetics, Yale School of Medicine, P.O. Box 208082, New Haven, CT, 06520-8082, USA.
| |
Collapse
|
20
|
Integrated analysis of long noncoding RNA and mRNA expression profile in children with obesity by microarray analysis. Sci Rep 2018; 8:8750. [PMID: 29884798 PMCID: PMC5993825 DOI: 10.1038/s41598-018-27113-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 05/30/2018] [Indexed: 12/29/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) have an important role in adipose tissue function and energy metabolism homeostasis, and abnormalities may lead to obesity. To investigate whether lncRNAs are involved in childhood obesity, we investigated the differential expression profile of lncRNAs in obese children compared with non-obese children. A total number of 1268 differentially expressed lncRNAs and 1085 differentially expressed mRNAs were identified. Gene Ontology (GO) and pathway analysis revealed that these lncRNAs were involved in varied biological processes, including the inflammatory response, lipid metabolic process, osteoclast differentiation and fatty acid metabolism. In addition, the lncRNA-mRNA co-expression network and the protein-protein interaction (PPI) network were constructed to identify hub regulatory lncRNAs and genes based on the microarray expression profiles. This study for the first time identifies an expression profile of differentially expressed lncRNAs in obese children and indicated hub lncRNA RP11-20G13.3 attenuated adipogenesis of preadipocytes, which is conducive to the search for new diagnostic and therapeutic strategies of childhood obesity.
Collapse
|
21
|
Zhang J, Yuan Y, Wei Z, Ren J, Hou X, Yang D, Cai S, Chen C, Tan M, Chen GG, Wu K, He Y. Crosstalk between prognostic long noncoding RNAs and messenger RNAs as transcriptional hallmarks in gastric cancer. Epigenomics 2018; 10:433-443. [PMID: 29402138 DOI: 10.2217/epi-2017-0136] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
AIM Our study investigated the significance of the crosstalk between long noncoding RNAs (lncRNAs) and mRNAs in gastric cancer (GC). METHODS lncRNA and mRNA expression profiling data in 671 GC tumors and 77 nontumorous gastric tissues were retrieved from the gene expression omnibus database: GSE54129, GSE13911, GSE19826, GSE79973, GSE15459 and GSE66229. Differentially expressed analysis, RNA coexpression network construction, gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analyses were conducted in this study. RESULTS Using differentially expressed and prognostic lncRNAs or mRNAs in GC, we constructed the lncRNA-mRNA coexpression networks. This network involved with vital GO and KEGG pathways. CONCLUSION Our study reveals coexpressed lncRNAs and mRNAs as transcriptional hallmarks in GC patients which provide interesting information regarding the incidence and outcome of GC.
Collapse
Affiliation(s)
- Jian Zhang
- Division of Gastrointestinal Surgery & Gastric Cancer Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
| | - Yujie Yuan
- Division of Gastrointestinal Surgery & Gastric Cancer Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
| | - Zhewei Wei
- Division of Gastrointestinal Surgery & Gastric Cancer Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
| | - Jianwei Ren
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, PR China.,Department of Surgery, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, PR China
| | - Xun Hou
- Division of Gastrointestinal Surgery & Gastric Cancer Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
| | - Dongjie Yang
- Division of Gastrointestinal Surgery & Gastric Cancer Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
| | - Sirong Cai
- Division of Gastrointestinal Surgery & Gastric Cancer Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
| | - Chuangqi Chen
- Division of Gastrointestinal Surgery & Gastric Cancer Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
| | - Min Tan
- Division of Gastrointestinal Surgery & Gastric Cancer Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
| | - George Gong Chen
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, PR China.,Department of Surgery, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, PR China
| | - Kaiming Wu
- Division of Gastrointestinal Surgery & Gastric Cancer Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
| | - Yulong He
- Division of Gastrointestinal Surgery & Gastric Cancer Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
| |
Collapse
|
22
|
He Q, Liu Y, Sun W. Statistical analysis of non-coding RNA data. Cancer Lett 2018; 417:161-167. [PMID: 29306017 DOI: 10.1016/j.canlet.2017.12.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 12/13/2017] [Accepted: 12/20/2017] [Indexed: 12/15/2022]
Abstract
With rapid progress in high-throughput genome technology, the study of noncoding RNA has arisen as a highly popular topic in biomedical research. Noncoding RNA plays fundamental roles in cell proliferation, cell differentiation and epigenetic regulation, and the study of noncoding RNA will yield novel insights into gene regulation and provide new clues for disease treatment. However, due to the large volume and diverse functions of noncoding RNAs, the analysis of these RNAs has proved to be a challenging task. In this review, we review the commonly used computational tools for the identification of noncoding RNAs, and discuss popular statistical tools for their analysis. Due to the large body of noncoding RNA classes, we focus on the analysis of microRNA and long noncoding RNA, two of the most widely studied classes of noncoding RNAs. Specific examples are provided to show the context of the analysis. This review aims to provide up-to-date information on existing tools and methods for identifying and analyzing noncoding RNA.
Collapse
Affiliation(s)
- Qianchuan He
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
| | - Yang Liu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Wei Sun
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
| |
Collapse
|
23
|
Wang W, Zhao Z, Yang F, Wang H, Wu F, Liang T, Yan X, Li J, Lan Q, Wang J, Zhao J. An immune-related lncRNA signature for patients with anaplastic gliomas. J Neurooncol 2017; 136:263-271. [PMID: 29170907 DOI: 10.1007/s11060-017-2667-6] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 11/11/2017] [Indexed: 12/26/2022]
Abstract
We investigated immune-related long non-coding RNAs (lncRNAs) that may be exploited as potential therapeutic targets in anaplastic gliomas. We obtained 572 lncRNAs and 317 immune genes from the Chinese Glioma Genome Atlas microarray and constructed immune-related lncRNAs co-expression networks to identify immune-related lncRNAs. Two additional datasets (GSE16011, REMBRANDT) were used for validation. Gene set enrichment analysis and principal component analysis were used for functional annotation. Immune-lncRNAs co-expression networks were constructed. Nine immune-related lncRNAs (SNHG8, PGM5-AS1, ST20-AS1, LINC00937, AGAP2-AS1, MIR155HG, TUG1, MAPKAPK5-AS1, and HCG18) signature was identified in patients with anaplastic gliomas. Patients in the low-risk group showed longer overall survival (OS) and progression-free survival than those in the high-risk group (P < 0.0001; P < 0.0001). Additionally, patients in the high-risk group displayed no-deletion of chromosomal arms 1p and/or 19q, isocitrate dehydrogenase wild-type, classical and mesenchymal TCGA subtype, G3 CGGA subtype, and lower Karnofsky performance score (KPS). Moreover, the signature was an independent factor and was significantly associated with the OS (P = 0.000, hazard ratio (HR) = 1.434). These findings were further validated in two additional datasets (GSE16011, REMBRANDT). Low-risk and high-risk groups displayed different immune status based on principal components analysis. Our results showed that the nine immune-related lncRNAs signature has prognostic value for anaplastic gliomas.
Collapse
Affiliation(s)
- Wen Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, No. 6 Tiantan Xili, Dongcheng District, Beijing, 100050, China.,Department of Neurosurgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215123, China.,Chinese Glioma Cooperative Group (CGCG), Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Zheng Zhao
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100050, China.,Chinese Glioma Cooperative Group (CGCG), Beijing, China
| | - Fan Yang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, No. 6 Tiantan Xili, Dongcheng District, Beijing, 100050, China.,Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100050, China.,Chinese Glioma Cooperative Group (CGCG), Beijing, China
| | - Haoyuan Wang
- Department of Neurosurgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, China.,Chinese Glioma Cooperative Group (CGCG), Beijing, China
| | - Fan Wu
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100050, China.,Chinese Glioma Cooperative Group (CGCG), Beijing, China
| | - Tingyu Liang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, No. 6 Tiantan Xili, Dongcheng District, Beijing, 100050, China.,Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100050, China.,Chinese Glioma Cooperative Group (CGCG), Beijing, China
| | - Xiaoyan Yan
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100050, China.,Chinese Glioma Cooperative Group (CGCG), Beijing, China
| | - Jiye Li
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100050, China
| | - Qing Lan
- Department of Neurosurgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215123, China
| | - Jiangfei Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, No. 6 Tiantan Xili, Dongcheng District, Beijing, 100050, China. .,Chinese Glioma Cooperative Group (CGCG), Beijing, China. .,China National Clinical Research Center for Neurological Diseases, Beijing, China.
| | - Jizong Zhao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, No. 6 Tiantan Xili, Dongcheng District, Beijing, 100050, China. .,Department of Neurosurgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215123, China. .,China National Clinical Research Center for Neurological Diseases, Beijing, China.
| |
Collapse
|