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Wei B, Yue Q, Ka Y, Sun C, Zhao Y, Ning X, Jin Y, Gao J, Wu Y, Liu W. Identification and Validation of IFI44 as a Novel Biomarker for Primary Sjögren's Syndrome. J Inflamm Res 2024; 17:5723-5740. [PMID: 39219820 PMCID: PMC11366250 DOI: 10.2147/jir.s477490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024] Open
Abstract
Background Primary Sjögren's syndrome (pSS) is an autoimmune condition marked by lymphocyte infiltration in the exocrine glands. Our study aimed to identify a novel biomarker for pSS to improve its diagnosis and treatment. Methods The gene expression profiles of pSS were obtained from the Gene Expression Omnibus (GEO) database. The specific differentially expressed genes (DEGs) were screened by the Least Absolute Shrinkage and Selection Operator (LASSO), Random Forest (RF), and Recursive Feature Elimination with Support Vector Machines (SVM-RFE). A biomarker was picked out based on correlation and diagnostic performance, the connection between the biomarker and clinical traits and immune infiltrating cells was explored, and the biomarker's protein expression level in the serum of pSS patients was detected by enzyme-linked immunosorbent assay (ELISA). The competitive endogenous RNA (ceRNA) network regulated by the biomarker was predicted to verify the reliability of the biomarker in diagnosing pSS. Results IFI44, XAF1, GBP1, EIF2AK2, IFI27, and IFI6 showed prominent diagnostic ability, with the high accuracy (AUC = 0.859) and significance (R ≥ 0.8) of IFI44 within the training dataset. IFI44 strongly exhibited a negative correlation with resting NK cells, macrophages M0, and eosinophils, and a positive correlation with activated dendritic cells, naive B cells, and activated CD4 memory T cells. Furthermore, IFI44 was significantly positively correlated with clinical traits such as IgG, SSA, SSB, ANA, and ESSDAI, with its protein expression level in the serum of pSS patients being notably elevated compared to controls (p < 0.001). Finally, the ceRNA regulatory network showed that hsa-miR-944, hsa-miR-9-5p, hsa-miR-126-5p, and hsa-miR-335-3p were significantly targeted IFI44, suggesting that IFI44 may serve as a dependable biomarker for pSS. Conclusion In this study, we dug out IFI44 as a biomarker for pSS, systematically studied the potential regulatory mechanism of IFI44, and verified its reliability as a biomarker for pSS.
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Affiliation(s)
- Bowen Wei
- Department of Rheumatism and Immunity, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, People’s Republic of China
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, People’s Republic of China
| | - Qingyun Yue
- Department of Rheumatism and Immunity, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, People’s Republic of China
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, People’s Republic of China
| | - Yuxiu Ka
- Department of Rheumatism and Immunity, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, People’s Republic of China
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, People’s Republic of China
| | - Chenyang Sun
- Department of Rheumatism and Immunity, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, People’s Republic of China
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, People’s Republic of China
| | - Yuxing Zhao
- Department of Rheumatism and Immunity, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, People’s Republic of China
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, People’s Republic of China
| | - Xiaomei Ning
- Department of Rheumatism and Immunity, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, People’s Republic of China
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, People’s Republic of China
| | - Yue Jin
- Department of Rheumatism and Immunity, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, People’s Republic of China
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, People’s Republic of China
| | - Jingyue Gao
- Department of Rheumatism and Immunity, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, People’s Republic of China
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, People’s Republic of China
| | - Yuanhao Wu
- Department of Rheumatism and Immunity, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, People’s Republic of China
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, People’s Republic of China
| | - Wei Liu
- Department of Rheumatism and Immunity, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, People’s Republic of China
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, People’s Republic of China
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Yang Y, Chen X, Liao X, Jiang W, Zhou Y, Sun Y, Zheng B. Identification of MAP1LC3A as a promising mitophagy-related gene in polycystic ovary syndrome. Sci Rep 2024; 14:16982. [PMID: 39043888 PMCID: PMC11266624 DOI: 10.1038/s41598-024-67969-9] [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: 03/17/2024] [Accepted: 07/18/2024] [Indexed: 07/25/2024] Open
Abstract
Increasing evidence suggests that mitophagy is crucially involved in the progression of polycystic ovary syndrome (PCOS). Exploration of PCOS-specific biomarkers related to mitophagy is expected to provide critical insights into disease pathogenesis. In this study, we employed bioinformatic analyses and machine learning algorithms to determine novel biomarkers for PCOS that may be tied with mitophagy. A grand total of 12 differential expressed mitophagy-related genes (DE-MRGs) associated with PCOS were identified. TOMM5 and MAP1LC3A among the 12 DE-MRGs were recognized as potential marker genes by LASSO, RF and SVM-RFE algorithms. The area under the ROC curve (AUROC) of MAP1LC3A were all greater than 0.8 both in the training set and validation sets. The CIBERSORT analysis indicated a potential association between alterations in the immune microenvironment of PCOS individuals and MAP1LC3A expression. In addition, we found that MAP1LC3A was positively related to the testosterone levels of PCOS patients. Overall, MAP1LC3A was identified as optimal PCOS-specific biomarkers related to mitophagy. Our findings created a diagnostic strength and offered a perspective for investigating the mitophagy process in PCOS.
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Affiliation(s)
- Yizhen Yang
- Reproductive Medicine Center of Fujian Maternity and Child Health Hospital, Fuzhou, 350001, Fujian, China
- Fujian Maternal-Fetal Clinical Medicine Research Center, Fuzhou, 350001, Fujian, China
| | - Xiaojing Chen
- Reproductive Medicine Center of Fujian Maternity and Child Health Hospital, Fuzhou, 350001, Fujian, China
- Fujian Maternal-Fetal Clinical Medicine Research Center, Fuzhou, 350001, Fujian, China
| | - Xiuhua Liao
- Reproductive Medicine Center of Fujian Maternity and Child Health Hospital, Fuzhou, 350001, Fujian, China
| | - Wenwen Jiang
- Reproductive Medicine Center of Fujian Maternity and Child Health Hospital, Fuzhou, 350001, Fujian, China
| | - Yuan Zhou
- Reproductive Medicine Center of Fujian Maternity and Child Health Hospital, Fuzhou, 350001, Fujian, China
| | - Yan Sun
- Reproductive Medicine Center of Fujian Maternity and Child Health Hospital, Fuzhou, 350001, Fujian, China.
- Fujian Maternal-Fetal Clinical Medicine Research Center, Fuzhou, 350001, Fujian, China.
| | - Beihong Zheng
- Reproductive Medicine Center of Fujian Maternity and Child Health Hospital, Fuzhou, 350001, Fujian, China.
- Fujian Maternal-Fetal Clinical Medicine Research Center, Fuzhou, 350001, Fujian, China.
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Tian Z, Yu S, Cai R, Zhang Y, Liu Q, Zhu Y. SH3GL2 and MMP17 as lung adenocarcinoma biomarkers: a machine-learning based approach. Biochem Biophys Rep 2024; 38:101693. [PMID: 38571554 PMCID: PMC10987888 DOI: 10.1016/j.bbrep.2024.101693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 03/19/2024] [Accepted: 03/19/2024] [Indexed: 04/05/2024] Open
Abstract
Objective Using bioinformatics machine learning methods, our research aims to identify the potential key genes associated with Lung adenocarcinoma (LUAD). Methods We obtained two gene expression profiling microarrays (GSE68571 and GSE74706) from the public Gene Expression Omnibus (GEO) database at the National Centre for Biotechnology Information (NCBI). The purpose was to identify Differentially Expressed Genes (DEGs) between the lung adenocarcinoma group and the healthy control group. The limma R package in R was utilized for this analysis. For the differential gene diagnosis of lung adenocarcinoma, we employed the least absolute shrinkage and selection operator (LASSO) regression and SVM-RFE screening crossover. To evaluate the performance, ROC curves were plotted. We performed immuno-infiltration analysis using CIBERSORT. Finally, we validated the key genes through qRT-PCR and Western-blot verification, then downregulated MMP17 gene expression, upregulated SH3GL2 gene expression, and performed CCK8 experiments. Results A total of 32 Differentially Expressed Genes (DEGs) were identified. Two diagnostic marker genes, SH3GL2 and MMP17, were selected by employing LASSO and SVM-RFE machine learning methods. In Lung adenocarcinoma cells, the expression of MMP17 was observed to be elevated compared to normal lung epithelial cells in the control group (P < 0.05). In contrast, a down-regulation of SH3GL2 was found in Lung adenocarcinoma cells (P < 0.05). Finally, we downregulated MMP17 and upregulated SH3GL2 gene expression, then the CCK8 showed that the proliferation of both lung cancer cells was inhibited. Conclusion SH3GL2 and MMP17 are expected to be potential biomarkers for Lung adenocarcinoma.
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Affiliation(s)
- Zengjian Tian
- General Hospital of Ningxia Medical University, Yinchuan, Ningxia, 750004, China
| | - Shilong Yu
- General Hospital of Ningxia Medical University, Yinchuan, Ningxia, 750004, China
| | - Ruizhi Cai
- General Hospital of Ningxia Medical University, Yinchuan, Ningxia, 750004, China
| | - Yinghui Zhang
- General Hospital of Ningxia Medical University, Yinchuan, Ningxia, 750004, China
| | - Qilun Liu
- General Hospital of Ningxia Medical University, Yinchuan, Ningxia, 750004, China
| | - Yongzhao Zhu
- Institute of Medical Sciences, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, 750004, China
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Mao Y, Hou X, Fu S, Luan J. Transcriptomic and machine learning analyses identify hub genes of metabolism and host immune response that are associated with the progression of breast capsular contracture. Genes Dis 2024; 11:101087. [PMID: 38292203 PMCID: PMC10825289 DOI: 10.1016/j.gendis.2023.101087] [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: 07/11/2023] [Revised: 08/03/2023] [Accepted: 08/16/2023] [Indexed: 02/01/2024] Open
Abstract
Capsular contracture is a prevalent and severe complication that affects the postoperative outcomes of patients who receive silicone breast implants. At present, prosthesis replacement is the major treatment for capsular contracture after both breast augmentation procedures and breast reconstruction following breast cancer surgery. However, the mechanism(s) underlying breast capsular contracture remains unclear. This study aimed to identify the biological features of breast capsular contracture and reveal the potential underlying mechanism using RNA sequencing. Sample tissues from 12 female patients (15 breast capsules) were divided into low capsular contracture (LCC) and high capsular contracture (HCC) groups based on the Baker grades. Subsequently, 41 lipid metabolism-related genes were identified through enrichment analysis, and three of these genes were identified as candidate genes by SVM-RFE and LASSO algorithms. We then compared the proportions of the 22 types of immune cells between the LCC and HCC groups using a CIBERSORT analysis and explored the correlation between the candidate hub features and immune cells. Notably, PRKAR2B was positively correlated with the differentially clustered immune cells, which were M1 macrophages and follicular helper T cells (area under the ROC = 0.786). In addition, the expression of PRKAR2B at the mRNA or protein level was lower in the HCC group than in the LCC group. Potential molecular mechanisms were identified based on the expression levels in the high and low PRKAR2B groups. Our findings indicate that PRKAR2B is a novel diagnostic biomarker for breast capsular contracture and might also influence the grade and progression of capsular contracture.
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Affiliation(s)
- Yukun Mao
- Breast Plastic and Reconstructive Surgery Center, Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100144, China
| | - Xueying Hou
- Breast Plastic and Reconstructive Surgery Center, Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100144, China
| | - Su Fu
- Breast Plastic and Reconstructive Surgery Center, Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100144, China
| | - Jie Luan
- Breast Plastic and Reconstructive Surgery Center, Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100144, China
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Lou Y, Li PH, Liu XQ, Wang TX, Liu YL, Chen CC, Ma KL. ITGAM-mediated macrophages contribute to basement membrane damage in diabetic nephropathy and atherosclerosis. BMC Nephrol 2024; 25:72. [PMID: 38413872 PMCID: PMC10900706 DOI: 10.1186/s12882-024-03505-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 02/15/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Diabetic nephropathy (DN) and atherosclerosis (AS) are prevalent and severe complications associated with diabetes, exhibiting lesions in the basement membrane, an essential component found within the glomerulus, tubules, and arteries. These lesions contribute significantly to the progression of both diseases, however, the precise underlying mechanisms, as well as any potential shared pathogenic processes between them, remain elusive. METHODS Our study analyzed transcriptomic profiles from DN and AS patients, sourced from the Gene Expression Omnibus database. A combination of integrated bioinformatics approaches and machine learning models were deployed to identify crucial genes connected to basement membrane lesions in both conditions. The role of integrin subunit alpha M (ITGAM) was further explored using immune infiltration analysis and genetic correlation studies. Single-cell sequencing analysis was employed to delineate the expression of ITGAM across different cell types within DN and AS tissues. RESULTS Our analyses identified ITGAM as a key gene involved in basement membrane alterations and revealed its primary expression within macrophages in both DN and AS. ITGAM was significantly correlated with tissue immune infiltration within these diseases. Furthermore, the expression of genes encoding core components of the basement membrane was influenced by the expression level of ITGAM. CONCLUSION Our findings suggest that macrophages may contribute to basement membrane lesions in DN and AS through the action of ITGAM. Moreover, therapeutic strategies that target ITGAM may offer potential avenues to mitigate basement membrane lesions in these two diabetes-related complications.
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Affiliation(s)
- Yude Lou
- Department of Nephrology, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310009, China
| | - Peng Hui Li
- Institute of Immunology, School of Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Xiao Qi Liu
- Department of Nephrology, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310009, China
| | - Tian Xiang Wang
- Department of Nephrology, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310009, China
| | - Yi Lan Liu
- Department of Nephrology, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310009, China
| | - Chen Chen Chen
- Department of Basic Medicine Sciences, School of Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Kun Ling Ma
- Department of Nephrology, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310009, China.
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Liu J, Feng L, Jia Q, Meng J, Zhao Y, Ren L, Yan Z, Wang M, Qin J. A comprehensive bioinformatics analysis identifies mitophagy biomarkers and potential Molecular mechanisms in hypertensive nephropathy. J Biomol Struct Dyn 2024:1-20. [PMID: 38334110 DOI: 10.1080/07391102.2024.2311344] [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: 07/31/2023] [Accepted: 12/05/2023] [Indexed: 02/10/2024]
Abstract
Mitophagy, the selective removal of damaged mitochondria, plays a critical role in kidney diseases, but its involvement in hypertensive nephropathy (HTN) is not well understood. To address this gap, we investigated mitophagy-related genes in HTN, identifying potential biomarkers for diagnosis and treatment. Transcriptome datasets from the Gene Expression Omnibus database were analyzed, resulting in the identification of seven mitophagy related differentially expressed genes (MR-DEGs), namely PINK1, ULK1, SQSTM1, ATG5, ATG12, MFN2, and UBA52. Further, we explored the correlation between MR-DEGs, immune cells, and inflammatory factors. The identified genes demonstrated a strong correlation with Mast cells, T-cells, TGFβ3, IL13, and CSF3. Machine learning techniques were employed to screen important genes, construct diagnostic models, and evaluate their accuracy. Consensus clustering divided the HTN patients into two mitophagy subgroups, with Subgroup 2 showing higher levels of immune cell infiltration and inflammatory factors. The functions of their proteins primarily involve complement, coagulation, lipids, and vascular smooth muscle contraction. Single-cell RNA sequencing revealed that mitophagy was most significant in proximal tubule cells (PTC) in HTN patients. Pseudotime analysis of PTC confirmed the expression changes observed in the transcriptome. Intercellular communication analysis suggested that mitophagy might regulate PTC's participation in intercellular crosstalk. Notably, specific transcription factors such as HNF4A, PPARA, and STAT3 showed strong correlations with mitophagy-related genes in PTC, indicating their potential role in modulating PTC function and influencing the onset and progression of HTN. This study offers a comprehensive analysis of mitophagy in HTN, enhancing our understanding of the pathogenesis, diagnosis, and treatment of HTN.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jiayou Liu
- The Second Clinical Medical College, Beijing University of Chinese Medicine, Beijing, China
| | - Luda Feng
- Department of Nephropathy, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Qi Jia
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Jia Meng
- Department of Nephropathy, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Yun Zhao
- Department of Nephropathy, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Lei Ren
- Department of Nephropathy, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Ziming Yan
- Department of Nephropathy, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Manrui Wang
- The Second Clinical Medical College, Beijing University of Chinese Medicine, Beijing, China
| | - Jianguo Qin
- Department of Nephropathy, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
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Liao C, Peng TW, Li XM, Chen ZC, Wang MY, Ye X, Lan Y, Fu X, An G. Identification of ferroptotic genes and phenotypes in idiopathic nonobstructive azoospermia. Syst Biol Reprod Med 2023; 69:410-422. [PMID: 37782778 DOI: 10.1080/19396368.2023.2257352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 08/23/2023] [Indexed: 10/04/2023]
Abstract
Effective treatments for nonobstructive azoospermia (NOA), which affects 1% of all men globally, are limited by undefined pathogenic mechanisms, especially in idiopathic NOA (iNOA). Here, we tried to identify the functional ferroptosis-related genes and phenotypes involved in iNOA. Differentially expressed ferroptotic genes were identified from iNOA mRNA microarray datasets by bioinformatic analyses, and these ferroptotic genes were subsequently filtered by various algorithms. Then, receiver operating characteristic (ROC) curves were generated to evaluate the diagnostic ability of the abovementioned genes for iNOA. Generally, 11 differentially expressed ferroptotic genes were downregulated, and five genes were upregulated in iNOA samples. Four genes, including DUSP1, GPX4, HSD17B11, and SLC2A8, were technically selected and determined to be potential biomarkers for iNOA. Subsequently, similar expression levels were validated at both the RNA and protein levels in the iNOA specimens. Finally, morphologic and biochemical assays were applied to define the ferroptotic phenotypes in testes. The ferroptotic features, like shrunken mitochondria with electron-dense membranes and a reduction in cristae were observed across various cell types within iNOA patients, accompanied by the overload of ferrous ions and increased lipid peroxidation production. Our findings demonstrated that these ferroptosis genes could be involved in the underlying pathogenesis mechanisms of iNOA by regulating ferroptosis and serve as potential diagnostic biomarkers. Also, the ferroptotic phenotypes were identified in iNOA patients.
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Affiliation(s)
- Chen Liao
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine; Guangdong Provincial Key Laboratory for Major Obstetric Diseases; Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology; Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affifiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, P.R. China
- Key Laboratory for Reproductive Medicine of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P.R. China
| | - Tian-Wen Peng
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine; Guangdong Provincial Key Laboratory for Major Obstetric Diseases; Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology; Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affifiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, P.R. China
- Key Laboratory for Reproductive Medicine of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P.R. China
| | - Xiao-Min Li
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine; Guangdong Provincial Key Laboratory for Major Obstetric Diseases; Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology; Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affifiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, P.R. China
- Key Laboratory for Reproductive Medicine of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P.R. China
| | - Zhi-Cong Chen
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine; Guangdong Provincial Key Laboratory for Major Obstetric Diseases; Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology; Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affifiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, P.R. China
- Key Laboratory for Reproductive Medicine of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P.R. China
| | - Mu-Ye Wang
- Department of Anesthesiology, Guangdong Provincial Key Laboratory for Major Obstetric Diseases; Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affifiliated Hospital of Guangzhou Medical University, Guangdong, P.R. China
| | - Xin Ye
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine; Guangdong Provincial Key Laboratory for Major Obstetric Diseases; Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology; Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affifiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, P.R. China
- Key Laboratory for Reproductive Medicine of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P.R. China
| | - Yu Lan
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine; Guangdong Provincial Key Laboratory for Major Obstetric Diseases; Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology; Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affifiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, P.R. China
- Key Laboratory for Reproductive Medicine of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P.R. China
| | - Xin Fu
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine; Guangdong Provincial Key Laboratory for Major Obstetric Diseases; Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology; Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affifiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, P.R. China
- Key Laboratory for Reproductive Medicine of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P.R. China
| | - Geng An
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine; Guangdong Provincial Key Laboratory for Major Obstetric Diseases; Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology; Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affifiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, P.R. China
- Key Laboratory for Reproductive Medicine of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P.R. China
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Liu ZY, Liu F, Cao Y, Peng SL, Pan HW, Hong XQ, Zheng PF. ACSL1, CH25H, GPCPD1, and PLA2G12A as the potential lipid-related diagnostic biomarkers of acute myocardial infarction. Aging (Albany NY) 2023; 15:1394-1411. [PMID: 36863716 PMCID: PMC10042701 DOI: 10.18632/aging.204542] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 02/13/2023] [Indexed: 03/04/2023]
Abstract
Lipid metabolism plays an essential role in the genesis and progress of acute myocardial infarction (AMI). Herein, we identified and verified latent lipid-related genes involved in AMI by bioinformatic analysis. Lipid-related differentially expressed genes (DEGs) involved in AMI were identified using the GSE66360 dataset from the Gene Expression Omnibus (GEO) database and R software packages. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted to analyze lipid-related DEGs. Lipid-related genes were identified by two machine learning techniques: least absolute shrinkage and selection operator (LASSO) regression and support vector machine recursive feature elimination (SVM-RFE). The receiver operating characteristic (ROC) curves were used to descript diagnostic accuracy. Furthermore, blood samples were collected from AMI patients and healthy individuals, and real-time quantitative polymerase chain reaction (RT-qPCR) was used to determine the RNA levels of four lipid-related DEGs. Fifty lipid-related DEGs were identified, 28 upregulated and 22 downregulated. Several enrichment terms related to lipid metabolism were found by GO and KEGG enrichment analyses. After LASSO and SVM-RFE screening, four genes (ACSL1, CH25H, GPCPD1, and PLA2G12A) were identified as potential diagnostic biomarkers for AMI. Moreover, the RT-qPCR analysis indicated that the expression levels of four DEGs in AMI patients and healthy individuals were consistent with bioinformatics analysis results. The validation of clinical samples suggested that 4 lipid-related DEGs are expected to be diagnostic markers for AMI and provide new targets for lipid therapy of AMI.
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Affiliation(s)
- Zheng-Yu Liu
- Department of Cardiology, Hunan Provincial People's Hospital, Changsha 410000, China
- Department of Epidemiology, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), Changsha 410000, China
- Clinical Medicine Research Center of Heart Failure of Hunan Province, Changsha 410000, China
| | - Fen Liu
- Department of Epidemiology, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), Changsha 410000, China
- Clinical Medicine Research Center of Heart Failure of Hunan Province, Changsha 410000, China
- The First Affiliated Hospital of Hunan Normal University (Hunan Provincial People's Hospital), Changsha 410000, China
| | - Yan Cao
- Department of Epidemiology, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), Changsha 410000, China
- Clinical Medicine Research Center of Heart Failure of Hunan Province, Changsha 410000, China
- Department of Emergency, Hunan Provincial People's Hospital, Changsha 410000, China
| | - Shao-Liang Peng
- Department of Epidemiology, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), Changsha 410000, China
- Clinical Data Center, Hunan Provincial People's Hospital, Changsha 410000, China
| | - Hong-Wei Pan
- Department of Cardiology, Hunan Provincial People's Hospital, Changsha 410000, China
- Department of Epidemiology, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), Changsha 410000, China
- Clinical Medicine Research Center of Heart Failure of Hunan Province, Changsha 410000, China
| | - Xiu-Qin Hong
- Department of Epidemiology, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), Changsha 410000, China
- Clinical Medicine Research Center of Heart Failure of Hunan Province, Changsha 410000, China
- The First Affiliated Hospital of Hunan Normal University (Hunan Provincial People's Hospital), Changsha 410000, China
| | - Peng-Fei Zheng
- Department of Cardiology, Hunan Provincial People's Hospital, Changsha 410000, China
- Department of Epidemiology, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), Changsha 410000, China
- Clinical Medicine Research Center of Heart Failure of Hunan Province, Changsha 410000, China
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9
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He J, Li X. Identification and Validation of Aging-Related Genes in Idiopathic Pulmonary Fibrosis. Front Genet 2022; 13:780010. [PMID: 35211155 PMCID: PMC8863089 DOI: 10.3389/fgene.2022.780010] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 01/19/2022] [Indexed: 12/13/2022] Open
Abstract
Aging plays a significant role in the occurrence and development of idiopathic pulmonary fibrosis (IPF). In this study, we aimed to identify and verify potential aging-associated genes involved in IPF using bioinformatic analysis. The mRNA expression profile dataset GSE150910 available in the Gene Expression Omnibus (GEO) database and R software were used to identify the differentially expressed aging-related genes involved in IPF. Hub gene expression was validated by other GEO datasets. Gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed on differentially expressed aging-related genes. Subsequently, aging-related genes were further screened using three techniques (least absolute shrinkage and selection operator (LASSO) regression, support vector machine, and random forest), and the receiver operating characteristic curves were plotted based on screening results. Finally, real-time quantitative polymerase chain reaction (qRT-PCR) was performed to verify the RNA expression of the six differentially expressed aging-related genes using the blood samples of patients with IPF and healthy individuals. Sixteen differentially expressed aging-related genes were detected, of which the expression of 12 were upregulated and four were downregulated. GO and KEGG enrichment analyses indicated the presence of several enriched terms related to senescence and apoptotic mitochondrial changes. Further screening by LASSO regression, support vector machine, and random forest identified six genes (IGF1, RET, IGFBP2, CDKN2A, JUN, and TFAP2A) that could serve as potential diagnostic biomarkers for IPF. Furthermore, qRT-PCR analysis indicated that among the above-mentioned six aging-related genes, only the expression levels of IGF1, RET, and IGFBP2 in patients with IPF and healthy individuals were consistent with the results of bioinformatic analysis. In conclusion, bioinformatics analysis identified 16 potential aging-related genes associated with IPF, and clinical sample validation suggested that among these, IGF1, RET, and IGFBP2 might play a role in the incidence and prognosis of IPF. Our findings may help understand the pathogenesis of IPF.
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Affiliation(s)
- Jie He
- Clinical Medical College of Chengdu Medical College, Chengdu, China.,Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Xiaoyan Li
- Clinical Medical College of Chengdu Medical College, Chengdu, China.,Department of Endocrinology, The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
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10
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Yang YY, Gao ZX, Mao ZH, Liu DW, Liu ZS, Wu P. Identification of ULK1 as a novel mitophagy-related gene in diabetic nephropathy. Front Endocrinol (Lausanne) 2022; 13:1079465. [PMID: 36743936 PMCID: PMC9889542 DOI: 10.3389/fendo.2022.1079465] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 12/28/2022] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Accumulating evidence indicates that mitophagy is crucial for the development of diabetic nephropathy (DN). However, little is known about the key genes involved. The present study is to identify the potential mitophagy-related genes (MRGs) in DN. METHODS Five datasets were obtained from the Gene Expression Omnibus (GEO) database and were split into the training and validation set. Then the differentially expressed MRGs were screened and further analyzed for GO and KEGG enrichment. Next, three algorithms (SVM-RFE, LASSO and RF) were used to identify hub genes. The ROC curves were plotted based on the hub genes. We then used the CIBERSORT algorithm to assess the infiltration of 22 types of immune cells and explore the correlation between hub genes and immune cells. Finally, the Nephroseq V5 tool was used to analyze the correlation between hub genes and GFR in DN patients. RESULTS Compared with the tubulointerstitium, the expression of MRGs was more noticeably varied in the glomeruli. Twelve DE-MRGs were identified in glomerular samples, of which 11 genes were down-regulated and only MFN1 was up-regulated. GO and KEGG analysis indicated that several enrichment terms were associated with changes in autophagy. Three genes (MFN1, ULK1 and PARK2) were finally determined as potential hub genes by three algorithms. In the training set, the AUROC of MFN1, ULK1 and PARK2 were 0.839, 0.906 and 0.842. However, the results of the validation set demonstrated that MFN1 and PARK2 had no significant difference in distinguishing DN samples from healthy controls, while the AUROC of ULK1 was 0.894. Immune infiltration analysis using CIBERSORT showed that ULK1 was positively related to neutrophils, whereas negatively related to M1 and M2 macrophages. Finally, ULK1 was positively correlated with GFR in Nephroseq database. CONCLUSIONS ULK1 is a potential biomarker for DN and may influence the development of diabetic nephropathy by regulating mitophagy.
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Affiliation(s)
- Yuan-Yuan Yang
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Institute of Nephrology, Zhengzhou University, Zhengzhou, China
- Henan Province Research Center for Kidney Disease, Zhengzhou, China
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, China
| | - Zhong-Xiuzi Gao
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Institute of Nephrology, Zhengzhou University, Zhengzhou, China
- Henan Province Research Center for Kidney Disease, Zhengzhou, China
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, China
| | - Zi-Hui Mao
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Institute of Nephrology, Zhengzhou University, Zhengzhou, China
- Henan Province Research Center for Kidney Disease, Zhengzhou, China
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, China
| | - Dong-Wei Liu
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Institute of Nephrology, Zhengzhou University, Zhengzhou, China
- Henan Province Research Center for Kidney Disease, Zhengzhou, China
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, China
| | - Zhang-Suo Liu
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Institute of Nephrology, Zhengzhou University, Zhengzhou, China
- Henan Province Research Center for Kidney Disease, Zhengzhou, China
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, China
- *Correspondence: Peng Wu, ; Zhang-Suo Liu,
| | - Peng Wu
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Institute of Nephrology, Zhengzhou University, Zhengzhou, China
- Henan Province Research Center for Kidney Disease, Zhengzhou, China
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, China
- *Correspondence: Peng Wu, ; Zhang-Suo Liu,
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11
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Mufford MS, van der Meer D, Andreassen OA, Ramesar R, Stein DJ, Dalvie S. A review of systems biology research of anxiety disorders. ACTA ACUST UNITED AC 2021; 43:414-423. [PMID: 33053074 PMCID: PMC8352731 DOI: 10.1590/1516-4446-2020-1090] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 06/24/2020] [Indexed: 01/04/2023]
Abstract
The development of "omic" technologies and deep phenotyping may facilitate a systems biology approach to understanding anxiety disorders. Systems biology approaches incorporate data from multiple modalities (e.g., genomic, neuroimaging) with functional analyses (e.g., animal and tissue culture models) and mathematical modeling (e.g., machine learning) to investigate pathological biophysical networks at various scales. Here we review: i) the neurobiology of anxiety disorders; ii) how systems biology approaches have advanced this work; and iii) the clinical implications and future directions of this research. Systems biology approaches have provided an improved functional understanding of candidate biomarkers and have suggested future potential for refining the diagnosis, prognosis, and treatment of anxiety disorders. The systems biology approach for anxiety disorders is, however, in its infancy and in some instances is characterized by insufficient power and replication. The studies reviewed here represent important steps to further untangling the pathophysiology of anxiety disorders.
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Affiliation(s)
- Mary S Mufford
- South African Medical Research Council Genomic and Precision Medicine Research Unit, Division of Human Genetics, Institute of Infectious Disease and Molecular Medicine, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Dennis van der Meer
- Division of Mental Health and Addiction, Norwegian Centre for Mental Disorders Research (NORMENT), Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,School of Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, Netherlands
| | - Ole A Andreassen
- Division of Mental Health and Addiction, Norwegian Centre for Mental Disorders Research (NORMENT), Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Raj Ramesar
- South African Medical Research Council Genomic and Precision Medicine Research Unit, Division of Human Genetics, Institute of Infectious Disease and Molecular Medicine, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Dan J Stein
- South African Medical Research Council (SAMRC), Unit on Risk & Resilience in Mental Disorders, Department of Psychiatry and Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Shareefa Dalvie
- South African Medical Research Council (SAMRC), Unit on Risk & Resilience in Mental Disorders, Department of Psychiatry and Neuroscience Institute, University of Cape Town, Cape Town, South Africa
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12
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Tsai CH, Chen PC, Liu DS, Kuo YY, Hsieh TT, Chiang DL, Lai F, Wu CT. Panic attack prediction using wearable devices and machine learning: Development and cohort study (Preprint). JMIR Med Inform 2021; 10:e33063. [PMID: 35166679 PMCID: PMC8889475 DOI: 10.2196/33063] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/08/2021] [Accepted: 01/02/2022] [Indexed: 12/18/2022] Open
Abstract
Background A panic attack (PA) is an intense form of anxiety accompanied by multiple somatic presentations, leading to frequent emergency department visits and impairing the quality of life. A prediction model for PAs could help clinicians and patients monitor, control, and carry out early intervention for recurrent PAs, enabling more personalized treatment for panic disorder (PD). Objective This study aims to provide a 7-day PA prediction model and determine the relationship between a future PA and various features, including physiological factors, anxiety and depressive factors, and the air quality index (AQI). Methods We enrolled 59 participants with PD (Diagnostic and Statistical Manual of Mental Disorders, 5th edition, and the Mini International Neuropsychiatric Interview). Participants used smartwatches (Garmin Vívosmart 4) and mobile apps to collect their sleep, heart rate (HR), activity level, anxiety, and depression scores (Beck Depression Inventory [BDI], Beck Anxiety Inventory [BAI], State-Trait Anxiety Inventory state anxiety [STAI-S], State-Trait Anxiety Inventory trait anxiety [STAI-T], and Panic Disorder Severity Scale Self-Report) in their real life for a duration of 1 year. We also included AQIs from open data. To analyze these data, our team used 6 machine learning methods: random forests, decision trees, linear discriminant analysis, adaptive boosting, extreme gradient boosting, and regularized greedy forests. Results For 7-day PA predictions, the random forest produced the best prediction rate. Overall, the accuracy of the test set was 67.4%-81.3% for different machine learning algorithms. The most critical variables in the model were questionnaire and physiological features, such as the BAI, BDI, STAI, MINI, average HR, resting HR, and deep sleep duration. Conclusions It is possible to predict PAs using a combination of data from questionnaires and physiological and environmental data.
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Affiliation(s)
- Chan-Hen Tsai
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei City, Taiwan
- Department of Psychiatry, En Chu Kong Hospital, New Taipei City, Taiwan
| | - Pei-Chen Chen
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei City, Taiwan
| | - Ding-Shan Liu
- Department of Computer Science and Information Engineering, National Taiwan University, Taipei City, Taiwan
| | - Ying-Ying Kuo
- Department of Psychiatry, En Chu Kong Hospital, New Taipei City, Taiwan
| | - Tsung-Ting Hsieh
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei City, Taiwan
| | - Dai-Lun Chiang
- Financial Technology Applications Program, Ming Chuan University, Taoyuan City, Taiwan
| | - Feipei Lai
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei City, Taiwan
- Department of Computer Science and Information Engineering, National Taiwan University, Taipei City, Taiwan
| | - Chia-Tung Wu
- Department of Computer Science and Information Engineering, National Taiwan University, Taipei City, Taiwan
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13
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Lai CH. Biomarkers in Panic Disorder. CURRENT PSYCHIATRY RESEARCH AND REVIEWS 2021. [DOI: 10.2174/2666082216999200918163245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Panic disorder (PD) is a kind of anxiety disorder that impacts the life quality
and functional perspectives in patients. However, the pathophysiological study of PD seems still
inadequate and many unresolved issues need to be clarified.
Objectives:
In this review article of biomarkers in PD, the investigator will focus on the findings of
magnetic resonance imaging (MRI) of the brain in the pathophysiology study. The MRI biomarkers
would be divided into several categories, on the basis of structural and functional perspectives.
Methods:
The structural category would include the gray matter and white matter tract studies. The
functional category would consist of functional MRI (fMRI), resting-state fMRI (Rs-fMRI), and
magnetic resonance spectroscopy (MRS). The PD biomarkers revealed by the above methodologies
would be discussed in this article.
Results:
For the gray matter perspectives, the PD patients would have alterations in the volumes of
fear network structures, such as the amygdala, parahippocampal gyrus, thalamus, anterior cingulate
cortex, insula, and frontal regions. For the white matter tract studies, the PD patients seemed to have
alterations in the fasciculus linking the fear network regions, such as the anterior thalamic radiation,
uncinate fasciculus, fronto-occipital fasciculus, and superior longitudinal fasciculus. For the fMRI
studies in PD, the significant results also focused on the fear network regions, such as the amygdala,
hippocampus, thalamus, insula, and frontal regions. For the Rs-fMRI studies, PD patients seemed to
have alterations in the regions of the default mode network and fear network model. At last, the
MRS results showed alterations in neuron metabolites of the hippocampus, amygdala, occipital
cortex, and frontal regions.
Conclusion:
The MRI biomarkers in PD might be compatible with the extended fear network model
hypothesis in PD, which included the amygdala, hippocampus, thalamus, insula, frontal regions, and
sensory-related cortex.
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Affiliation(s)
- Chien-Han Lai
- Department of Psychiatry, Institute of Biophotonics, National Yang-Ming University, Taipei, Taiwan
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14
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Schwarzmeier H, Leehr EJ, Böhnlein J, Seeger FR, Roesmann K, Gathmann B, Herrmann MJ, Siminski N, Junghöfer M, Straube T, Grotegerd D, Dannlowski U. Theranostic markers for personalized therapy of spider phobia: Methods of a bicentric external cross-validation machine learning approach. Int J Methods Psychiatr Res 2020; 29:e1812. [PMID: 31814209 PMCID: PMC7301283 DOI: 10.1002/mpr.1812] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 09/18/2019] [Accepted: 10/08/2019] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVES Embedded in the Collaborative Research Center "Fear, Anxiety, Anxiety Disorders" (CRC-TRR58), this bicentric clinical study aims at identifying biobehavioral markers of treatment (non-)response by applying machine learning methodology with an external cross-validation protocol. We hypothesize that a priori prediction of treatment (non-)response is possible in a second, independent sample based on multimodal markers. METHODS One-session virtual reality exposure treatment (VRET) with patients with spider phobia was conducted on two sites. Clinical, neuroimaging, and genetic data were assessed at baseline, post-treatment and after 6 months. The primary and secondary outcomes defining treatment response are as follows: 30% reduction regarding the individual score in the Spider Phobia Questionnaire and 50% reduction regarding the individual distance in the behavioral avoidance test. RESULTS N = 204 patients have been included (n = 100 in Würzburg, n = 104 in Münster). Sample characteristics for both sites are comparable. DISCUSSION This study will offer cross-validated theranostic markers for predicting the individual success of exposure-based therapy. Findings will support clinical decision-making on personalized therapy, bridge the gap between basic and clinical research, and bring stratified therapy into reach. The study is registered at ClinicalTrials.gov (ID: NCT03208400).
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Affiliation(s)
- Hanna Schwarzmeier
- Department of Psychiatry, Psychosomatics, and Psychotherapy, Center for Mental HealthUniversity Hospital of WürzburgWürzburgGermany
| | | | - Joscha Böhnlein
- Department of Psychiatry and PsychotherapyUniversity of MünsterMünsterGermany
| | - Fabian Reinhard Seeger
- Department of Psychiatry, Psychosomatics, and Psychotherapy, Center for Mental HealthUniversity Hospital of WürzburgWürzburgGermany
| | - Kati Roesmann
- Institute for Biomagnetism and BiosignalanalysisUniversity of MünsterMünsterGermany
- Otto‐Creutzfeld Center for Cognitive and Behavioral NeuroscienceUniversity of MünsterMünsterGermany
| | - Bettina Gathmann
- Institute of Medical Psychology and Systems NeuroscienceUniversity of MünsterMünsterGermany
| | - Martin J. Herrmann
- Department of Psychiatry, Psychosomatics, and Psychotherapy, Center for Mental HealthUniversity Hospital of WürzburgWürzburgGermany
| | - Niklas Siminski
- Department of Psychiatry, Psychosomatics, and Psychotherapy, Center for Mental HealthUniversity Hospital of WürzburgWürzburgGermany
| | - Markus Junghöfer
- Institute for Biomagnetism and BiosignalanalysisUniversity of MünsterMünsterGermany
- Otto‐Creutzfeld Center for Cognitive and Behavioral NeuroscienceUniversity of MünsterMünsterGermany
| | - Thomas Straube
- Institute of Medical Psychology and Systems NeuroscienceUniversity of MünsterMünsterGermany
- Otto‐Creutzfeld Center for Cognitive and Behavioral NeuroscienceUniversity of MünsterMünsterGermany
| | - Dominik Grotegerd
- Department of Psychiatry and PsychotherapyUniversity of MünsterMünsterGermany
| | - Udo Dannlowski
- Department of Psychiatry and PsychotherapyUniversity of MünsterMünsterGermany
- Otto‐Creutzfeld Center for Cognitive and Behavioral NeuroscienceUniversity of MünsterMünsterGermany
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15
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Nguyen AH, Marsh P, Schmiess-Heine L, Burke PJ, Lee A, Lee J, Cao H. Cardiac tissue engineering: state-of-the-art methods and outlook. J Biol Eng 2019; 13:57. [PMID: 31297148 PMCID: PMC6599291 DOI: 10.1186/s13036-019-0185-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 06/03/2019] [Indexed: 12/17/2022] Open
Abstract
The purpose of this review is to assess the state-of-the-art fabrication methods, advances in genome editing, and the use of machine learning to shape the prospective growth in cardiac tissue engineering. Those interdisciplinary emerging innovations would move forward basic research in this field and their clinical applications. The long-entrenched challenges in this field could be addressed by novel 3-dimensional (3D) scaffold substrates for cardiomyocyte (CM) growth and maturation. Stem cell-based therapy through genome editing techniques can repair gene mutation, control better maturation of CMs or even reveal its molecular clock. Finally, machine learning and precision control for improvements of the construct fabrication process and optimization in tissue-specific clonal selections with an outlook of cardiac tissue engineering are also presented.
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Affiliation(s)
- Anh H. Nguyen
- Electrical and Computer Engineering Department, University of Alberta, Edmonton, Alberta Canada
- Electrical Engineering and Computer Science Department, University of California Irvine, Irvine, CA USA
| | - Paul Marsh
- Electrical Engineering and Computer Science Department, University of California Irvine, Irvine, CA USA
| | - Lauren Schmiess-Heine
- Electrical Engineering and Computer Science Department, University of California Irvine, Irvine, CA USA
| | - Peter J. Burke
- Electrical Engineering and Computer Science Department, University of California Irvine, Irvine, CA USA
- Biomedical Engineering Department, University of California Irvine, Irvine, CA USA
- Chemical Engineering and Materials Science Department, University of California Irvine, Irvine, CA USA
| | - Abraham Lee
- Biomedical Engineering Department, University of California Irvine, Irvine, CA USA
- Mechanical and Aerospace Engineering Department, University of California Irvine, Irvine, CA USA
| | - Juhyun Lee
- Bioengineering Department, University of Texas at Arlington, Arlington, TX USA
| | - Hung Cao
- Electrical Engineering and Computer Science Department, University of California Irvine, Irvine, CA USA
- Biomedical Engineering Department, University of California Irvine, Irvine, CA USA
- Henry Samueli School of Engineering, University of California, Irvine, USA
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16
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Ebert DD, Harrer M, Apolinário-Hagen J, Baumeister H. Digital Interventions for Mental Disorders: Key Features, Efficacy, and Potential for Artificial Intelligence Applications. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1192:583-627. [PMID: 31705515 DOI: 10.1007/978-981-32-9721-0_29] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Mental disorders are highly prevalent and often remain untreated. Many limitations of conventional face-to-face psychological interventions could potentially be overcome through Internet-based and mobile-based interventions (IMIs). This chapter introduces core features of IMIs, describes areas of application, presents evidence on the efficacy of IMIs as well as potential effect mechanisms, and delineates how Artificial Intelligence combined with IMIs may improve current practices in the prevention and treatment of mental disorders in adults. Meta-analyses of randomized controlled trials clearly show that therapist-guided IMIs can be highly effective for a broad range of mental health problems. Whether the effects of unguided IMIs are also clinically relevant, particularly under routine care conditions, is less clear. First studies on IMIs for the prevention of mental disorders have shown promising results. Despite limitations and challenges, IMIs are increasingly implemented into routine care worldwide. IMIs are also well suited for applications of Artificial Intelligence and Machine Learning, which provides ample opportunities to improve the identification and treatment of mental disorders. Together with methodological innovations, these approaches may also deepen our understanding of how psychological interventions work, and why. Ethical and professional restraints as well as potential contraindications of IMIs, however, should also be considered. In sum, IMIs have a high potential for improving the prevention and treatment of mental health disorders across various indications, settings, and populations. Therefore, implementing IMIs into routine care as both adjunct and alternative to face-to-face treatment is highly desirable. Technological advancements may further enhance the variability and flexibility of IMIs, and thus even further increase their impact in people's lives in the future.
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Affiliation(s)
- David Daniel Ebert
- Department of Clinical Psychology, Vrije Universiteit Amsterdam, Van der Boechorststraat 1, 1881 BT, Amsterdam, The Netherlands.
| | - Mathias Harrer
- Clinical Psychology and Psychotherapy, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | | | - Harald Baumeister
- Clinical Psychology and Psychotherapy, University of Ulm, Ulm, Germany
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17
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Khalsa SS, Adolphs R, Cameron OG, Critchley HD, Davenport PW, Feinstein JS, Feusner JD, Garfinkel SN, Lane RD, Mehling WE, Meuret AE, Nemeroff CB, Oppenheimer S, Petzschner FH, Pollatos O, Rhudy JL, Schramm LP, Simmons WK, Stein MB, Stephan KE, Van den Bergh O, Van Diest I, von Leupoldt A, Paulus MP. Interoception and Mental Health: A Roadmap. BIOLOGICAL PSYCHIATRY. COGNITIVE NEUROSCIENCE AND NEUROIMAGING 2018; 3:501-513. [PMID: 29884281 PMCID: PMC6054486 DOI: 10.1016/j.bpsc.2017.12.004] [Citation(s) in RCA: 445] [Impact Index Per Article: 63.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/20/2017] [Accepted: 12/10/2017] [Indexed: 12/29/2022]
Abstract
Interoception refers to the process by which the nervous system senses, interprets, and integrates signals originating from within the body, providing a moment-by-moment mapping of the body's internal landscape across conscious and unconscious levels. Interoceptive signaling has been considered a component process of reflexes, urges, feelings, drives, adaptive responses, and cognitive and emotional experiences, highlighting its contributions to the maintenance of homeostatic functioning, body regulation, and survival. Dysfunction of interoception is increasingly recognized as an important component of different mental health conditions, including anxiety disorders, mood disorders, eating disorders, addictive disorders, and somatic symptom disorders. However, a number of conceptual and methodological challenges have made it difficult for interoceptive constructs to be broadly applied in mental health research and treatment settings. In November 2016, the Laureate Institute for Brain Research organized the first Interoception Summit, a gathering of interoception experts from around the world, with the goal of accelerating progress in understanding the role of interoception in mental health. The discussions at the meeting were organized around four themes: interoceptive assessment, interoceptive integration, interoceptive psychopathology, and the generation of a roadmap that could serve as a guide for future endeavors. This review article presents an overview of the emerging consensus generated by the meeting.
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Affiliation(s)
- Sahib S Khalsa
- Laureate Institute for Brain Research, University of Tulsa, Tulsa, Oklahoma; Oxley College of Health Sciences, University of Tulsa, Tulsa, Oklahoma.
| | - Ralph Adolphs
- California Institute of Technology, Pasadena, California
| | - Oliver G Cameron
- Department of Psychiatry, University of Michigan, Ann Arbor, Michigan
| | - Hugo D Critchley
- Sackler Centre for Consciousness Science, University of Sussex, Brighton, United Kingdom
| | - Paul W Davenport
- Department of Physiology, University of Florida, Gainesville, Florida
| | - Justin S Feinstein
- Laureate Institute for Brain Research, University of Tulsa, Tulsa, Oklahoma; Oxley College of Health Sciences, University of Tulsa, Tulsa, Oklahoma
| | - Jamie D Feusner
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, California
| | - Sarah N Garfinkel
- Sackler Centre for Consciousness Science, University of Sussex, Brighton, United Kingdom
| | - Richard D Lane
- Department of Psychiatry, University of Arizona, Tucson, Arizona
| | - Wolf E Mehling
- Department of Family and Community Medicine, University of California, San Francisco, San Francisco, California
| | - Alicia E Meuret
- Department of Psychology, Southern Methodist University, Dallas, Texas
| | - Charles B Nemeroff
- Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, Florida
| | | | - Frederike H Petzschner
- Translational Neuromodeling Unit, Institute for Biomedical Engineering, University of Zurich, Zurich, Switzerland
| | - Olga Pollatos
- Department of Clinical and Health Psychology, Institute of Psychology and Education, Ulm University, Ulm, Germany
| | - Jamie L Rhudy
- Department of Psychology, University of Tulsa, Tulsa, Oklahoma
| | - Lawrence P Schramm
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland; Department of Neuroscience, Johns Hopkins University, Baltimore, Maryland
| | - W Kyle Simmons
- Laureate Institute for Brain Research, University of Tulsa, Tulsa, Oklahoma; Oxley College of Health Sciences, University of Tulsa, Tulsa, Oklahoma
| | - Murray B Stein
- Department of Psychiatry, University of California, San Diego, San Diego, California
| | - Klaas E Stephan
- Translational Neuromodeling Unit, Institute for Biomedical Engineering, University of Zurich, Zurich, Switzerland
| | | | - Ilse Van Diest
- Department of Health Psychology, University of Leuven, Leuven, Belgium
| | | | - Martin P Paulus
- Laureate Institute for Brain Research, University of Tulsa, Tulsa, Oklahoma
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