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Zhu Y, Chen Y, Xu J, Zu Y. Unveiling the Potential of Migrasomes: A Machine-Learning-Driven Signature for Diagnosing Acute Myocardial Infarction. Biomedicines 2024; 12:1626. [PMID: 39062199 PMCID: PMC11274667 DOI: 10.3390/biomedicines12071626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 07/16/2024] [Accepted: 07/19/2024] [Indexed: 07/28/2024] Open
Abstract
BACKGROUND Recent studies have demonstrated that the migrasome, a newly functional extracellular vesicle, is potentially significant in the occurrence, progression, and diagnosis of cardiovascular diseases. Nonetheless, its diagnostic significance and biological mechanism in acute myocardial infarction (AMI) have yet to be fully explored. METHODS To remedy this gap, we employed an integrative machine learning (ML) framework composed of 113 ML combinations within five independent AMI cohorts to establish a predictive migrasome-related signature (MS). To further elucidate the biological mechanism underlying MS, we implemented single-cell RNA sequencing (scRNA-seq) of cardiac Cd45+ cells from AMI-induced mice. Ultimately, we conducted mendelian randomization (MR) and molecular docking to unveil the therapeutic effectiveness of MS. RESULTS MS demonstrated robust predictive performance and superior generalization, driven by the optimal combination of Stepglm and Lasso, on the expression of nine migrasome genes (BMP1, ITGB1, NDST1, TSPAN1, TSPAN18, TSPAN2, TSPAN4, TSPAN7, TSPAN9, and WNT8A). Notably, ITGB1 was found to be predominantly expressed in cardiac macrophages in AMI-induced mice, mechanically regulating macrophage transformation between anti-inflammatory and pro-inflammatory. Furthermore, we showed a positive causality between genetic predisposition towards ITGB1 expression and AMI risk, positioning it as a causative gene. Finally, we showed that ginsenoside Rh1, which interacts closely with ITGB1, could represent a novel therapeutic approach for repressing ITGB1. CONCLUSIONS Our MS has implications in forecasting and curving AMI to inform future diagnostic and therapeutic strategies for AMI.
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Affiliation(s)
- Yihao Zhu
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 201306, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Yuxi Chen
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 201306, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Jiajin Xu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China
| | - Yao Zu
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 201306, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
- Marine Biomedical Science and Technology Innovation Platform of Lin-Gang Special Area, Shanghai 201306, China
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Zhu Y, Chen Y, Zu Y. Leveraging a neutrophil-derived PCD signature to predict and stratify patients with acute myocardial infarction: from AI prediction to biological interpretation. J Transl Med 2024; 22:612. [PMID: 38956669 PMCID: PMC11221097 DOI: 10.1186/s12967-024-05415-0] [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: 12/11/2023] [Accepted: 06/19/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND Programmed cell death (PCD) has recently been implicated in modulating the removal of neutrophils recruited in acute myocardial infarction (AMI). Nonetheless, the clinical significance and biological mechanism of neutrophil-related PCD remain unexplored. METHODS We employed an integrative machine learning-based computational framework to generate a predictive neutrophil-derived PCD signature (NPCDS) within five independent microarray cohorts from the peripheral blood of AMI patients. Non-negative matrix factorization was leveraged to develop an NPCDS-based AMI subtype. To elucidate the biological mechanism underlying NPCDS, we implemented single-cell transcriptomics on Cd45+ cells isolated from the murine heart of experimental AMI. We finally conducted a Mendelian randomization (MR) study and molecular docking to investigate the therapeutic value of NPCDS on AMI. RESULTS We reported the robust and superior performance of NPCDS in AMI prediction, which contributed to an optimal combination of random forest and stepwise regression fitted on nine neutrophil-related PCD genes (MDM2, PTK2B, MYH9, IVNS1ABP, MAPK14, GNS, MYD88, TLR2, CFLAR). Two divergent NPCDS-based subtypes of AMI were revealed, in which subtype 1 was characterized as inflammation-activated with more vibrant neutrophil activities, whereas subtype 2 demonstrated the opposite. Mechanically, we unveiled the expression dynamics of NPCDS to regulate neutrophil transformation from a pro-inflammatory phase to an anti-inflammatory phase in AMI. We uncovered a significant causal association between genetic predisposition towards MDM2 expression and the risk of AMI. We also found that lidoflazine, isotetrandrine, and cepharanthine could stably target MDM2. CONCLUSION Altogether, NPCDS offers significant implications for prediction, stratification, and therapeutic management for AMI.
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Affiliation(s)
- Yihao Zhu
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, People's Republic of China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, People's Republic of China
| | - Yuxi Chen
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, People's Republic of China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, People's Republic of China
| | - Yao Zu
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, People's Republic of China.
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, People's Republic of China.
- Marine Biomedical Science and Technology Innovation Platform of Lin-Gang Special Area, Shanghai, 201306, People's Republic of China.
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Li F, Bai W, Zhang Y, Zhang Z, Zhang D, Shen N, Yuan J, Zhao G, Wang X. Construction of an economical xylose-utilizing Saccharomyces cerevisiae and its ethanol fermentation. FEMS Yeast Res 2024; 24:foae001. [PMID: 38268490 PMCID: PMC10855017 DOI: 10.1093/femsyr/foae001] [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: 03/05/2023] [Revised: 01/03/2024] [Accepted: 01/23/2024] [Indexed: 01/26/2024] Open
Abstract
Traditional industrial Saccharomyces cerevisiae could not metabolize xylose due to the lack of a specific enzyme system for the reaction from xylose to xylulose. This study aims to metabolically remould industrial S. cerevisiae for the purpose of utilizing both glucose and xylose with high efficiency. Heterologous gene xylA from Piromyces and homologous genes related to xylose utilization were selected to construct expression cassettes and integrated into genome. The engineered strain was domesticated with industrial material under optimizing conditions subsequently to further improve xylose utilization rates. The resulting S. cerevisiae strain ABX0928-0630 exhibits a rapid growth rate and possesses near 100% xylose utilization efficiency to produce ethanol with industrial material. Pilot-scale fermentation indicated the predominant feature of ABX0928-0630 for industrial application, with ethanol yield of 0.48 g/g sugars after 48 hours and volumetric xylose consumption rate of 0.87 g/l/h during the first 24 hours. Transcriptome analysis during the modification and domestication process revealed a significant increase in the expression level of pathways associated with sugar metabolism and sugar sensing. Meanwhile, genes related to glycerol lipid metabolism exhibited a pattern of initial increase followed by a subsequent decrease, providing a valuable reference for the construction of efficient xylose-fermenting strains.
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Affiliation(s)
- Fan Li
- Nutrition and Health Research Institute, COFCO Corporation, No. 4 Road, South District, Beiqijia Town, Changping District, Beijing 102209, China
- COFCO Biochemical and Bioenergy (Zhaodong) Co., Ltd., No. 24, Zhaolan Road, Zhaodong City, Suihua, Heilongjiang 151100, China
- COFCO Corporation, COFCO Fortune Plaza, No.8, Chao Yang Men South St., Chao Yang District, Beijing 100020, China
| | - Wenxin Bai
- Nutrition and Health Research Institute, COFCO Corporation, No. 4 Road, South District, Beiqijia Town, Changping District, Beijing 102209, China
| | - Yuan Zhang
- Nutrition and Health Research Institute, COFCO Corporation, No. 4 Road, South District, Beiqijia Town, Changping District, Beijing 102209, China
- COFCO Corporation, COFCO Fortune Plaza, No.8, Chao Yang Men South St., Chao Yang District, Beijing 100020, China
| | - Zijian Zhang
- Nutrition and Health Research Institute, COFCO Corporation, No. 4 Road, South District, Beiqijia Town, Changping District, Beijing 102209, China
| | - Deguo Zhang
- COFCO Corporation, COFCO Fortune Plaza, No.8, Chao Yang Men South St., Chao Yang District, Beijing 100020, China
- COFCO Biotechnology Co., Ltd., No. 1, Zhongliang Avenue, Yuhui District, Bengbu, Anhui 233010, China
| | - Naidong Shen
- Nutrition and Health Research Institute, COFCO Corporation, No. 4 Road, South District, Beiqijia Town, Changping District, Beijing 102209, China
- COFCO Corporation, COFCO Fortune Plaza, No.8, Chao Yang Men South St., Chao Yang District, Beijing 100020, China
| | - Jingwei Yuan
- COFCO Biochemical and Bioenergy (Zhaodong) Co., Ltd., No. 24, Zhaolan Road, Zhaodong City, Suihua, Heilongjiang 151100, China
- COFCO Corporation, COFCO Fortune Plaza, No.8, Chao Yang Men South St., Chao Yang District, Beijing 100020, China
| | - Guomiao Zhao
- Nutrition and Health Research Institute, COFCO Corporation, No. 4 Road, South District, Beiqijia Town, Changping District, Beijing 102209, China
- COFCO Corporation, COFCO Fortune Plaza, No.8, Chao Yang Men South St., Chao Yang District, Beijing 100020, China
| | - Xiaoyan Wang
- Nutrition and Health Research Institute, COFCO Corporation, No. 4 Road, South District, Beiqijia Town, Changping District, Beijing 102209, China
- COFCO Corporation, COFCO Fortune Plaza, No.8, Chao Yang Men South St., Chao Yang District, Beijing 100020, China
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