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Qin X, Liu J. Nanoformulations for the diagnosis and treatment of metabolic dysfunction-associated steatohepatitis. Acta Biomater 2024:S1742-7061(24)00326-X. [PMID: 38879104 DOI: 10.1016/j.actbio.2024.06.014] [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: 12/30/2023] [Revised: 05/25/2024] [Accepted: 06/10/2024] [Indexed: 06/29/2024]
Abstract
Metabolic dysfunction-associated steatohepatitis (MASH) is a progressive phase of metabolic dysfunction-associated steatotic liver disease (MASLD) that develops into irreversible liver cirrhosis and hepatocellular carcinoma, ultimately necessitating liver transplantation as the sole life-saving option. However, given the drawbacks of liver transplantation, including invasiveness, chronic immunosuppression, and a lack of donor livers, prompt diagnosis and effective treatment are indispensable. Due to the limitations of liver biopsy and conventional imaging modalities in diagnosing MASH, as well as the potential hazards associated with liver-protecting medicines, numerous nanoformulations have been created for MASH theranostics. Particularly, there has been significant study interest in artificial nanoparticles, natural biomaterials, and bionic nanoparticles that exhibit exceptional biocompatibility and bioavailability. In this review, we summarized extracellular vesicles (EVs)-based omics analysis and Fe3O4-based functional magnetic nanoparticles as magnetic resonance imaging (MRI) contrast agents for MASH diagnosis. Additionally, artificial nanoparticles such as organic and inorganic nanoparticles, as well as natural biomaterials such as cells and cell-derived EVs and bionic nanoparticles including cell membrane-coated nanoparticles, have also been reported for MASH treatment owing to their specific targeting and superior therapeutic effect. This review has the potential to stimulate advancements in nanoformulation fabrication techniques. By exploring their compatibility with cell biology, it could lead to the creation of innovative material systems for efficient theragnostic uses for MASH. STATEMENT OF SIGNIFICANCE: People with metabolic dysfunction-associated steatohepatitis (MASH) will progress to fibrosis, cirrhosis, or even liver cancer. It is imperative to establish effective theragnostic techniques to stop MASH from progressing into a lethal condition. In our review, we summarize the advancement of artificial, natural, and bionic nanoparticles applied in MASH theragnosis. Furthermore, the issues that need to be resolved for these cutting-edge techniques are summarized to realize a more significant clinical impact. We forecast the key fields that will advance further as nanotechnology and MASH research progress. Generally, our discovery has significant implications for the advancement of nanoformulation fabrication techniques, and their potential to be compatible with cell biology could lead to the creation of innovative materials systems for effective MASH theragnostic.
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Affiliation(s)
- Xueying Qin
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225001, PR China; The Key Laboratory of Syndrome Differentiation and Treatment of Gastric Cancer of the State Administration of Traditional Chinese Medicine, Yangzhou, 225001, PR China
| | - Jingjing Liu
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225001, PR China; The Key Laboratory of Syndrome Differentiation and Treatment of Gastric Cancer of the State Administration of Traditional Chinese Medicine, Yangzhou, 225001, PR China.
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2
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Ding T, He W, Yan H, Wei Z, Zeng X, Hao X. Metabolic profiling in tissues and urine of patients with prostatic lesions and the diagnostic value of urine extracellular vesicles metabolites in prostate cancer. Clin Chim Acta 2024; 556:117845. [PMID: 38403146 DOI: 10.1016/j.cca.2024.117845] [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: 09/17/2023] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 02/27/2024]
Abstract
BACKGROUND Prostate cancer (PCa) lacks convenient and highly specific diagnostic markers. Although the value of extracellular vesicles (EV) in oncology is widely recognized, the diagnostic value of EV metabolites requires further exploration. This study aimed to explore the diagnostic value of urine EV (u-EV) metabolomics in PCa. METHODS We first detected metabolites in paired tissues cells (cells), tissue EV (t-EVs), u-EVs, and urine samples in cohort 1 (8 PCa vs. 5 benign prostatic hypertrophy, BPH) to prob the feasibility of EV metabolites as diagnostic markers. We then analyzed the value of u-EVs as markers for PCa diagnosis and typing in the expanded sample cohort (60 PCa vs. 40 BPH). RESULTS U-EV metabolites were more consistent with those in tissue-derived samples (cells and t-EVs) than those in urine, and more differential metabolites between BPH and PCa were identified in u-EV. Subsequently, we used a random forest model to construct a panel of six metabolites for PCa, which showed an area under the curve (AUC) of 0.833 in training cohort and 0.844 in validation cohort. We also found significantly differentially expressed metabolites between PCa subtypes (Gleason ≤ 7 vs. Gleason > 7 and localized vs. metastasis), demonstrating the value of EV metabolites in PCa typing and prognostic assessment. CONCLUSION Metabolomic analysis of u-EVs is a promising source of noninvasive markers for PCa diagnosis.
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Affiliation(s)
- Ting Ding
- Department of Clinical Laboratory Medicine, Xijing Hospital, Fourth Military Medical University (Air Force Medical University), Xi'an, China; School of Medicine, Northwest University, Xi'an, China
| | - Weixiang He
- Department of Urology, Xijing Hospital, Fourth Military Medical University (Air Force Medical University), Xi'an, China
| | - Hua Yan
- The National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, China
| | - Zhen Wei
- School of Medicine, Northwest University, Xi'an, China; Shanxi Lifegen Co., Ltd., Xi'an, China
| | - Xianfei Zeng
- School of Medicine, Northwest University, Xi'an, China; Shanxi Lifegen Co., Ltd., Xi'an, China.
| | - Xiaoke Hao
- Department of Clinical Laboratory Medicine, Xijing Hospital, Fourth Military Medical University (Air Force Medical University), Xi'an, China; School of Medicine, Northwest University, Xi'an, China.
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3
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Sun M, Zhang H, Liu J, Chen J, Cui Y, Wang S, Zhang X, Yang Z. Extracellular Vesicles: A New Star for Gene Drug Delivery. Int J Nanomedicine 2024; 19:2241-2264. [PMID: 38465204 PMCID: PMC10924919 DOI: 10.2147/ijn.s446224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/20/2024] [Indexed: 03/12/2024] Open
Abstract
Recently, gene therapy has become a subject of considerable research and has been widely evaluated in various disease models. Though it is considered as a stand-alone agent for COVID-19 vaccination, gene therapy is still suffering from the following drawbacks during its translation from the bench to the bedside: the high sensitivity of exogenous nucleic acids to enzymatic degradation; the severe side effects induced either by exogenous nucleic acids or components in the formulation; and the difficulty to cross the barriers before reaching the therapeutic target. Therefore, for the successful application of gene therapy, a safe and reliable transport vector is urgently needed. Extracellular vesicles (EVs) are the ideal candidate for the delivery of gene drugs owing to their low immunogenicity, good biocompatibility and low toxicity. To better understand the properties of EVs and their advantages as gene drug delivery vehicles, this review covers from the origin of EVs to the methods of EVs generation, as well as the common methods of isolation and purification in research, with their pros and cons discussed. Meanwhile, the engineering of EVs for gene drugs is also highlighted. In addition, this paper also presents the progress in the EVs-mediated delivery of microRNAs, small interfering RNAs, messenger RNAs, plasmids, and antisense oligonucleotides. We believe this review will provide a theoretical basis for the development of gene drugs.
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Affiliation(s)
- Man Sun
- School of Life Sciences, Jilin University, Changchun, 130012, People’s Republic of China
| | - Huan Zhang
- School of Life Sciences, Jilin University, Changchun, 130012, People’s Republic of China
| | - Jiayi Liu
- School of Life Sciences, Jilin University, Changchun, 130012, People’s Republic of China
| | - Jiayi Chen
- School of Life Sciences, Jilin University, Changchun, 130012, People’s Republic of China
| | - Yaxin Cui
- School of Life Sciences, Jilin University, Changchun, 130012, People’s Republic of China
| | - Simiao Wang
- School of Life Sciences, Jilin University, Changchun, 130012, People’s Republic of China
| | - Xiangyu Zhang
- Department of General Surgery, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, 310020, People’s Republic of China
| | - Zhaogang Yang
- School of Life Sciences, Jilin University, Changchun, 130012, People’s Republic of China
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4
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Ni F, Zhu Q, Li H, Liu F, Chen H. Efficient preparation of high-purity and intact mesenchymal stem cell-derived extracellular vesicles. Anal Bioanal Chem 2024; 416:1797-1808. [PMID: 38355844 DOI: 10.1007/s00216-024-05193-0] [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: 10/20/2023] [Revised: 01/09/2024] [Accepted: 02/01/2024] [Indexed: 02/16/2024]
Abstract
Mesenchymal stem cell-derived extracellular vesicles (MSC-EVs) have shown great promise for regeneration and immunomodulation. However, efficient and scalable methods for their preparation are still lacking. In this study, we present the adoption of a label-free technique known as "EXODUS" to isolate and purify MSC-EVs from the conditioned medium. Our findings indicate that EXODUS can rapidly isolate EVs from 10 mL of conditioned medium with a 5-fold higher yield compared to conventional approaches, including ultracentrifugation (UC) and polyethylene glycol precipitation (PEG) methods. Additionally, pre-storing the conditioned medium at 4°C for 1 week resulted in a ~2-fold higher yield of MSC-EVs compared to the freshly prepared medium. However, storing the purified EV particles at 4°C for 1 month led to a 2-fold reduction in particle concentration. Furthermore, we found that MSC-EVs isolated using EXODUS exhibit higher expression levels of EV markers such as Alix, Flotillin1, CD81, and TSG101 in comparison to PEG and UC methods. We also discovered that MSC-EVs isolated using EXODUS are enriched in response to cytokine, collagen-containing extracellular matrix, and calcium ion binding compared to PEG method and enriched in extracellular structure organization, extracellular matrix, and extracellular matrix structure constituents compared to UC. Finally, we demonstrated that MSC-EVs isolated using EXODUS exhibit greater potential in animal organ development, tissue development, and anatomical structure morphogenesis compared to the UC. These findings suggest that EXODUS is a suitable method for the large-scale preparation of high-quality MSC-EVs for various clinical applications.
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Affiliation(s)
- Fangfang Ni
- National Engineering Technology Research Center for Ophthalmology and Optometry, School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Qingfu Zhu
- National Engineering Technology Research Center for Ophthalmology and Optometry, School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Hengrui Li
- National Engineering Technology Research Center for Ophthalmology and Optometry, School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Fei Liu
- National Engineering Technology Research Center for Ophthalmology and Optometry, School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China.
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
| | - Hao Chen
- National Engineering Technology Research Center for Ophthalmology and Optometry, School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China.
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Zheng TL, Sha JC, Deng Q, Geng S, Xiao SY, Yang WJ, Byrne CD, Targher G, Li YY, Wang XX, Wu D, Zheng MH. Object detection: A novel AI technology for the diagnosis of hepatocyte ballooning. Liver Int 2024; 44:330-343. [PMID: 38014574 DOI: 10.1111/liv.15799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/02/2023] [Accepted: 11/12/2023] [Indexed: 11/29/2023]
Abstract
Metabolic dysfunction-associated fatty liver disease (MAFLD) has reached epidemic proportions worldwide and is the most frequent cause of chronic liver disease in developed countries. Within the spectrum of liver disease in MAFLD, steatohepatitis is a progressive form of liver disease and hepatocyte ballooning (HB) is a cardinal pathological feature of steatohepatitis. The accurate and reproducible diagnosis of HB is therefore critical for the early detection and treatment of steatohepatitis. Currently, a diagnosis of HB relies on pathological examination by expert pathologists, which may be a time-consuming and subjective process. Hence, there has been interest in developing automated methods for diagnosing HB. This narrative review briefly discusses the development of artificial intelligence (AI) technology for diagnosing fatty liver disease pathology over the last 30 years and provides an overview of the current research status of AI algorithms for the identification of HB, including published articles on traditional machine learning algorithms and deep learning algorithms. This narrative review also provides a summary of object detection algorithms, including the principles, historical developments, and applications in the medical image analysis. The potential benefits of object detection algorithms for HB diagnosis (specifically those combined with a transformer architecture) are discussed, along with the future directions of object detection algorithms in HB diagnosis and the potential applications of generative AI on transformer architecture in this field. In conclusion, object detection algorithms have huge potential for the identification of HB and could make the diagnosis of MAFLD more accurate and efficient in the near future.
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Affiliation(s)
- Tian-Lei Zheng
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China
- Artificial Intelligence Unit, Department of Medical Equipment Management, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Jun-Cheng Sha
- Department of Interventional Radiology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Qian Deng
- Department of Histopathology, Ningbo Clinical Pathology Diagnosis Center, Ningbo, China
| | - Shi Geng
- Artificial Intelligence Unit, Department of Medical Equipment Management, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Shu-Yuan Xiao
- Department of Pathology, University of Chicago Medicine, Chicago, Illinois, USA
| | - Wen-Jun Yang
- Department of Pathology, the Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Christopher D Byrne
- Southampton National Institute for Health and Care Research Biomedical Research Centre, University Hospital Southampton, Southampton General Hospital, and University of Southampton, Southampton, UK
| | - Giovanni Targher
- Department of Medicine, University of Verona, Verona, Italy
- IRCSS Sacro Cuore - Don Calabria Hospital, Negrar di Valpolicella, Italy
| | - Yang-Yang Li
- Department of Pathology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiang-Xue Wang
- Institute for AI in Medicine, School of Artificial Intelligence, Nanjing University of Information Science and Technology, Nanjing, China
| | - Di Wu
- Department of Pathology, Xuzhou Central Hospital, Xuzhou, China
| | - Ming-Hua Zheng
- MAFLD Research Center, Department of Hepatology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Institute of Hepatology, Wenzhou Medical University, Wenzhou, China
- Key Laboratory of Diagnosis and Treatment for the Development of Chronic Liver Disease in Zhejiang Province, Wenzhou, China
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Wei R, Teng Y, Han C, Wei S, Li L, Liu H, Hu S, Kang B, Xu H. Multi-omics reveals goose fatty liver formation from metabolic reprogramming. Front Vet Sci 2024; 11:1122904. [PMID: 38348107 PMCID: PMC10859500 DOI: 10.3389/fvets.2024.1122904] [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: 12/14/2022] [Accepted: 01/08/2024] [Indexed: 02/15/2024] Open
Abstract
To comprehensively provide insight into goose fatty liver formation, we performed an integrative analysis of the liver transcriptome, lipidome, and amino acid metabolome, as well as peripheral adipose tissue transcriptome analysis using samples collected from the overfed geese and normally fed geese. Transcriptome analysis showed that liver metabolism pathways were mainly enriched in glucolipid metabolism, amino acid metabolism, inflammation response, and cell cycle; peripheral adipose tissue and the liver cooperatively regulated liver lipid accumulation during overfeeding. Liver lipidome patterns obviously changed after overfeeding, and 157 different lipids were yielded. In the liver amino acid metabolome, the level of Lys increased after overfeeding. In summary, this is the first study describing goose fatty liver formation from an integrative analysis of transcriptome, lipidome, and amino acid metabolome, which will provide a whole new dimension to understanding the mechanism of goose fatty liver formation.
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Affiliation(s)
- Rongxue Wei
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yongqiang Teng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Chunchun Han
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Shouhai Wei
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Liang Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Hehe Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Shenqiang Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Bo Kang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Hengyong Xu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
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Jang HJ, Shim KS, Lee J, Park JH, Kang SJ, Shin YM, Lee JB, Baek W, Yoon JK. Engineering of Cell Derived-Nanovesicle as an Alternative to Exosome Therapy. Tissue Eng Regen Med 2024; 21:1-19. [PMID: 38066355 PMCID: PMC10764700 DOI: 10.1007/s13770-023-00610-4] [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: 10/04/2023] [Revised: 10/24/2023] [Accepted: 10/27/2023] [Indexed: 01/04/2024] Open
Abstract
BACKGROUND Exosomes, nano-sized vesicles ranging between 30 and 150 nm secreted by human cells, play a pivotal role in long-range intercellular communication and have attracted significant attention in the field of regenerative medicine. Nevertheless, their limited productivity and cost-effectiveness pose challenges for clinical applications. These issues have recently been addressed by cell-derived nanovesicles (CDNs), which are physically synthesized exosome-mimetic nanovesicles from parent cells, as a promising alternative to exosomes. CDNs exhibit structural, physical, and biological properties similar to exosomes, containing intracellular protein and genetic components encapsulated by the cell plasma membrane. These characteristics allow CDNs to be used as regenerative medicine and therapeutics on their own, or as a drug delivery system. METHODS The paper reviews diverse methods for CDN synthesis, current analysis techniques, and presents engineering strategies to improve lesion targeting efficiency and/or therapeutic efficacy. RESULTS CDNs, with their properties similar to those of exosomes, offer a cost-effective and highly productive alternative due to their non-living biomaterial nature, nano-size, and readiness for use, allowing them to overcome several limitations of conventional cell therapy methods. CONCLUSION Ongoing research and enhancement of CDNs engineering, along with comprehensive safety assessments and stability analysis, exhibit vast potential to advance regenerative medicine by enabling the development of efficient therapeutic interventions.
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Affiliation(s)
- Hye-Jeong Jang
- Department of Systems Biotechnology, Chung-Ang University, Anseong-Si, Gyeonggi-Do, 17546, Republic of Korea
| | - Kyu-Sik Shim
- Department of Plastic and Reconstructive Surgery, Institute for Human Tissue Restoration, Severance Hospital, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Jinah Lee
- Department of Biological Science, Research Institute of Women's Health, Brain Korea 21 Project, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Joo Hyeon Park
- Department of Biological Science, Research Institute of Women's Health, Brain Korea 21 Project, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Seong-Jun Kang
- Department of Systems Biotechnology, Chung-Ang University, Anseong-Si, Gyeonggi-Do, 17546, Republic of Korea
| | - Young Min Shin
- Department of Biological Science, Research Institute of Women's Health, Brain Korea 21 Project, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Jung Bok Lee
- Department of Biological Science, Research Institute of Women's Health, Brain Korea 21 Project, Sookmyung Women's University, Seoul, 04310, Republic of Korea.
| | - Wooyeol Baek
- Department of Plastic and Reconstructive Surgery, Institute for Human Tissue Restoration, Severance Hospital, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
| | - Jeong-Kee Yoon
- Department of Systems Biotechnology, Chung-Ang University, Anseong-Si, Gyeonggi-Do, 17546, Republic of Korea.
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Zhu X, Shen A, Li N, Feng S, Tang T, Zhang Y, Jing J, Zhong X, Xie L, Huang S, Liu B, Lv L. Identification of stable reference genes for relative quantification of long RNA expression in urinary extracellular vesicles. JOURNAL OF EXTRACELLULAR BIOLOGY 2024; 3:e136. [PMID: 38938675 PMCID: PMC11080903 DOI: 10.1002/jex2.136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 12/07/2023] [Accepted: 12/24/2023] [Indexed: 06/29/2024]
Abstract
Urinary extracellular vesicles (uEVs) are rich in valuable biomolecule information which are increasingly recognized as potential biomarkers for various diseases. uEV long RNAs are among the critical cargos capable of providing unique transcriptome information of the source cells. However, consensus regarding ideal reference genes for relative long RNAs quantification in uEVs is not available as of date. Here we explored stable reference genes through profiling the long RNA expression by RNA-seq following unsupervised analysis and validation studies. Candidate reference genes were identified using four algorithms: NormFinder, GeNorm, BestKeeper and the Delta Ct method, followed by validation. RNA profile showed uEVs contained abundant long RNAs information and the core transcriptome was related to cellular structures, especially ribosome which functions mainly as translation, protein and RNA binding molecules. Analysis of RNA-seq data identified RPL18A, RPL11, RPL27, RACK1, RPSA, RPL41, H1-2, RPL4, GAPDH, RPS27A as candidate reference genes. RT-qPCR validation revealed that RPL41, RPSA and RPL18A were reliable reference genes for long RNA quantification in uEVs from patients with diabetes mellitus (DM), diabetic nephropathy (DN), IgA nephropathy (IgAN) and prostate cancer (PCA). Interestingly, RPL41 also outperformed traditional reference genes in renal tissues of DN and IgAN, as well as in plasma EVs of several types of cancers. The stable reference genes identified in this study may facilitate development of uEVs as novel biomarkers and increase the accuracy and comparability of biomarker studies.
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Affiliation(s)
- Xiao‐Xiao Zhu
- Institute of Nephrology, Zhong Da HospitalSoutheast University School of MedicineNanjingChina
| | - An‐Ran Shen
- Institute of Nephrology, Zhong Da HospitalSoutheast University School of MedicineNanjingChina
| | - Ning Li
- Institute of Nephrology, Zhong Da HospitalSoutheast University School of MedicineNanjingChina
| | - Song‐Tao Feng
- Institute of Nephrology, Zhong Da HospitalSoutheast University School of MedicineNanjingChina
| | - Tao‐Tao Tang
- Institute of Nephrology, Zhong Da HospitalSoutheast University School of MedicineNanjingChina
| | - Yue Zhang
- Institute of Nephrology, Zhong Da HospitalSoutheast University School of MedicineNanjingChina
| | - Jing Jing
- Institute of Nephrology, Zhong Da HospitalSoutheast University School of MedicineNanjingChina
| | - Xin Zhong
- Institute of Nephrology, Zhong Da HospitalSoutheast University School of MedicineNanjingChina
| | - Li‐Jun Xie
- Institute of Nephrology, Zhong Da HospitalSoutheast University School of MedicineNanjingChina
| | - Sheng‐Lin Huang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Bi‐Cheng Liu
- Institute of Nephrology, Zhong Da HospitalSoutheast University School of MedicineNanjingChina
| | - Lin‐Li Lv
- Institute of Nephrology, Zhong Da HospitalSoutheast University School of MedicineNanjingChina
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9
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Barreiro K, Dwivedi OP, Rannikko A, Holthöfer H, Tuomi T, Groop PH, Puhka M. Capturing the Kidney Transcriptome by Urinary Extracellular Vesicles-From Pre-Analytical Obstacles to Biomarker Research. Genes (Basel) 2023; 14:1415. [PMID: 37510317 PMCID: PMC10379145 DOI: 10.3390/genes14071415] [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: 05/26/2023] [Revised: 06/30/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
Urinary extracellular vesicles (uEV) hold non-invasive RNA biomarkers for genitourinary tract diseases. However, missing knowledge about reference genes and effects of preanalytical choices hinder biomarker studies. We aimed to assess how preanalytical variables (urine storage temperature, isolation workflow) affect diabetic kidney disease (DKD)-linked miRNAs or kidney-linked miRNAs and mRNAs (kidney-RNAs) in uEV isolates and to discover stable reference mRNAs across diverse uEV datasets. We studied nine raw and normalized sequencing datasets including healthy controls and individuals with prostate cancer or type 1 diabetes with or without albuminuria. We focused on kidney-RNAs reviewing literature for DKD-linked miRNAs from kidney tissue, cell culture and uEV/urine experiments. RNAs were analyzed by expression heatmaps, hierarchical clustering and selecting stable mRNAs with normalized counts (>200) and minimal coefficient of variation. Kidney-RNAs were decreased after urine storage at -20 °C vs. -80 °C. Isolation workflows captured kidney-RNAs with different efficiencies. Ultracentrifugation captured DKD -linked miRNAs that separated healthy and diabetic macroalbuminuria groups. Eleven mRNAs were stably expressed across the datasets. Hence, pre-analytical choices had variable effects on kidney-RNAs-analyzing kidney-RNAs complemented global correlation, which could fade differences in some relevant RNAs. Replicating prior DKD-marker results and discovery of candidate reference mRNAs encourages further uEV biomarker studies.
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Affiliation(s)
- Karina Barreiro
- Institute for Molecular Medicine Finland FIMM, HiLIFE, University of Helsinki, 00290 Helsinki, Finland
- Institute for Molecular Medicine Finland FIMM, EV and HiPREP Core, University of Helsinki, 00290 Helsinki, Finland
| | - Om Prakash Dwivedi
- Institute for Molecular Medicine Finland FIMM, HiLIFE, University of Helsinki, 00290 Helsinki, Finland
| | - Antti Rannikko
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
- Department of Urology, University of Helsinki, Helsinki University Hospital, 00290 Helsinki, Finland
| | - Harry Holthöfer
- Institute for Molecular Medicine Finland FIMM, HiLIFE, University of Helsinki, 00290 Helsinki, Finland
- III Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Tiinamaija Tuomi
- Institute for Molecular Medicine Finland FIMM, HiLIFE, University of Helsinki, 00290 Helsinki, Finland
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, 214 28 Malmö, Sweden
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, 00290 Helsinki, Finland
- Endocrinology, Abdominal Centre, Helsinki University Hospital, 00029 Helsinki, Finland
| | - Per-Henrik Groop
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, 00290 Helsinki, Finland
- Department of Nephrology, University of Helsinki, Helsinki University Hospital, 00290 Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3800, Australia
| | - Maija Puhka
- Institute for Molecular Medicine Finland FIMM, HiLIFE, University of Helsinki, 00290 Helsinki, Finland
- Institute for Molecular Medicine Finland FIMM, EV and HiPREP Core, University of Helsinki, 00290 Helsinki, Finland
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10
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Musso G, Saba F, Cassader M, Gambino R. Lipidomics in pathogenesis, progression and treatment of nonalcoholic steatohepatitis (NASH): Recent advances. Prog Lipid Res 2023; 91:101238. [PMID: 37244504 DOI: 10.1016/j.plipres.2023.101238] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 05/20/2023] [Accepted: 05/21/2023] [Indexed: 05/29/2023]
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a chronic liver disease affecting up to 30% of the general adult population. NAFLD encompasses a histological spectrum ranging from pure steatosis to non-alcoholic steatohepatitis (NASH). NASH can progress to cirrhosis and is becoming the most common indication for liver transplantation, as a result of increasing disease prevalence and of the absence of approved treatments. Lipidomic readouts of liver blood and urine samples from experimental models and from NASH patients disclosed an abnormal lipid composition and metabolism. Collectively, these changes impair organelle function and promote cell damage, necro-inflammation and fibrosis, a condition termed lipotoxicity. We will discuss the lipid species and metabolic pathways leading to NASH development and progression to cirrhosis, as well as and those species that can contribute to inflammation resolution and fibrosis regression. We will also focus on emerging lipid-based therapeutic opportunities, including specialized proresolving lipid molecules and macrovesicles contributing to cell-to-cell communication and NASH pathophysiology.
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Affiliation(s)
- Giovanni Musso
- Dept of Emergency Medicine, San Luigi Gonzaga University Hospital, Orbassano, Turin, Italy.
| | - Francesca Saba
- Dept. of Medical Sciences, San Giovanni Battista Hospital, University of Turin, Turin, Italy
| | - Maurizio Cassader
- Dept. of Medical Sciences, San Giovanni Battista Hospital, University of Turin, Turin, Italy
| | - Roberto Gambino
- Dept. of Medical Sciences, San Giovanni Battista Hospital, University of Turin, Turin, Italy
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11
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Fan S, Poetsch A. Proteomic Research of Extracellular Vesicles in Clinical Biofluid. Proteomes 2023; 11:proteomes11020018. [PMID: 37218923 DOI: 10.3390/proteomes11020018] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/14/2023] [Accepted: 04/28/2023] [Indexed: 05/24/2023] Open
Abstract
Extracellular vesicles (EVs), the lipid bilayer membranous structures of particles, are produced and released from almost all cells, including eukaryotes and prokaryotes. The versatility of EVs has been investigated in various pathologies, including development, coagulation, inflammation, immune response modulation, and cell-cell communication. Proteomics technologies have revolutionized EV studies by enabling high-throughput analysis of their biomolecules to deliver comprehensive identification and quantification with rich structural information (PTMs, proteoforms). Extensive research has highlighted variations in EV cargo depending on vesicle size, origin, disease, and other features. This fact has sparked activities to use EVs for diagnosis and treatment to ultimately achieve clinical translation with recent endeavors summarized and critically reviewed in this publication. Notably, successful application and translation require a constant improvement of methods for sample preparation and analysis and their standardization, both of which are areas of active research. This review summarizes the characteristics, isolation, and identification approaches for EVs and the recent advances in EVs for clinical biofluid analysis to gain novel knowledge by employing proteomics. In addition, the current and predicted future challenges and technical barriers are also reviewed and discussed.
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Affiliation(s)
- Shipan Fan
- School of Basic Medical Sciences, Nanchang University, Nanchang 330021, China
| | - Ansgar Poetsch
- Queen Mary School, Medical College, Nanchang University, Nanchang 330021, China
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12
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Gu D, Ding Y, Jiang X, Shen B, Musante L, Holthofer H, Zou H. Diabetes with kidney injury may change the abundance and cargo of urinary extracellular vesicles. Front Endocrinol (Lausanne) 2023; 14:1085133. [PMID: 37077361 PMCID: PMC10107408 DOI: 10.3389/fendo.2023.1085133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/03/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND Urinary extracellular vesicles (uEVs) are derived from epithelia facing the renal tubule lumen in the kidney and urogenital tract; they may carry protein biomarkers of renal dysfunction and structural injury. However, there are scarce studies focusing on uEVs in diabetes with kidney injury. MATERIALS AND METHODS A community-based epidemiological survey was performed, and the participants were randomly selected for our study. uEVs were enriched by dehydrated dialysis method, quantified by Coomassie Bradford protein assay, and adjusted by urinary creatinine (UCr). Then, they identified by transmission electron microscopy (TEM), nanoparticle track analysis (NTA), and western blot of tumor susceptibility gene 101. RESULTS Decent uEVs with a homogeneous distribution were finally obtained, presenting a membrane-encapsulated structure like cup-shaped or roundish under TEM, having active Brownian motion, and presenting the main peak between 55 and 110 nm under NTA. The Bradford protein assay showed that the protein concentrations of uEVs were 0.02 ± 0.02, 0.04 ± 0.05, 0.05 ± 0.04, 0.07 ± 0.08, and 0.11 ± 0.15 μg/mg UCr, respectively, in normal controls and in prediabetes, diabetes with normal proteinuria, diabetes with microalbuminuria, and diabetes with macroproteinuria groups after adjusting the protein concentration with UCr by calculating the vesicles-to-creatinine ratio. CONCLUSION The protein concentration of uEVs in diabetes with kidney injury increased significantly than the normal controls before and after adjusting the UCr. Therefore, diabetes with kidney injury may change the abundance and cargo of uEVs, which may be involved in the physiological and pathological changes of diabetes.
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Affiliation(s)
- Dongfeng Gu
- Department of Nephrology and Transplantation Center, Zhengzhou People’s Hospital, Henan University of Chinese Medicine, Zhengzhou, China
| | - Yanan Ding
- Department of Nephrology and Transplantation Center, Zhengzhou People’s Hospital, Henan University of Chinese Medicine, Zhengzhou, China
| | - Xin Jiang
- Department of Nephrology and Transplantation Center, Zhengzhou People’s Hospital, Henan University of Chinese Medicine, Zhengzhou, China
| | - Beili Shen
- Department of Nephrology and Transplantation Center, Zhengzhou People’s Hospital, Henan University of Chinese Medicine, Zhengzhou, China
| | - Luca Musante
- Division of Nephrology and Center for Immunity, Inflammation and Regenerative Medicine, Department of Medicine, University of Virginia, Charlottesville, VA, United States
| | - Harry Holthofer
- Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hequn Zou
- Department of Nephrology, South China Hospital of Shenzhen University, Shenzhen, China
- *Correspondence: Hequn Zou,
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13
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Wei R, Ning R, Han C, Wei S, Teng Y, Li L, Liu H, Hu S, Kang B, Xu H. Lipidomics analysis reveals new insights into the goose fatty liver formation. Poult Sci 2022; 102:102428. [PMID: 36586388 PMCID: PMC9811251 DOI: 10.1016/j.psj.2022.102428] [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: 09/02/2022] [Revised: 10/31/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022] Open
Abstract
Our previous study described the mechanism of goose fatty liver formation from cell culture and transcriptome. However, how lipidome of goose liver response to overfeeding is unclear. In this study, we used the same batch of geese (control group and corn flour overfeeding group) to explore the lipidome changes and underlying metabolic mechanisms of goose fatty liver formation. Liquid chromatography-mass spectrometry (LC-MS) was provided to lipidome detection. Liver lipidomics profiles analysis was performed by principal component analysis (PCA), partial least squares-discriminant analysis (PLS-DA) and orthogonal partial least squares-discriminant analysis (OPLS-DA), different lipids were identified and annotated, and the enriched metabolic pathways were showed. The results of PCA, PLS-DA, and OPLS-DA displayed a clear separation and discrimination between control group and corn flour overfeeding group. Two hundred and fifty-one different lipids were yielded, which were involved in triglyceride (TG), diglyceride (DG), phosphatidic acids (PA), phosphatidylinositols (PI), phosphatidylethanolamines (PE), phosphatidylcholines (PC), lyso-phosphatidylcholines (LPC), monogalactosylmonoacylglycerol (MGMG), sphingolipids (SM), ceramides (Cer), and hexaglycosylceramides (Hex1Cer). Different lipids were enriched in glycerophospholipid metabolism, glycerolipid metabolism, phosphatidylinositol signaling system, inositol phosphate metabolism, glycosylphosphatidylinositol (GPI)-anchor biosynthesis and sphingolipid metabolism. In conclusion, this is the first report describing the goose fatty liver formation from lipidomics, this study might provide some insights into the underlying glucolipid metabolism disorders in the process of fatty liver formation.
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Affiliation(s)
- Rongxue Wei
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China
| | - Rong Ning
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China
| | - Chunchun Han
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China.
| | - Shouhai Wei
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China
| | - Yongqiang Teng
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China
| | - Liang Li
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China
| | - Hehe Liu
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China
| | - Shengqiang Hu
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China
| | - Bo Kang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China
| | - Hengyong Xu
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China
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