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Li Y, Dong T, Wan S, Xiong R, Jin S, Dai Y, Guan C. Application of multi-omics techniques to androgenetic alopecia: Current status and perspectives. Comput Struct Biotechnol J 2024; 23:2623-2636. [PMID: 39021583 PMCID: PMC11253216 DOI: 10.1016/j.csbj.2024.06.026] [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: 03/10/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 07/20/2024] Open
Abstract
The rapid advancement of sequencing technologies has enabled the generation of vast datasets, allowing for the in-depth analysis of sequencing data. This analysis has facilitated the validation of novel pathogenesis hypotheses for understanding and treating diseases through ex vivo and in vivo experiments. Androgenetic alopecia (AGA), a common hair loss disorder, has been a key focus of investigators attempting to uncover its underlying mechanisms. Abnormal changes in mRNA, proteins, and metabolites have been identified in individuals with AGA, and future developments in sequencing technologies may reveal new biomarkers for AGA. By integrating multiple omics analysis datasets such as genomics, transcriptomics, proteomics, and metabolomics-along with clinical phenotype data-we can achieve a comprehensive understanding of the molecular underpinnings of AGA. This review summarizes the data-mining studies conducted on various omics analysis datasets as related to AGA that have been adopted to interpret the biological data obtained from different omics layers. We herein discuss the challenges of integrative omics analyses, and suggest that collaborative multi-omics studies can enhance the understanding of the complete pathomechanism(s) of AGA by focusing on the interaction networks comprising DNA, RNA, proteins, and metabolites.
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Affiliation(s)
- Yujie Li
- Hangzhou Third Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou 310009, China
| | - Tingru Dong
- Hangzhou Third Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou 310009, China
| | - Sheng Wan
- Hangzhou Third Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou 310009, China
- Department of Dermatology, Hangzhou Third People's Hospital, Hangzhou 310009, China
| | - Renxue Xiong
- Hangzhou Third Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou 310009, China
- Department of Dermatology, Hangzhou Third People's Hospital, Hangzhou 310009, China
| | - Shiyu Jin
- Hangzhou Third Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou 310009, China
| | - Yeqin Dai
- Hangzhou Third Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou 310009, China
- Department of Dermatology, Hangzhou Third People's Hospital, Hangzhou 310009, China
| | - Cuiping Guan
- Hangzhou Third Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou 310009, China
- Department of Dermatology, Hangzhou Third People's Hospital, Hangzhou 310009, China
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Khan NLA, Muhandiram S, Dissanayake K, Godakumara K, Midekessa G, Andronowska A, Heath PR, Kodithuwakku S, Hart AR, Fazeli A. Effect of 3D and 2D cell culture systems on trophoblast extracellular vesicle physico-chemical characteristics and potency. Front Cell Dev Biol 2024; 12:1382552. [PMID: 38835509 PMCID: PMC11148233 DOI: 10.3389/fcell.2024.1382552] [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: 02/05/2024] [Accepted: 04/30/2024] [Indexed: 06/06/2024] Open
Abstract
The growing understanding of the role of extracellular vesicles (EVs) in embryo-maternal communication has sparked considerable interest in their therapeutic potential within assisted reproductive technology, particularly in enhancing implantation success. However, the major obstacle remains the large-scale production of EVs, and there is still a gap in understanding how different culture systems affect the characteristics of the EVs. In the current study, trophoblast analogue human chorionic carcinoma cell line was cultivated in both conventional monolayer culture (2D) and as spheroids in suspension culture (3D) and how the cell growth environment affects the physical, biochemical and cellular signalling properties of EVs produced by them was studied. Interestingly, the 3D system was more active in secreting EVs compared to the 2D system, while no significant differences were observed in terms of morphology, size, and classical EV protein marker expression between EVs derived from the two culture systems. There were substantial differences in the proteomic cargo profile and cellular signalling potency of EVs derived from the two culture systems. Notably, 2D EVs were more potent in inducing a cellular response in endometrial epithelial cells (EECs) compared to 3D EVs. Therefore, it is essential to recognize that the biological activity of EVs depends not only on the cell of origin but also on the cellular microenvironment of the parent cell. In conclusion, caution is warranted when selecting an EV production platform, especially for assessing the functional and therapeutic potential of EVs through in vitro studies.
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Affiliation(s)
- Norhayati Liaqat Ali Khan
- Division of Clinical Medicine, School of Medicine and Population Health, The Medical School, University of Sheffield, Sheffield, United Kingdom
- Centre of Preclinical Science Studies, Faculty of Dentistry, University Teknologi MARA (UiTM), Sg. Buloh, Selangor, Malaysia
| | - Subhashini Muhandiram
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Keerthie Dissanayake
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia
- Department of Pathophysiology, Institute of Biomedicine and Translational Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Kasun Godakumara
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia
- Department of Pathophysiology, Institute of Biomedicine and Translational Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Getnet Midekessa
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia
- Department of Pathophysiology, Institute of Biomedicine and Translational Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Aneta Andronowska
- Department of Hormonal Action Mechanisms, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Paul R Heath
- Division of Clinical Medicine, School of Medicine and Population Health, The Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Suranga Kodithuwakku
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia
- Department of Animal Science, Faculty of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka
| | - Amber Rose Hart
- Division of Clinical Medicine, School of Medicine and Population Health, The Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Alireza Fazeli
- Division of Clinical Medicine, School of Medicine and Population Health, The Medical School, University of Sheffield, Sheffield, United Kingdom
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia
- Department of Pathophysiology, Institute of Biomedicine and Translational Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia
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Schueler J, Sjöman H, Kriesi C. Sensor extended imaging workflow for creating fit for purpose models in basic and applied cell biology. Commun Biol 2024; 7:170. [PMID: 38341479 PMCID: PMC10858951 DOI: 10.1038/s42003-024-05843-0] [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: 03/21/2023] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
While various engineering disciplines spent years on developing methods and workflows to increase their R&D efficiency, the field of cell biology has seen limited evolution in the fundamental approaches to interact with living cells. Perturbations are mostly of chemical nature, and physiologically relevant contexts and stimuli are left with limited attention, resulting in a solution space constrained within the boundaries of presently manageable perturbations. To predict in the laboratory how a drug will work in a human patient, cell biology must have a closer look at life and strive to mimic the human being in all his complexity. By implementing an iterative process from perturbation to measurement and vice versa, the authors suggest using a sensor-extended imaging workflow to implement product development practices to cell biology, opening a physiologically relevant solution space for the development of truly translational and predictive fit for purpose in vitro cell models.
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Affiliation(s)
- Julia Schueler
- Charles River Germany GmbH, Am Flughafen 12-14, 79111, Freiburg, Germany.
| | - Heikki Sjöman
- Vitroscope AS, Leirfossvegen 5d, 7037, Trondheim, Norway
| | - Carlo Kriesi
- Vitroscope AS, Leirfossvegen 5d, 7037, Trondheim, Norway
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Tian CM, Yang MF, Xu HM, Zhu MZ, Yue NN, Zhang Y, Shi RY, Yao J, Wang LS, Liang YJ, Li DF. Stem cell-derived intestinal organoids: a novel modality for IBD. Cell Death Discov 2023; 9:255. [PMID: 37479716 PMCID: PMC10362068 DOI: 10.1038/s41420-023-01556-1] [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: 04/28/2023] [Revised: 07/06/2023] [Accepted: 07/12/2023] [Indexed: 07/23/2023] Open
Abstract
The organoids represent one of the greatest revolutions in the biomedical field in the past decade. This three-dimensional (3D) micro-organ cultured in vitro has a structure highly similar to that of the tissue and organ. Using the regeneration ability of stem cells, a 3D organ-like structure called intestinal organoids is established, which can mimic the characteristics of real intestinal organs, including morphology, function, and personalized response to specific stimuli. Here, we discuss current stem cell-based organ-like 3D intestinal models, including understanding the molecular pathophysiology, high-throughput screening drugs, drug efficacy testing, toxicological evaluation, and organ-based regeneration of inflammatory bowel disease (IBD). We summarize the advances and limitations of the state-of-the-art reconstruction platforms for intestinal organoids. The challenges, advantages, and prospects of intestinal organs as an in vitro model system for precision medicine are also discussed. Key applications of stem cell-derived intestinal organoids. Intestinal organoids can be used to model infectious diseases, develop new treatments, drug screens, precision medicine, and regenerative medicine.
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Affiliation(s)
- Cheng-Mei Tian
- Department of Gastroenterology, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, China
- Department of Emergency, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, China
| | - Mei-Feng Yang
- Department of Hematology, Yantian District People's Hospital, Shenzhen, 518020, Guangdong, China
| | - Hao-Ming Xu
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, 51000, China
| | - Min-Zheng Zhu
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, 51000, China
| | - Ning-Ning Yue
- Department of Gastroenterology, Shenzhen People's Hospital The Second Clinical Medical College, Jinan University, Shenzhen, 518020, Guangdong, China
| | - Yuan Zhang
- Department of Medical Administration, Huizhou Institute of Occupational Diseases Control and Prevention, Huizhou, 516000, Guangdong, China
| | - Rui-Yue Shi
- Department of Gastroenterology, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, China.
| | - Jun Yao
- Department of Gastroenterology, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, China.
| | - Li-Sheng Wang
- Department of Gastroenterology, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, China.
| | - Yu-Jie Liang
- Department of Child and Adolescent Psychiatry, Shenzhen Kangning Hospital, Shenzhen, 518020, Guangdong, China.
| | - De-Feng Li
- Department of Gastroenterology, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, China.
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Tevlek A, Kecili S, Ozcelik OS, Kulah H, Tekin HC. Spheroid Engineering in Microfluidic Devices. ACS OMEGA 2023; 8:3630-3649. [PMID: 36743071 PMCID: PMC9893254 DOI: 10.1021/acsomega.2c06052] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 12/12/2022] [Indexed: 05/27/2023]
Abstract
Two-dimensional (2D) cell culture techniques are commonly employed to investigate biophysical and biochemical cellular responses. However, these culture methods, having monolayer cells, lack cell-cell and cell-extracellular matrix interactions, mimicking the cell microenvironment and multicellular organization. Three-dimensional (3D) cell culture methods enable equal transportation of nutrients, gas, and growth factors among cells and their microenvironment. Therefore, 3D cultures show similar cell proliferation, apoptosis, and differentiation properties to in vivo. A spheroid is defined as self-assembled 3D cell aggregates, and it closely mimics a cell microenvironment in vitro thanks to cell-cell/matrix interactions, which enables its use in several important applications in medical and clinical research. To fabricate a spheroid, conventional methods such as liquid overlay, hanging drop, and so forth are available. However, these labor-intensive methods result in low-throughput fabrication and uncontrollable spheroid sizes. On the other hand, microfluidic methods enable inexpensive and rapid fabrication of spheroids with high precision. Furthermore, fabricated spheroids can also be cultured in microfluidic devices for controllable cell perfusion, simulation of fluid shear effects, and mimicking of the microenvironment-like in vivo conditions. This review focuses on recent microfluidic spheroid fabrication techniques and also organ-on-a-chip applications of spheroids, which are used in different disease modeling and drug development studies.
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Affiliation(s)
- Atakan Tevlek
- METU
MEMS Research and Application Center, Ankara 06800, Turkey
| | - Seren Kecili
- The
Department of Bioengineering, Izmir Institute
of Technology, Urla, Izmir 35430, Turkey
| | - Ozge S. Ozcelik
- The
Department of Bioengineering, Izmir Institute
of Technology, Urla, Izmir 35430, Turkey
| | - Haluk Kulah
- METU
MEMS Research and Application Center, Ankara 06800, Turkey
- The
Department of Electrical and Electronics Engineering, Middle East Technical University, Ankara 06800, Turkey
| | - H. Cumhur Tekin
- METU
MEMS Research and Application Center, Ankara 06800, Turkey
- The
Department of Bioengineering, Izmir Institute
of Technology, Urla, Izmir 35430, Turkey
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