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Su Y, Yu Z, Yang Y, Wong KC, Li X. Distribution-Agnostic Deep Learning Enables Accurate Single-Cell Data Recovery and Transcriptional Regulation Interpretation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307280. [PMID: 38380499 DOI: 10.1002/advs.202307280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 01/16/2024] [Indexed: 02/22/2024]
Abstract
Single-cell RNA sequencing (scRNA-seq) is a robust method for studying gene expression at the single-cell level, but accurately quantifying genetic material is often hindered by limited mRNA capture, resulting in many missing expression values. Existing imputation methods rely on strict data assumptions, limiting their broader application, and lack reliable supervision, leading to biased signal recovery. To address these challenges, authors developed Bis, a distribution-agnostic deep learning model for accurately recovering missing sing-cell gene expression from multiple platforms. Bis is an optimal transport-based autoencoder model that can capture the intricate distribution of scRNA-seq data while addressing the characteristic sparsity by regularizing the cellular embedding space. Additionally, they propose a module using bulk RNA-seq data to guide reconstruction and ensure expression consistency. Experimental results show Bis outperforms other models across simulated and real datasets, showcasing superiority in various downstream analyses including batch effect removal, clustering, differential expression analysis, and trajectory inference. Moreover, Bis successfully restores gene expression levels in rare cell subsets in a tumor-matched peripheral blood dataset, revealing developmental characteristics of cytokine-induced natural killer cells within a head and neck squamous cell carcinoma microenvironment.
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Affiliation(s)
- Yanchi Su
- School of Artificial Intelligence, Jilin University, Changchun, 130012, China
| | - Zhuohan Yu
- School of Artificial Intelligence, Jilin University, Changchun, 130012, China
| | - Yuning Yang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Ka-Chun Wong
- Department of Computer Science, City University of Hong Kong, Hong Kong SAR, 999077, China
| | - Xiangtao Li
- School of Artificial Intelligence, Jilin University, Changchun, 130012, China
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Darwish T, Swaidan NT, Emara MM. Stress Factors as Possible Regulators of Pluripotent Stem Cell Survival and Differentiation. BIOLOGY 2023; 12:1119. [PMID: 37627003 PMCID: PMC10452095 DOI: 10.3390/biology12081119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/02/2023] [Accepted: 08/05/2023] [Indexed: 08/27/2023]
Abstract
In recent years, extensive research efforts have been directed toward pluripotent stem cells, primarily due to their remarkable capacity for pluripotency. This unique attribute empowers these cells to undergo self-renewal and differentiate into various cell types originating from the ectoderm, mesoderm, and endoderm germ layers. The delicate balance and precise regulation of self-renewal and differentiation are essential for the survival and functionality of these cells. Notably, exposure to specific environmental stressors can activate numerous transcription factors, initiating a diverse array of stress response pathways. These pathways play pivotal roles in regulating gene expression and protein synthesis, ultimately aiming to preserve cell survival and maintain cellular functions. Reactive oxygen species, heat shock, hypoxia, osmotic stress, DNA damage, endoplasmic reticulum stress, and mechanical stress are among the examples of such stressors. In this review, we comprehensively discuss the impact of environmental stressors on the growth of embryonic cells. Furthermore, we provide a summary of the distinct stress response pathways triggered when pluripotent stem cells are exposed to different environmental stressors. Additionally, we highlight recent discoveries regarding the role of such stressors in the generation, differentiation, and self-renewal of induced pluripotent stem cells.
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Affiliation(s)
| | | | - Mohamed M. Emara
- Basic Medical Sciences Department, College of Medicine, QU Health, Qatar University, 2713 Doha, Qatar
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Kobayashi M, Tomoda K, Morihara H, Asahi M, Shimizu T, Kumagai S. Non-thermal atmospheric-pressure plasma potentiates mesodermal differentiation of human induced pluripotent stem cells. Heliyon 2022; 8:e12009. [PMID: 36506411 PMCID: PMC9727642 DOI: 10.1016/j.heliyon.2022.e12009] [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: 04/11/2022] [Revised: 09/08/2022] [Accepted: 11/23/2022] [Indexed: 12/03/2022] Open
Abstract
Non-thermal atmospheric-pressure plasma has been used for biological applications, including sterilization and stimulation of cell growth and differentiation. Here, we demonstrate that plasma exposure influences the differentiation pattern of human induced pluripotent stem cells (hiPSCs). We treated hiPSCs with dielectric barrier-discharge air plasma and found an exposure dose that does not kill hiPSCs. Immunohistochemical staining for E-CADHERIN showed that the exposure affected cell-cell attachment and doubled the average size of the hiPSCs. Analysis of mRNAs in embryoid bodies (EBs) from plasma-treated hiPSCs revealed repression of ectoderm genes, including WNT1, and increased expression of mesoderm genes. Importantly, hiPSCs deficient in DNA repair only displayed minimal damage after plasma exposure. Collectively, our results suggest that plasma treatment can be another tool for directing the fate of pluripotent stem cells without disrupting their genomic integrity.
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Affiliation(s)
- Mime Kobayashi
- Division of Biological Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan,Department of Pharmacology, Osaka Medical and Pharmaceutical University, 2-7 Daigaku-machi, Takatsuki, Osaka 569-8686, Japan,Corresponding author.
| | - Kiichiro Tomoda
- Department of Pharmacology, Osaka Medical and Pharmaceutical University, 2-7 Daigaku-machi, Takatsuki, Osaka 569-8686, Japan,Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA,Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Hirofumi Morihara
- Department of Pharmacology, Osaka Medical and Pharmaceutical University, 2-7 Daigaku-machi, Takatsuki, Osaka 569-8686, Japan
| | - Michio Asahi
- Department of Pharmacology, Osaka Medical and Pharmaceutical University, 2-7 Daigaku-machi, Takatsuki, Osaka 569-8686, Japan
| | - Tetsuji Shimizu
- Research Institute for Advanced Electronics and Photonics, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8560, Japan
| | - Shinya Kumagai
- Department of Electrical and Electronic Engineering, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya 468-8502, Japan
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Thanaskody K, Jusop AS, Tye GJ, Wan Kamarul Zaman WS, Dass SA, Nordin F. MSCs vs. iPSCs: Potential in therapeutic applications. Front Cell Dev Biol 2022; 10:1005926. [PMID: 36407112 PMCID: PMC9666898 DOI: 10.3389/fcell.2022.1005926] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/21/2022] [Indexed: 01/24/2023] Open
Abstract
Over the past 2 decades, mesenchymal stem cells (MSCs) have attracted a lot of interest as a unique therapeutic approach for a variety of diseases. MSCs are capable of self-renewal and multilineage differentiation capacity, immunomodulatory, and anti-inflammatory properties allowing it to play a role in regenerative medicine. Furthermore, MSCs are low in tumorigenicity and immune privileged, which permits the use of allogeneic MSCs for therapies that eliminate the need to collect MSCs directly from patients. Induced pluripotent stem cells (iPSCs) can be generated from adult cells through gene reprogramming with ectopic expression of specific pluripotency factors. Advancement in iPS technology avoids the destruction of embryos to make pluripotent cells, making it free of ethical concerns. iPSCs can self-renew and develop into a plethora of specialized cells making it a useful resource for regenerative medicine as they may be created from any human source. MSCs have also been used to treat individuals infected with the SARS-CoV-2 virus. MSCs have undergone more clinical trials than iPSCs due to high tumorigenicity, which can trigger oncogenic transformation. In this review, we discussed the overview of mesenchymal stem cells and induced pluripotent stem cells. We briefly present therapeutic approaches and COVID-19-related diseases using MSCs and iPSCs.
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Affiliation(s)
- Kalaiselvaan Thanaskody
- Centre for Tissue Engineering and Regenerative Medicine (CTERM), Faculty of Medicine, University Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Amirah Syamimi Jusop
- Centre for Tissue Engineering and Regenerative Medicine (CTERM), Faculty of Medicine, University Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Gee Jun Tye
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Malaysia
| | - Wan Safwani Wan Kamarul Zaman
- Department of Biomedical Engineering, Faculty of Engineering, Universiti Malaya, Kuala Lumpur, Malaysia,Centre for Innovation in Medical Engineering (CIME), Department of Biomedical Engineering, Faculty of Engineering, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Sylvia Annabel Dass
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Malaysia
| | - Fazlina Nordin
- Centre for Tissue Engineering and Regenerative Medicine (CTERM), Faculty of Medicine, University Kebangsaan Malaysia, Kuala Lumpur, Malaysia,*Correspondence: Fazlina Nordin,
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Li F, Ye Y, Lei X, Zhang W. Effects of Microgravity on Early Embryonic Development and Embryonic Stem Cell Differentiation: Phenotypic Characterization and Potential Mechanisms. Front Cell Dev Biol 2021; 9:797167. [PMID: 34926474 PMCID: PMC8675004 DOI: 10.3389/fcell.2021.797167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/15/2021] [Indexed: 11/20/2022] Open
Abstract
With the development of science and technology, mankind’s exploration of outer space has increased tremendously. Settling in outer space or on other planets could help solve the Earth’s resource crisis, but such settlement will first face the problem of reproduction. There are considerable differences between outer space and the Earth’s environment, with the effects of gravity being one of the most significant. Studying the possible effects and underlying mechanisms of microgravity on embryonic stem cell (ESC) differentiation and embryonic development could help provide solutions to healthy living and reproduction in deep space. This article summarizes recent research progress on the effects of microgravity on ESCs and early embryonic development and proposes hypotheses regarding the potential mechanisms. In addition, we discuss the controversies and key questions in the field and indicate directions for future research.
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Affiliation(s)
- Feng Li
- Department of Urinary Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Ying Ye
- Cam-Su Genomic Resource Center, Medical College of Soochow University, Suzhou, China
| | - Xiaohua Lei
- Center for Energy Metabolism and Reproduction, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Wensheng Zhang
- Cam-Su Genomic Resource Center, Medical College of Soochow University, Suzhou, China.,Department of Physiology, School of Basic Medical Sciences, Binzhou Medical University, Yantai, China
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Torizal FG, Kim SM, Horiguchi I, Inamura K, Suzuki I, Morimura T, Nishikawa M, Sakai Y. Production of homogenous size-controlled human induced pluripotent stem cell aggregates using ring-shaped culture vessel. J Tissue Eng Regen Med 2021; 16:254-266. [PMID: 34923748 DOI: 10.1002/term.3278] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 10/23/2021] [Accepted: 12/16/2021] [Indexed: 01/01/2023]
Abstract
Aggregate size is an important parameter that determines the cell fate and quality of the resulting human-induced pluripotent stem cells (hiPSCs). Nowadays, large-scale suspension culture is a common method for scaling-up the biomanufacturing of hiPSCs to realize their practical application. However, this culture system exhibits a complex hydrodynamic condition resulting from the different mixing conditions of culture media, which potentially produce non-uniform aggregates, which may decrease the quality of the cell yield. Here, we performed expansion in a ring-shaped culture vessel and compared it with three other suspension-based culture systems to evaluate the uniformity and characteristics of hiPSC aggregates. Morphologically, the hiPSC aggregates formed and expanded in the ring-shaped culture vessel, resulting in small and uniform aggregates compared to the other culture systems. This aggregate population showed a decent mass transfer required for the exchange of biochemical substances, such as nutrients, growth factors, oxygen, and waste metabolic products, inside the aggregates. Thus, better metabolic performance and pluripotency markers were achieved in this system. Interestingly, all culture systems used in this study showed different tendencies in embryoid body differentiation. The smaller aggregates produced by sphere ring and dish bag tended to differentiate toward ectodermal and mesodermal lineages, while predominantly larger aggregates from the 6-well plates and spinner flask exhibited more potential for endodermal lineage. Our study demonstrates the production of a decent homogenous aggregate population by providing equal hydrodynamic force through the ring-shaped culture vessel design, which may be further upscaled to produce a large number of hiPSCs for clinical applications.
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Affiliation(s)
- Fuad Gandhi Torizal
- Department of Chemical Systems Engineering, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Japan.,Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Japan
| | - Seong Min Kim
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Japan
| | - Ikki Horiguchi
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan
| | - Kousuke Inamura
- Department of Chemical Systems Engineering, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Japan
| | - Ikumi Suzuki
- Division of Biotechnology Industrial Equipments, Fukoku Ltd, Saitama, Japan
| | - Takashi Morimura
- Division of Biotechnology Industrial Equipments, Fukoku Ltd, Saitama, Japan
| | - Masaki Nishikawa
- Department of Chemical Systems Engineering, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Japan
| | - Yasuyuki Sakai
- Department of Chemical Systems Engineering, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Japan.,Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Japan
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Bernardo A, Malara M, Bertuccini L, De Nuccio C, Visentin S, Minghetti L. The Antihypertensive Drug Telmisartan Protects Oligodendrocytes from Cholesterol Accumulation and Promotes Differentiation by a PPAR-γ-Mediated Mechanism. Int J Mol Sci 2021; 22:ijms22179434. [PMID: 34502342 PMCID: PMC8431237 DOI: 10.3390/ijms22179434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/23/2021] [Accepted: 08/27/2021] [Indexed: 12/13/2022] Open
Abstract
Our previous studies have demonstrated that specific peroxisome proliferator-activated receptor-γ (PPAR-γ) agonists play a fundamental role in oligodendrocyte progenitor (OP) differentiation, protecting them against oxidative and inflammatory damage. The antihypertensive drug Telmisartan (TLM) was shown to act as a PPAR-γ modulator. This study investigates the TLM effect on OP differentiation and validates its capability to restore damage in a pharmacological model of Niemann-Pick type C (NPC) disease through a PPAR-γ-mediated mechanism. For the first time in purified OPs, we demonstrate that TLM-induced PPAR-γ activation downregulates the type 1 angiotensin II receptor (AT1), the level of which naturally decreases during differentiation. Like other PPAR-γ agonists, we show that TLM promotes peroxisomal proliferation and promotes OP differentiation. Furthermore, TLM can offset the OP maturation arrest induced by a lysosomal cholesterol transport inhibitor (U18666A), which reproduces an NPC1-like phenotype. In the NPC1 model, TLM also reduces cholesterol accumulation within peroxisomal and lysosomal compartments and the contacts between lysosomes and peroxisomes, revealing that TLM can regulate intracellular cholesterol transport, crucial for myelin formation. Altogether, these data indicate a new potential use of TLM in hypomyelination pathologies such as NPC1, underlining the possible repositioning of the drug already used in other pathologies.
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Affiliation(s)
- Antonietta Bernardo
- National Center for Research and Preclinical and Clinical Evaluation of Drugs, Istituto Superiore di Sanità, 00169 Rome, Italy;
- Correspondence: ; Tel.: +39-06-4990-2927
| | | | - Lucia Bertuccini
- Core Facilities, Istituto Superiore di Sanità, 00169 Rome, Italy;
| | - Chiara De Nuccio
- Research Coordination and Support Service, Istituto Superiore di Sanità, 00169 Rome, Italy; (C.D.N.); (L.M.)
| | - Sergio Visentin
- National Center for Research and Preclinical and Clinical Evaluation of Drugs, Istituto Superiore di Sanità, 00169 Rome, Italy;
| | - Luisa Minghetti
- Research Coordination and Support Service, Istituto Superiore di Sanità, 00169 Rome, Italy; (C.D.N.); (L.M.)
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