1
|
Li Y, Fan C, Hu Y, Zhang W, Li H, Wang Y, Xu Z. Multi-cohort validation: A comprehensive exploration of prognostic marker in clear cell renal cell carcinoma. Int Immunopharmacol 2024; 135:112300. [PMID: 38781609 DOI: 10.1016/j.intimp.2024.112300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 05/07/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024]
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common form of RCC. It is characterized by resistance to traditional radiotherapy and chemotherapy, as well as an unfavorable clinical prognosis. Although TYMP is implicated in the advancement of tumor progression, the role of TYMP in ccRCC is still not understood. Heightened TYMP expression was identified in ccRCC through database mining and confirmed in RCC cell lines. Indeed, TYMP knockdown impacted RCC cell proliferation, migration, and invasion in vitro. TYMP showed a positive correlation with clinicopathological parameters (histological grade, pathological stage). Moreover, patients with high TYMP expression were indicative of poor prognosis in TCGA-ccRCC and external cohorts. The results of single-cell analysis showed that the distribution of TYMP was predominantly observed in monocytes and macrophages. Furthermore, there is a significant association between TYMP and immune status. Methylation analysis further elucidated the relationship between TYMP expression and multiple methylation sites. Drug sensitivity analysis unveiled potential pharmaceutical options. Additionally, mutation analyses identified an association between TYMP and the ccRCC driver genes like BAP1 and ROS1. In summary, TYMP may serve as a reliable prognostic indicator for ccRCC.
Collapse
Affiliation(s)
- Yifei Li
- Zhejiang Key Laboratory of Intelligent Cancer Biomarker Discovery and Translation, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Congcong Fan
- Zhejiang Key Laboratory of Intelligent Cancer Biomarker Discovery and Translation, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Yuhang Hu
- Zhejiang Key Laboratory of Intelligent Cancer Biomarker Discovery and Translation, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Weizhi Zhang
- Zhejiang Key Laboratory of Intelligent Cancer Biomarker Discovery and Translation, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Hang Li
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Yining Wang
- Zhejiang Key Laboratory of Intelligent Cancer Biomarker Discovery and Translation, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Ziqiang Xu
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China.
| |
Collapse
|
2
|
Yanagihara K, Hayashi Y, Liu Y, Yamaguchi T, Hemmi Y, Kokunugi M, Yamada KU, Fukumoto K, Suga M, Terada S, Nikawa H, Kawabata K, Furue M. Trisomy 12 compromises the mesendodermal differentiation propensity of human pluripotent stem cells. In Vitro Cell Dev Biol Anim 2024; 60:521-534. [PMID: 38169039 PMCID: PMC11126453 DOI: 10.1007/s11626-023-00824-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 09/08/2023] [Indexed: 01/05/2024]
Abstract
Trisomy 12 is one of the most frequent chromosomal abnormalities in cultured human pluripotent stem cells (hPSCs). Although potential oncogenic properties and augmented cell cycle caused by trisomy 12 have been reported, the consequences of trisomy 12 in terms of cell differentiation, which is the basis for regenerative medicine, drug development, and developmental biology studies, have not yet been investigated. Here, we report that trisomy 12 compromises the mesendodermal differentiation of hPSCs. We identified sublines of hPSCs carrying trisomy 12 after their prolonged culture. Transcriptome analysis revealed that these hPSC sublines carried abnormal gene expression patterns in specific signaling pathways in addition to cancer-related cell cycle pathways. These hPSC sublines showed a lower propensity for mesendodermal differentiation in embryoid bodies cultured in a serum-free medium. BMP4-induced exit from the self-renewal state was impaired in the trisomy 12 hPSC sublines, with less upregulation of key transcription factor gene expression. As a consequence, the differentiation efficiency of hematopoietic and hepatic lineages was also impaired in the trisomy 12 hPSC sublines. We reveal that trisomy 12 disrupts the genome-wide expression patterns that are required for proper mesendodermal differentiation.
Collapse
Affiliation(s)
- Kana Yanagihara
- Laboratory of Stem Cell Cultures, National Institutes of Biomedical Innovation, Health, and Nutrition, 7-6-8, Saito-Asagi, Osaka, Ibaraki, 567-0085, Japan
| | - Yohei Hayashi
- iPS Cell Advanced Characterization and Development Team, RIKEN Bioresource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan.
| | - Yujung Liu
- Laboratory of Stem Cell Cultures, National Institutes of Biomedical Innovation, Health, and Nutrition, 7-6-8, Saito-Asagi, Osaka, Ibaraki, 567-0085, Japan
| | - Tomoko Yamaguchi
- Laboratory of Cell Model for Drug Discovery, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8, Saito-Asagi, Osaka, Ibaraki, 567-0085, Japan
| | - Yasuko Hemmi
- iPS Cell Advanced Characterization and Development Team, RIKEN Bioresource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Minako Kokunugi
- Laboratory of Stem Cell Cultures, National Institutes of Biomedical Innovation, Health, and Nutrition, 7-6-8, Saito-Asagi, Osaka, Ibaraki, 567-0085, Japan
- Department of Oral Biology & Engineering Integrated Health Sciences, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kozue Uchio Yamada
- Laboratory of Animal Models for Human Diseases, National Institutes of Biomedical Innovation, Health, and Nutrition, 7-6-8, Saito-Asagi, Osaka, Ibaraki, 567-0085, Japan
| | - Ken Fukumoto
- Laboratory of Stem Cell Cultures, National Institutes of Biomedical Innovation, Health, and Nutrition, 7-6-8, Saito-Asagi, Osaka, Ibaraki, 567-0085, Japan
- Department of Applied Chemistry and Biotechnology, University of Fukui, Fukui City, 3-9-1 Bunkyo, Fukui, 910-8507, Japan
| | - Mika Suga
- Laboratory of Stem Cell Cultures, National Institutes of Biomedical Innovation, Health, and Nutrition, 7-6-8, Saito-Asagi, Osaka, Ibaraki, 567-0085, Japan
| | - Satoshi Terada
- Department of Applied Chemistry and Biotechnology, University of Fukui, Fukui City, 3-9-1 Bunkyo, Fukui, 910-8507, Japan
| | - Hiroki Nikawa
- Department of Oral Biology & Engineering Integrated Health Sciences, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kenji Kawabata
- Laboratory of Cell Model for Drug Discovery, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8, Saito-Asagi, Osaka, Ibaraki, 567-0085, Japan
| | - Miho Furue
- Laboratory of Stem Cell Cultures, National Institutes of Biomedical Innovation, Health, and Nutrition, 7-6-8, Saito-Asagi, Osaka, Ibaraki, 567-0085, Japan.
- Cel-MiM, Ltd., Tokyo, Japan.
| |
Collapse
|
3
|
Aoi T, Asaka I, Akutsu H, Ito Y, Kataoka K, Kanda Y, Kojima H, Sekino Y, Suemori H, Nakagawa M, Nakamura K, Nakamura Y, Fujii M, Furue M, Yamazaki D. Secondary Publication: Proposal for Points of Consideration for Pluripotent Stem Cell Culture. In Vitro Cell Dev Biol Anim 2024; 60:563-568. [PMID: 38472720 PMCID: PMC11126491 DOI: 10.1007/s11626-024-00863-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 01/31/2024] [Indexed: 03/14/2024]
Abstract
Human pluripotent stem cells, such as human embryonic stem cells and human induced pluripotent stem cells, are used in basic research and various applied fields, including drug discovery and regenerative medicine. Stem cell technologies have developed rapidly in recent years, and the supply of culture materials has improved. This has facilitated the culture of human pluripotent stem cells and has enabled an increasing number of researchers and bioengineers to access this technology. At the same time, it is a challenge to share the basic concepts and techniques of this technology among researchers and technicians to ensure the reproducibility of research results. Human pluripotent stem cells differ from conventional somatic cells in many aspects, and many points need to be considered in their handling, even for those experienced in cell culture. Therefore, we have prepared this proposal, "Points of Consideration for Pluripotent Stem Cell Culture," to promote the effective use of human pluripotent stem cells. This proposal includes seven items to be considered and practices to be confirmed before using human pluripotent stem cells. These are laws/guidelines and consent/material transfer agreements, diversity of pluripotent stem cells, culture materials, thawing procedure, media exchange and cell passaging, freezing procedure, and culture management. We aim for the concept of these points of consideration to be shared by researchers and technicians involved in the cell culture of pluripotent stem cells. In this way, we hope the reliability of research using pluripotent stem cells can be improved, and cell culture technology will advance.
Collapse
Affiliation(s)
- Takashi Aoi
- Division of Stem Cell Medicine, Graduate School of Medicine, Kobe University, Kobe, Hyogo, 650-0017, Japan
| | - Isao Asaka
- Department of Fundamental Cell Technology, Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Hidenori Akutsu
- Center for Regenerative Medicine, National Center for Child Health and Development, Tokyo, 157-8538, Japan
| | - Yuzuru Ito
- Faculty of Life and Environmental Sciences (Bioindustrial Sciences), University of Tsukuba, Tsukuba, Ibaraki, 305-8972, Japan
| | - Ken Kataoka
- Department of Life Science, Faculty of Science, Okayama University of Science, Okayama, 700‑0005, Japan
| | - Yasunari Kanda
- Division of Pharmacology, National Institute of Health Sciences, Kawasaki, Kanagawa, 210-0821, Japan
| | - Hajime Kojima
- Japanese Center for the Validation of Alternative Methods, National Institute of Health Sciences, Kawasaki, Kanagawa, 210-0821, Japan
| | - Yuko Sekino
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-Ku, Tokyo, 113-8657, Japan
| | - Hirofumi Suemori
- Division of Clinical Basis for ES Cell Research, Institute for Frontier Life and Medical Sciences, Center for Human ES Cell Research, Kyoto University, 53 Kawahara-Cho, Shogoin, Sakyo-Ku, Kyoto, 606-8507, Japan
| | - Masato Nakagawa
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Kazuaki Nakamura
- Department of Pharmacology, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Research Center, Tsukuba, 305-0074, Japan
| | - Makiko Fujii
- Department of Genomic Oncology and Oral Medicine, Graduate School of Biomedical and Health Science, Hiroshima University, Hiroshima, 834-8553, Japan
| | - Miho Furue
- Laboratory of Stem Cell Cultures, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 567-0085, Japan.
- Cel-MiM, Ltd., Tokyo, Japan.
| | - Daiju Yamazaki
- Division of Pharmacology, National Institute of Health Sciences, Kawasaki, Kanagawa, 210-0821, Japan
| |
Collapse
|
4
|
Wu Z, Shen S, Mizikovsky D, Cao Y, Naval-Sanchez M, Tan SZ, Alvarez YD, Sun Y, Chen X, Zhao Q, Kim D, Yang P, Hill TA, Jones A, Fairlie DP, Pébay A, Hewitt AW, Tam PPL, White MD, Nefzger CM, Palpant NJ. Wnt dose escalation during the exit from pluripotency identifies tranilast as a regulator of cardiac mesoderm. Dev Cell 2024; 59:705-722.e8. [PMID: 38354738 DOI: 10.1016/j.devcel.2024.01.019] [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: 03/08/2023] [Revised: 10/27/2023] [Accepted: 01/23/2024] [Indexed: 02/16/2024]
Abstract
Wnt signaling is a critical determinant of cell lineage development. This study used Wnt dose-dependent induction programs to gain insights into molecular regulation of stem cell differentiation. We performed single-cell RNA sequencing of hiPSCs responding to a dose escalation protocol with Wnt agonist CHIR-99021 during the exit from pluripotency to identify cell types and genetic activity driven by Wnt stimulation. Results of activated gene sets and cell types were used to build a multiple regression model that predicts the efficiency of cardiomyocyte differentiation. Cross-referencing Wnt-associated gene expression profiles to the Connectivity Map database, we identified the small-molecule drug, tranilast. We found that tranilast synergistically activates Wnt signaling to promote cardiac lineage differentiation, which we validate by in vitro analysis of hiPSC differentiation and in vivo analysis of developing quail embryos. Our study provides an integrated workflow that links experimental datasets, prediction models, and small-molecule databases to identify drug-like compounds that control cell differentiation.
Collapse
Affiliation(s)
- Zhixuan Wu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sophie Shen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Dalia Mizikovsky
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yuanzhao Cao
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Marina Naval-Sanchez
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Siew Zhuan Tan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yanina D Alvarez
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yuliangzi Sun
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Xiaoli Chen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Qiongyi Zhao
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Daniel Kim
- Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Pengyi Yang
- Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Timothy A Hill
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Alun Jones
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David P Fairlie
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Alice Pébay
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC 3010, Australia; Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Alex W Hewitt
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7000, Australia
| | - Patrick P L Tam
- Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Melanie D White
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Christian M Nefzger
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, QLD 4067, Australia
| | - Nathan J Palpant
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.
| |
Collapse
|
5
|
Fatima N, Saif Ur Rahman M, Qasim M, Ali Ashfaq U, Ahmed U, Masoud MS. Transcriptional Factors Mediated Reprogramming to Pluripotency. Curr Stem Cell Res Ther 2024; 19:367-388. [PMID: 37073151 DOI: 10.2174/1574888x18666230417084518] [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: 12/18/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 04/20/2023]
Abstract
A unique kind of pluripotent cell, i.e., Induced pluripotent stem cells (iPSCs), now being targeted for iPSC synthesis, are produced by reprogramming animal and human differentiated cells (with no change in genetic makeup for the sake of high efficacy iPSCs formation). The conversion of specific cells to iPSCs has revolutionized stem cell research by making pluripotent cells more controllable for regenerative therapy. For the past 15 years, somatic cell reprogramming to pluripotency with force expression of specified factors has been a fascinating field of biomedical study. For that technological primary viewpoint reprogramming method, a cocktail of four transcription factors (TF) has required: Kruppel-like factor 4 (KLF4), four-octamer binding protein 34 (OCT3/4), MYC and SOX2 (together referred to as OSKM) and host cells. IPS cells have great potential for future tissue replacement treatments because of their ability to self-renew and specialize in all adult cell types, although factor-mediated reprogramming mechanisms are still poorly understood medically. This technique has dramatically improved performance and efficiency, making it more useful in drug discovery, disease remodeling, and regenerative medicine. Moreover, in these four TF cocktails, more than 30 reprogramming combinations were proposed, but for reprogramming effectiveness, only a few numbers have been demonstrated for the somatic cells of humans and mice. Stoichiometry, a combination of reprogramming agents and chromatin remodeling compounds, impacts kinetics, quality, and efficiency in stem cell research.
Collapse
Affiliation(s)
- Nazira Fatima
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
| | - Muhammad Saif Ur Rahman
- Institute of Advanced Studies, Shenzhen University, Shenzhen, 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Muhammad Qasim
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Uzair Ahmed
- EMBL Partnership Institute for Genome Editing Technologies, Vilnius University, Vilnius, 10257, Lithuania
| | - Muhammad Shareef Masoud
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| |
Collapse
|
6
|
Yang X, Chen D, Sun Q, Wang Y, Xia Y, Yang J, Lin C, Dang X, Cen Z, Liang D, Wei R, Xu Z, Xi G, Xue G, Ye C, Wang LP, Zou P, Wang SQ, Rivera-Fuentes P, Püntener S, Chen Z, Liu Y, Zhang J, Zhao Y. A live-cell image-based machine learning strategy for reducing variability in PSC differentiation systems. Cell Discov 2023; 9:53. [PMID: 37280224 DOI: 10.1038/s41421-023-00543-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 03/13/2023] [Indexed: 06/08/2023] Open
Abstract
The differentiation of pluripotent stem cells (PSCs) into diverse functional cell types provides a promising solution to support drug discovery, disease modeling, and regenerative medicine. However, functional cell differentiation is currently limited by the substantial line-to-line and batch-to-batch variabilities, which severely impede the progress of scientific research and the manufacturing of cell products. For instance, PSC-to-cardiomyocyte (CM) differentiation is vulnerable to inappropriate doses of CHIR99021 (CHIR) that are applied in the initial stage of mesoderm differentiation. Here, by harnessing live-cell bright-field imaging and machine learning (ML), we realize real-time cell recognition in the entire differentiation process, e.g., CMs, cardiac progenitor cells (CPCs), PSC clones, and even misdifferentiated cells. This enables non-invasive prediction of differentiation efficiency, purification of ML-recognized CMs and CPCs for reducing cell contamination, early assessment of the CHIR dose for correcting the misdifferentiation trajectory, and evaluation of initial PSC colonies for controlling the start point of differentiation, all of which provide a more invulnerable differentiation method with resistance to variability. Moreover, with the established ML models as a readout for the chemical screen, we identify a CDK8 inhibitor that can further improve the cell resistance to the overdose of CHIR. Together, this study indicates that artificial intelligence is able to guide and iteratively optimize PSC differentiation to achieve consistently high efficiency across cell lines and batches, providing a better understanding and rational modulation of the differentiation process for functional cell manufacturing in biomedical applications.
Collapse
Affiliation(s)
- Xiaochun Yang
- State Key Laboratory of Natural and Biomimetic Drugs, MOE Key Laboratory of Cell Proliferation and Differentiation, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Daichao Chen
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Qiushi Sun
- Beijing Key Lab of Traffic Data Analysis and Mining, School of Computer and Information Technology, Beijing Jiaotong University, Beijing, China
| | - Yao Wang
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Yu Xia
- College of Engineering, Peking University, Beijing, China
| | - Jinyu Yang
- College of Engineering, Peking University, Beijing, China
| | - Chang Lin
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China
| | - Xin Dang
- State Key Laboratory of Natural and Biomimetic Drugs, MOE Key Laboratory of Cell Proliferation and Differentiation, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Zimu Cen
- State Key Laboratory of Natural and Biomimetic Drugs, MOE Key Laboratory of Cell Proliferation and Differentiation, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Dongdong Liang
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Rong Wei
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Ze Xu
- State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing, China
| | - Guangyin Xi
- State Key Laboratory of Natural and Biomimetic Drugs, MOE Key Laboratory of Cell Proliferation and Differentiation, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Gang Xue
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Can Ye
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Li-Peng Wang
- State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing, China
| | - Peng Zou
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Shi-Qiang Wang
- State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing, China
| | | | - Salome Püntener
- Department of Chemistry, University of Zurich, Zurich, Switzerland
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédéral de Lausanne, Lausanne, Switzerland
| | - Zhixing Chen
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
- Institute of Molecular Medicine, National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Yi Liu
- Beijing Key Lab of Traffic Data Analysis and Mining, School of Computer and Information Technology, Beijing Jiaotong University, Beijing, China.
| | - Jue Zhang
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
- College of Engineering, Peking University, Beijing, China.
| | - Yang Zhao
- State Key Laboratory of Natural and Biomimetic Drugs, MOE Key Laboratory of Cell Proliferation and Differentiation, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
| |
Collapse
|
7
|
Sustained intrinsic WNT and BMP4 activation impairs hESC differentiation to definitive endoderm and drives the cells towards extra-embryonic mesoderm. Sci Rep 2021; 11:8242. [PMID: 33859268 PMCID: PMC8050086 DOI: 10.1038/s41598-021-87547-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 03/31/2021] [Indexed: 12/13/2022] Open
Abstract
We identified a human embryonic stem cell subline that fails to respond to the differentiation cues needed to obtain endoderm derivatives, differentiating instead into extra-embryonic mesoderm. RNA-sequencing analysis showed that the subline has hyperactivation of the WNT and BMP4 signalling. Modulation of these pathways with small molecules confirmed them as the cause of the differentiation impairment. While activation of WNT and BMP4 in control cells resulted in a loss of endoderm differentiation and induction of extra-embryonic mesoderm markers, inhibition of these pathways in the subline restored its ability to differentiate. Karyotyping and exome sequencing analysis did not identify any changes in the genome that could account for the pathway deregulation. These findings add to the increasing evidence that different responses of stem cell lines to differentiation protocols are based on genetic and epigenetic factors, inherent to the line or acquired during cell culture.
Collapse
|
8
|
Gene Editing Correction of a Urea Cycle Defect in Organoid Stem Cell Derived Hepatocyte-like Cells. Int J Mol Sci 2021; 22:ijms22031217. [PMID: 33530582 PMCID: PMC7865883 DOI: 10.3390/ijms22031217] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 12/17/2022] Open
Abstract
Urea cycle disorders are enzymopathies resulting from inherited deficiencies in any genes of the cycle. In severe cases, currently available therapies are marginally effective, with liver transplantation being the only definitive treatment. Donor liver availability can limit even this therapy. Identification of novel therapeutics for genetic-based liver diseases requires models that provide measurable hepatic functions and phenotypes. Advances in stem cell and genome editing technologies could provide models for the investigation of cell-based genetic diseases, as well as the platforms for drug discovery. This report demonstrates a practical, and widely applicable, approach that includes the successful reprogramming of somatic cells from a patient with a urea cycle defect, their genetic correction and differentiation into hepatic organoids, and the subsequent demonstration of genetic and phenotypic change in the edited cells consistent with the correction of the defect. While individually rare, there is a large number of other genetic-based liver diseases. The approach described here could be applied to a broad range and a large number of patients with these hepatic diseases where it could serve as an in vitro model, as well as identify successful strategies for corrective cell-based therapy.
Collapse
|
9
|
Eskandarian P, Bagherzadeh Mohasefi J, Pirnejad H, Niazkhani Z. Prediction of future gene expression profile by analyzing its past variation pattern. Gene Expr Patterns 2021; 39:119166. [PMID: 33444808 DOI: 10.1016/j.gep.2021.119166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/28/2020] [Accepted: 01/07/2021] [Indexed: 01/21/2023]
Abstract
A number of initial Hematopoietic Stem Cells (HSC) are considered in a container that are able to divide into HSCs or differentiate into various types of descendant cells. In this paper, a method is designed to predict an approximate gene expression profile (GEP) for future descendant cells resulted from HSC division/differentiation. First, the GEP prediction problem is modeled into a multivariate time series prediction problem. A novel method called EHSCP (Extended Hematopoietic Stem Cell Prediction) is introduced which is an artificial neural machine to solve the problem. EHSCP accepts the initial sequence of measured GEPs as input and predicts GEPs of future descendant cells. This prediction can be performed for multiple stages of cell division/differentiation. EHSCP considers the GEP sequence as time series and computes correlation between input time series. Two novel artificial neural units called PLSTM (Parametric Long Short Term Memory) and MILSTM (Multi-Input LSTM) are designed. PLSTM makes EHSCP able to consider this correlation in output prediction. Since there exist thousands of time series in GEP prediction, a hierarchical encoder is proposed that computes this correlation using 101 MILSTMs. EHSCP is trained using 155 datasets and is evaluated on 39 test datasets. These evaluations show that EHSCP surpasses existing methods in terms of prediction accuracy and number of correctly-predicted division/differentiation stages. In these evaluations, number of correctly-predicted stages in EHSCP was 128 when as many as 8 initial stages were given.
Collapse
Affiliation(s)
- Parinaz Eskandarian
- Department of Computer Engineering, Urmia Branch, Islamic Azad University, Urmia, Iran.
| | - Jamshid Bagherzadeh Mohasefi
- Department of Computer Engineering, Urmia Branch, Islamic Azad University, Urmia, Iran; Department of Electrical and Computer Engineering, Urmia University, Urmia, Iran.
| | - Habibollah Pirnejad
- Patient Safety Research Center, Clinical Research Institute, Urmia University of Medical Sciences, Urmia, Iran.
| | - Zahra Niazkhani
- Nephrology and Kidney Transplant Research Center, Clinical Research Institute, Urmia University of Medical Sciences, Urmia, Iran.
| |
Collapse
|
10
|
Fang M, Liu LP, Zhou H, Li YM, Zheng YW. Practical choice for robust and efficient differentiation of human pluripotent stem cells. World J Stem Cells 2020; 12:752-760. [PMID: 32952856 PMCID: PMC7477655 DOI: 10.4252/wjsc.v12.i8.752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 04/30/2020] [Accepted: 07/01/2020] [Indexed: 02/06/2023] Open
Abstract
Human pluripotent stem cells (hPSCs) have the distinct advantage of being able to differentiate into cells of all three germ layers. Target cells or tissues derived from hPSCs have many uses such as drug screening, disease modeling, and transplantation therapy. There are currently a wide variety of differentiation methods available. However, most of the existing differentiation methods are unreliable, with uneven differentiation efficiency and poor reproducibility. At the same time, it is difficult to choose the optimal method when faced with so many differentiation schemes, and it is time-consuming and costly to explore a new differentiation approach. Thus, it is critical to design a robust and efficient method of differentiation. In this review article, we summarize a comprehensive approach in which hPSCs are differentiated into target cells or organoids including brain, liver, blood, melanocytes, and mesenchymal cells. This was accomplished by employing an embryoid body-based three-dimensional (3D) suspension culture system with multiple cells co-cultured. The method has high stable differentiation efficiency compared to the conventional 2D culture and can meet the requirements of clinical application. Additionally, ex vivo co-culture models might be able to constitute organoids that are highly similar or mimic human organs for potential organ transplantation in the future.
Collapse
Affiliation(s)
- Mei Fang
- Institute of Regenerative Medicine, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang 212001, Jiangsu Province, China
| | - Li-Ping Liu
- Institute of Regenerative Medicine, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang 212001, Jiangsu Province, China
| | - Hang Zhou
- Institute of Regenerative Medicine, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang 212001, Jiangsu Province, China
| | - Yu-Mei Li
- Institute of Regenerative Medicine, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang 212001, Jiangsu Province, China
| | - Yun-Wen Zheng
- Institute of Regenerative Medicine, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang 212001, Jiangsu Province, China
- School of Biotechnology and Heath Sciences, Wuyi University, Jiangmen 529020, Guangdong Province, China
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, University of Tsukuba Faculty of Medicine, Tsukuba, Ibaraki 305-8575, Japan
- Yokohama City University School of Medicine, Yokohama, Kanagawa 234-0006, Japan
- Division of Regenerative Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, the University of Tokyo, Tokyo 108-8639, Japan
| |
Collapse
|
11
|
Cytotoxicity assay using a human pluripotent stem cell-derived cranial neural crest cell model. In Vitro Cell Dev Biol Anim 2020; 56:505-510. [PMID: 32812205 DOI: 10.1007/s11626-020-00491-0] [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: 03/27/2020] [Accepted: 08/06/2020] [Indexed: 10/23/2022]
Abstract
Cleft lip and palate are the most common congenital abnormalities that occur early in pregnancy. The majority of cranial mesenchyme is derived from cranial neural crest cells that differentiate into odontoblasts, cartilage, craniofacial bone, and connective tissue. A subset of these cells differentiates into cranial ganglia. We have previously reported an induction protocol of cranial neural crest cell-like cells from human pluripotent stem cells. This study tested detection of the cytotoxic sensitivities of dental materials, including titanium ions, palladium ions, and hydroxyethyl methacrylate, on the cell viability of induced cranial neural crest cell-like cells (iNC-LCs) derived from Tic human induced pluripotent stem cell (hiPSC) line. Further, the sensitivity was compared with those of human fetal lung fibroblastic cell line MRC-5, which is origin of Tic hiPSC, and osteoblastic cell line MC3T3-E1 which was derived from mouse calvaria. The results suggested that this cell-based assay system using iNC-LCs is a potential method for in vitro screening as an alternative to animal testing to predict toxic effects of dental materials on early craniofacial development.
Collapse
|
12
|
Evaluating the efficacy of small molecules for neural differentiation of common marmoset ESCs and iPSCs. Neurosci Res 2019; 155:1-11. [PMID: 31586586 DOI: 10.1016/j.neures.2019.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 09/12/2019] [Accepted: 09/26/2019] [Indexed: 12/15/2022]
Abstract
The common marmoset (marmoset; Callithrix jacchus) harbors various desired features as a non-human primate (NHP) model for neuroscience research. Recently, efforts have been made to induce neural cells in vitro from marmoset pluripotent stem cells (PSCs), including embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), which are characterized by their capacity to differentiate into all cell types from the three germ layers. Successful generation of marmoset neural cells is not only invaluable for understanding neural development and for modeling neurodegenerative and psychiatric disorders, but is also necessary for the phenotypic screening of genetically-modified marmosets. However, differences in the differentiation propensity among PSC lines hamper the applicability and the reproducibility of differentiation methods. To overcome this limitation, we evaluated the efficacy of small molecules for neural differentiation of marmoset ESCs (cjESCs) and iPSCs using multiple differentiation methods. By immunochemical and transcriptomic analyses, we confirmed that our methods using the small molecules are efficient for various differentiation protocols by either enhancing the yield of a mixture of neural cells including both neurons and glial cells, or a pure population of neurons. Collectively, our findings optimized in vitro neural differentiation methods for marmoset PSCs, which would ultimately help enhance the utility of the animal model in neuroscience.
Collapse
|
13
|
Liu LP, Zheng YW. Predicting differentiation potential of human pluripotent stem cells: Possibilities and challenges. World J Stem Cells 2019; 11:375-382. [PMID: 31396366 PMCID: PMC6682503 DOI: 10.4252/wjsc.v11.i7.375] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/12/2019] [Accepted: 06/20/2019] [Indexed: 02/06/2023] Open
Abstract
The capability of human pluripotent stem cell (hPSC) lines to propagate indefinitely and differentiate into derivatives of three embryonic germ layers makes these cells be powerful tools for basic scientific research and promising agents for translational medicine. However, variations in differentiation tendency and efficiency as well as pluripotency maintenance necessitate the selection of hPSC lines for the intended applications to save time and cost. To screen the qualified cell lines and exclude problematic cell lines, their pluripotency must be confirmed initially by traditional methods such as teratoma formation or by high-throughput gene expression profiling assay. Additionally, their differentiation potential, particularly the lineage-specific differentiation propensities of hPSC lines, should be predicted in an early stage. As a complement to the teratoma assay, RNA sequencing data provide a quantitative estimate of the differentiation ability of hPSCs in vivo. Moreover, multiple scorecards have been developed based on selected gene sets for predicting the differentiation potential into three germ layers or the desired cell type many days before terminal differentiation. For clinical application of hPSCs, the malignant potential of the cells must also be evaluated. A combination of histologic examination of teratoma with quantitation of gene expression data derived from teratoma tissue provides safety-related predictive information by detecting immature teratomas, malignancy marker expression, and other parameters. Although various prediction methods are available, distinct limitations remain such as the discordance of results between different assays and requirement of a long time and high labor and cost, restricting their wide applications in routine studies. Therefore, simpler and more rapid detection assays with high specificity and sensitivity that can be used to monitor the status of hPSCs at any time and fewer targeted markers that are more specific for a given desired cell type are urgently needed.
Collapse
Affiliation(s)
- Li-Ping Liu
- Institute of Regenerative Medicine, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang 212001, Jiangsu Province, China
- University of Tsukuba Faculty of Medicine, Tsukuba, Ibaraki 305-8575, Japan
| | - Yun-Wen Zheng
- Institute of Regenerative Medicine, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang 212001, Jiangsu Province, China
- University of Tsukuba Faculty of Medicine, Tsukuba, Ibaraki 305-8575, Japan
- Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| |
Collapse
|
14
|
Guo NN, Liu LP, Zhang YX, Cai YT, Guo Y, Zheng YW, Li YM. Early prediction of the differentiation potential during the formation of human iPSC-derived embryoid bodies. Biochem Biophys Res Commun 2019; 516:673-679. [PMID: 31248595 DOI: 10.1016/j.bbrc.2019.06.081] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 06/16/2019] [Indexed: 12/16/2022]
Abstract
Induced pluripotent stem cells (iPSCs) show huge variations in their differentiation potential, even in the same condition. However, methods for predicting these differentiation tendencies, especially in the early stage of differentiation, are still scarce. This study aimed to establish a simple and practical system to predict the differentiation tendency of iPSC lines using embryoid bodies (EBs) with identified parameters in the early stage. We compared four human iPSC lines in terms of the morphology and maintenance of EBs and their gene expression levels of specific markers for three germ-layers. Furthermore, the differentiation potentials of these iPSC lines into melanocytes, which are ectoderm-derived cells, were also compared and correlated with the above parameters. The results showed that iPSC lines forming regular, smooth, and not cystic EBs, which could be maintained in culture for a relatively longer time, also expressed higher levels of ectoderm-specific markers and lower levels of mesoderm/endoderm markers. Additionally, these iPSC lines showed greater potential in melanocyte differentiation using EB-based protocol, and the induced melanocytes expressed melanocytic markers and presented characteristics that were similar to those of normal human melanocytes. By contrast, iPSC lines that formed cystic EBs with bright or dark cavities and expressed relatively lower levels of ectoderm-specific markers failed in the melanocyte differentiation. Collectively, the differentiation tendency of human iPSC lines may be predicted by specific parameters in the EB stage. The formation and maintenance of optimal EBs and the expression of germ layer-specific markers are particularly important and practical for the prediction assay in the early stage.
Collapse
Affiliation(s)
- Ning-Ning Guo
- Jiangsu University Institute of Regenerative Medicine, The Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, 212001, China
| | - Li-Ping Liu
- Jiangsu University Institute of Regenerative Medicine, The Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, 212001, China
| | - Yi-Xuan Zhang
- Jiangsu University Institute of Regenerative Medicine, The Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, 212001, China
| | - Yu-Tian Cai
- Jiangsu University Institute of Regenerative Medicine, The Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, 212001, China
| | - Yuan Guo
- Jiangsu University Institute of Regenerative Medicine, The Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, 212001, China
| | - Yun-Wen Zheng
- Jiangsu University Institute of Regenerative Medicine, The Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, 212001, China; University of Tsukuba Faculty of Medicine, Tsukuba, Ibaraki, 305-8575, Japan; Yokohama City University School of Medicine, Yokohama, Kanagawa, 236-0004, Japan.
| | - Yu-Mei Li
- Jiangsu University Institute of Regenerative Medicine, The Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, 212001, China.
| |
Collapse
|
15
|
Zhang BP, Huang ZH, Dong C. Biliary atresia combined with progressive familial intrahepatic cholestasis type 3: A case report and review of the literature. Medicine (Baltimore) 2019; 98:e15593. [PMID: 31083246 PMCID: PMC6531222 DOI: 10.1097/md.0000000000015593] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 04/04/2019] [Accepted: 04/16/2019] [Indexed: 01/26/2023] Open
Abstract
RATIONALE Neonatal cholestasis is one of the most serious diseases in infancy. Progressive familial intrahepatic cholestasis (PFIC) is a disease that leads to intrahepatic cholestasis. It is one of the common causes of neonatal cholestasis in addition to biliary atresia (BA). The differential diagnosis of neonatal cholestasis is clinically challenging for pediatricians. PATIENT CONCERNS A 4-month-old female presented with severe jaundice, pruritus, and pale stool for 20 days. Abnormally strong echoes near the portal area, an abnormally small gallbladder with an irregularly stiff wall, and splenomegaly were identified on abdominal ultrasound. Blood tests showed elevated alanine aminotransferase, total bilirubin, conjugated bilirubin, gamma-glutamyltranspeptidase, and total bile acid levels. DIAGNOSIS Intraoperative cholangiography showed BA. ABCB4 gene mutation IVS13+6G>A/G was confirmed by genetic testing. The patient was diagnosed with BA combined with PFIC3. INTERVENTIONS Kasai portoenterostomy and ursodeoxycholic acid were used for treatment. OUTCOMES Her clinical symptoms and blood tests improved gradually. No recurrence was noted during 1 year of follow-up. LESSONS Additional examinations, such as genetic testing, should be considered in patients with BA who had refractory jaundice after Kasai portoenterostomy in order to exclude intrahepatic cholestasis.
Collapse
Affiliation(s)
- Ben-Ping Zhang
- Department of Endocrinology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | | | | |
Collapse
|
16
|
Hayashi Y, Ohnuma K, Furue MK. Pluripotent Stem Cell Heterogeneity. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1123:71-94. [DOI: 10.1007/978-3-030-11096-3_6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
17
|
Mashimo Y, Yoshioka M, Tokunaga Y, Fockenberg C, Terada S, Koyama Y, Shibata-Seki T, Yoshimoto K, Sakai R, Hakariya H, Liu L, Akaike T, Kobatake E, How SE, Uesugi M, Chen Y, Kamei KI. Fabrication of a Multiplexed Artificial Cellular MicroEnvironment Array. J Vis Exp 2018. [PMID: 30247461 DOI: 10.3791/57377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Cellular microenvironments consist of a variety of cues, such as growth factors, extracellular matrices, and intercellular interactions. These cues are well orchestrated and are crucial in regulating cell functions in a living system. Although a number of researchers have attempted to investigate the correlation between environmental factors and desired cellular functions, much remains unknown. This is largely due to the lack of a proper methodology to mimic such environmental cues in vitro, and simultaneously test different environmental cues on cells. Here, we report an integrated platform of microfluidic channels and a nanofiber array, followed by high-content single-cell analysis, to examine stem cell phenotypes altered by distinct environmental factors. To demonstrate the application of this platform, this study focuses on the phenotypes of self-renewing human pluripotent stem cells (hPSCs). Here, we present the preparation procedures for a nanofiber array and the microfluidic structure in the fabrication of a Multiplexed Artificial Cellular MicroEnvironment (MACME) array. Moreover, overall steps of the single-cell profiling, cell staining with multiple fluorescent markers, multiple fluorescence imaging, and statistical analyses, are described.
Collapse
Affiliation(s)
- Yasumasa Mashimo
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University; Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology
| | - Momoko Yoshioka
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University
| | - Yumie Tokunaga
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University
| | | | - Shiho Terada
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University
| | - Yoshie Koyama
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University
| | - Teiko Shibata-Seki
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology
| | - Koki Yoshimoto
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University
| | - Risako Sakai
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University
| | - Hayase Hakariya
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University
| | - Li Liu
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University
| | - Toshihiro Akaike
- Biomaterials Center for Regenerative Medical Engineering, Foundation for Advancement of International Science
| | - Eiry Kobatake
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology
| | - Siew-Eng How
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah
| | - Motonari Uesugi
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University; Institute for Chemical Research, Kyoto University
| | - Yong Chen
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University; Ecole Normale Supérieure
| | - Ken-Ichiro Kamei
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University;
| |
Collapse
|
18
|
Keller A, Dziedzicka D, Zambelli F, Markouli C, Sermon K, Spits C, Geens M. Genetic and epigenetic factors which modulate differentiation propensity in human pluripotent stem cells. Hum Reprod Update 2018; 24:162-175. [PMID: 29377992 DOI: 10.1093/humupd/dmx042] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 11/23/2017] [Accepted: 12/22/2017] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Human pluripotent stem cell (hPSC) lines are known to have a bias in their differentiation. This gives individual cell lines a propensity to preferentially differentiate towards one germ layer or cell type over others. Chromosomal aberrations, mitochondrial mutations, genetic diversity and epigenetic variance are the main drivers of this phenomenon, and can lead to a wide range of phenotypes. OBJECTIVE AND RATIONALE Our aim is to provide a comprehensive overview of the different factors which influence differentiation propensity. Specifically, we sought to highlight known genetic variances and their mechanisms, in addition to more general observations from larger abnormalities. Furthermore, we wanted to provide an up-to-date list of a growing number of predictive indicators which are able to identify differentiation propensity before the initiation of differentiation. As differentiation propensity can lead to difficulties in both research as well as clinical translation, our thorough overview could be a useful tool. SEARCH METHODS Combinations of the following key words were applied as search criteria in the PubMed database: embryonic stem cells, induced pluripotent stem cells, differentiation propensity (also: potential, efficiency, capacity, bias, variability), epigenetics, chromosomal abnormalities, genetic aberrations, X chromosome inactivation, mitochondrial function, mitochondrial metabolism, genetic diversity, reprogramming, predictive marker, residual stem cell, clinic. Only studies in English were included, ranging from 2000 to 2017, with a majority ranging from 2010 to 1017. Further manuscripts were added from cross-references. OUTCOMES Differentiation propensity is affected by a wide variety of (epi)genetic factors. These factors clearly lead to a loss of differentiation capacity, preference towards certain cell types and oftentimes, phenotypes which begin to resemble cancer. Broad changes in (epi)genetics, such as aneuploidies or wide-ranging modifications to the epigenetic landscape tend to lead to extensive, less definite changes in differentiation capacity, whereas more specific abnormalities often have precise ramifications in which certain cell types become more preferential. Furthermore, there appears to be a greater, though often less considered, contribution to differentiation propensity by factors such as mitochondria and inherent genetic diversity. Varied differentiation capacity can also lead to potential consequences in the clinical translation of hPSC, including the occurrence of residual undifferentiated stem cells, and the transplantation of potentially transformed cells. WIDER IMPLICATIONS As hPSC continue to advance towards the clinic, our understanding of them progresses as well. As a result, the challenges faced become more numerous, but also more clear. If the transition to the clinic is to be achieved with a minimum number of potential setbacks, thorough evaluation of the cells will be an absolute necessity. Altered differentiation propensity represents at least one such hurdle, for which researchers and eventually clinicians will need to find solutions. Already, steps are being taken to tackle the issue, though further research will be required to evaluate any long-term risks it poses.
Collapse
Affiliation(s)
- Alexander Keller
- Research group Reproduction and Genetics (REGE), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Jette, Belgium
| | - Dominika Dziedzicka
- Research group Reproduction and Genetics (REGE), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Jette, Belgium
| | - Filippo Zambelli
- Research group Reproduction and Genetics (REGE), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Jette, Belgium
| | - Christina Markouli
- Research group Reproduction and Genetics (REGE), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Jette, Belgium
| | - Karen Sermon
- Research group Reproduction and Genetics (REGE), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Jette, Belgium
| | - Claudia Spits
- Research group Reproduction and Genetics (REGE), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Jette, Belgium
| | - Mieke Geens
- Research group Reproduction and Genetics (REGE), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Jette, Belgium
| |
Collapse
|
19
|
Jaramillo M, Yeh H, Yarmush ML, Uygun BE. Decellularized human liver extracellular matrix (hDLM)-mediated hepatic differentiation of human induced pluripotent stem cells (hIPSCs). J Tissue Eng Regen Med 2018; 12:e1962-e1973. [PMID: 29222839 DOI: 10.1002/term.2627] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 08/31/2017] [Accepted: 11/30/2017] [Indexed: 12/30/2022]
Abstract
Liver tissue engineering has emerged as a promising approach in organ transplantation but has been hampered by the lack of a reliable and readily available cell source. Human induced pluripotent stem cells hiPSCs have been highlighted as a desirable source, due to their differentiation potential, ability to self-renew, and the possibility of making patient-specific cells. We developed a decellularization protocol that efficiently removes cellular material while retaining extracellular matrix components. Subsequently, hiPSCs were differentiated on decellularized human liver extracellular matrix (hDLM) scaffolds using an established hepatic differentiation protocol. We demonstrate that using hDLM leads to upregulation markers of hepatic functions when compared with standard differentiation conditions. In addition, expression of a number of hepatic transcription and nuclear factors were found to be within levels comparable with those of primary human adult hepatocytes. Analysis of progression of differentiation on hDLM demonstrated that hepatic developmental marker expression was consistent with hepatic development. The hDLM-derived cells exhibited key hepatic characteristics that were comparable with those observed in primary neonatal human hepatocytes. We investigated the optimal timing of the introduction of hDLM into the differentiation protocol and found that the best results are obtained when cells are plated on hDLM since the earliest stages and accompanied by a progressive loss of sensitivity to substrate composition at later stages. The significance of this work is that it allows for the development of differentiation protocols that take into account signals from extracellular matrix, closely recapitulating of the in vivo micro-environment and resulting in cells that are phenotypically closer to mature hepatocytes.
Collapse
Affiliation(s)
- Maria Jaramillo
- Center for Engineering in Medicine, Massachusetts General Hospital, Harvard Medical School, Shriners Hospitals for Children, Boston, MA, USA.,Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Heidi Yeh
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Martin L Yarmush
- Center for Engineering in Medicine, Massachusetts General Hospital, Harvard Medical School, Shriners Hospitals for Children, Boston, MA, USA.,Department of Surgery, Massachusetts General Hospital, Boston, MA, USA.,Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, USA
| | - Basak E Uygun
- Center for Engineering in Medicine, Massachusetts General Hospital, Harvard Medical School, Shriners Hospitals for Children, Boston, MA, USA.,Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| |
Collapse
|
20
|
Kamei KI, Mashimo Y, Yoshioka M, Tokunaga Y, Fockenberg C, Terada S, Koyama Y, Nakajima M, Shibata-Seki T, Liu L, Akaike T, Kobatake E, How SE, Uesugi M, Chen Y. Microfluidic-Nanofiber Hybrid Array for Screening of Cellular Microenvironments. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1603104. [PMID: 28272774 DOI: 10.1002/smll.201603104] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 01/06/2017] [Indexed: 06/06/2023]
Abstract
Cellular microenvironments are generally sophisticated, but crucial for regulating the functions of human pluripotent stem cells (hPSCs). Despite tremendous effort in this field, the correlation between the environmental factors-especially the extracellular matrix and soluble cell factors-and the desired cellular functions remains largely unknown because of the lack of appropriate tools to recapitulate in vivo conditions and/or simultaneously evaluate the interplay of different environment factors. Here, a combinatorial platform is developed with integrated microfluidic channels and nanofibers, associated with a method of high-content single-cell analysis, to study the effects of environmental factors on stem cell phenotype. Particular attention is paid to the dependence of hPSC short-term self-renewal on the density and composition of extracellular matrices and initial cell seeding densities. Thus, this combinatorial approach provides insights into the underlying chemical and physical mechanisms that govern stem cell fate decisions.
Collapse
Affiliation(s)
- Ken-Ichiro Kamei
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Yasumasa Mashimo
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto, 606-8501, Japan
- Department of Environmental Chemistry and Engineering, Graduate School of Interdisciplinary Science and Engineering, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan
| | - Momoko Yoshioka
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Yumie Tokunaga
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Christopher Fockenberg
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Shiho Terada
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Yoshie Koyama
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Minako Nakajima
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Teiko Shibata-Seki
- Department of Environmental Chemistry and Engineering, Graduate School of Interdisciplinary Science and Engineering, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan
| | - Li Liu
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Toshihiro Akaike
- Department of Biomolecular Engineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 259 Nagatsuta, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan
- Biomaterials Center for Regenerative Medical Engineering, Foundation for Advancement of International Science, Kasuga, Tsukuba-shi, Ibaraki, 305-0821, Japan
| | - Eiry Kobatake
- Department of Environmental Chemistry and Engineering, Graduate School of Interdisciplinary Science and Engineering, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan
| | - Siew-Eng How
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu, Sabah, 88400, Malaysia
| | - Motonari Uesugi
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto, 606-8501, Japan
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Yong Chen
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto, 606-8501, Japan
- Ecole Normale Supérieure, CNRS-ENS-UPMC UMR 8640, 24 Rue Lhomond, Paris, 75005, France
| |
Collapse
|