1
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Ishikawa M, Sugino S, Masuda Y, Tarumoto Y, Seto Y, Taniyama N, Wagai F, Yamauchi Y, Kojima Y, Kiryu H, Yusa K, Eiraku M, Mochizuki A. RENGE infers gene regulatory networks using time-series single-cell RNA-seq data with CRISPR perturbations. Commun Biol 2023; 6:1290. [PMID: 38155269 PMCID: PMC10754834 DOI: 10.1038/s42003-023-05594-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 11/15/2023] [Indexed: 12/30/2023] Open
Abstract
Single-cell RNA-seq analysis coupled with CRISPR-based perturbation has enabled the inference of gene regulatory networks with causal relationships. However, a snapshot of single-cell CRISPR data may not lead to an accurate inference, since a gene knockout can influence multi-layered downstream over time. Here, we developed RENGE, a computational method that infers gene regulatory networks using a time-series single-cell CRISPR dataset. RENGE models the propagation process of the effects elicited by a gene knockout on its regulatory network. It can distinguish between direct and indirect regulations, which allows for the inference of regulations by genes that are not knocked out. RENGE therefore outperforms current methods in the accuracy of inferring gene regulatory networks. When used on a dataset we derived from human-induced pluripotent stem cells, RENGE yielded a network consistent with multiple databases and literature. Accurate inference of gene regulatory networks by RENGE would enable the identification of key factors for various biological systems.
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Affiliation(s)
- Masato Ishikawa
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan.
| | - Seiichi Sugino
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
| | - Yoshie Masuda
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
| | - Yusuke Tarumoto
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
| | - Yusuke Seto
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
| | - Nobuko Taniyama
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
| | - Fumi Wagai
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
| | - Yuhei Yamauchi
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
| | - Yasuhiro Kojima
- Laboratory of Computational Life Science, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
| | - Hisanori Kiryu
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan
| | - Kosuke Yusa
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
| | - Mototsugu Eiraku
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, 606-8507, Japan
| | - Atsushi Mochizuki
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
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2
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Yoo DH, Im YS, Oh JY, Gil D, Kim YO. DUSP6 is a memory retention feedback regulator of ERK signaling for cellular resilience of human pluripotent stem cells in response to dissociation. Sci Rep 2023; 13:5683. [PMID: 37029196 PMCID: PMC10082014 DOI: 10.1038/s41598-023-32567-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 03/29/2023] [Indexed: 04/09/2023] Open
Abstract
Cultured human pluripotent stem cells (hPSCs) grow as colonies that require breakdown into small clumps for further propagation. Although cell death mechanism by single-cell dissociation of hPSCs has been well defined, how hPSCs respond to the deadly stimulus and recover the original status remains unclear. Here we show that dissociation of hPSCs immediately activates ERK, which subsequently activates RSK and induces DUSP6, an ERK-specific phosphatase. Although the activation is transient, DUSP6 expression persists days after passaging. DUSP6 depletion using the CRISPR/Cas9 system reveals that DUSP6 suppresses the ERK activity over the long term. Elevated ERK activity by DUSP6 depletion increases both viability of hPSCs after single-cell dissociation and differentiation propensity towards mesoderm and endoderm lineages. These findings provide new insights into how hPSCs respond to dissociation in order to maintain pluripotency.
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Affiliation(s)
- Dae Hoon Yoo
- Division of Intractable Disease Research, Korea National Institute of Health, Osong, Cheongju, 28160, Republic of Korea
| | - Young Sam Im
- Division of Intractable Disease Research, Korea National Institute of Health, Osong, Cheongju, 28160, Republic of Korea
| | - Ji Young Oh
- Division of Intractable Disease Research, Korea National Institute of Health, Osong, Cheongju, 28160, Republic of Korea
| | - Dayeon Gil
- Division of Intractable Disease Research, Korea National Institute of Health, Osong, Cheongju, 28160, Republic of Korea
| | - Yong-Ou Kim
- Division of Intractable Disease Research, Korea National Institute of Health, Osong, Cheongju, 28160, Republic of Korea.
- Center for National Stem Cell and Regenerative Medicine 202, Osongsaengmyung 2-Ro, Heundeok-Gu, Cheongju, Chungcheongbuk-Do, 28160, Republic of Korea.
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3
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Al-Akashi Z, Zujur D, Kamiya D, Kato T, Kondo T, Ikeya M. Selective vulnerability of human-induced pluripotent stem cells to dihydroorotate dehydrogenase inhibition during mesenchymal stem/stromal cell purification. Front Cell Dev Biol 2023; 11:1089945. [PMID: 36814599 PMCID: PMC9939518 DOI: 10.3389/fcell.2023.1089945] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/24/2023] [Indexed: 02/08/2023] Open
Abstract
The use of induced mesenchymal stem/stromal cells (iMSCs) derived from human induced pluripotent stem cells (hiPSCs) in regenerative medicine involves the risk of teratoma formation due to hiPSCs contamination in iMSCs. Therefore, eradicating the remaining undifferentiated hiPSCs is crucial for the effectiveness of the strategy. The present study demonstrates the Brequinar (BRQ)-induced inhibition of dihydroorotate dehydrogenase (DHODH), a key enzyme in de novo pyrimidine biosynthesis, selectively induces apoptosis, cell cycle arrest, and differentiation; furthermore, it promotes transcriptional changes and prevents the growth of 3-dimensional hiPSC aggregates. Contrastingly, BRQ-treated iMSCs showed no changes in survival, differentiation potential, or gene expression. The results suggest that BRQ is a potential agent for the effective purification of iMSCs from a mixed population of iMSCs and hiPSCs, which is a crucial step in successful iMSC-based therapy.
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Affiliation(s)
- Ziadoon Al-Akashi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Denise Zujur
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Daisuke Kamiya
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan,Takeda-CiRA Joint Program, Fujisawa, Kanagawa, Japan
| | - Tomohisa Kato
- Medical Research Institute, Kanazawa Medical University, Kanazawa, Japan
| | - Toru Kondo
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Makoto Ikeya
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan,Takeda-CiRA Joint Program, Fujisawa, Kanagawa, Japan,*Correspondence: Makoto Ikeya,
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4
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Kim H, Park K, Yon JM, Kim SW, Lee SY, Jeong I, Jang J, Lee S, Cho DW. Predicting multipotency of human adult stem cells derived from various donors through deep learning. Sci Rep 2022; 12:21614. [PMID: 36517519 PMCID: PMC9749643 DOI: 10.1038/s41598-022-25423-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 11/29/2022] [Indexed: 12/15/2022] Open
Abstract
Adult stem cell-based therapeutic approaches have great potential in regenerative medicine because of their immunoregulatory properties and multidifferentiation capacity. Nevertheless, the outcomes of stem cell‑based therapies to date have shown inconsistent efficacy owing to donor variation, thwarting the expectation of clinical effects. However, such donor dependency has been elucidated by biological consequences that current research could not predict. Here, we introduce cellular morphology-based prediction to determine the multipotency rate of human nasal turbinate stem cells (hNTSCs), aiming to predict the differentiation rate of keratocyte progenitors. We characterized the overall genes and morphologies of hNTSCs from five donors and compared stemness-related properties, including multipotency and specific lineages, using mRNA sequencing. It was demonstrated that transformation factors affecting the principal components were highly related to cell morphology. We then performed a convolutional neural network-based analysis, which enabled us to assess the multipotency level of each cell group based on their morphologies with 85.98% accuracy. Surprisingly, the trend in expression levels after ex vivo differentiation matched well with the deep learning prediction. These results suggest that AI‑assisted cellular behavioral prediction can be utilized to perform quantitative, non-invasive, single-cell, and multimarker characterizations of live stem cells for improved quality control in clinical cell therapies.
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Affiliation(s)
- Hyeonji Kim
- grid.49100.3c0000 0001 0742 4007Department of Mechanical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk 37673 South Korea
| | - Keonhyeok Park
- grid.49100.3c0000 0001 0742 4007Department of Mechanical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk 37673 South Korea
| | - Jung-Min Yon
- grid.411947.e0000 0004 0470 4224Department of Otolaryngology-Head and Neck Surgery, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, 06591 South Korea
| | - Sung Won Kim
- grid.411947.e0000 0004 0470 4224Department of Otolaryngology-Head and Neck Surgery, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, 06591 South Korea
| | - Soo Young Lee
- grid.49100.3c0000 0001 0742 4007Department of Mechanical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk 37673 South Korea
| | - Iljoo Jeong
- grid.49100.3c0000 0001 0742 4007Department of Mechanical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk 37673 South Korea
| | - Jinah Jang
- grid.49100.3c0000 0001 0742 4007Department of Mechanical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk 37673 South Korea ,grid.49100.3c0000 0001 0742 4007Department of Convergence IT Engineering, POSTECH, Pohang, Gyeongbuk 37673 South Korea ,grid.15444.300000 0004 0470 5454Institute of Convergence Science, Yonsei University, Seoul, 03722 South Korea
| | - Seungchul Lee
- grid.49100.3c0000 0001 0742 4007Department of Mechanical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk 37673 South Korea ,grid.15444.300000 0004 0470 5454Institute of Convergence Science, Yonsei University, Seoul, 03722 South Korea
| | - Dong-Woo Cho
- grid.49100.3c0000 0001 0742 4007Department of Mechanical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk 37673 South Korea ,grid.15444.300000 0004 0470 5454Institute of Convergence Science, Yonsei University, Seoul, 03722 South Korea
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5
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Improving the differentiation potential of pluripotent stem cells by optimizing culture conditions. Sci Rep 2022; 12:14147. [PMID: 35986054 PMCID: PMC9391418 DOI: 10.1038/s41598-022-18400-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/10/2022] [Indexed: 11/22/2022] Open
Abstract
Embryoid cells and induced pluripotent stem cells (iPSCs) are pluripotent stem cells (PSCs). They retain differentiation and self-renewal potential. However, the differentiation potential of PSCs can be changed by the culture medium. PSCs retain their differentiation potential when cultured with medium that supports the glycolytic pathway, showing high expression of chromodomain-helicase-DNA-binding protein 7 (CHD7), but lose their differentiation potential with medium that supports mitochondrial function, showing reduced levels of CHD7. Labeling cells by their copy number variant profile revealed that genetically different PSC populations can be cultured by medium selection. Another factor that defines the self-renewal potential of PSCs is culture condition. PSCs form colonies as they grow, and spontaneous differentiation inevitably occurs along the rim of these colonies in areas that lack cell-to-cell contact; because of this, undifferentiated cell populations would diminish if differentiated cells are not removed properly. Seeding cells on a less potent cell-binding material may minimize the inclusion of differentiated cells, exploiting the reduced adhesive properties of differentiated cells. Culturing cells with medium that supports the glycolytic pathway, using CHD7 as a biomarker for differentiation potential, and culturing cells on less sticky material can improve the differentiation potential of already established PSC clones.
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6
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Etezadi F, Le MNT, Shahsavarani H, Alipour A, Moazzezy N, Samani S, Amanzadeh A, Pahlavan S, Bonakdar S, Shokrgozar MA, Hasegawa K. Optimization of a PDMS-Based Cell Culture Substrate for High-Density Human-Induced Pluripotent Stem Cell Adhesion and Long-Term Differentiation into Cardiomyocytes under a Xeno-Free Condition. ACS Biomater Sci Eng 2022; 8:2040-2052. [PMID: 35468288 DOI: 10.1021/acsbiomaterials.2c00162] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Despite the numerous advantages of PDMS-based substrates in various biomedical applications, they are limited by their highly hydrophobic surface that does not optimally interact with cells for attachment and growth. Hence, the lack of lengthy and straightforward procedures for high-density cell production on the PDMS-based substrate is one of the significant challenges in cell production in the cell therapy field. In this study, we found that the PDMS substrate coated with a combination of polydopamine (PDA) and laminin-511 E8 fragments (PDA + LME8-coated PDMS) can support human-induced pluripotent stem cell (hiPSC) attachment and growth for the long term and satisfy their demands of differentiation into cardiomyocytes (iCMs). Compared with prior studies, the density of hiPSCs and their adhesion time on the PDMS surface were increased during iCM production. Although the differentiated iCMs beat and produce mechanical forces, which disturb cellular attachments, the iCMs on the PDA + LME8-coated PDMS substrate showed dramatically better attachment than the control condition. Further, the substrate required less manipulation by enabling one-step seeding throughout the process in iCM formation from hiPSCs under animal-free conditions. In light of the results achieved, the PDA + LME8-coated PDMS substrate will be an up-and-coming tool for cardiomyocyte production for cell therapy and tissue engineering, microfluidics, and organ-on-chip platforms.
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Affiliation(s)
- Fatemeh Etezadi
- National Cell Bank of Iran, Pasteur Institute of Iran, No. 69, Pasteur Ave, Tehran 1316943551, Iran.,Institute for Integrated Cell-Material Sciences (iCeMS), Institute for Advanced Study, Kyoto University, Kyoto 606-8501, Japan.,Laboratory of Regenerative Medicine and Biomedical Innovations, Pasteur Institute of Iran, No. 69, Pasteur Ave, Tehran 1316943551, Iran
| | - Minh Nguyen Tuyet Le
- Institute for Integrated Cell-Material Sciences (iCeMS), Institute for Advanced Study, Kyoto University, Kyoto 606-8501, Japan
| | - Hosein Shahsavarani
- Laboratory of Regenerative Medicine and Biomedical Innovations, Pasteur Institute of Iran, No. 69, Pasteur Ave, Tehran 1316943551, Iran.,Department of Cell and Molecular Sciences, Faculty of Life Science and Biotechnology, Shahid Beheshti University, 1983963113 Tehran, Iran
| | - Atefeh Alipour
- Department of Nanobiotechnology, Pasteur Institute of Iran, No. 69, Pasteur Ave, Tehran 1316943551, Iran
| | - Neda Moazzezy
- Molecular Biology Department, Pasteur Institute of Iran, No. 69, Pasteur Ave, Tehran 1316943551, Iran
| | - Saeed Samani
- Department of Tissue Engineering & Applied Cell Sciences, TUMS School of Advanced Technologies in Medicine, No. 88, Italia St, Tehran, 1417755469, Iran
| | - Amir Amanzadeh
- National Cell Bank of Iran, Pasteur Institute of Iran, No. 69, Pasteur Ave, Tehran 1316943551, Iran
| | - Sara Pahlavan
- Department of Stem Cells and Development Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACERCR, Banihashem Ave, Tehran 16635-148, Iran
| | - Shahin Bonakdar
- National Cell Bank of Iran, Pasteur Institute of Iran, No. 69, Pasteur Ave, Tehran 1316943551, Iran
| | - Mohammad Ali Shokrgozar
- National Cell Bank of Iran, Pasteur Institute of Iran, No. 69, Pasteur Ave, Tehran 1316943551, Iran
| | - Kouichi Hasegawa
- Institute for Integrated Cell-Material Sciences (iCeMS), Institute for Advanced Study, Kyoto University, Kyoto 606-8501, Japan
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7
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Schock EN, York JR, LaBonne C. The developmental and evolutionary origins of cellular pluripotency in the vertebrate neural crest. Semin Cell Dev Biol 2022; 138:36-44. [PMID: 35534333 DOI: 10.1016/j.semcdb.2022.04.008] [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: 10/30/2021] [Revised: 03/28/2022] [Accepted: 04/10/2022] [Indexed: 11/30/2022]
Abstract
Neural crest cells are central to vertebrate development and evolution, endowing vertebrates with a "new head" that resulted in morphological, physiological, and behavioral features that allowed vertebrates to become active predators. One remarkable feature of neural crest cells is their multi-germ layer potential that allows for the formation of both ectodermal (pigmentation, peripheral glia, sensory neurons) and mesenchymal (connective tissue, cartilage/bone, dermis) cell types. Understanding the cellular and evolutionary origins of this broad cellular potential in the neural crest has been a long-standing focus for developmental biologists. Here, we review recent work that has demonstrated that neural crest cells share key features with pluripotent blastula stem cells, including expression of the Yamanaka stem cell factors (Oct3/4, Klf4, Sox2, c-Myc). These shared features suggest that pluripotency is either retained in the neural crest from blastula stages or subsequently reactivated as the neural crest forms. We highlight the cellular and molecular parallels between blastula stem cells and neural crest cells and discuss the work that has led to current models for the cellular origins of broad potential in the crest. Finally, we explore how these themes can provide new insights into how and when neural crest cells and pluripotency evolved in vertebrates and the evolutionary relationship between these populations.
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Affiliation(s)
| | | | - Carole LaBonne
- Dept. of Molecular Biosciences; NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, United States.
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8
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Ke M, Chong CM, Zhu Q, Zhang K, Cai CZ, Lu JH, Qin D, Su H. Comprehensive Perspectives on Experimental Models for Parkinson's Disease. Aging Dis 2021; 12:223-246. [PMID: 33532138 PMCID: PMC7801282 DOI: 10.14336/ad.2020.0331] [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: 02/24/2020] [Accepted: 03/31/2020] [Indexed: 11/19/2022] Open
Abstract
Parkinson’s disease (PD) ranks second among the most common neurodegenerative diseases, characterized by progressive and selective loss of dopaminergic neurons. Various cross-species preclinical models, including cellular models and animal models, have been established through the decades to study the etiology and mechanism of the disease from cell lines to nonhuman primates. These models are aimed at developing effective therapeutic strategies for the disease. None of the current models can replicate all major pathological and clinical phenotypes of PD. Selection of the model for PD largely relies on our interest of study. In this review, we systemically summarized experimental PD models, including cellular and animal models used in preclinical studies, to understand the pathogenesis of PD. This review is intended to provide current knowledge about the application of these different PD models, with focus on their strengths and limitations with respect to their contributions to the assessment of the molecular pathobiology of PD and identification of the therapeutic strategies for the disease.
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Affiliation(s)
- Minjing Ke
- 1State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Cheong-Meng Chong
- 1State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Qi Zhu
- 1State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Ke Zhang
- 1State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Cui-Zan Cai
- 1State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Jia-Hong Lu
- 1State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Dajiang Qin
- 2Guangzhou Regenerative Medicine and Health Guangdong Laboratory, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,3South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Huanxing Su
- 1State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
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9
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Yao H, Hannum DF, Zhai Y, Hill SF, Albanus RD'O, Lou W, Skidmore JM, Sanchez G, Saiakhova A, Bielas SL, Scacheri P, Ljungman M, Parker SCJ, Martin DM. CHD7 promotes neural progenitor differentiation in embryonic stem cells via altered chromatin accessibility and nascent gene expression. Sci Rep 2020; 10:17445. [PMID: 33060836 PMCID: PMC7562747 DOI: 10.1038/s41598-020-74537-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 09/30/2020] [Indexed: 01/09/2023] Open
Abstract
CHARGE syndrome, a rare multiple congenital anomaly condition, is caused by haploinsufficiency of the chromatin remodeling protein gene CHD7 (Chromodomain helicase DNA binding protein 7). Brain abnormalities and intellectual disability are commonly observed in individuals with CHARGE, and neuronal differentiation is reduced in CHARGE patient-derived iPSCs and conditional knockout mouse brains. However, the mechanisms of CHD7 function in nervous system development are not well understood. In this study, we asked whether CHD7 promotes gene transcription in neural progenitor cells via changes in chromatin accessibility. We used Chd7 null embryonic stem cells (ESCs) derived from Chd7 mutant mouse blastocysts as a tool to investigate roles of CHD7 in neuronal and glial differentiation. Loss of Chd7 significantly reduced neuronal and glial differentiation. Sholl analysis showed that loss of Chd7 impaired neuronal complexity and neurite length in differentiated neurons. Genome-wide studies demonstrated that loss of Chd7 leads to modified chromatin accessibility (ATAC-seq) and differential nascent expression (Bru-Seq) of neural-specific genes. These results suggest that CHD7 acts preferentially to alter chromatin accessibility of key genes during the transition of NPCs to neurons to promote differentiation. Our results form a basis for understanding the cell stage-specific roles for CHD7-mediated chromatin remodeling during cell lineage acquisition.
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Affiliation(s)
- Hui Yao
- Department of Pediatrics, University of Michigan, 8220C MSRB III, 1150 W. Medical Center Dr., Ann Arbor, MI, 48109-5652, USA
| | - Douglas F Hannum
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Yiwen Zhai
- Department of Pediatrics, University of Michigan, 8220C MSRB III, 1150 W. Medical Center Dr., Ann Arbor, MI, 48109-5652, USA.,Center of Genetic and Prenatal Diagnosis, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Sophie F Hill
- College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI, USA
| | | | - Wenjia Lou
- Department of Pediatrics, University of Michigan, 8220C MSRB III, 1150 W. Medical Center Dr., Ann Arbor, MI, 48109-5652, USA
| | - Jennifer M Skidmore
- Department of Pediatrics, University of Michigan, 8220C MSRB III, 1150 W. Medical Center Dr., Ann Arbor, MI, 48109-5652, USA
| | - Gilson Sanchez
- Department of Pediatrics, University of Michigan, 8220C MSRB III, 1150 W. Medical Center Dr., Ann Arbor, MI, 48109-5652, USA
| | - Alina Saiakhova
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Stephanie L Bielas
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Peter Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Stephen C J Parker
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.,Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Donna M Martin
- Department of Pediatrics, University of Michigan, 8220C MSRB III, 1150 W. Medical Center Dr., Ann Arbor, MI, 48109-5652, USA. .,Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
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10
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Dieterich W, Neurath MF, Zopf Y. Intestinal ex vivo organoid culture reveals altered programmed crypt stem cells in patients with celiac disease. Sci Rep 2020; 10:3535. [PMID: 32103108 PMCID: PMC7044285 DOI: 10.1038/s41598-020-60521-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 02/12/2020] [Indexed: 11/30/2022] Open
Abstract
The ex vivo generation of gastrointestinal organoids from crypt stem cells opens up the possibility of new research approaches investigating gastrointestinal diseases. We used this technology to study differences between healthy controls and patients with celiac disease (CD). We noticed distinct dissimilarities in the phenotypes of organoids between our study groups and found considerable variations in their gene expression. Extracellular matrix genes involved in epithelial-mesenchymal transition are expressed most differently. In addition, we demonstrated epigenetic modifications that might be responsible for the different organoid gene expression thus accounting for a deranged crypt/villus axis development in CD. The organoids have proven valuable to demonstrate fundamental differences in duodenal derived organoids between healthy controls and patients with CD and thus are a suitable tool to gain new insights in pathogenesis of CD.
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Affiliation(s)
- Walburga Dieterich
- Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany. .,Hector Center of Excellence for Nutrition, Exercise, and Sports, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.
| | - Markus F Neurath
- Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Yurdagül Zopf
- Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.,Hector Center of Excellence for Nutrition, Exercise, and Sports, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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11
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Imai A, Yamashita A, Ota MS. High-fat diet increases labial groove formation in maxillary incisors and is related to aging in C57BL/6 mice. J Oral Biosci 2019; 62:58-63. [PMID: 31862385 DOI: 10.1016/j.job.2019.12.003] [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: 10/24/2019] [Revised: 12/04/2019] [Accepted: 12/04/2019] [Indexed: 10/25/2022]
Abstract
OBJECTIVES The aim of this study was to explore the relationship between the consumption of a high-fat diet and aging-dependent formation of maxillary incisor grooves in C57BL/6 mice, and to identify putative maxillary incisor groove-related genes. METHODS We fed 2-month-old and 16-month-old C57BL/6 mice on either a chow diet or a high-fat diet for three months and observed changes in maxillary incisor grooves. We examined tissue sections of the maxillary incisors with grooves and carried out transcriptome analysis of the apical tissue fragments of maxillary incisors with/without grooves. RESULTS Consumption of a high-fat diet for three months resulted in significant increases in both body weight and the number of incisor grooves. Both the number and frequency of incisor grooves increased in an age-dependent manner from 26 to 28 months, during which time an additional groove appeared. There was abnormal differentiation and apoptosis of ameloblasts on the labial surface at the grooves of the maxillary incisors. Transcriptome analysis identified 23 genes as being specific to 24-month-old mice; these included several genes related to apoptosis and cell differentiation. CONCLUSIONS The study findings indicate that, in C57BL/6 mice, consumption of a high-fat diet increases labial groove formation in maxillary incisors, which is related to aging of the tissue stem cells in the apical root end of the teeth.
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Affiliation(s)
- Atsuko Imai
- The Division of Clinical Nutrition, Department of Food and Nutrition, Japan Women's University, Bunkyo-ku, Tokyo, Japan
| | - Atsuko Yamashita
- Laboratory of Anatomy and Physiology, Department of Food and Nutrition, Japan Women's University, Bunkyo-ku, Tokyo, Japan
| | - Masato S Ota
- Laboratory of Anatomy and Physiology, Department of Food and Nutrition, Japan Women's University, Bunkyo-ku, Tokyo, Japan.
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12
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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.
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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
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13
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Yamamoto T, Hatabayashi K, Arita M, Yajima N, Takenaka C, Suzuki T, Takahashi M, Oshima Y, Hara K, Kagawa K, Kawamata S. Kynurenine signaling through the aryl hydrocarbon receptor maintains the undifferentiated state of human embryonic stem cells. Sci Signal 2019; 12:12/587/eaaw3306. [PMID: 31239324 DOI: 10.1126/scisignal.aaw3306] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Kynurenine, which is generated from tryptophan by indoleamine 2,3-dioxygenase 1 (IDO1), binds to the aryl hydrocarbon receptor (AhR). Here, we report that kynurenine was produced by undifferentiated human embryonic stem cells (hESCs) and by induced pluripotent stem cells (iPSCs). In undifferentiated hESCs, kynurenine stimulated the AhR to promote the expression of self-renewal genes. The kynurenine-AhR complex also stimulated the expression of IDO1 and AHR, activating a positive feedback loop. Inhibition of IDO1 activity reduced the proliferation of undifferentiated ESCs but did not stimulate their differentiation. Substantial amounts of free kynurenine were present in the culture medium, providing a paracrine signal for maintenance of the undifferentiated state. Kynurenine was not present in the medium of differentiated ESCs or iPSCs. When ESCs were induced to undergo ectodermal differentiation, the abundance of kynurenine in the medium was reduced through activation of the main kynurenine catabolic pathway mediated by kynurenine aminotransferase 2 (KAT2, also known as AADAT), resulting in the secretion of 2-aminoadipic acid (2-AAA) into the culture medium. Inhibition of KAT2 activity blocked ectodermal differentiation. Thus, kynurenine metabolism plays an important role in the maintenance of the undifferentiated state and in ectodermal differentiation. Furthermore, kynurenine in the culture medium is a biomarker for the undifferentiated state, whereas the presence of 2-AAA in the culture medium is a biomarker of ESCs and iPSCs that have committed to differentiate along the ectoderm lineage.
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Affiliation(s)
- Takako Yamamoto
- Research & Development Center for Cell Therapy, Foundation for Biomedical Research and Innovation, 2-2 Minatojima Minami-machi, Chuo-ku, Kobe 650-0047, Japan
| | - Kunitada Hatabayashi
- Innovative Technology Planning Department, Tokyo Electron Limited, Akasaka Biz Tower, 5-3-1 Akasaka, Minato-Ku, Tokyo 107-6325, Japan
| | - Mao Arita
- Research & Development Center for Cell Therapy, Foundation for Biomedical Research and Innovation, 2-2 Minatojima Minami-machi, Chuo-ku, Kobe 650-0047, Japan
| | - Nobuyuki Yajima
- Research & Development Center for Cell Therapy, Foundation for Biomedical Research and Innovation, 2-2 Minatojima Minami-machi, Chuo-ku, Kobe 650-0047, Japan
| | - Chiemi Takenaka
- Research & Development Center for Cell Therapy, Foundation for Biomedical Research and Innovation, 2-2 Minatojima Minami-machi, Chuo-ku, Kobe 650-0047, Japan
| | - Takashi Suzuki
- Analytical and Measuring Instruments Division, Shimadzu Corporation, 1 Nishinokyo, Kuwahara-cho, Nagagyo-ku, Kyoto 604-8511, Japan
| | - Masatoshi Takahashi
- Analytical and Measuring Instruments Division, Shimadzu Corporation, 1 Nishinokyo, Kuwahara-cho, Nagagyo-ku, Kyoto 604-8511, Japan
| | - Yasuhiro Oshima
- Innovative Technology Planning Department, Tokyo Electron Limited, Akasaka Biz Tower, 5-3-1 Akasaka, Minato-Ku, Tokyo 107-6325, Japan
| | - Keisuke Hara
- Innovative Technology Planning Department, Tokyo Electron Limited, Akasaka Biz Tower, 5-3-1 Akasaka, Minato-Ku, Tokyo 107-6325, Japan
| | - Kenichi Kagawa
- Innovative Technology Planning Department, Tokyo Electron Limited, Akasaka Biz Tower, 5-3-1 Akasaka, Minato-Ku, Tokyo 107-6325, Japan
| | - Shin Kawamata
- Research & Development Center for Cell Therapy, Foundation for Biomedical Research and Innovation, 2-2 Minatojima Minami-machi, Chuo-ku, Kobe 650-0047, Japan. .,Riken Center for Developmental Biology, 2-1 Minatojima Minami-machi, Chuo-ku, Kobe 650-0047, Japan
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14
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Ohashi F, Miyagawa S, Yasuda S, Miura T, Kuroda T, Itoh M, Kawaji H, Ito E, Yoshida S, Saito A, Sameshima T, Kawai J, Sawa Y, Sato Y. CXCL4/PF4 is a predictive biomarker of cardiac differentiation potential of human induced pluripotent stem cells. Sci Rep 2019; 9:4638. [PMID: 30874579 PMCID: PMC6420577 DOI: 10.1038/s41598-019-40915-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 02/21/2019] [Indexed: 12/23/2022] Open
Abstract
Selection of human induced pluripotent stem cell (hiPSC) lines with high cardiac differentiation potential is important for regenerative therapy and drug screening. We aimed to identify biomarkers for predicting cardiac differentiation potential of hiPSC lines by comparing the gene expression profiles of six undifferentiated hiPSC lines with different cardiac differentiation capabilities. We used three platforms of gene expression analysis, namely, cap analysis of gene expression (CAGE), mRNA array, and microRNA array to efficiently screen biomarkers related to cardiac differentiation of hiPSCs. Statistical analysis revealed candidate biomarker genes with significant correlation between the gene expression levels in the undifferentiated hiPSCs and their cardiac differentiation potential. Of the candidate genes, PF4 was validated as a biomarker expressed in undifferentiated hiPSCs with high potential for cardiac differentiation in 13 additional hiPSC lines. Our observations suggest that PF4 may be a useful biomarker for selecting hiPSC lines appropriate for the generation of cardiomyocytes.
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Affiliation(s)
- Fumiya Ohashi
- Division of Cell-Based Therapeutic Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan.,Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, 2-2 Yamada-oka, Suita, Osaka, 565-0871, Japan.,Department of Cellular & Gene Therapy Products, Osaka University Graduate School of Pharmaceutical Sciences, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Terumo Corporation, 1500 Inokuchi, Nakai-machi, Ashigarakami-gun, Kanagawa, 259-0151, Japan
| | - Shigeru Miyagawa
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, 2-2 Yamada-oka, Suita, Osaka, 565-0871, Japan
| | - Satoshi Yasuda
- Division of Cell-Based Therapeutic Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Takumi Miura
- Division of Cell-Based Therapeutic Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Takuya Kuroda
- Division of Cell-Based Therapeutic Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Masayoshi Itoh
- Preventive Medicine and Diagnosis Innovation Program, RIKEN Center, 1-7-22, Suehirocho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Hideya Kawaji
- Preventive Medicine and Diagnosis Innovation Program, RIKEN Center, 1-7-22, Suehirocho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.,Preventive Medicine and Applied Genomics Unit, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Emiko Ito
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, 2-2 Yamada-oka, Suita, Osaka, 565-0871, Japan
| | - Shohei Yoshida
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, 2-2 Yamada-oka, Suita, Osaka, 565-0871, Japan
| | - Atsuhiro Saito
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, 2-2 Yamada-oka, Suita, Osaka, 565-0871, Japan
| | - Tadashi Sameshima
- Terumo Corporation, 1500 Inokuchi, Nakai-machi, Ashigarakami-gun, Kanagawa, 259-0151, Japan
| | - Jun Kawai
- Preventive Medicine and Diagnosis Innovation Program, RIKEN Center, 1-7-22, Suehirocho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Yoshiki Sawa
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, 2-2 Yamada-oka, Suita, Osaka, 565-0871, Japan
| | - Yoji Sato
- Division of Cell-Based Therapeutic Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan. .,Department of Cellular & Gene Therapy Products, Osaka University Graduate School of Pharmaceutical Sciences, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan. .,Department of Quality Assurance Science for Pharmaceuticals, Nagoya City University Graduate School of Pharmaceutical Sciences, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi, 467-8603, Japan. .,Department of Translational Pharmaceutical Sciences, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka, 812-8582, Japan. .,LiSE Laboratory, Kanagawa Institute of Industrial Science and Technology, 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-0821, Japan.
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15
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Machado RAC, Schneider H, DeOcesano-Pereira C, Lichtenstein F, Andrade F, Fujita A, Trombetta-Lima M, Weller M, Bowman-Colin C, Sogayar MC. CHD7 promotes glioblastoma cell motility and invasiveness through transcriptional modulation of an invasion signature. Sci Rep 2019; 9:3952. [PMID: 30850678 PMCID: PMC6408455 DOI: 10.1038/s41598-019-39564-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 01/10/2019] [Indexed: 01/21/2023] Open
Abstract
Chromatin remodeler proteins exert an important function in promoting dynamic modifications in the chromatin architecture, performing a central role in regulating gene transcription. Deregulation of these molecular machines may lead to striking perturbations in normal cell function. The CHD7 gene is a member of the chromodomain helicase DNA-binding family and, when mutated, has been shown to be the cause of the CHARGE syndrome, a severe developmental human disorder. Moreover, CHD7 has been described to be essential for neural stem cells and it is also highly expressed or mutated in a number of human cancers. However, its potential role in glioblastoma has not yet been tested. Here, we show that CHD7 is up-regulated in human glioma tissues and we demonstrate that CHD7 knockout (KO) in LN-229 glioblastoma cells suppresses anchorage-independent growth and spheroid invasion in vitro. Additionally, CHD7 KO impairs tumor growth and increases overall survival in an orthotopic mouse xenograft model. Conversely, ectopic overexpression of CHD7 in LN-428 and A172 glioblastoma cell lines increases cell motility and invasiveness in vitro and promotes LN-428 tumor growth in vivo. Finally, RNA-seq analysis revealed that CHD7 modulates a specific transcriptional signature of invasion-related target genes. Further studies should explore clinical-translational implications for glioblastoma treatment.
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Affiliation(s)
- Raquel A C Machado
- Department of Biochemistry, Chemistry Institute, University of São Paulo, São Paulo 05508-000 SP, Brazil
- Cell and Molecular Therapy Center (NUCEL), Internal Medicine Department, School of Medicine, University of São Paulo, São Paulo 05360-130 SP, Brazil
| | - Hannah Schneider
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Carlos DeOcesano-Pereira
- Cell and Molecular Therapy Center (NUCEL), Internal Medicine Department, School of Medicine, University of São Paulo, São Paulo 05360-130 SP, Brazil
- Centre of Excellence in New Target Discovery (CENTD), Butantan Institute, São Paulo, SP, Brazil
| | - Flavio Lichtenstein
- Centre of Excellence in New Target Discovery (CENTD), Butantan Institute, São Paulo, SP, Brazil
| | - Fernando Andrade
- Department of Computer Science, Institute of Mathematics and Statistics, University of São Paulo, São Paulo, Brazil
| | - André Fujita
- Department of Computer Science, Institute of Mathematics and Statistics, University of São Paulo, São Paulo, Brazil
| | - Marina Trombetta-Lima
- Cell and Molecular Therapy Center (NUCEL), Internal Medicine Department, School of Medicine, University of São Paulo, São Paulo 05360-130 SP, Brazil
| | - Michael Weller
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Christian Bowman-Colin
- Cell and Molecular Therapy Center (NUCEL), Internal Medicine Department, School of Medicine, University of São Paulo, São Paulo 05360-130 SP, Brazil.
- Dana Farber Cancer Institute, Harvard Medical School, 1 Jimmi Fund Way - SM808, Boston, MA, USA.
| | - Mari Cleide Sogayar
- Department of Biochemistry, Chemistry Institute, University of São Paulo, São Paulo 05508-000 SP, Brazil.
- Cell and Molecular Therapy Center (NUCEL), Internal Medicine Department, School of Medicine, University of São Paulo, São Paulo 05360-130 SP, Brazil.
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16
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Zimta AA, Baru O, Badea M, Buduru SD, Berindan-Neagoe I. The Role of Angiogenesis and Pro-Angiogenic Exosomes in Regenerative Dentistry. Int J Mol Sci 2019; 20:ijms20020406. [PMID: 30669338 PMCID: PMC6359271 DOI: 10.3390/ijms20020406] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 01/04/2019] [Accepted: 01/15/2019] [Indexed: 02/07/2023] Open
Abstract
Dental surgeries can result in traumatic wounds that provoke major discomfort and have a high risk of infection. In recent years, density research has taken a keen interest in finding answers to this problem by looking at the latest results made in regenerative medicine and adapting them to the specificities of oral tissue. One of the undertaken directions is the study of angiogenesis as an integrative part of oral tissue regeneration. The stimulation of this process is intended to enhance the local availability of stem cells, oxygen levels, nutrient supply, and evacuation of toxic waste. For a successful stimulation of local angiogenesis, two major cellular components must be considered: the stem cells and the vascular endothelial cells. The exosomes are extracellular vesicles, which mediate the communication between two cell types. In regenerative dentistry, the analysis of exosome miRNA content taps into the extended communication between these cell types with the purpose of improving the regenerative potential of oral tissue. This review analyzes the stem cells available for the dentistry, the molecular cargo of their exosomes, and the possible implications these may have for a future therapeutic induction of angiogenesis in the oral wounds.
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Affiliation(s)
- Alina-Andreea Zimta
- MEDFUTURE-Research Center for Advanced Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy, 23 Marinescu Street, 400337 Cluj-Napoca, Romania.
| | - Oana Baru
- Department of Preventive Dentistry, Faculty of Dental Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400083 Cluj-Napoca, Romania.
| | - Mandra Badea
- Department of Preventive Dentistry, Faculty of Dental Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400083 Cluj-Napoca, Romania.
| | - Smaranda Dana Buduru
- Prosthetics and Dental materials, Faculty of Dental Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, 32 Clinicilor Street, 400006 Cluj-Napoca, Romania.
- Stomestet Stomatology Clinic, Calea Manastur 68A Street, 400658 Cluj-Napoca, Romania.
| | - Ioana Berindan-Neagoe
- MEDFUTURE-Research Center for Advanced Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy, 23 Marinescu Street, 400337 Cluj-Napoca, Romania.
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy, 23 Marinescu Street, 400337 Cluj-Napoca, Romania.
- Department of Functional Genomics and Experimental Pathology, The Oncology Institute "Prof. Dr. Ion Chiricuta", Republicii 34th street, 400015 Cluj-Napoca, Romania.
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17
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The Role of DNA/Histone Modifying Enzymes and Chromatin Remodeling Complexes in Testicular Germ Cell Tumors. Cancers (Basel) 2018; 11:cancers11010006. [PMID: 30577487 PMCID: PMC6357018 DOI: 10.3390/cancers11010006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 12/10/2018] [Accepted: 12/18/2018] [Indexed: 12/22/2022] Open
Abstract
It is well established that cancer cells exhibit alterations in chromatin structure and accessibility. Indeed, the dysregulation of many protein-coding players with enzymatic activity (DNA and histone-modifying enzymes) and chromatin remodelers have been depicted in various tumor models in recent years. Still, little attention has been directed towards testicular germ cell tumors (TGCTs)-representing the most common neoplasm among young adult Caucasian men-with most studies focusing on exploring the role of DNA methyltransferases (DNMTs) and DNA demethylases (TETs). TGCTs represent a complex tumor model, associated with developmental and embryogenesis-related phenomena, and display seldom (cyto)genetic aberrations, leaving room for Epigenetics to explain such morphological and clinical diversity. Herein, we have summarized the major findings that were reported in literature regarding the dysregulation of DNA/histone-modifying enzymes and chromatin remodelers in TGCTs. Additionally, we performed in silico analysis of The Cancer Genome Atlas database to find the most relevant of those players in TGCTs. We concluded that several DNA/histone-modifying enzymes and chromatin remodelers may serve as biomarkers for subtyping, dictating prognosis and survival, and, possibly, for serving as targets of directed, less toxic therapies.
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18
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Kasah S, Oddy C, Basson MA. Autism-linked CHD gene expression patterns during development predict multi-organ disease phenotypes. J Anat 2018; 233:755-769. [PMID: 30277262 DOI: 10.1111/joa.12889] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2018] [Indexed: 12/24/2022] Open
Abstract
Recent large-scale exome sequencing studies have identified mutations in several members of the CHD (Chromodomain Helicase DNA-binding protein) gene family in neurodevelopmental disorders. Mutations in the CHD2 gene have been linked to developmental delay, intellectual disability, autism and seizures, CHD8 mutations to autism and intellectual disability, whereas haploinsufficiency of CHD7 is associated with executive dysfunction and intellectual disability. In addition to these neurodevelopmental features, a wide range of other developmental defects are associated with mutants of these genes, especially with regards to CHD7 haploinsufficiency, which is the primary cause of CHARGE syndrome. Whilst the developmental expression of CHD7 has been reported previously, limited information on the expression of CHD2 and CHD8 during development is available. Here, we compare the expression patterns of all three genes during mouse development directly. We find high, widespread expression of these genes at early stages of development that gradually becomes restricted during later developmental stages. Chd2 and Chd8 are widely expressed in the developing central nervous system (CNS) at all stages of development, with moderate expression remaining in the neocortex, hippocampus, olfactory bulb and cerebellum of the postnatal brain. Similarly, Chd7 expression is seen throughout the CNS during late embryogenesis and early postnatal development, with strong enrichment in the cerebellum, but displays low expression in the cortex and neurogenic niches in early life. In addition to expression in the brain, novel sites of Chd2 and Chd8 expression are reported. These findings suggest additional roles for these genes in organogenesis and predict that mutation of these genes may predispose individuals to a range of other, non-neurological developmental defects.
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Affiliation(s)
- Sahrunizam Kasah
- Centre for Craniofacial and Regenerative Biology, King's College London, London, UK
| | - Christopher Oddy
- Centre for Craniofacial and Regenerative Biology, King's College London, London, UK
| | - M Albert Basson
- Centre for Craniofacial and Regenerative Biology, King's College London, London, UK.,MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
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