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Zhong Z, Du J, Zhu X, Guan L, Hu Y, Zhang P, Wang H. Highly efficient conversion of mouse fibroblasts into functional hepatic cells under chemical induction. J Mol Cell Biol 2024; 15:mjad071. [PMID: 37996395 PMCID: PMC11121195 DOI: 10.1093/jmcb/mjad071] [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: 12/06/2022] [Revised: 06/25/2023] [Accepted: 11/22/2023] [Indexed: 11/25/2023] Open
Abstract
Previous studies have shown that hepatocyte-like cells can be generated from fibroblasts using either lineage-specific transcription factors or chemical induction methods. However, these methods have their own deficiencies that restrict the therapeutic applications of such induced hepatocytes. In this study, we present a transgene-free, highly efficient chemical-induced direct reprogramming approach to generate hepatocyte-like cells from mouse embryonic fibroblasts (MEFs). Using a small molecule cocktail (SMC) as an inducer, MEFs can be directly reprogrammed into hepatocyte-like cells, bypassing the intermediate stages of pluripotent and immature hepatoblasts. These chemical-induced hepatocyte-like cells (ciHeps) closely resemble mature primary hepatocytes in terms of morphology, biological behavior, gene expression patterns, marker expression levels, and hepatic functions. Furthermore, transplanted ciHeps can integrate into the liver, promote liver regeneration, and improve survival rates in mice with acute liver damage. ciHeps can also ameliorate liver fibrosis caused by chronic injuries and enhance liver function. Notably, ciHeps exhibit no tumorigenic potential either in vitro or in vivo. Mechanistically, SMC-induced mesenchymal-to-epithelial transition and suppression of SNAI1 contribute to the fate conversion of fibroblasts into ciHeps. These results indicate that this transgene-free, chemical-induced direct reprogramming technique has the potential to serve as a valuable means of producing alternative hepatocytes for both research and therapeutic purposes. Additionally, this method also sheds light on the direct reprogramming of other cell types under chemical induction.
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Affiliation(s)
- Zhi Zhong
- Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- National Center for Liver Cancer, Naval Medical University, Shanghai 201805, China
| | - Jiangchuan Du
- National Center for Liver Cancer, Naval Medical University, Shanghai 201805, China
| | - Xiangjie Zhu
- National Center for Liver Cancer, Naval Medical University, Shanghai 201805, China
- Institute of Metabolism and Integrative Biology, Fudan University, Shanghai 200438, China
| | - Lingting Guan
- National Center for Liver Cancer, Naval Medical University, Shanghai 201805, China
| | - Yanyu Hu
- National Center for Liver Cancer, Naval Medical University, Shanghai 201805, China
| | - Peilin Zhang
- National Center for Liver Cancer, Naval Medical University, Shanghai 201805, China
| | - Hongyang Wang
- Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- National Center for Liver Cancer, Naval Medical University, Shanghai 201805, China
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Song Y, Soto J, Wong SY, Wu Y, Hoffman T, Akhtar N, Norris S, Chu J, Park H, Kelkhoff DO, Ang CE, Wernig M, Kasko A, Downing TL, Poo MM, Li S. Biphasic regulation of epigenetic state by matrix stiffness during cell reprogramming. SCIENCE ADVANCES 2024; 10:eadk0639. [PMID: 38354231 PMCID: PMC10866547 DOI: 10.1126/sciadv.adk0639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 01/12/2024] [Indexed: 02/16/2024]
Abstract
We investigate how matrix stiffness regulates chromatin reorganization and cell reprogramming and find that matrix stiffness acts as a biphasic regulator of epigenetic state and fibroblast-to-neuron conversion efficiency, maximized at an intermediate stiffness of 20 kPa. ATAC sequencing analysis shows the same trend of chromatin accessibility to neuronal genes at these stiffness levels. Concurrently, we observe peak levels of histone acetylation and histone acetyltransferase (HAT) activity in the nucleus on 20 kPa matrices, and inhibiting HAT activity abolishes matrix stiffness effects. G-actin and cofilin, the cotransporters shuttling HAT into the nucleus, rises with decreasing matrix stiffness; however, reduced importin-9 on soft matrices limits nuclear transport. These two factors result in a biphasic regulation of HAT transport into nucleus, which is directly demonstrated on matrices with dynamically tunable stiffness. Our findings unravel a mechanism of the mechano-epigenetic regulation that is valuable for cell engineering in disease modeling and regenerative medicine applications.
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Affiliation(s)
- Yang Song
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Jennifer Soto
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Sze Yue Wong
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Yifan Wu
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Tyler Hoffman
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Navied Akhtar
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92617, USA
| | - Sam Norris
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Julia Chu
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hyungju Park
- Division of Neurobiology, Department of Molecular and Cell Biology, Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Structure and Function of Neural Network, Korea Brain Research Institute (KBRI), Daegu 41068, South Korea
| | - Douglas O. Kelkhoff
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Cheen Euong Ang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Pathology and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Marius Wernig
- Department of Pathology and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Andrea Kasko
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Timothy L. Downing
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92617, USA
| | - Mu-ming Poo
- Division of Neurobiology, Department of Molecular and Cell Biology, Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA
- Institute of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Song Li
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
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3
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Dhanjal DS, Singh R, Sharma V, Nepovimova E, Adam V, Kuca K, Chopra C. Advances in Genetic Reprogramming: Prospects from Developmental Biology to Regenerative Medicine. Curr Med Chem 2024; 31:1646-1690. [PMID: 37138422 DOI: 10.2174/0929867330666230503144619] [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: 11/12/2022] [Revised: 03/13/2023] [Accepted: 03/16/2023] [Indexed: 05/05/2023]
Abstract
The foundations of cell reprogramming were laid by Yamanaka and co-workers, who showed that somatic cells can be reprogrammed into pluripotent cells (induced pluripotency). Since this discovery, the field of regenerative medicine has seen advancements. For example, because they can differentiate into multiple cell types, pluripotent stem cells are considered vital components in regenerative medicine aimed at the functional restoration of damaged tissue. Despite years of research, both replacement and restoration of failed organs/ tissues have remained elusive scientific feats. However, with the inception of cell engineering and nuclear reprogramming, useful solutions have been identified to counter the need for compatible and sustainable organs. By combining the science underlying genetic engineering and nuclear reprogramming with regenerative medicine, scientists have engineered cells to make gene and stem cell therapies applicable and effective. These approaches have enabled the targeting of various pathways to reprogramme cells, i.e., make them behave in beneficial ways in a patient-specific manner. Technological advancements have clearly supported the concept and realization of regenerative medicine. Genetic engineering is used for tissue engineering and nuclear reprogramming and has led to advances in regenerative medicine. Targeted therapies and replacement of traumatized , damaged, or aged organs can be realized through genetic engineering. Furthermore, the success of these therapies has been validated through thousands of clinical trials. Scientists are currently evaluating induced tissue-specific stem cells (iTSCs), which may lead to tumour-free applications of pluripotency induction. In this review, we present state-of-the-art genetic engineering that has been used in regenerative medicine. We also focus on ways that genetic engineering and nuclear reprogramming have transformed regenerative medicine and have become unique therapeutic niches.
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Affiliation(s)
- Daljeet Singh Dhanjal
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Reena Singh
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Varun Sharma
- Head of Bioinformatic Division, NMC Genetics India Pvt. Ltd., Gurugram, India
| | - Eugenie Nepovimova
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, 50003, Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, Brno, CZ 613 00, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Purkynova 123, Brno, CZ-612 00, Czech Republic
| | - Kamil Kuca
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, 50003, Czech Republic
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, 50005, Czech Republic
| | - Chirag Chopra
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
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Zhang J, Wang Y, Guo J, Zhang N, He J, Zhou Z, Wu F. Direct Reprogramming of Mouse Fibroblasts to Osteoblast-like Cells Using Runx2/Dlx5 Factors on Engineered Stiff Hydrogels. ACS APPLIED MATERIALS & INTERFACES 2023; 15:59209-59223. [PMID: 38102996 DOI: 10.1021/acsami.3c14777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Direct reprogramming of somatic cells into functional cells still faces major limitations in terms of efficiency and achieving functional maturity of the reprogramed cells. While different approaches have been developed commonly based on exploiting biochemical signals, introducing appropriate mechanical cues that stimulate the reprogramming process is rarely reported. In this study, collagen-coated polyacrylamide (PAM) hydrogels with stiffness close to that of collagenous bone (40 kPa) were adopted to augment the direct reprogramming process of mouse fibroblasts to osteoblastic-like cells. The results suggested that culturing cells on a hydrogel substrate enhanced the overexpression of osteogenic transcription factors using nonviral vectors and improved the yield of osteoblast-like cells. Particularly, a synergistic effect on achieving osteogenic functionality has been observed for the mechanical cues and overexpression of transcriptional factors, leading to enhanced osteogenic transformation and production of bone mineral matrix. Animal experiments suggested that reprogramed cells generated on matrix hydrogels accelerated bone regeneration and stimulated ectopic osteogenesis. Mechanism analysis suggested the critical involvement of actomyosin contraction and mechanical signal-mediated pathways like the RhoA-ROCK pathway, leading to a synergistic effect on the key transcriptional processes, including chromatin remodeling, nuclear translocation, and epigenetic transition. This study provides insights into the mechanical cue-enhanced direct reprogramming and cell therapy.
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Affiliation(s)
- Junwei Zhang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, PR China
| | - Yao Wang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, PR China
| | - Jing Guo
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, PR China
| | - Nihui Zhang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, PR China
| | - Jing He
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, PR China
| | - Zongke Zhou
- Orthopedic Research Institute & Department of Orthopedics, West China Hospital of Sichuan University, Chengdu 610041, Sichuan, China
| | - Fang Wu
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, PR China
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5
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Park S, Lee J, Ahn KS, Shim HW, Yoon J, Hyun J, Lee JH, Jang S, Yoo KH, Jang Y, Kim T, Kim HK, Lee MR, Jang J, Shim H, Kim H. Cyclic Stretch Promotes Cellular Reprogramming Process through Cytoskeletal-Nuclear Mechano-Coupling and Epigenetic Modification. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303395. [PMID: 37727069 PMCID: PMC10646259 DOI: 10.1002/advs.202303395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/27/2023] [Indexed: 09/21/2023]
Abstract
Advancing the technologies for cellular reprogramming with high efficiency has significant impact on regenerative therapy, disease modeling, and drug discovery. Biophysical cues can tune the cell fate, yet the precise role of external physical forces during reprogramming remains elusive. Here the authors show that temporal cyclic-stretching of fibroblasts significantly enhances the efficiency of induced pluripotent stem cell (iPSC) production. Generated iPSCs are proven to express pluripotency markers and exhibit in vivo functionality. Bulk RNA-sequencing reveales that cyclic-stretching enhances biological characteristics required for pluripotency acquisition, including increased cell division and mesenchymal-epithelial transition. Of note, cyclic-stretching activates key mechanosensitive molecules (integrins, perinuclear actins, nesprin-2, and YAP), across the cytoskeletal-to-nuclear space. Furthermore, stretch-mediated cytoskeletal-nuclear mechano-coupling leads to altered epigenetic modifications, mainly downregulation in H3K9 methylation, and its global gene occupancy change, as revealed by genome-wide ChIP-sequencing and pharmacological inhibition tests. Single cell RNA-sequencing further identifies subcluster of mechano-responsive iPSCs and key epigenetic modifier in stretched cells. Collectively, cyclic-stretching activates iPSC reprogramming through mechanotransduction process and epigenetic changes accompanied by altered occupancy of mechanosensitive genes. This study highlights the strong link between external physical forces with subsequent mechanotransduction process and the epigenetic changes with expression of related genes in cellular reprogramming, holding substantial implications in the field of cell biology, tissue engineering, and regenerative medicine.
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Saadeldin IM, Bang S, Maigoro AY, Yun SH, Kim SI, Lee S, Cho J. Proteomic Analysis and Reprogramming Potential of the Porcine Intra-Ooplasmic Nanovesicles. Cell Reprogram 2023; 25:238-250. [PMID: 37725012 DOI: 10.1089/cell.2023.0050] [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] [Indexed: 09/21/2023] Open
Abstract
Oocytes contain reprogramming machinery that can transform somatic cells into totipotent cells. In this study, we aimed to isolate and characterize nanovesicles from mature porcine oocytes and described them for the first time as "intra-ooplasmic vesicles (IOVs)". Isolated IOVs had an average diameter of 186.3 ± 10.8 nm. Proteomic analysis revealed 467 peptide reads, with the top 20 proteins related to reprogramming, antioxidative defense, cytoskeleton, heat shock proteins, and metabolism. Protein-protein interaction and gene ontology analysis indicated that these proteins were involved in various biological pathways, including protein folding, metabolism, and cellular responses to stress. Supplementing cultured fibroblasts with IOVs resulted in the expression of the pluripotency marker OCT4 and the early trophoblastic marker CDX2 and increased expression of the corresponding mRNAs together with increasing KLF4 and SALL4 expression. IOV treatment of fibroblasts for 14 consecutive days resulted in changes in cell morphology, with increased expression of ZEB2 and YBX3 as markers for epithelial-to-mesenchymal transition (EMT). These results provide a rationale for further characterization of IOVs, investigation of potential reprogramming capabilities for EMT, and the generation of induced pluripotent or oligopotent stem cells.
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Affiliation(s)
- Islam M Saadeldin
- Laboratory of Theriogenology, College of Veterinary Medicine, Chungnam National University, Daejeon, Republic of Korea
- Research Institute of Veterinary Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Seonggyu Bang
- Laboratory of Theriogenology, College of Veterinary Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Abdulkadir Y Maigoro
- Department of Life Sciences, Incheon National University, Incheon, Republic of Korea
| | - Sung Ho Yun
- Korea Basic Science Institute (KBSI), Ochang, Republic of Korea
| | - Seung Ii Kim
- Korea Basic Science Institute (KBSI), Ochang, Republic of Korea
| | - Sanghoon Lee
- Laboratory of Theriogenology, College of Veterinary Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Jongki Cho
- Laboratory of Theriogenology, College of Veterinary Medicine, Chungnam National University, Daejeon, Republic of Korea
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Sahito JZA, Deng S, Qin L, Xiao L, Zhang D, Huang B. CeRNA Network Reveals the Circular RNA Characterization in Goat Ear Fibroblasts Reprogramming into Mammary Epithelial Cells. Genes (Basel) 2023; 14:1831. [PMID: 37895180 PMCID: PMC10606430 DOI: 10.3390/genes14101831] [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: 07/27/2023] [Revised: 08/18/2023] [Accepted: 08/22/2023] [Indexed: 10/29/2023] Open
Abstract
Circular RNAs (circRNAs) are a type of non-coding RNA that play a crucial role in the development and lactation of mammary glands in mammals. A total of 107 differentially expressed circRNAs (DE circRNAs) were found, of which 52 were up-regulated and 55 were down-regulated. We also found that DE circRNA host genes were mainly involved in GO terms related to the development process of mammary epithelial cells and KEGG pathways were mostly related to mammary epithelial cells, lactation, and gland development. Protein network analysis found that DE circRNAs can competitively bind to miRNAs as key circRNAs by constructing a circRNA-miRNA-mRNA network. CircRNAs competitively bind to miRNAs (miR-10b-3p, miR-671-5p, chi-miR-200c, chi-miR-378-3p, and chi-miR-30e-5p) involved in goat mammary gland development, mammary epithelial cells, and lactation, affecting the expression of core genes (CDH2, MAPK1, ITGB1, CAMSAP2, and MAPKAPK5). Here, we generated CiMECs and systematically explored the differences in the transcription profile for the first time using whole-transcriptome sequencing. We also analyzed the interaction among mRNA, miRNA, and cirRNA and predicted that circRNA plays an important role in the maintenance of mammary epithelial cells.
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Affiliation(s)
- Jam Zaheer Ahmed Sahito
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (J.Z.A.S.); (S.D.); (L.Q.); (L.X.); (D.Z.)
| | - Shan Deng
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (J.Z.A.S.); (S.D.); (L.Q.); (L.X.); (D.Z.)
| | - Liangshan Qin
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (J.Z.A.S.); (S.D.); (L.Q.); (L.X.); (D.Z.)
| | - Lianggui Xiao
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (J.Z.A.S.); (S.D.); (L.Q.); (L.X.); (D.Z.)
| | - Dandan Zhang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (J.Z.A.S.); (S.D.); (L.Q.); (L.X.); (D.Z.)
- Guangxi Key Laboratory of Eye Health, The People’s Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical Sciences, Nanning, 530021, China
| | - Ben Huang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (J.Z.A.S.); (S.D.); (L.Q.); (L.X.); (D.Z.)
- Guangxi Key Laboratory of Eye Health, The People’s Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical Sciences, Nanning, 530021, China
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Soto J, Song Y, Wu Y, Chen B, Park H, Akhtar N, Wang P, Hoffman T, Ly C, Sia J, Wong S, Kelkhoff DO, Chu J, Poo M, Downing TL, Rowat AC, Li S. Reduction of Intracellular Tension and Cell Adhesion Promotes Open Chromatin Structure and Enhances Cell Reprogramming. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2300152. [PMID: 37357983 PMCID: PMC10460843 DOI: 10.1002/advs.202300152] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 05/13/2023] [Indexed: 06/27/2023]
Abstract
The role of transcription factors and biomolecules in cell type conversion has been widely studied. Yet, it remains unclear whether and how intracellular mechanotransduction through focal adhesions (FAs) and the cytoskeleton regulates the epigenetic state and cell reprogramming. Here, it is shown that cytoskeletal structures and the mechanical properties of cells are modulated during the early phase of induced neuronal (iN) reprogramming, with an increase in actin cytoskeleton assembly induced by Ascl1 transgene. The reduction of actin cytoskeletal tension or cell adhesion at the early phase of reprogramming suppresses the expression of mesenchymal genes, promotes a more open chromatin structure, and significantly enhances the efficiency of iN conversion. Specifically, reduction of intracellular tension or cell adhesion not only modulates global epigenetic marks, but also decreases DNA methylation and heterochromatin marks and increases euchromatin marks at the promoter of neuronal genes, thus enhancing the accessibility for gene activation. Finally, micro- and nano-topographic surfaces that reduce cell adhesions enhance iN reprogramming. These novel findings suggest that the actin cytoskeleton and FAs play an important role in epigenetic regulation for cell fate determination, which may lead to novel engineering approaches for cell reprogramming.
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Affiliation(s)
- Jennifer Soto
- Department of BioengineeringUniversity of CaliforniaLos AngelesCA90095USA
| | - Yang Song
- Department of BioengineeringUniversity of CaliforniaLos AngelesCA90095USA
| | - Yifan Wu
- Department of BioengineeringUniversity of CaliforniaLos AngelesCA90095USA
| | - Binru Chen
- Department of BioengineeringUniversity of CaliforniaLos AngelesCA90095USA
| | - Hyungju Park
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCA94720USA
| | - Navied Akhtar
- Department of Biomedical EngineeringUniversity of CaliforniaIrvineCA92617USA
| | - Peng‐Yuan Wang
- Department of BioengineeringUniversity of CaliforniaLos AngelesCA90095USA
- Oujiang LaboratoryKey Laboratory of Alzheimer's Disease of Zhejiang ProvinceInstitute of AgingWenzhou Medical UniversityWenzhouZhejiang325024China
| | - Tyler Hoffman
- Department of BioengineeringUniversity of CaliforniaLos AngelesCA90095USA
| | - Chau Ly
- Department of BioengineeringUniversity of CaliforniaLos AngelesCA90095USA
- Department of Integrative Biology and PhysiologyUniversity of CaliforniaLos AngelesCA90095USA
| | - Junren Sia
- Department of BioengineeringUniversity of CaliforniaBerkeleyCA94720USA
| | - SzeYue Wong
- Department of BioengineeringUniversity of CaliforniaBerkeleyCA94720USA
| | | | - Julia Chu
- Department of BioengineeringUniversity of CaliforniaBerkeleyCA94720USA
| | - Mu‐Ming Poo
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCA94720USA
| | - Timothy L. Downing
- Department of Biomedical EngineeringUniversity of CaliforniaIrvineCA92617USA
| | - Amy C. Rowat
- Department of BioengineeringUniversity of CaliforniaLos AngelesCA90095USA
- Department of Integrative Biology and PhysiologyUniversity of CaliforniaLos AngelesCA90095USA
| | - Song Li
- Department of BioengineeringUniversity of CaliforniaLos AngelesCA90095USA
- Department of MedicineUniversity of CaliforniaLos AngelesCA90095USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell ResearchUniversity of California, Los AngelesLos AngelesCA90095USA
- Jonsson Comprehensive Cancer CenterDavid Geffen School of MedicineUniversity of California, Los AngelesLos AngelesCA90095USA
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9
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Wang G, Wang Y, Lyu Y, He H, Liuyang S, Wang J, Sun S, Cheng L, Fu Y, Zhu J, Zhong X, Yang Z, Chen Q, Li C, Guan J, Deng H. Chemical-induced epigenome resetting for regeneration program activation in human cells. Cell Rep 2023; 42:112547. [PMID: 37224020 DOI: 10.1016/j.celrep.2023.112547] [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: 11/09/2022] [Revised: 01/30/2023] [Accepted: 05/04/2023] [Indexed: 05/26/2023] Open
Abstract
Human somatic cells can be reprogrammed to pluripotent stem cells by small molecules through an intermediate stage with a regeneration signature, but how this regeneration state is induced remains largely unknown. Here, through integrated single-cell analysis of transcriptome, we demonstrate that the pathway of human chemical reprogramming with regeneration state is distinct from that of transcription-factor-mediated reprogramming. Time-course construction of chromatin landscapes unveils hierarchical histone modification remodeling underlying the regeneration program, which involved sequential enhancer recommissioning and mirrored the reversal process of regeneration potential lost in organisms as they mature. In addition, LEF1 is identified as a key upstream regulator for regeneration gene program activation. Furthermore, we reveal that regeneration program activation requires sequential enhancer silencing of somatic and proinflammatory programs. Altogether, chemical reprogramming resets the epigenome through reversal of the loss of natural regeneration, representing a distinct concept for cellular reprogramming and advancing the development of regenerative therapeutic strategies.
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Affiliation(s)
- Guan Wang
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China; State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Yanglu Wang
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China; Academy for Advanced Interdisciplinary Studies, The Center for Biomed-X Research, Peking University, Beijing, China
| | - Yulin Lyu
- School of Life Sciences, Center for Bioinformatics, Center for Statistical Science, Peking University, Beijing, China
| | - Huanjing He
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Shijia Liuyang
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Jinlin Wang
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Shicheng Sun
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Lin Cheng
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yao Fu
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Jialiang Zhu
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Xinxing Zhong
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China; State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Zhihan Yang
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Qijing Chen
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Cheng Li
- School of Life Sciences, Center for Bioinformatics, Center for Statistical Science, Peking University, Beijing, China.
| | - Jingyang Guan
- Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing, China.
| | - Hongkui Deng
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China; State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China.
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10
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Yang S, Hu H, Kung H, Zou R, Dai Y, Hu Y, Wang T, Lv T, Yu J, Li F. Organoids: The current status and biomedical applications. MedComm (Beijing) 2023; 4:e274. [PMID: 37215622 PMCID: PMC10192887 DOI: 10.1002/mco2.274] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 04/22/2023] [Accepted: 04/27/2023] [Indexed: 05/24/2023] Open
Abstract
Organoids are three-dimensional (3D) miniaturized versions of organs or tissues that are derived from cells with stem potential and can self-organize and differentiate into 3D cell masses, recapitulating the morphology and functions of their in vivo counterparts. Organoid culture is an emerging 3D culture technology, and organoids derived from various organs and tissues, such as the brain, lung, heart, liver, and kidney, have been generated. Compared with traditional bidimensional culture, organoid culture systems have the unique advantage of conserving parental gene expression and mutation characteristics, as well as long-term maintenance of the function and biological characteristics of the parental cells in vitro. All these features of organoids open up new opportunities for drug discovery, large-scale drug screening, and precision medicine. Another major application of organoids is disease modeling, and especially various hereditary diseases that are difficult to model in vitro have been modeled with organoids by combining genome editing technologies. Herein, we introduce the development and current advances in the organoid technology field. We focus on the applications of organoids in basic biology and clinical research, and also highlight their limitations and future perspectives. We hope that this review can provide a valuable reference for the developments and applications of organoids.
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Affiliation(s)
- Siqi Yang
- Division of Biliary Tract SurgeryDepartment of General SurgeryWest China HospitalSichuan UniversityChengduSichuan ProvinceChina
| | - Haijie Hu
- Division of Biliary Tract SurgeryDepartment of General SurgeryWest China HospitalSichuan UniversityChengduSichuan ProvinceChina
| | - Hengchung Kung
- Krieger School of Arts and SciencesJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Ruiqi Zou
- Division of Biliary Tract SurgeryDepartment of General SurgeryWest China HospitalSichuan UniversityChengduSichuan ProvinceChina
| | - Yushi Dai
- Division of Biliary Tract SurgeryDepartment of General SurgeryWest China HospitalSichuan UniversityChengduSichuan ProvinceChina
| | - Yafei Hu
- Division of Biliary Tract SurgeryDepartment of General SurgeryWest China HospitalSichuan UniversityChengduSichuan ProvinceChina
| | - Tiantian Wang
- Key Laboratory of Rehabilitation Medicine in Sichuan ProvinceWest China HospitalSichuan UniversityChengduSichuanChina
| | - Tianrun Lv
- Division of Biliary Tract SurgeryDepartment of General SurgeryWest China HospitalSichuan UniversityChengduSichuan ProvinceChina
| | - Jun Yu
- Departments of MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
- Departments of OncologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Fuyu Li
- Division of Biliary Tract SurgeryDepartment of General SurgeryWest China HospitalSichuan UniversityChengduSichuan ProvinceChina
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11
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Temporary and permanent control of partially specified Boolean networks. Biosystems 2023; 223:104795. [PMID: 36377120 DOI: 10.1016/j.biosystems.2022.104795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 10/16/2022] [Accepted: 10/19/2022] [Indexed: 01/11/2023]
Abstract
Boolean networks (BNs) are a well-accepted modelling formalism in computational systems biology. Nevertheless, modellers often cannot identify only a single BN that matches the biological reality. The typical reasons for this is insufficient knowledge or a lack of experimental data. Formally, this uncertainty can be expressed using partially specified Boolean networks (PSBNs), which encode the wide range of network candidates into a single structure. In this paper, we target the control of PSBNs. The goal of BN control is to find perturbations which guarantee stabilisation of the system in the desired state. Specifically, we consider variable perturbations (gene knock-out and over-expression) with three types of application time-window: one-step, temporary, and permanent. While the control of fully specified BNs is a thoroughly explored topic, control of PSBNs introduces additional challenges that we address in this paper. In particular, the unspecified components of the model cause a significant amount of additional state space explosion. To address this issue, we propose a fully symbolic methodology that can represent the numerous system variants in a compact form. In fully specified models, the efficiency of a perturbation is characterised by the count of perturbed variables (the perturbation size). However, in the case of a PSBN, a perturbation might work only for a subset of concrete BN models. To that end, we introduce and quantify perturbation robustness. This metric characterises how efficient the given perturbation is with respect to the model uncertainty. Finally, we evaluate the novel control methods using non-trivial real-world PSBN models. We inspect the method's scalability and efficiency with respect to the size of the state space and the number of unspecified components. We also compare the robustness metrics for all three perturbation types. Our experiments support the hypothesis that one-step perturbations are significantly less robust than temporary and permanent ones.
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12
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Kdimati S, Bürtin F, Linnebacher M, Mullins CS. Patient-Derived Organoids for In Vivo Validation of In Vitro Data. Methods Mol Biol 2023; 2589:111-126. [PMID: 36255621 DOI: 10.1007/978-1-0716-2788-4_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Patient-derived organoids are promising tumor models for functional validation of next-generation sequencing-based therapy recommendations. In times of rapidly advancing precision oncology approaches in everyday clinical processes, reliable and valid tumor models are required. Tumor organoids consist of tumor "stem" cells, differentiated (epithelial) tumor, and stroma cells. The cellular architecture and interactions closely mimic the original patient tumor. These organoids can be implanted into immunodeficient mice, generating patient-derived organoid-derived xenografts, thus enabling in vitro to in vivo transfer. Most importantly, the high clinical relevance of PDO models is maintained in this conversion. This protocol describes in detail the methods and techniques as well as the materials necessary to generate in vitro PDO and in vivo PDO-derived xenograft models. The elaborate process description starts with the processing of freshly obtained tumor tissue. The proceedings include tissue processing, organoid culturing, PDO implantation into immunodeficient mice, tumor explantation, and finally tumor preservation. All these proceedings are described in this timely chronological order. This protocol will enable researchers to generate PDO models from freshly received tumor tissue and generate PDO-derived xenografts. Models generated according to these methods are suitable for a very broad research spectrum.
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Affiliation(s)
- Said Kdimati
- Department of General Surgery, Molecular Oncology and Immunotherapy, Rostock, Germany
| | - Florian Bürtin
- Department of General Surgery, Molecular Oncology and Immunotherapy, Rostock, Germany
| | - Michael Linnebacher
- Department of General Surgery, Molecular Oncology and Immunotherapy, Rostock, Germany
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13
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Guan J, Wang G, Wang J, Zhang Z, Fu Y, Cheng L, Meng G, Lyu Y, Zhu J, Li Y, Wang Y, Liuyang S, Liu B, Yang Z, He H, Zhong X, Chen Q, Zhang X, Sun S, Lai W, Shi Y, Liu L, Wang L, Li C, Lu S, Deng H. Chemical reprogramming of human somatic cells to pluripotent stem cells. Nature 2022; 605:325-331. [PMID: 35418683 DOI: 10.1038/s41586-022-04593-5] [Citation(s) in RCA: 132] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 03/01/2022] [Indexed: 12/17/2022]
Abstract
Cellular reprogramming can manipulate the identity of cells to generate the desired cell types1-3. The use of cell intrinsic components, including oocyte cytoplasm and transcription factors, can enforce somatic cell reprogramming to pluripotent stem cells4-7. By contrast, chemical stimulation by exposure to small molecules offers an alternative approach that can manipulate cell fate in a simple and highly controllable manner8-10. However, human somatic cells are refractory to chemical stimulation owing to their stable epigenome2,11,12 and reduced plasticity13,14; it is therefore challenging to induce human pluripotent stem cells by chemical reprogramming. Here we demonstrate, by creating an intermediate plastic state, the chemical reprogramming of human somatic cells to human chemically induced pluripotent stem cells that exhibit key features of embryonic stem cells. The whole chemical reprogramming trajectory analysis delineated the induction of the intermediate plastic state at the early stage, during which chemical-induced dedifferentiation occurred, and this process was similar to the dedifferentiation process that occurs in axolotl limb regeneration. Moreover, we identified the JNK pathway as a major barrier to chemical reprogramming, the inhibition of which was indispensable for inducing cell plasticity and a regeneration-like program by suppressing pro-inflammatory pathways. Our chemical approach provides a platform for the generation and application of human pluripotent stem cells in biomedicine. This study lays foundations for developing regenerative therapeutic strategies that use well-defined chemicals to change cell fates in humans.
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Affiliation(s)
- Jingyang Guan
- MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Guan Wang
- MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Jinlin Wang
- MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
| | - Zhengyuan Zhang
- MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yao Fu
- MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Lin Cheng
- MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Gaofan Meng
- MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yulin Lyu
- School of Life Sciences, Center for Bioinformatics, Center for Statistical Science, Peking University, Beijing, China
| | - Jialiang Zhu
- MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yanqin Li
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Yanglu Wang
- MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Shijia Liuyang
- MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Bei Liu
- MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Zirun Yang
- MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Huanjing He
- MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Xinxing Zhong
- MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Qijing Chen
- MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Xu Zhang
- MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Shicheng Sun
- MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Weifeng Lai
- MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yan Shi
- MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Lulu Liu
- MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Lipeng Wang
- MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Cheng Li
- School of Life Sciences, Center for Bioinformatics, Center for Statistical Science, Peking University, Beijing, China
| | - Shichun Lu
- Faculty of Hepato-Pancreato-Biliary Surgery, Chinese PLA General Hospital, Institute of Hepatobiliary Surgery of Chinese PLA, Key Laboratory of Digital Hepatobiliary Surgery, PLA, Beijing, China.
| | - Hongkui Deng
- MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China. .,State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China.
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14
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Lim J, Yoon J, Shin M, Lee KB, Choi JW. Biomolecular Electron Controller Composed of Nanobiohybrid with Electrically Released Complex for Spatiotemporal Control of Neuronal Differentiation. SMALL METHODS 2022; 6:e2100912. [PMID: 35174997 DOI: 10.1002/smtd.202100912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/11/2021] [Indexed: 06/14/2023]
Abstract
In vitro spatiotemporal control of cell differentiation is a critical issue in several biomedical fields such as stem cell therapy and regenerative medicine, as it enables the generation of heterogeneous tissue structures similar to those of their native counterparts. However, the simultaneous control of both spatial and temporal cell differentiation poses important challenges, and therefore no previous studies have achieved this goal. Here, the authors develop a cell differentiation biomolecular electron controller ("Biomoletron") composed of recombinant proteins, DNA, Au nanoparticles, peptides, and an electrically released complex with retinoic acid (RA) to spatiotemporally control SH-SY5Y cell differentiation. RA is only released from the Biomoletron when the complex is electrically stimulated, thus demonstrating the temporal control of SH-SY5Y cell differentiation. Furthermore, by introducing a patterned Au substrate that allows controlling the area where the Biomoletron is immobilized, spatiotemporal differentiation of the SH-SY5Y cell is successfully achieved. Therefore, the proposed Biomoletron-mediated differentiation method provides a promising strategy for spatiotemporal cell differentiation control with applications in regenerative medicine and cell therapy.
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Affiliation(s)
- Joungpyo Lim
- Department of Chemical & Biomolecular Engineering, Sogang University, Mapo-gu, Seoul, 04107, Republic of Korea
| | - Jinho Yoon
- Department of Chemical & Biomolecular Engineering, Sogang University, Mapo-gu, Seoul, 04107, Republic of Korea
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Minkyu Shin
- Department of Chemical & Biomolecular Engineering, Sogang University, Mapo-gu, Seoul, 04107, Republic of Korea
| | - Ki-Bum Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Jeong-Woo Choi
- Department of Chemical & Biomolecular Engineering, Sogang University, Mapo-gu, Seoul, 04107, Republic of Korea
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15
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Ambattu LA, Gelmi A, Yeo LY. Short-Duration High Frequency MegaHertz-Order Nanomechanostimulation Drives Early and Persistent Osteogenic Differentiation in Mesenchymal Stem Cells. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2106823. [PMID: 35023629 DOI: 10.1002/smll.202106823] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 12/12/2021] [Indexed: 06/14/2023]
Abstract
Stem cell fate can be directed through the application of various external physical stimuli, enabling a controlled approach to targeted differentiation. Studies involving the use of dynamic mechanical cues driven by vibrational excitation to date have, however, been limited to low frequency (Hz to kHz) forcing over extended durations (typically continuous treatment for >7 days). Contrary to previous assertions that there is little benefit in applying frequencies beyond 1 kHz, we show here that high frequency MHz-order mechanostimulation in the form of nanoscale amplitude surface reflected bulk waves are capable of triggering differentiation of human mesenchymal stem cells from various donor sources toward an osteoblast lineage, with early, short time stimuli inducing long-term osteogenic commitment. More specifically, rapid treatments (10 min daily over 5 days) of the high frequency (10 MHz) mechanostimulation are shown to trigger significant upregulation in early osteogenic markers (RUNX2, COL1A1) and sustained increase in late markers (osteocalcin, osteopontin) through a mechanistic pathway involving piezo channel activation and Rho-associated protein kinase signaling. Given the miniaturizability and low cost of the devices, the possibility for upscaling the platform toward practical bioreactors, to address a pressing need for more efficient stem cell differentiation technologies in the pursuit of translatable regenerative medicine strategies, is ensivaged.
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Affiliation(s)
- Lizebona August Ambattu
- Micro/Nanophysics Research Laboratory, School of Engineering, RMIT University, Melbourne, Victoria, 3000, Australia
| | - Amy Gelmi
- School of Science, RMIT University, Melbourne, Victoria, 3000, Australia
| | - Leslie Y Yeo
- Micro/Nanophysics Research Laboratory, School of Engineering, RMIT University, Melbourne, Victoria, 3000, Australia
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16
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Cell Transdifferentiation and Reprogramming in Disease Modeling: Insights into the Neuronal and Cardiac Disease Models and Current Translational Strategies. Cells 2021; 10:cells10102558. [PMID: 34685537 PMCID: PMC8533873 DOI: 10.3390/cells10102558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 08/29/2021] [Accepted: 09/01/2021] [Indexed: 02/07/2023] Open
Abstract
Cell transdifferentiation and reprogramming approaches in recent times have enabled the manipulation of cell fate by enrolling exogenous/artificial controls. The chemical/small molecule and regulatory components of transcription machinery serve as potential tools to execute cell transdifferentiation and have thereby uncovered new avenues for disease modeling and drug discovery. At the advanced stage, one can believe these methods can pave the way to develop efficient and sensitive gene therapy and regenerative medicine approaches. As we are beginning to learn about the utility of cell transdifferentiation and reprogramming, speculations about its applications in translational therapeutics are being largely anticipated. Although clinicians and researchers are endeavoring to scale these processes, we lack a comprehensive understanding of their mechanism(s), and the promises these offer for targeted and personalized therapeutics are scarce. In the present report, we endeavored to provide a detailed review of the original concept, methods and modalities enrolled in the field of cellular transdifferentiation and reprogramming. A special focus is given to the neuronal and cardiac systems/diseases towards scaling their utility in disease modeling and drug discovery.
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17
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Zhang Y, Huang S, Zhong W, Chen W, Yao B, Wang X. 3D organoids derived from the small intestine: An emerging tool for drug transport research. Acta Pharm Sin B 2021; 11:1697-1707. [PMID: 34386316 PMCID: PMC8343122 DOI: 10.1016/j.apsb.2020.12.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/29/2020] [Accepted: 09/23/2020] [Indexed: 12/14/2022] Open
Abstract
Small intestine in vitro models play a crucial role in drug transport research. Although conventional 2D cell culture models, such as Caco-2 monolayer, possess many advantages, they should be interpreted with caution because they have relatively poor physiologically reproducible phenotypes and functions. With the development of 3D culture technology, pluripotent stem cells (PSCs) and adult somatic stem cells (ASCs) show remarkable self-organization characteristics, which leads to the development of intestinal organoids. Based on previous studies, this paper reviews the application of intestinal 3D organoids in drug transport mediated by P-glycoprotein (P-gp), breast cancer resistance protein (BCRP) and multidrug resistance protein 2 (MRP2). The advantages and limitations of this model are also discussed. Although there are still many challenges, intestinal 3D organoid model has the potential to be an excellent tool for drug transport research.
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Key Words
- 3D organoid
- ASCs, adult somatic stem cells
- BCRP, breast cancer resistance protein
- BMP, bone morphogenetic protein
- CDF, 5(6)-carboxy-2′,7′-dichlorofluorescein
- Caco-2 cell monolayer
- DDI, drug–drug interactions
- Drug transporter
- EGF, epidermal growth factor
- ER, efflux ratio
- ESCs, embryonic stem cells
- FGF, fibroblast growth factor
- Lgr5+, leucine-rich-repeat-containing G-protein-coupled receptor 5 positive
- MCT, monocarboxylate transporter protein
- MRP2, multidrug resistance protein 2
- NBD, nucleotide-binding domain
- OATP, organic anion transporting polypeptide
- OCT, organic cation transporter
- OCTN, carnitine/organic cation transporter
- P-glycoprotein
- P-gp, P-glycoprotein
- PEPT, peptide transporter protein
- PMAT, plasma membrane monoamine transporter
- PSCs, pluripotent stem cells
- Papp, apparent permeability coefficient
- Rh123, rhodamine 123
- SLC, solute carrier
- Small intestine
- TEER, transepithelial electrical resistance
- TMDs, transmembrane domains
- cMOAT, canalicular multispecific organic anion transporter
- iPSCs, induced pluripotent stem cells
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Affiliation(s)
- Yuanjin Zhang
- Changning Maternity and Infant Health Hospital, East China Normal University, Shanghai 200051, China
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Shengbo Huang
- Changning Maternity and Infant Health Hospital, East China Normal University, Shanghai 200051, China
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Weiguo Zhong
- Changning Maternity and Infant Health Hospital, East China Normal University, Shanghai 200051, China
| | - Wenxia Chen
- Changning Maternity and Infant Health Hospital, East China Normal University, Shanghai 200051, China
| | - Bingyi Yao
- Changning Maternity and Infant Health Hospital, East China Normal University, Shanghai 200051, China
| | - Xin Wang
- Changning Maternity and Infant Health Hospital, East China Normal University, Shanghai 200051, China
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
- Corresponding author. Tel.: +86 21 2420 6564; fax: +86 21 5434 4922.
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18
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Pan SH, Zhao N, Feng X, Jie Y, Jin ZB. Conversion of mouse embryonic fibroblasts into neural crest cells and functional corneal endothelia by defined small molecules. SCIENCE ADVANCES 2021; 7:7/23/eabg5749. [PMID: 34088673 PMCID: PMC8177713 DOI: 10.1126/sciadv.abg5749] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 04/20/2021] [Indexed: 05/06/2023]
Abstract
Reprogramming of somatic cells into desired functional cell types by small molecules has vast potential for developing cell replacement therapy. Here, we developed a stepwise strategy to generate chemically induced neural crest cells (ciNCCs) and chemically induced corneal endothelial cells (ciCECs) from mouse fibroblasts using defined small molecules. The ciNCCs exhibited typical NCC features and could differentiate into ciCECs using another chemical combination in vitro. The resulting ciCECs showed consistent gene expression profiles and self-renewal capacity to those of primary CECs. Notably, these ciCECs could be cultured for as long as 30 passages and still retain the CEC features in defined medium. Transplantation of these ciCECs into an animal model reversed corneal opacity. Our chemical approach for direct reprogramming of mouse fibroblasts into ciNCCs and ciCECs provides an alternative cell source for regeneration of corneal endothelia and other tissues derived from neural crest.
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Affiliation(s)
- Shao-Hui Pan
- Institute of Stem Cell Research, The Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Ning Zhao
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology and Visual Science Key Laboratory, Beijing 100730, China
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University and Capital Medical University, Beijing Tongren Hospital, Beijing 100730, China
| | - Xiang Feng
- Institute of Stem Cell Research, The Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Ying Jie
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology and Visual Science Key Laboratory, Beijing 100730, China
| | - Zi-Bing Jin
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology and Visual Science Key Laboratory, Beijing 100730, China.
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University and Capital Medical University, Beijing Tongren Hospital, Beijing 100730, China
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19
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Akinci E, Hamilton MC, Khowpinitchai B, Sherwood RI. Using CRISPR to understand and manipulate gene regulation. Development 2021; 148:dev182667. [PMID: 33913466 PMCID: PMC8126405 DOI: 10.1242/dev.182667] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Understanding how genes are expressed in the correct cell types and at the correct level is a key goal of developmental biology research. Gene regulation has traditionally been approached largely through observational methods, whereas perturbational approaches have lacked precision. CRISPR-Cas9 has begun to transform the study of gene regulation, allowing for precise manipulation of genomic sequences, epigenetic functionalization and gene expression. CRISPR-Cas9 technology has already led to the discovery of new paradigms in gene regulation and, as new CRISPR-based tools and methods continue to be developed, promises to transform our knowledge of the gene regulatory code and our ability to manipulate cell fate. Here, we discuss the current and future application of the emerging CRISPR toolbox toward predicting gene regulatory network behavior, improving stem cell disease modeling, dissecting the epigenetic code, reprogramming cell fate and treating diseases of gene dysregulation.
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Affiliation(s)
- Ersin Akinci
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Department of Agricultural Biotechnology, Faculty of Agriculture, Akdeniz University, Antalya, 07070, Turkey
| | - Marisa C. Hamilton
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Benyapa Khowpinitchai
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Richard I. Sherwood
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Hubrecht Institute, 3584 CT, Utrecht, The Netherlands
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20
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Teschendorff AE, Feinberg AP. Statistical mechanics meets single-cell biology. Nat Rev Genet 2021; 22:459-476. [PMID: 33875884 PMCID: PMC10152720 DOI: 10.1038/s41576-021-00341-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2021] [Indexed: 02/07/2023]
Abstract
Single-cell omics is transforming our understanding of cell biology and disease, yet the systems-level analysis and interpretation of single-cell data faces many challenges. In this Perspective, we describe the impact that fundamental concepts from statistical mechanics, notably entropy, stochastic processes and critical phenomena, are having on single-cell data analysis. We further advocate the need for more bottom-up modelling of single-cell data and to embrace a statistical mechanics analysis paradigm to help attain a deeper understanding of single-cell systems biology.
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Affiliation(s)
- Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China. .,UCL Cancer Institute, University College London, London, UK.
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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21
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Song Y, Soto J, Wang P, An Q, Zhang X, Hong S, Lee LP, Fan G, Yang L, Li S. Asymmetric Cell Division of Fibroblasts is An Early Deterministic Step to Generate Elite Cells during Cell Reprogramming. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2003516. [PMID: 33854891 PMCID: PMC8025021 DOI: 10.1002/advs.202003516] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/28/2020] [Indexed: 05/30/2023]
Abstract
Cell reprogramming is considered a stochastic process, and it is not clear which cells are prone to be reprogrammed and whether a deterministic step exists. Here, asymmetric cell division (ACD) at the early stage of induced neuronal (iN) reprogramming is shown to play a deterministic role in generating elite cells for reprogramming. Within one day, fibroblasts underwent ACD, with one daughter cell being converted into an iN precursor and the other one remaining as a fibroblast. Inhibition of ACD significantly inhibited iN conversion. Moreover, the daughter cells showed asymmetric DNA segregation and histone marks during cytokinesis, and the cells inheriting newly replicated DNA strands during ACD became iN precursors. These results unravel a deterministic step at the early phase of cell reprogramming and demonstrate a novel role of ACD in cell phenotype change. This work also supports a novel hypothesis that daughter cells with newly replicated DNA strands are elite cells for reprogramming, which remains to be tested in various reprogramming processes.
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Affiliation(s)
- Yang Song
- Department of BioengineeringUniversity of California Los AngelesLos AngelesCA90095USA
| | - Jennifer Soto
- Department of BioengineeringUniversity of California Los AngelesLos AngelesCA90095USA
| | - Pingping Wang
- Department of BioengineeringUniversity of California Los AngelesLos AngelesCA90095USA
| | - Qin An
- Department of Human GeneticsUniversity of California Los AngelesLos AngelesCA90095USA
| | - Xuexiang Zhang
- Department of BioengineeringUniversity of California Los AngelesLos AngelesCA90095USA
| | - SoonGweon Hong
- Division of Engineering in MedicineDepartment of MedicineBrigham and Women's HospitalHarvard Medical SchoolBostonMA02115USA
| | - Luke P. Lee
- Division of Engineering in MedicineDepartment of MedicineBrigham and Women's HospitalHarvard Medical SchoolBostonMA02115USA
- Department of BioengineeringDepartment of Electrical Engineering and Computer ScienceUniversity of California at BerkeleyBerkeleyCAUSA
- Institute of Quantum BiophysicsDepartment of BiophysicsSungkyunkwan UniversitySuwon16419Korea
| | - Guoping Fan
- Department of Human GeneticsUniversity of California Los AngelesLos AngelesCA90095USA
| | - Li Yang
- College of BioengineeringChongqing UniversityChongqing400044China
| | - Song Li
- Department of BioengineeringUniversity of California Los AngelesLos AngelesCA90095USA
- Department of MedicineUniversity of California Los AngelesLos AngelesCA90095USA
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22
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Yu J. Vascularized Organoids: A More Complete Model. Int J Stem Cells 2020; 14:127-137. [PMID: 33377457 PMCID: PMC8138664 DOI: 10.15283/ijsc20143] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/01/2020] [Accepted: 11/30/2020] [Indexed: 11/19/2022] Open
Abstract
As an emerging research model in vitro, organoids have achieved major progress in recapitulating morphological aspects of organs and personalized precision therapy. Various organoids have been currently constructed in vitro (e.g., brain, heart, liver, and gastrointestinal). Though there are prominent advantages on microstructures and partial functions, most of them have been encountering a frustrating challenge that stromal components (e.g., blood vessels) are in short supplement, which has imposed the main dilemma on the application of such model ex vivo. As advanced technologies, co-culturing pluripotent stem cells, mesenchymal stem cells, with endothelial cells on 3D substrate matrix, are leaping forward, a novel model of an organoid with vascularization is formed. The mentioned contribute to the construction of the functional organoids derived from corresponding tissues, making them more reliable in stem cell research and clinical medicine. The present study overall summarizes progress of the evolution, applications and prospects of vascularized organoids.
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Affiliation(s)
- Jin Yu
- Department of Oncology, Affiliated Zhongshan Hospital of Dalian University, Dalian, China
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23
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O'Connor SK, Katz DB, Oswald SJ, Groneck L, Guilak F. Formation of Osteochondral Organoids from Murine Induced Pluripotent Stem Cells. Tissue Eng Part A 2020; 27:1099-1109. [PMID: 33191853 DOI: 10.1089/ten.tea.2020.0273] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Osteoarthritis is a debilitating joint disease that is characterized by pathologic changes in both cartilage and bone, potentially involving cross talk between these tissues that is complicated by extraneous factors that are difficult to study in vivo. To create a model system of these cartilage-bone interactions, we developed an osteochondral organoid from murine induced pluripotent stem cells (iPSCs). Using this approach, we grew organoids from a single cell type through time-dependent sequential exposure of growth factors, namely transforming growth factor β-3 and bone morphogenic protein 2, to mirror bone development through endochondral ossification. The result is a cartilaginous region and a calcified bony region comprising an organoid with the potential for joint disease drug screening and investigation of genetic risk in a patient or disease-specific manner. Furthermore, we also investigated the possibility of the differentiated cells within the organoid to revert to a pluripotent state. It was found that while the cells themselves maintain the capacity for reinduction of pluripotency, encapsulation in the newly formed 3D matrix prevents this process from occurring, which could have implications for future clinical use of iPSCs.
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Affiliation(s)
- Shannon K O'Connor
- Department of Orthopaedic Surgery, Washington University in St. Louis, St. Louis, Missouri, USA.,Shriners Hospitals for Children, St. Louis, St. Louis, Missouri, USA.,Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
| | - Dakota B Katz
- Department of Orthopaedic Surgery, Washington University in St. Louis, St. Louis, Missouri, USA.,Shriners Hospitals for Children, St. Louis, St. Louis, Missouri, USA.,Department of Biomedical Engineering, Washington University, St. Louis, Missouri, USA.,Center of Regenerative Medicine, Washington University, St. Louis, Missouri, USA
| | - Sara J Oswald
- Department of Orthopaedic Surgery, Washington University in St. Louis, St. Louis, Missouri, USA.,Shriners Hospitals for Children, St. Louis, St. Louis, Missouri, USA.,Center of Regenerative Medicine, Washington University, St. Louis, Missouri, USA
| | - Logan Groneck
- Department of Orthopaedic Surgery, Washington University in St. Louis, St. Louis, Missouri, USA.,Shriners Hospitals for Children, St. Louis, St. Louis, Missouri, USA.,Department of Biomedical Engineering, Washington University, St. Louis, Missouri, USA
| | - Farshid Guilak
- Department of Orthopaedic Surgery, Washington University in St. Louis, St. Louis, Missouri, USA.,Shriners Hospitals for Children, St. Louis, St. Louis, Missouri, USA.,Department of Biomedical Engineering, Washington University, St. Louis, Missouri, USA.,Center of Regenerative Medicine, Washington University, St. Louis, Missouri, USA
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24
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Li Y, Tang P, Cai S, Peng J, Hua G. Organoid based personalized medicine: from bench to bedside. CELL REGENERATION (LONDON, ENGLAND) 2020; 9:21. [PMID: 33135109 PMCID: PMC7603915 DOI: 10.1186/s13619-020-00059-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 09/04/2020] [Indexed: 12/11/2022]
Abstract
Three-dimensional cultured organoids have become a powerful in vitro research tool that preserves genetic, phenotypic and behavioral trait of in vivo organs, which can be established from both pluripotent stem cells and adult stem cells. Organoids derived from adult stem cells can be established directly from diseased epithelium and matched normal tissues, and organoids can also be genetically manipulated by CRISPR-Cas9 technology. Applications of organoids in basic research involve the modeling of human development and diseases, including genetic, infectious and malignant diseases. Importantly, accumulating evidence suggests that biobanks of patient-derived organoids for many cancers and cystic fibrosis have great value for drug development and personalized medicine. In addition, organoids hold promise for regenerative medicine. In the present review, we discuss the applications of organoids in the basic and translational research.
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Affiliation(s)
- Yaqi Li
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Peiyuan Tang
- Institute of Radiation Medicine, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Sanjun Cai
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Junjie Peng
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Guoqiang Hua
- Institute of Radiation Medicine, Fudan University Shanghai Cancer Center, Shanghai, 200032, China. .,Cancer institute, Fudan University Shanghai Cancer Center, Shanghai, 230032, China.
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25
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Ullah I, Seo K, Wi H, Kim Y, Lee S, Ock SA. Induction of the differentiation of porcine bone marrow mesenchymal stem cells into premature hepatocyte-like cells in an indirect coculture system with primary hepatocytes. Anim Cells Syst (Seoul) 2020; 24:289-298. [PMID: 33209203 PMCID: PMC7646558 DOI: 10.1080/19768354.2020.1823473] [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] [Indexed: 02/06/2023] Open
Abstract
Liver transplantation is currently the only option for patients with end-stage liver disease. Thus, other alternate therapeutic strategies are needed. Bone marrow mesenchymal stem cells (BM-MSCs) are nonhematopoietic cells present in the bone marrow stroma that serve as precursors cells for various other cells. In this study, we evaluated the differentiation of porcine BM-MSCs into hepatocyte-like cells using three types of culture systems: hepatic induction medium (HIM), HIM/primary hepatocyte culture supernatant (HCS; 1:1 ratio), and a hepatocyte coculture system (HCCS; primary hepatocytes in the upper chamber, and BM-MSCs in the lower chamber). Primary hepatocytes were isolated from anesthetized healthy 1-month-old pigs by enzymatic digestion. Hepatic-specific marker expression (albumin [ALB], transferrin [TF], α-fetoprotein [AFP]), glycogen storage, low-density lipoprotein, and indocyanine green uptake were evaluated. Upregulation of hepatic-specific markers (ALB, TF, and AFP) was observed by real-time polymerase chain reaction in the HCCS group. Periodic acid-Schiff staining revealed enhanced glycogen storage in hepatocyte-like cells from the HCCS group compared with that from the HIM/HCS group. Furthermore, hepatocyte like-cells in the HCCS group showed improved LDL and ICG uptake than those in the other groups. Overall, our current study revealed that indirect coculture of primary hepatocytes and BM-MSCs enhanced the differentiation efficacy of BM-MSCs into hepatocyte-like cells by unknown useful soluble factors, including paracrine factors.
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Affiliation(s)
- Imran Ullah
- Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, Wanju-gun, Republic of Korea.,Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Kangmin Seo
- Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, Wanju-gun, Republic of Korea
| | - Hayeon Wi
- Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, Wanju-gun, Republic of Korea
| | - Youngim Kim
- Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, Wanju-gun, Republic of Korea
| | - Seunghoon Lee
- Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, Wanju-gun, Republic of Korea
| | - Sun A Ock
- Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, Wanju-gun, Republic of Korea
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26
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Zeng F, Zhang Y, Han X, Weng J, Gao Y. Liver Buds and Liver Organoids: New Tools for Liver Development, Disease and Medical Application. Stem Cell Rev Rep 2020; 15:774-784. [PMID: 31863336 DOI: 10.1007/s12015-019-09909-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The current understanding and effective treatment of liver disease is far from satisfactory. Liver organoids and liver buds (LBs) transforming cell culture from two dimensions(2D) to three dimensions(3D) has provided infinite possibilities for stem cells to use in clinic. Recent technological advances in the 3D culture have shown the potentiality of liver organoids and LBs as the promising tool to model in vitro liver diseases. The induced LBs and liver organoids provide a platform for cell-based therapy, liver disease models, liver organogenesis and drugs screening. And its genetic heterogeneity supplies a way for the realization of precision medicine.
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Affiliation(s)
- Fanhong Zeng
- Second Department of Hepatobiliary Surgery, Zhujiang Hospital, State Key Laboratory of Organ Failure Research, Co-Innovation Center for Organ Failure Research, Southern Medical University, 253 Gongye Street, Haizhu, Guangzhou, 510280, China
| | - Yue Zhang
- Second Department of Hepatobiliary Surgery, Zhujiang Hospital, State Key Laboratory of Organ Failure Research, Co-Innovation Center for Organ Failure Research, Southern Medical University, 253 Gongye Street, Haizhu, Guangzhou, 510280, China
| | - Xu Han
- Second Department of Hepatobiliary Surgery, Zhujiang Hospital, State Key Laboratory of Organ Failure Research, Co-Innovation Center for Organ Failure Research, Southern Medical University, 253 Gongye Street, Haizhu, Guangzhou, 510280, China
| | - Jun Weng
- Second Department of Hepatobiliary Surgery, Zhujiang Hospital, State Key Laboratory of Organ Failure Research, Co-Innovation Center for Organ Failure Research, Southern Medical University, 253 Gongye Street, Haizhu, Guangzhou, 510280, China.
| | - Yi Gao
- Second Department of Hepatobiliary Surgery, Zhujiang Hospital, State Key Laboratory of Organ Failure Research, Co-Innovation Center for Organ Failure Research, Southern Medical University, 253 Gongye Street, Haizhu, Guangzhou, 510280, China.
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27
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Green DW, Watson JA, Watson GS, Stamboulis A. Sequenced Somatic Cell Reprogramming and Differentiation Inside Nested Hydrogel Droplets. ACTA ACUST UNITED AC 2020; 4:e2000071. [PMID: 32597033 DOI: 10.1002/adbi.202000071] [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: 03/09/2020] [Revised: 05/06/2020] [Indexed: 11/08/2022]
Abstract
The efficient genesis of pluripotent cells or therapeutic cells for regenerative medicine involves several external manipulations and conditioning protocols, which drives down clinical applicability. Automated programming of the genesis by microscale physical forces and chronological biochemistry can increase clinical success. The design and fabrication of nested polysaccharide droplets (millimeter-sized) with cell sustaining properties of natural tissues and intrinsic properties for time and space evolution of cell transformation signals between somatic cells, pluripotent cells and differentiated therapeutic cells in a swift and efficient manner without the need for laborious external manipulation are reported. Cells transform between phenotypic states by having single and double nested droplets constituted with extracellular matrix proteins and reprogramming, and differentiation factors infused chronologically across the droplet space. The cell transformation into germ layer cells and bone cells is successfully tested in vitro and in vivo and promotes the formation of new bone tissues. Thus, nested droplets with BMP-2 loaded guests synthesize mineralized bone tissue plates along the length of a cranial non-union bone defect at 4 weeks. The advantages of sequenced somatic cell reprogramming and differentiation inside an individual hydrogel module without external manipulation, promoted by formulating tissue mimetic physical, mechanical, and chemical microenvironments are shown.
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Affiliation(s)
- David W Green
- School of Metallurgy and Materials, Healthcare Technologies Institute, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Jolanta A Watson
- School of Science and Engineering, University of the Sunshine Coast, Fraser Coast, Hervey Bay, QLD, 4655, Australia
| | - Gregory S Watson
- School of Science and Engineering, University of the Sunshine Coast, Fraser Coast, Hervey Bay, QLD, 4655, Australia
| | - Artemis Stamboulis
- School of Metallurgy and Materials, Healthcare Technologies Institute, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
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28
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Fang J, Hsueh YY, Soto J, Sun W, Wang J, Gu Z, Khademhosseini A, Li S. Engineering Biomaterials with Micro/Nanotechnologies for Cell Reprogramming. ACS NANO 2020; 14:1296-1318. [PMID: 32011856 PMCID: PMC10067273 DOI: 10.1021/acsnano.9b04837] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Cell reprogramming is a revolutionized biotechnology that offers a powerful tool to engineer cell fate and function for regenerative medicine, disease modeling, drug discovery, and beyond. Leveraging advances in biomaterials and micro/nanotechnologies can enhance the reprogramming performance in vitro and in vivo through the development of delivery strategies and the control of biophysical and biochemical cues. In this review, we present an overview of the state-of-the-art technologies for cell reprogramming and highlight the recent breakthroughs in engineering biomaterials with micro/nanotechnologies to improve reprogramming efficiency and quality. Finally, we discuss future directions and challenges for reprogramming technologies and clinical translation.
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Affiliation(s)
- Jun Fang
- Department of Bioengineering , University of California, Los Angeles , Los Angeles , California 90095 , United States
- Department of Medicine , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Yuan-Yu Hsueh
- Department of Bioengineering , University of California, Los Angeles , Los Angeles , California 90095 , United States
- Division of Plastic Surgery, Department of Surgery, College of Medicine , National Cheng Kung University Hospital , Tainan 70456 , Taiwan
| | - Jennifer Soto
- Department of Bioengineering , University of California, Los Angeles , Los Angeles , California 90095 , United States
- Department of Medicine , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Wujin Sun
- Department of Bioengineering , University of California, Los Angeles , Los Angeles , California 90095 , United States
- Center for Minimally Invasive Therapeutics (C-MIT), California NanoSystems Institute , University of California, Los Angeles , Los Angles , California 90095 , United States
| | - Jinqiang Wang
- Department of Bioengineering , University of California, Los Angeles , Los Angeles , California 90095 , United States
- Center for Minimally Invasive Therapeutics (C-MIT), California NanoSystems Institute , University of California, Los Angeles , Los Angles , California 90095 , United States
| | - Zhen Gu
- Department of Bioengineering , University of California, Los Angeles , Los Angeles , California 90095 , United States
- Center for Minimally Invasive Therapeutics (C-MIT), California NanoSystems Institute , University of California, Los Angeles , Los Angles , California 90095 , United States
- Jonsson Comprehensive Cancer Center , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Ali Khademhosseini
- Department of Bioengineering , University of California, Los Angeles , Los Angeles , California 90095 , United States
- Center for Minimally Invasive Therapeutics (C-MIT), California NanoSystems Institute , University of California, Los Angeles , Los Angles , California 90095 , United States
- Department of Chemical and Biomolecular Engineering , University of California, Los Angeles , Los Angeles , California 90095 , United States
- Department of Radiology , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Song Li
- Department of Bioengineering , University of California, Los Angeles , Los Angeles , California 90095 , United States
- Department of Medicine , University of California, Los Angeles , Los Angeles , California 90095 , United States
- Center for Minimally Invasive Therapeutics (C-MIT), California NanoSystems Institute , University of California, Los Angeles , Los Angles , California 90095 , United States
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29
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Epigenetic Control of a Local Chromatin Landscape. Int J Mol Sci 2020; 21:ijms21030943. [PMID: 32023873 PMCID: PMC7038174 DOI: 10.3390/ijms21030943] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/28/2020] [Accepted: 01/29/2020] [Indexed: 12/11/2022] Open
Abstract
Proper regulation of the chromatin landscape is essential for maintaining eukaryotic cell identity and diverse cellular processes. The importance of the epigenome comes, in part, from the ability to influence gene expression through patterns in DNA methylation, histone tail modification, and chromatin architecture. Decades of research have associated this process of chromatin regulation and gene expression with human diseased states. With the goal of understanding how chromatin dysregulation contributes to disease, as well as preventing or reversing this type of dysregulation, a multidisciplinary effort has been launched to control the epigenome. Chemicals that alter the epigenome have been used in labs and in clinics since the 1970s, but more recently there has been a shift in this effort towards manipulating the chromatin landscape in a locus-specific manner. This review will provide an overview of chromatin biology to set the stage for the type of control being discussed, evaluate the recent technological advances made in controlling specific regions of chromatin, and consider the translational applications of these works.
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30
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Song Y, Soto J, Chen B, Yang L, Li S. Cell engineering: Biophysical regulation of the nucleus. Biomaterials 2020; 234:119743. [PMID: 31962231 DOI: 10.1016/j.biomaterials.2019.119743] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 12/02/2019] [Accepted: 12/25/2019] [Indexed: 12/12/2022]
Abstract
Cells live in a complex and dynamic microenvironment, and a variety of microenvironmental cues can regulate cell behavior. In addition to biochemical signals, biophysical cues can induce not only immediate intracellular responses, but also long-term effects on phenotypic changes such as stem cell differentiation, immune cell activation and somatic cell reprogramming. Cells respond to mechanical stimuli via an outside-in and inside-out feedback loop, and the cell nucleus plays an important role in this process. The mechanical properties of the nucleus can directly or indirectly modulate mechanotransduction, and the physical coupling of the cell nucleus with the cytoskeleton can affect chromatin structure and regulate the epigenetic state, gene expression and cell function. In this review, we will highlight the recent progress in nuclear biomechanics and mechanobiology in the context of cell engineering, tissue remodeling and disease development.
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Affiliation(s)
- Yang Song
- Department of Bioengineering, University of California, Los Angeles, CA, USA; School of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Jennifer Soto
- Department of Bioengineering, University of California, Los Angeles, CA, USA
| | - Binru Chen
- Department of Bioengineering, University of California, Los Angeles, CA, USA
| | - Li Yang
- School of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Song Li
- Department of Bioengineering, University of California, Los Angeles, CA, USA; Department of Medicine, University of California, Los Angeles, CA, USA.
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Generation of functional hepatocyte-like cells from human bone marrow mesenchymal stem cells by overexpression of transcription factor HNF4α and FOXA2. Hepatobiliary Pancreat Dis Int 2019; 18:546-556. [PMID: 31230960 DOI: 10.1016/j.hbpd.2019.03.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/05/2019] [Indexed: 02/05/2023]
Abstract
BACKGROUND Our previous study showed that overexpression of hepatocyte nuclear factor 4α (HNF4α) could directly promote mesenchymal stem cells (MSCs) to differentiate into hepatocyte-like cells. However, the efficiency of hepatic differentiation remains low. The purpose of our study was to establish an MSC cell line that overexpressed HNF4α and FOXA2 genes to obtain an increased hepatic differentiation efficiency and hepatocyte-like cells with more mature hepatocyte functions. METHODS Successful establishment of high-level HNF4α and FOXA2 co-overexpression in human induced hepatocyte-like cells (hiHep cells) was verified by flow cytometry, immunofluorescence and RT-PCR. Measurements of albumin (ALB), urea, glucose, indocyanine green (ICG) uptake and release, cytochrome P450 (CYP) activity and gene expression were used to analyze mature hepatic functions of hiHep cells. RESULTS hiHep cells efficiently express HNF4α and FOXA2 genes and proteins, exhibit typical epithelial morphology and acquire mature hepatocyte-like cell functions, including ALB secretion, urea production, ICG uptake and release, and glycogen storage. hiHep cells can be activated by CYP inducers. The percentage of both ALB and α-1-antitrypsin (AAT)-positive cells was approximately 72.6%. The expression levels of hepatocyte-specific genes (ALB, AAT, and CYP1A1) and liver drug transport-related genes (ABCB1, ABCG2, and SLC22A18) in hiHep cells were significantly higher than those in MSCs-Vector cells. The hiHep cells did not form tumors after subcutaneous xenograft in BALB/c nude mice after 2 months. CONCLUSION This study provides an accessible, feasible and efficient strategy to generate hiHep cells from MSCs.
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Liang J, Wang N, He J, Du J, Guo Y, Li L, Wu W, Yao C, Li Z, Kee K. Induction of Sertoli-like cells from human fibroblasts by NR5A1 and GATA4. eLife 2019; 8:48767. [PMID: 31710289 PMCID: PMC6881147 DOI: 10.7554/elife.48767] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 11/09/2019] [Indexed: 12/13/2022] Open
Abstract
Sertoli cells are essential nurse cells in the testis that regulate the process of spermatogenesis and establish the immune-privileged environment of the blood-testis-barrier (BTB). Here, we report the in vitro reprogramming of fibroblasts to human induced Sertoli-like cells (hiSCs). Initially, five transcriptional factors and a gene reporter carrying the AMH promoter were utilized to obtain the hiSCs. We further reduce the number of reprogramming factors to two, NR5A1 and GATA4, and show that these hiSCs have transcriptome profiles and cellular properties that are similar to those of primary human Sertoli cells. Moreover, hiSCs can sustain the viability of spermatogonia cells harvested from mouse seminiferous tubules. hiSCs suppress the proliferation of human T lymphocytes and protect xenotransplanted human cells in mice with normal immune systems. hiSCs also allow us to determine a gene associated with Sertoli cell only syndrome (SCO), CX43, is indeed important in regulating the maturation of Sertoli cells.
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Affiliation(s)
- Jianlin Liang
- Center for Stem Cell Biology and Regenerative Medicine, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China.,Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Nan Wang
- Center for Stem Cell Biology and Regenerative Medicine, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Jing He
- Center for Stem Cell Biology and Regenerative Medicine, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Jian Du
- Center for Stem Cell Biology and Regenerative Medicine, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Yahui Guo
- Center for Stem Cell Biology and Regenerative Medicine, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Lin Li
- Center for Stem Cell Biology and Regenerative Medicine, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Wenbo Wu
- National Institute of Biological Sciences, Beijing, China
| | - Chencheng Yao
- Department of Andrology, the Center for Men's Health, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai General Hospital, Shanghai, China
| | - Zheng Li
- Department of Andrology, the Center for Men's Health, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai General Hospital, Shanghai, China
| | - Kehkooi Kee
- Center for Stem Cell Biology and Regenerative Medicine, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China.,Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.,Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
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33
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Synthetic biology for improving cell fate decisions and tissue engineering outcomes. Emerg Top Life Sci 2019; 3:631-643. [PMID: 33523179 DOI: 10.1042/etls20190091] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/02/2019] [Accepted: 10/07/2019] [Indexed: 02/07/2023]
Abstract
Synthetic biology is a relatively new field of science that combines aspects of biology and engineering to create novel tools for the construction of biological systems. Using tools within synthetic biology, stem cells can then be reprogrammed and differentiated into a specified cell type. Stem cells have already proven to be largely beneficial in many different therapies and have paved the way for tissue engineering and regenerative medicine. Although scientists have made great strides in tissue engineering, there still remain many questions to be answered in regard to regeneration. Presented here is an overview of synthetic biology, common tools built within synthetic biology, and the way these tools are being used in stem cells. Specifically, this review focuses on how synthetic biologists engineer genetic circuits to dynamically control gene expression while also introducing emerging topics such as genome engineering and synthetic transcription factors. The findings mentioned in this review show the diverse use of stem cells within synthetic biology and provide a foundation for future research in tissue engineering with the use of synthetic biology tools. Overall, the work done using synthetic biology in stem cells is in its early stages, however, this early work is leading to new approaches for repairing diseased and damaged tissues and organs, and further expanding the field of tissue engineering.
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Santorelli M, Lam C, Morsut L. Synthetic development: building mammalian multicellular structures with artificial genetic programs. Curr Opin Biotechnol 2019; 59:130-140. [PMID: 31128430 PMCID: PMC6778502 DOI: 10.1016/j.copbio.2019.03.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 03/08/2019] [Accepted: 03/24/2019] [Indexed: 12/28/2022]
Abstract
Synthetic biology efforts began in simple single-cell systems, which were relatively easy to manipulate genetically (Cameron et al., 2014). The field grew exponentially in the last two decades, and one of the latest frontiers are synthetic developmental programs for multicellular mammalian systems (Black et al., 2017; Wieland and Fussenegger, 2012) to genetically control features such as patterning or morphogenesis. These programs rely on engineered cell-cell communications, multicellular gene regulatory networks and effector genes. Here, we contextualize the first of these synthetic developmental programs, examine molecular and computational tools that can be used to generate next generation versions, and present the general logic that underpins these approaches. These advances are exciting as they represent a novel way to address both control and understanding in the field of developmental biology and tissue development (Elowitz and Lim, 2010; Velazquez et al., 2018; White et al., 2018; Morsut, 2017). This field is just at the beginning, and it promises to be of major interest in the upcoming years of biomedical research.
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Affiliation(s)
- Marco Santorelli
- The Eli and Edythe Broad CIRM Center, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, United States
| | - Calvin Lam
- The Eli and Edythe Broad CIRM Center, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, United States
| | - Leonardo Morsut
- The Eli and Edythe Broad CIRM Center, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, United States; Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, United States.
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35
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Qian Y, Ji C, Yue S, Zhao M. Exposure of low-dose fipronil enantioselectively induced anxiety-like behavior associated with DNA methylation changes in embryonic and larval zebrafish. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 249:362-371. [PMID: 30909129 DOI: 10.1016/j.envpol.2019.03.038] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/11/2019] [Accepted: 03/11/2019] [Indexed: 06/09/2023]
Abstract
Fipronil, a broad-spectrum chiral insecticide, has been documented to induce significant neurotoxicity to nontarget aquatic species; however, whether its neurotoxicity behaves enantioselectively and what molecular mechanisms correspond to the neurotoxicity remain unanswered. To date, few investigations have focused on the genomic mechanisms responsible for the enantioselective toxicity of chiral pesticides. The epigenetic modifications, especially DNA methylation, caused by the pesticides are also blind spot of the research works. Video tracking showed that R-fipronil exhibited more intense neurotoxicity, as well as the induction of more severe anxiety-like behavior, such as boosted swimming speed and dysregulated photoperiodic locomotion, to embryonic and larval zebrafish compared with S-fipronil. The MeDIP-Seq analysis, combined with Gene Ontology and KEGG, revealed that R-fipronil disrupted five signaling pathways (MAPK, Calcium signaling, Neuroactive ligand-receptor interaction, Purine metabolism, and Endocytosis) to a greater extent than S-fipronil through the hypermethylation of several important neuro-related genes, whereas no significant alterations of global DNA methylation were observed on the two enantiomers. To summarize, our data indicated that the fipronil-conducted enantioselective neurotoxicity likely applied its enantioselectivity by the dysregulation of DNA methylation. Our study also provided novel epigenetic insights into the study of enantioselective biological effects and the relevant underlying mechanisms of chiral insecticide.
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Affiliation(s)
- Yi Qian
- College of Life Science, Taizhou University, Taizhou, Zhejiang, 318000, China
| | - Chenyang Ji
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, China
| | - Siqing Yue
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, China
| | - Meirong Zhao
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, China.
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Celikkaya H, Cosacak MI, Papadimitriou C, Popova S, Bhattarai P, Biswas SN, Siddiqui T, Wistorf S, Nevado-Alcalde I, Naumann L, Mashkaryan V, Brandt K, Freudenberg U, Werner C, Kizil C. GATA3 Promotes the Neural Progenitor State but Not Neurogenesis in 3D Traumatic Injury Model of Primary Human Cortical Astrocytes. Front Cell Neurosci 2019; 13:23. [PMID: 30809125 PMCID: PMC6380212 DOI: 10.3389/fncel.2019.00023] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 01/18/2019] [Indexed: 01/05/2023] Open
Abstract
Astrocytes are abundant cell types in the vertebrate central nervous system and can act as neural stem cells in specialized niches where they constitutively generate new neurons. Outside the stem cell niches, however, these glial cells are not neurogenic. Although injuries in the mammalian central nervous system lead to profound proliferation of astrocytes, which cluster at the lesion site to form a gliotic scar, neurogenesis does not take place. Therefore, a plausible regenerative therapeutic option is to coax the endogenous reactive astrocytes to a pre-neurogenic progenitor state and use them as an endogenous reservoir for repair. However, little is known on the mechanisms that promote the neural progenitor state after injuries in humans. Gata3 was previously found to be a mechanism that zebrafish brain uses to injury-dependent induction of neural progenitors. However, the effects of GATA3 in human astrocytes after injury are not known. Therefore, in this report, we investigated how overexpression of GATA3 in primary human astrocytes would affect the neurogenic potential before and after injury in 2D and 3D cultures. We found that primary human astrocytes are unable to induce GATA3 after injury. Lentivirus-mediated overexpression of GATA3 significantly increased the number of GFAP/SOX2 double positive astrocytes and expression of pro-neural factor ASCL1, but failed to induce neurogenesis, suggesting that GATA3 is required for enhancing the neurogenic potential of primary human astrocytes and is not sufficient to induce neurogenesis alone.
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Affiliation(s)
- Hilal Celikkaya
- German Center for Neurodegenerative Diseases, Helmholtz Association, Dresden, Germany.,Center for Regenerative Therapies Dresden, TU Dresden, Dresden, Germany
| | - Mehmet Ilyas Cosacak
- German Center for Neurodegenerative Diseases, Helmholtz Association, Dresden, Germany
| | | | - Stanislava Popova
- German Center for Neurodegenerative Diseases, Helmholtz Association, Dresden, Germany.,Center for Regenerative Therapies Dresden, TU Dresden, Dresden, Germany
| | - Prabesh Bhattarai
- German Center for Neurodegenerative Diseases, Helmholtz Association, Dresden, Germany
| | - Srijeeta Nag Biswas
- German Center for Neurodegenerative Diseases, Helmholtz Association, Dresden, Germany.,Center for Regenerative Therapies Dresden, TU Dresden, Dresden, Germany
| | - Tohid Siddiqui
- German Center for Neurodegenerative Diseases, Helmholtz Association, Dresden, Germany
| | - Sabrina Wistorf
- German Center for Neurodegenerative Diseases, Helmholtz Association, Dresden, Germany
| | - Isabel Nevado-Alcalde
- German Center for Neurodegenerative Diseases, Helmholtz Association, Dresden, Germany
| | - Lisa Naumann
- German Center for Neurodegenerative Diseases, Helmholtz Association, Dresden, Germany
| | - Violeta Mashkaryan
- German Center for Neurodegenerative Diseases, Helmholtz Association, Dresden, Germany.,Center for Regenerative Therapies Dresden, TU Dresden, Dresden, Germany
| | - Kerstin Brandt
- German Center for Neurodegenerative Diseases, Helmholtz Association, Dresden, Germany
| | - Uwe Freudenberg
- Center for Regenerative Therapies Dresden, TU Dresden, Dresden, Germany.,Max Bergmann Center of Biomaterials Dresden, Leibniz Institute of Polymer Research Dresden, Dresden, Germany
| | - Carsten Werner
- Center for Regenerative Therapies Dresden, TU Dresden, Dresden, Germany.,Max Bergmann Center of Biomaterials Dresden, Leibniz Institute of Polymer Research Dresden, Dresden, Germany
| | - Caghan Kizil
- German Center for Neurodegenerative Diseases, Helmholtz Association, Dresden, Germany.,Center for Regenerative Therapies Dresden, TU Dresden, Dresden, Germany
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37
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Liu Y, Siles L, Postigo A, Dean DC. Epigenetically distinct sister chromatids and asymmetric generation of tumor initiating cells. Cell Cycle 2018; 17:2221-2229. [PMID: 30290712 DOI: 10.1080/15384101.2018.1532254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Cancer stem cells (CSC) are thought to be an important source of cancer cells in tumors of different origins. Mounting evidence suggests they are generated reversibly from existing cancer cells, and supply new cancer cells during tumor progression and following therapy. Elegant lineage mapping stud(ies are identifying progenitors, and in some cases differentiated cells, as targets of transformation in a variety of tumors. Recent evidence suggests resulting tumor initiating cells (TIC) might be distinct from CSC. Molecular pathways leading from cells of tumor origin to precancerous lesions and cancer cells are only beginning to be unraveled. We review a pathway where asymmetric division of precancerous cells generates TIC in a K-Ras-initiated model of lung cancer. And, we compare unexpected steps in this asymmetric division to those evident in well-studied stem cell models.
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Affiliation(s)
- Yongqing Liu
- a Molecular Targets Program , James Graham Brown Cancer Center , Louisville , Kentucky.,b Department of Ophthalmology and Visual Sciences.,c Birth Defects Center , University of Louisville Health Sciences Center
| | - Laura Siles
- d Group of Transcriptional Regulation of Gene Expression , Institut d'Investigacions BiomèdiquesAugust Pi i Sunyer (IDIBAPS) , Barcelona , Spain
| | - Antonio Postigo
- a Molecular Targets Program , James Graham Brown Cancer Center , Louisville , Kentucky.,d Group of Transcriptional Regulation of Gene Expression , Institut d'Investigacions BiomèdiquesAugust Pi i Sunyer (IDIBAPS) , Barcelona , Spain.,e ICREA , Barcelona , Spain
| | - Douglas C Dean
- a Molecular Targets Program , James Graham Brown Cancer Center , Louisville , Kentucky.,b Department of Ophthalmology and Visual Sciences.,c Birth Defects Center , University of Louisville Health Sciences Center
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Rauch C, Feifel E, Kern G, Murphy C, Meier F, Parson W, Beilmann M, Jennings P, Gstraunthaler G, Wilmes A. Differentiation of human iPSCs into functional podocytes. PLoS One 2018; 13:e0203869. [PMID: 30222766 PMCID: PMC6141081 DOI: 10.1371/journal.pone.0203869] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 08/29/2018] [Indexed: 12/13/2022] Open
Abstract
Podocytes play a critical role in glomerular barrier function, both in health and disease. However, in vivo terminally differentiated podocytes are difficult to be maintained in in vitro culture. Induced pluripotent stem cells (iPSCs) offer the unique possibility for directed differentiation into mature podocytes. The current differentiation protocol to generate iPSC-derived podocyte-like cells provides a robust and reproducible method to obtain podocyte-like cells after 10 days that can be employed in in vitro research and biomedical engineering. Previous published protocols were improved by testing varying differentiation media, growth factors, seeding densities, and time course conditions. Modifications were made to optimize and simplify the one-step differentiation procedure. In contrast to earlier protocols, adherent cells for differentiation were used, the use of fetal bovine serum (FBS) was reduced to a minimum, and thus ß-mercaptoethanol could be omitted. The plating densities of iPSC stocks as well as the seeding densities for differentiation cultures turned out to be a crucial parameter for differentiation results. Conditionally immortalized human podocytes served as reference controls. iPSC-derived podocyte-like cells showed a typical podocyte-specific morphology and distinct expression of podocyte markers synaptopodin, podocin, nephrin and WT-1 after 10 days of differentiation as assessed by immunofluorescence staining or Western blot analysis. qPCR results showed a downregulation of pluripotency markers Oct4 and Sox-2 and a 9-fold upregulation of the podocyte marker synaptopodin during the time course of differentiation. Cultured podocytes exhibited endocytotic uptake of albumin. In toxicological assays, matured podocytes clearly responded to doxorubicin (Adriamycin™) with morphological alterations and a reduction in cell viability after 48 h of incubation.
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Affiliation(s)
- Caroline Rauch
- Division of Physiology, Medical University Innsbruck, Innsbruck Austria
| | - Elisabeth Feifel
- Division of Physiology, Medical University Innsbruck, Innsbruck Austria
| | - Georg Kern
- Division of Physiology, Medical University Innsbruck, Innsbruck Austria
| | - Cormac Murphy
- Division of Molecular and Computational Toxicology, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Florian Meier
- Boehringer Ingelheim Pharma GmbH & Co. KG, Nonclinical Drug Safety Germany, Biberach an der Riss, Germany
| | - Walther Parson
- Institute of Legal Medicine, Medical University Innsbruck, Innsbruck, Austria
| | - Mario Beilmann
- Boehringer Ingelheim Pharma GmbH & Co. KG, Nonclinical Drug Safety Germany, Biberach an der Riss, Germany
| | - Paul Jennings
- Division of Physiology, Medical University Innsbruck, Innsbruck Austria.,Division of Molecular and Computational Toxicology, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | | | - Anja Wilmes
- Division of Physiology, Medical University Innsbruck, Innsbruck Austria.,Division of Molecular and Computational Toxicology, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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39
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Identification of protein kinase inhibitors to reprogram breast cancer cells. Cell Death Dis 2018; 9:915. [PMID: 30206213 PMCID: PMC6133942 DOI: 10.1038/s41419-018-1002-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/09/2018] [Accepted: 05/11/2018] [Indexed: 12/22/2022]
Abstract
Direct reversion of cancers into normal-like tissues is an ideal strategy for cancer treatment. Recent reports have showed that defined transcription factors can induce reprogramming of cancer cells into pluripotent stem cells, supporting this notion. Here, we have developed a reprogramming method that uses a conceptually unique strategy for breast cancer cell treatment. We have screened a kinase inhibitor library and found that Rho-associated protein kinase (ROCK) and mammalian target of rapamycin (mTOR) kinase inhibitors can substitute for all transcription factors to be sufficient to reprogram breast cancer cells into progenitor cells. Furthermore, ROCK–mTOR inhibitors could reprogram breast cancer cells to another terminal lineage-adipogenic cells. Genome-wide transcriptional analysis shows that the induced fat-like cells have a profile different from breast cancer cells and similar to that of normal adipocytes. In vitro and in vivo tumorigenesis assays have shown that induced fat-like cells lose proliferation and tumorigenicity. Moreover, reprogramming treatment with ROCK–mTOR inhibitors prevents breast cancer local recurrence in mice. Currently, ROCK–mTOR inhibitors are already used as antitumor drugs in patients, thus, this reprogramming strategy has significant potential to move rapidly toward clinical trials for breast cancer treatment.
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40
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Yuan J, Zhang F, Hallahan D, Zhang Z, He L, Wu LG, You M, Yang Q. Reprogramming glioblastoma multiforme cells into neurons by protein kinase inhibitors. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2018; 37:181. [PMID: 30071868 PMCID: PMC6090992 DOI: 10.1186/s13046-018-0857-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 07/19/2018] [Indexed: 02/08/2023]
Abstract
Background Reprogramming of cancers into normal-like tissues is an innovative strategy for cancer treatment. Recent reports demonstrate that defined factors can reprogram cancer cells into pluripotent stem cells. Glioblastoma multiforme (GBM) is the most common and aggressive malignant brain tumor in humans. Despite multimodal therapy, the outcome for patients with GBM is still poor. Therefore, developing novel therapeutic strategy is a critical requirement. Methods We have developed a novel reprogramming method that uses a conceptually unique strategy for GBM treatment. We screened a kinase inhibitor library to find which candidate inhibitors under reprogramming condition can reprogram GBM cells into neurons. The induced neurons are identified whether functional and loss of tumorigenicity. Results We have found that mTOR and ROCK kinase inhibitors are sufficient to reprogram GBM cells into neural-like cells and “normal” neurons. The induced neurons expressed neuron-specific proteins, generated action potentials and neurotransmitter receptor-mediated currents. Genome-wide transcriptional analysis showed that the induced neurons had a profile different from GBM cells and were similar to that of control neurons induced by established methods. In vitro and in vivo tumorigenesis assays showed that induced neurons lost their proliferation ability and tumorigenicity. Moreover, reprogramming treatment with ROCK-mTOR inhibitors prevented GBM local recurrence in mice. Conclusion This study indicates that ROCK and mTOR inhibitors-based reprogramming treatment prevents GBM local recurrence. Currently ROCK-mTOR inhibitors are used as anti-tumor drugs in patients, so this reprogramming strategy has significant potential to move rapidly toward clinical trials. Electronic supplementary material The online version of this article (10.1186/s13046-018-0857-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jie Yuan
- Cancer Biology Division, Department of Radiation Oncology, Washington University School of Medicine, 4511 Forest Park, St. Louis, MO, 63108, USA.,Medical Center of Stomatology, the First Affiliated Hospital of Jinan University, Guangzhou, 510630, China.,School of Stomatology, Jinan University, Guangzhou, 510630, China
| | - Fan Zhang
- Cancer Biology Division, Department of Radiation Oncology, Washington University School of Medicine, 4511 Forest Park, St. Louis, MO, 63108, USA
| | - Dennis Hallahan
- Cancer Biology Division, Department of Radiation Oncology, Washington University School of Medicine, 4511 Forest Park, St. Louis, MO, 63108, USA
| | - Zhen Zhang
- Synaptic Transmission Section, National Institute of Neurological Disorders and Stroke, Bethesda, MD, 20892, USA
| | - Liming He
- Synaptic Transmission Section, National Institute of Neurological Disorders and Stroke, Bethesda, MD, 20892, USA
| | - Ling-Gang Wu
- Synaptic Transmission Section, National Institute of Neurological Disorders and Stroke, Bethesda, MD, 20892, USA
| | - Meng You
- Cancer Biology Division, Department of Radiation Oncology, Washington University School of Medicine, 4511 Forest Park, St. Louis, MO, 63108, USA
| | - Qin Yang
- Cancer Biology Division, Department of Radiation Oncology, Washington University School of Medicine, 4511 Forest Park, St. Louis, MO, 63108, USA.
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41
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Black JB, Gersbach CA. Synthetic transcription factors for cell fate reprogramming. Curr Opin Genet Dev 2018; 52:13-21. [PMID: 29803990 DOI: 10.1016/j.gde.2018.05.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 04/30/2018] [Accepted: 05/06/2018] [Indexed: 12/22/2022]
Abstract
The ability to reprogram cell lineage specification through the activity of master regulatory transcription factors has transformed disease modeling, drug screening, and cell therapy for regenerative medicine. Recent advances in the engineering of synthetic transcription factors to modulate endogenous gene expression networks and chromatin states have generated a new set of tools with unique advantages to study and enhance cell reprogramming methods. Several studies have applied synthetic transcription factors in various cell reprogramming paradigms in human and murine cells. Moreover, the adaption of CRISPR-based transcription factors for high-throughput screening will enable the systematic identification of optimal factors and gene network perturbations to improve current reprogramming protocols and enable conversion to more diverse, highly specified, and mature cell types. The rapid development of next-generation technologies with more robust and versatile functionality will continue to expand the application of synthetic transcription factors for cell reprogramming.
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Affiliation(s)
- Joshua B Black
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA; Department of Orthopaedic Surgery, Duke University Medical Center, Durham, NC 27710, USA.
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42
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Woods DC, Khrapko K, Tilly JL. Influence of Maternal Aging on Mitochondrial Heterogeneity, Inheritance, and Function in Oocytes and Preimplantation Embryos. Genes (Basel) 2018; 9:E265. [PMID: 29883421 PMCID: PMC5977205 DOI: 10.3390/genes9050265] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 05/11/2018] [Accepted: 05/14/2018] [Indexed: 12/15/2022] Open
Abstract
Contrasting the equal contribution of nuclear genetic material from maternal and paternal sources to offspring, passage of mitochondria, and thus mitochondrial DNA (mtDNA), is uniparental through the egg. Since mitochondria in eggs are ancestral to all somatic mitochondria of the next generation and to all cells of future generations, oocytes must prepare for the high energetic demands of maturation, fertilization and embryogenesis while simultaneously ensuring that their mitochondrial genomes are inherited in an undamaged state. Although significant effort has been made to understand how the mtDNA bottleneck and purifying selection act coordinately to prevent silent and unchecked spreading of invisible mtDNA mutations through the female germ line across successive generations, it is unknown if and how somatic cells of the immediate next generation are spared from inheritance of detrimental mtDNA molecules. Here, we review unique aspects of mitochondrial activity and segregation in eggs and early embryos, and how these events play into embryonic developmental competency in the face of advancing maternal age.
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Affiliation(s)
- Dori C Woods
- Laboratory for Aging and Infertility Research, Department of Biology, Northeastern University, Boston, MA 02115, USA.
| | - Konstantin Khrapko
- Laboratory for Aging and Infertility Research, Department of Biology, Northeastern University, Boston, MA 02115, USA.
| | - Jonathan L Tilly
- Laboratory for Aging and Infertility Research, Department of Biology, Northeastern University, Boston, MA 02115, USA.
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Bai F, Li Z, Umezawa A, Terada N, Jin S. Bacterial type III secretion system as a protein delivery tool for a broad range of biomedical applications. Biotechnol Adv 2018; 36:482-493. [PMID: 29409784 DOI: 10.1016/j.biotechadv.2018.01.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 01/08/2018] [Accepted: 01/30/2018] [Indexed: 12/16/2022]
Abstract
A protein delivery tool based on bacterial type III secretion system (T3SS) has been broadly applied in biomedical researches. In this review, we summarize various applications of the T3SS-mediate protein delivery which enables translocation of proteins directly into mammalian cells without protein purification. Some of the remarkable advancements include delivery of antigens for therapeutic vaccines, nucleases for genome editing, transcription factors for cellular reprogramming and stem cells differentiation, and signaling molecules for post-translational proteomics studies. With continued improvement of the T3SS-mediated protein delivery tools, even wider application of the technology is anticipated.
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Affiliation(s)
- Fang Bai
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Zhenpeng Li
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Akihiro Umezawa
- Department of Reproductive Biology, National Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Naohiro Terada
- Department of Pathology College of Medicine, University of Florida, Gainesville, FL 32610, United States
| | - Shouguang Jin
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China; Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, United States.
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Kajiwara K, Tanemoto T, Wada S, Karibe J, Ihara N, Ikemoto Y, Kawasaki T, Oishi Y, Samura O, Okamura K, Takada S, Akutsu H, Sago H, Okamoto A, Umezawa A. Fetal Therapy Model of Myelomeningocele with Three-Dimensional Skin Using Amniotic Fluid Cell-Derived Induced Pluripotent Stem Cells. Stem Cell Reports 2018; 8:1701-1713. [PMID: 28591652 PMCID: PMC5470234 DOI: 10.1016/j.stemcr.2017.05.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 05/11/2017] [Accepted: 05/12/2017] [Indexed: 01/28/2023] Open
Abstract
Myelomeningocele (MMC) is a congenital disease without genetic abnormalities. Neurological symptoms are irreversibly impaired after birth, and no effective treatment has been reported to date. Only surgical repairs have been reported so far. In this study, we performed antenatal treatment of MMC with an artificial skin using induced pluripotent stem cells (iPSCs) generated from a patient with Down syndrome (AF-T21-iPSCs) and twin-twin transfusion syndrome (AF-TTTS-iPSCs) to a rat model. We manufactured three-dimensional skin with epidermis generated from keratinocytes derived from AF-T21-iPSCs and AF-TTTS-iPSCs and dermis of human fibroblasts and collagen type I. For generation of epidermis, we developed a protocol using Y-27632 and epidermal growth factor. The artificial skin was successfully covered over MMC defect sites during pregnancy, implying a possible antenatal surgical treatment with iPSC technology.
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Affiliation(s)
- Kazuhiro Kajiwara
- Department of Reproductive Biology, Center for Regenerative Medicine, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan; Department of Obstetrics and Gynecology, The Jikei University School of Medicine, Tokyo 105-8471, Japan
| | - Tomohiro Tanemoto
- Department of Medical Science, Chiba University Graduate School of Medicine, Chiba 260-0856, Japan
| | - Seiji Wada
- Maternal-Fetal, Neonatal and Reproductive Medicine, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Jurii Karibe
- Department of Reproductive Biology, Center for Regenerative Medicine, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan
| | - Norimasa Ihara
- Department of Reproductive Biology, Center for Regenerative Medicine, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan
| | - Yu Ikemoto
- Department of Reproductive Biology, Center for Regenerative Medicine, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan
| | - Tomoyuki Kawasaki
- Department of Reproductive Biology, Center for Regenerative Medicine, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan
| | - Yoshie Oishi
- Department of Reproductive Biology, Center for Regenerative Medicine, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan
| | - Osamu Samura
- Department of Obstetrics and Gynecology, The Jikei University School of Medicine, Tokyo 105-8471, Japan
| | - Kohji Okamura
- Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Shuji Takada
- Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Hidenori Akutsu
- Department of Reproductive Biology, Center for Regenerative Medicine, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan
| | - Haruhiko Sago
- Maternal-Fetal, Neonatal and Reproductive Medicine, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Aikou Okamoto
- Department of Obstetrics and Gynecology, The Jikei University School of Medicine, Tokyo 105-8471, Japan
| | - Akihiro Umezawa
- Department of Reproductive Biology, Center for Regenerative Medicine, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan.
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JMJD1C Ensures Mouse Embryonic Stem Cell Self-Renewal and Somatic Cell Reprogramming through Controlling MicroRNA Expression. Stem Cell Reports 2017; 9:927-942. [PMID: 28826851 PMCID: PMC5599225 DOI: 10.1016/j.stemcr.2017.07.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 07/14/2017] [Accepted: 07/17/2017] [Indexed: 12/17/2022] Open
Abstract
The roles of histone demethylases (HDMs) for the establishment and maintenance of pluripotency are incompletely characterized. Here, we show that JmjC-domain-containing protein 1c (JMJD1C), an H3K9 demethylase, is required for mouse embryonic stem cell (ESC) self-renewal. Depletion of Jmjd1c leads to the activation of ERK/MAPK signaling and epithelial-to-mesenchymal transition (EMT) to induce differentiation of ESCs. Inhibition of ERK/MAPK signaling rescues the differentiation phenotype caused by Jmjd1c depletion. Mechanistically, JMJD1C, with the help of pluripotency factor KLF4, maintains ESC identity at least in part by regulating the expression of the miR-200 family and miR-290/295 cluster to suppress the ERK/MAPK signaling and EMT. Additionally, we uncover that JMJD1C ensures efficient generation and maintenance of induced pluripotent stem cells, at least partially through controlling the expression of microRNAs. Collectively, we propose an integrated model of epigenetic and transcriptional control mediated by the H3K9 demethylase for ESC self-renewal and somatic cell reprogramming. JMJD1C is required for the maintenance of ESC identity Depletion of Jmjd1c leads to the activation of ERK/MAPK signaling and EMT JMJD1C interplays with KLF4 to activate the expression of miR-200 family JMJD1C ensures efficient induction of pluripotency partially via miR-200 family
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Mullen AC, Wrana JL. TGF-β Family Signaling in Embryonic and Somatic Stem-Cell Renewal and Differentiation. Cold Spring Harb Perspect Biol 2017; 9:cshperspect.a022186. [PMID: 28108485 DOI: 10.1101/cshperspect.a022186] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Soon after the discovery of transforming growth factor-β (TGF-β), seminal work in vertebrate and invertebrate models revealed the TGF-β family to be central regulators of tissue morphogenesis. Members of the TGF-β family direct some of the earliest cell-fate decisions in animal development, coordinate complex organogenesis, and contribute to tissue homeostasis in the adult. Here, we focus on the role of the TGF-β family in mammalian stem-cell biology and discuss its wide and varied activities both in the regulation of pluripotency and in cell-fate commitment.
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Affiliation(s)
- Alan C Mullen
- Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02138
| | - Jeffrey L Wrana
- Lunenfeld-Tanenbam Research Institute, Mount Sinai Hospital and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1X5, Canada
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Skin-derived precursors from human subjects with Type 2 diabetes yield dysfunctional vascular smooth muscle cells. Clin Sci (Lond) 2017; 131:1801-1814. [PMID: 28424290 DOI: 10.1042/cs20170239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Revised: 04/16/2017] [Accepted: 04/19/2017] [Indexed: 01/04/2023]
Abstract
Objective: Few methods enable molecular and cellular studies of vascular aging or Type 2 diabetes (T2D). Here, we report a new approach to studying human vascular smooth muscle cell (VSMC) pathophysiology by examining VSMCs differentiated from progenitors found in skin. Approach and results: Skin-derived precursors (SKPs) were cultured from biopsies (N=164, ∼1 cm2) taken from the edges of surgical incisions of older adults (N=158; males 72%; mean age 62.7 ± 13 years) undergoing cardiothoracic surgery, and differentiated into VSMCs at high efficiency (>80% yield). The number of SKPs isolated from subjects with T2D was ∼50% lower than those without T2D (cells/g: 0.18 ± 0.03, N=58 versus 0.40 ± 0.05, N=100, P<0.05). Importantly, SKP-derived VSMCs from subjects with T2D had higher Fluo-5F-determined baseline cytosolic Ca2+ concentrations (AU: 1,968 ± 160, N=7 versus 1,386 ± 170, N=13, P<0.05), and a trend toward greater Ca2+ cycling responses to norepinephrine (NE) (AUC: 177,207 ± 24,669, N=7 versus 101,537 ± 15,881, N=20, P<0.08) despite a reduced frequency of Ca2+ cycling (events s-1 cell-1: 0.011 ± 0.004, N=8 versus 0.021 ± 0.003, N=19, P<0.05) than those without T2D. SKP-derived VSMCs from subjects with T2D also manifest enhanced sensitivity to phenylephrine (PE) in an impedance-based assay (EC50 nM: 72.3 ± 63.6, N=5 versus 3,684 ± 3,122, N=9, P<0.05), and impaired wound closure in vitro (% closure: 21.9 ± 3.6, N=4 versus 67.0 ± 10.3, N=4, P<0.05). Compared with aortic- and saphenous vein-derived primary VSMCs, SKP-derived VSMCs are functionally distinct, but mirror defects of T2D also exhibited by primary VSMCs. CONCLUSION Skin biopsies from older adults yield sufficient SKPs to differentiate VSMCs, which reveal abnormal phenotypes of T2D that survive differentiation and persist even after long-term normoglycemic culture.
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Wooten DJ, Quaranta V. Mathematical models of cell phenotype regulation and reprogramming: Make cancer cells sensitive again! Biochim Biophys Acta Rev Cancer 2017; 1867:167-175. [PMID: 28396217 DOI: 10.1016/j.bbcan.2017.04.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 04/03/2017] [Accepted: 04/04/2017] [Indexed: 02/06/2023]
Abstract
A cell's phenotype is the observable actualization of complex interactions between its genome, epigenome, and local environment. While traditional views in cancer have held that cellular and tumor phenotypes are largely functions of genomic instability, increasing attention has recently been given to epigenetic and microenvironmental influences. Such non-genetic factors allow cancer cells to experience intrinsic diversity and plasticity, and at the tumor level can result in phenotypic heterogeneity and treatment evasion. In 2006, Takahashi and Yamanaka exploited the epigenome's plasticity by "reprogramming" differentiated cells into a pluripotent state by inducing expression of a cocktail of four transcription factors. Recent advances in cancer biology have shown not only that cellular reprogramming is possible for malignant cells, but it may provide a foundation for future therapies. Nevertheless, cell reprogramming experiments are frequently plagued by low efficiency, activation of aberrant transcriptional programs, instability, and often rely on expertise gathered from systems which may not translate directly to cancer. Here, we review a theoretical framework tracing back to Waddington's epigenetic landscape which may be used to derive quantitative and qualitative understanding of cellular reprogramming. Implications for tumor heterogeneity, evolution and adaptation are discussed in the context of designing new treatments to re-sensitize recalcitrant tumors. This article is part of a Special Issue entitled: Evolutionary principles - heterogeneity in cancer?, edited by Dr. Robert A. Gatenby.
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Affiliation(s)
- David J Wooten
- Vanderbilt University School of Medicine, 2220 Pierce Ave., 446B, Nashville, TN 37232, United States
| | - Vito Quaranta
- Vanderbilt University School of Medicine, 2220 Pierce Ave., 446B, Nashville, TN 37232, United States.
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Chimenti I, Massai D, Morbiducci U, Beltrami AP, Pesce M, Messina E. Stem Cell Spheroids and Ex Vivo Niche Modeling: Rationalization and Scaling-Up. J Cardiovasc Transl Res 2017; 10:150-166. [PMID: 28289983 DOI: 10.1007/s12265-017-9741-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 02/27/2017] [Indexed: 02/08/2023]
Abstract
Improved protocols/devices for in vitro culture of 3D cell spheroids may provide essential cues for proper growth and differentiation of stem/progenitor cells (S/PCs) in their niche, allowing preservation of specific features, such as multi-lineage potential and paracrine activity. Several platforms have been employed to replicate these conditions and to generate S/PC spheroids for therapeutic applications. However, they incompletely reproduce the niche environment, with partial loss of its highly regulated network, with additional hurdles in the field of cardiac biology, due to debated resident S/PCs therapeutic potential and clinical translation. In this contribution, the essential niche conditions (metabolic, geometric, mechanical) that allow S/PCs maintenance/commitment will be discussed. In particular, we will focus on both existing bioreactor-based platforms for the culture of S/PC as spheroids, and on possible criteria for the scaling-up of niche-like spheroids, which could be envisaged as promising tools for personalized cardiac regenerative medicine, as well as for high-throughput drug screening.
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Affiliation(s)
- Isotta Chimenti
- Department of Medical Surgical Sciences and Biotechnology, "La Sapienza" University of Rome, Rome, Italy
| | - Diana Massai
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiac, Thoracic-, Transplantation and Vascular Surgery, Hannover Medical School, Hannover, Germany
| | - Umberto Morbiducci
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
| | | | - Maurizio Pesce
- Tissue Engineering Research Unit, "Centro Cardiologico Monzino", IRCCS, Milan, Italy
| | - Elisa Messina
- Department of Pediatrics and Infant Neuropsychiatry, "Umberto I" Hospital, "La Sapienza" University, Viale Regina Elena 324, 00161, Rome, Italy.
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50
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Fagnocchi L, Zippo A. Multiple Roles of MYC in Integrating Regulatory Networks of Pluripotent Stem Cells. Front Cell Dev Biol 2017; 5:7. [PMID: 28217689 PMCID: PMC5289991 DOI: 10.3389/fcell.2017.00007] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 01/20/2017] [Indexed: 12/20/2022] Open
Abstract
Pluripotent stem cells (PSCs) are defined by their self-renewal potential, which permits their unlimited propagation, and their pluripotency, being able to generate cell of the three embryonic lineages. These properties render PSCs a valuable tool for both basic and medical research. To induce and stabilize the pluripotent state, complex circuitries involving signaling pathways, transcription regulators and epigenetic mechanisms converge on a core transcriptional regulatory network of PSCs, thus determining their cell identity. Among the transcription factors, MYC represents a central hub, which modulates and integrates multiple mechanisms involved both in the maintenance of pluripotency and in cell reprogramming. Indeed, it instructs the PSC-specific cell cycle, metabolism and epigenetic landscape, contributes to limit exit from pluripotency and modulates signaling cascades affecting the PSC identity. Moreover, MYC extends its regulation on pluripotency by controlling PSC-specific non-coding RNAs. In this report, we review the MYC-controlled networks, which support the pluripotent state and discuss how their perturbation could affect cell identity. We further discuss recent finding demonstrating a central role of MYC in triggering epigenetic memory in PSCs, which depends on the establishment of a WNT-centered self-reinforcing circuit. Finally, we comment on the therapeutic implications of the role of MYC in affecting PSCs. Indeed, PSCs are used for both disease and cancer modeling and to derive cells for regenerative medicine. For these reasons, unraveling the MYC-mediated mechanism in those cells is fundamental to exploit their full potential and to identify therapeutic targets.
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Affiliation(s)
- Luca Fagnocchi
- Department of Epigenetics, Fondazione Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi" (INGM)Milan, Italy; Division of Pathology, Fondazione IRCCS Ca' Granda, Ospedale Maggiore PoliclinicoMilan, Italy
| | - Alessio Zippo
- Department of Epigenetics, Fondazione Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi" (INGM)Milan, Italy; Division of Pathology, Fondazione IRCCS Ca' Granda, Ospedale Maggiore PoliclinicoMilan, Italy
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