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Haviv D, Remšík J, Gatie M, Snopkowski C, Takizawa M, Pereira N, Bashkin J, Jovanovich S, Nawy T, Chaligne R, Boire A, Hadjantonakis AK, Pe'er D. The covariance environment defines cellular niches for spatial inference. Nat Biotechnol 2024:10.1038/s41587-024-02193-4. [PMID: 38565973 DOI: 10.1038/s41587-024-02193-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 02/28/2024] [Indexed: 04/04/2024]
Abstract
A key challenge of analyzing data from high-resolution spatial profiling technologies is to suitably represent the features of cellular neighborhoods or niches. Here we introduce the covariance environment (COVET), a representation that leverages the gene-gene covariate structure across cells in the niche to capture the multivariate nature of cellular interactions within it. We define a principled optimal transport-based distance metric between COVET niches that scales to millions of cells. Using COVET to encode spatial context, we developed environmental variational inference (ENVI), a conditional variational autoencoder that jointly embeds spatial and single-cell RNA sequencing data into a latent space. ENVI includes two decoders: one to impute gene expression across the spatial modality and a second to project spatial information onto single-cell data. ENVI can confer spatial context to genomics data from single dissociated cells and outperforms alternatives for imputing gene expression on diverse spatial datasets.
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Affiliation(s)
- Doron Haviv
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ján Remšík
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mohamed Gatie
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Catherine Snopkowski
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Meril Takizawa
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | | | - Tal Nawy
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ronan Chaligne
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Adrienne Boire
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Brain Tumor Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dana Pe'er
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Howard Hughes Medical Institute, New York, NY, USA.
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Haviv D, Gatie M, Hadjantonakis AK, Nawy T, Pe’er D. The covariance environment defines cellular niches for spatial inference. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.18.537375. [PMID: 37131616 PMCID: PMC10153165 DOI: 10.1101/2023.04.18.537375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The tsunami of new multiplexed spatial profiling technologies has opened a range of computational challenges focused on leveraging these powerful data for biological discovery. A key challenge underlying computation is a suitable representation for features of cellular niches. Here, we develop the covariance environment (COVET), a representation that can capture the rich, continuous multivariate nature of cellular niches by capturing the gene-gene covariate structure across cells in the niche, which can reflect the cell-cell communication between them. We define a principled optimal transport-based distance metric between COVET niches and develop a computationally efficient approximation to this metric that can scale to millions of cells. Using COVET to encode spatial context, we develop environmental variational inference (ENVI), a conditional variational autoencoder that jointly embeds spatial and single-cell RNA-seq data into a latent space. Two distinct decoders either impute gene expression across spatial modality, or project spatial information onto dissociated single-cell data. We show that ENVI is not only superior in the imputation of gene expression but is also able to infer spatial context to disassociated single-cell genomics data.
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Affiliation(s)
- Doron Haviv
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medicine; New York, NY 10065, USA
| | - Mohamed Gatie
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Tal Nawy
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Dana Pe’er
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Howard Hughes Medical Institute, New York, NY 10065, USA
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3
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Narayan G, Ronima K R, Thummer RP. Direct Reprogramming of Somatic Cells into Induced β-Cells: An Overview. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1410:171-189. [PMID: 36515866 DOI: 10.1007/5584_2022_756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The persistent shortage of insulin-producing islet mass or β-cells for transplantation in the ever-growing diabetic population worldwide is a matter of concern. To date, permanent cure to this medical complication is not available and soon after the establishment of lineage-specific reprogramming, direct β-cell reprogramming became a viable alternative for β-cell regeneration. Direct reprogramming is a straightforward and powerful technique that can provide an unlimited supply of cells by transdifferentiating terminally differentiated cells toward the desired cell type. This approach has been extensively used by multiple groups to reprogram non-β-cells toward insulin-producing β-cells. The β-cell identity has been achieved by various studies via ectopic expression of one or more pancreatic-specific transcription factors in somatic cells, bypassing the pluripotent state. This work highlights the importance of the direct reprogramming approaches (both integrative and non-integrative) in generating autologous β-cells for various applications. An in-depth understanding of the strategies and cell sources could prove beneficial for the efficient generation of integration-free functional insulin-producing β-cells for diabetic patients lacking endogenous β-cells.
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Affiliation(s)
- Gloria Narayan
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Ronima K R
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Rajkumar P Thummer
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India.
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Colarusso JL, Zhou Q. Direct Reprogramming of Different Cell Lineages into Pancreatic β-Like Cells. Cell Reprogram 2022; 24:252-258. [PMID: 35838597 PMCID: PMC9634980 DOI: 10.1089/cell.2022.0048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
One major goal of regenerative medicine is the production of pancreatic endocrine islets to treat insulin-dependent diabetic patients. Among the different methods developed to achieve this goal, a particularly promising approach is direct lineage reprogramming, in which non-β-cells are directly converted to glucose-responsive, insulin-secreting β-like cells. Efforts by different research groups have led to critical insights in the inducing factors necessary and types of somatic tissues suitable for direct conversion to β-like cells. Nevertheless, there is limited understanding of the molecular mechanisms underlying direct cell fate conversion. Significant challenges also remain in translating discoveries into therapeutics that will eventually benefit diabetic patients. This review aims to cover the advances made in the direct reprogramming of somatic cells into β-like cells and discuss the remaining challenges.
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Affiliation(s)
- Jonathan L. Colarusso
- Division of Regenerative Medicine, Department of Medicine, Ansary Stem Cell Institute, Weill Cornell Medicine, New York, New York, USA
| | - Qiao Zhou
- Division of Regenerative Medicine, Department of Medicine, Ansary Stem Cell Institute, Weill Cornell Medicine, New York, New York, USA
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5
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Wang YC, Wang ZJ, Zhang C, Ning BF. Cell reprogramming in liver with potential clinical correlations. J Dig Dis 2022; 23:13-21. [PMID: 34921720 DOI: 10.1111/1751-2980.13072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/13/2021] [Accepted: 12/15/2021] [Indexed: 12/11/2022]
Abstract
The theory of cell reprogramming has developed rapidly during the past decades. Cell reprogramming has been widely used in the construction of experimental models and cytotherapy for certain diseases. Hepatocyte-like cells that are important for the treatment of end-stage liver disease can now be obtained with a variety of reprogramming techniques. However, improving the differentiation status and physiological function of these cells remains challenging. Hepatocytes can transdifferentiate into other types of cells directly, whereas other types of cells can also transdifferentiate into hepatocyte-like cells both in vitro and in vivo. Moreover, cell reprogramming is to some extent similar to malignant cell transformation. During the initiation and progression of liver cancer, cell reprogramming is always associated with cancer metastasis and chemoresistance. In this review, we summarized the research related to cell reprogramming in liver and highlighted the potential effects of cell reprogramming in the pathogenesis and treatment of liver diseases.
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Affiliation(s)
- Yi Chuan Wang
- Clinical Cancer Institute, Center for Translational Medicine, Second Military Medical University, Shanghai, China
| | - Zhi Jie Wang
- Clinical Cancer Institute, Center for Translational Medicine, Second Military Medical University, Shanghai, China
| | - Cheng Zhang
- Department of Gastroenterology, Bethune International Peace Hospital, Shijiazhuang, Hebei Province, China
| | - Bei Fang Ning
- Department of Gastroenterology, Changzheng Hospital, Second Military Medical University, Shanghai, China
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Ruzittu S, Willnow D, Spagnoli FM. Direct Lineage Reprogramming: Harnessing Cell Plasticity between Liver and Pancreas. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a035626. [PMID: 31767653 DOI: 10.1101/cshperspect.a035626] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Direct lineage reprogramming of abundant and accessible cells into therapeutically useful cell types holds tremendous potential in regenerative medicine. To date, a number of different cell types have been generated by lineage reprogramming methods, including cells from the neural, cardiac, hepatic, and pancreatic lineages. The success of this strategy relies on developmental biology and the knowledge of cell-fate-defining transcriptional networks. Hepatocytes represent a prime target for β cell conversion for numerous reasons, including close developmental origin, accessibility, and regenerative potential. We present here an overview of pancreatic and hepatic development, with a particular focus on the mechanisms underlying the divergence between the two cell lineages. Additionally, we discuss to what extent this lineage relationship can be exploited in efforts to reprogram one cell type into the other and whether such an approach may provide a suitable strategy for regenerative therapies of diabetes.
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Affiliation(s)
- Silvia Ruzittu
- Centre for Stem Cell and Regenerative Medicine, King's College London, London SE1 9RT, United Kingdom.,Max Delbrück Center for Molecular Medicine (MDC), D-13125 Berlin, Germany
| | - David Willnow
- Centre for Stem Cell and Regenerative Medicine, King's College London, London SE1 9RT, United Kingdom
| | - Francesca M Spagnoli
- Centre for Stem Cell and Regenerative Medicine, King's College London, London SE1 9RT, United Kingdom
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Abstract
PURPOSE OF THE REVIEW Here, we review recent findings in the field of generating insulin-producing cells by pancreatic transcription factor (pTF)-induced liver transdifferentiation (TD). TD is the direct conversion of functional cell types from one lineage to another without passing through an intermediate stage of pluripotency. We address potential reasons for the restricted efficiency of TD and suggest modalities to overcome these challenges, to bring TD closer to its clinical implementation in autologous cell replacement therapy for insulin-dependent diabetes. RECENT FINDINGS Liver to pancreas TD is restricted to cells that are a priori predisposed to undergo the developmental process. In vivo, the predisposition of liver cells is affected by liver zonation and hepatic regeneration. The TD propensity of liver cells is related to permissive epigenome which could be extended to TD-resistant cells by specific soluble factors. An obligatory role for active Wnt signaling in continuously maintaining a "permissive" epigenome is suggested. Moreover, the restoration of the pancreatic niche and vasculature promotes the maturation of TD cells along the β cell function. Future studies on liver to pancreas TD should include the maturation of TD cells by 3D culture, the restoration of vasculature and the pancreatic niche, and the extension of TD propensity to TD-resistant cells by epigenetic modifications. Liver to pancreas TD is expected to result in the generation of custom-made "self" surrogate β cells for curing diabetes.
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Affiliation(s)
- Irit Meivar-Levy
- The Sheba Regenerative Medicine, Stem Cell and Tissue Engineering Center, Sheba Medical Center, 56261, Tel-Hashomer, Israel
- Dia-Cure, Institute of Medical Scientific Research Acad. Nicolae Cajal, University Titu Maiorescu, Bucharest, Romania
| | - Sarah Ferber
- The Sheba Regenerative Medicine, Stem Cell and Tissue Engineering Center, Sheba Medical Center, 56261, Tel-Hashomer, Israel.
- Dia-Cure, Institute of Medical Scientific Research Acad. Nicolae Cajal, University Titu Maiorescu, Bucharest, Romania.
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.
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Nowotschin S, Setty M, Kuo YY, Liu V, Garg V, Sharma R, Simon CS, Saiz N, Gardner R, Boutet SC, Church DM, Hoodless PA, Hadjantonakis AK, Pe'er D. The emergent landscape of the mouse gut endoderm at single-cell resolution. Nature 2019; 569:361-367. [PMID: 30959515 PMCID: PMC6724221 DOI: 10.1038/s41586-019-1127-1] [Citation(s) in RCA: 226] [Impact Index Per Article: 45.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 03/29/2019] [Indexed: 01/04/2023]
Abstract
Here we delineate the ontogeny of the mammalian endoderm by generating 112,217 single-cell transcriptomes, which represent all endoderm populations within the mouse embryo until midgestation. We use graph-based approaches to model differentiating cells, which provides a spatio-temporal characterization of developmental trajectories and defines the transcriptional architecture that accompanies the emergence of the first (primitive or extra-embryonic) endodermal population and its sister pluripotent (embryonic) epiblast lineage. We uncover a relationship between descendants of these two lineages, in which epiblast cells differentiate into endoderm at two distinct time points-before and during gastrulation. Trajectories of endoderm cells were mapped as they acquired embryonic versus extra-embryonic fates and as they spatially converged within the nascent gut endoderm, which revealed these cells to be globally similar but retain aspects of their lineage history. We observed the regionalized identity of cells along the anterior-posterior axis of the emergent gut tube, which reflects their embryonic or extra-embryonic origin, and the coordinated patterning of these cells into organ-specific territories.
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Affiliation(s)
- Sonja Nowotschin
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Manu Setty
- Computational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ying-Yi Kuo
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Vincent Liu
- Computational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Vidur Garg
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Roshan Sharma
- Computational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Claire S Simon
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nestor Saiz
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rui Gardner
- Flow Cytometry Core Facility, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Pamela A Hoodless
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia, Canada
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Dana Pe'er
- Computational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Hill CM, Banga A, Abrahante JE, Yuan C, Mutch LA, Janecek J, O'Brien T, Graham ML, Dutton JR. Establishing a Large-Animal Model for In Vivo Reprogramming of Bile Duct Cells into Insulin-Secreting Cells to Treat Diabetes. HUM GENE THER CL DEV 2017; 28:87-95. [PMID: 28363269 DOI: 10.1089/humc.2017.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Type 1 diabetes manifests as autoimmune destruction of beta cells requiring metabolic management with an exogenous replacement of insulin, either by repeated injection of recombinant insulin or by transplantation of allogeneic islets from cadaveric donors. Both of these approaches have severe limitations. Repeated insulin injection requires intensive blood glucose monitoring, is expensive, and is associated with decreased quality-of-life measures. Islet transplantation, while highly effective, is severely limited by shortage of donor organs. Clinical translation of beta cells derived from pluripotent stem cells is also not yet a reality, and alternative approaches to solving the replacement of lost beta cell function are required. In vivo direct reprogramming offers an attractive approach to generating new endogenous insulin-secreting cells by permanently altering the phenotype of somatic cells after transient expression of transcription factors. Previously, we have successfully restored control of blood glucose in diabetic mice by reprogramming liver cells into glucose-sensitive insulin-secreting cells after the transient, simultaneous delivery of three transcription factors (Pdx1, Ngn3, and MafA) to the liver of diabetic mice, using an adenoviral vector (Ad-PNM). Establishing a clinically relevant, large-animal model is a critical next step in translating this approach beyond the proof-of-principle stage in rodents and allowing investigation of vector design, dose and delivery, host response to vector infusion, and establishment of suitable criteria for measuring safety and efficacy. In this feasibility study we infused Ad-PNM into the liver of three diabetic cynomolgus macaques via portal vein catheter. Vector presence and cargo gene and protein expression were detected in liver tissue after infusion with no adverse effects. Refinement of immune suppression significantly extended the period of exogenous PNM expression. This pilot study establishes the suitability of this large-animal model to examine the translation of this approach for treating diabetes.
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Affiliation(s)
- Caitlin M Hill
- 1 Stem Cell Institute, McGuire Translational Research Facility, University of Minnesota , Minneapolis, Minnesota
| | - Anannya Banga
- 1 Stem Cell Institute, McGuire Translational Research Facility, University of Minnesota , Minneapolis, Minnesota
| | - Juan E Abrahante
- 2 University of Minnesota Informatics Institute, University of Minnesota , Minneapolis, Minnesota
| | - Ce Yuan
- 1 Stem Cell Institute, McGuire Translational Research Facility, University of Minnesota , Minneapolis, Minnesota.,5 Bioinformatics and Computational Biology Program, University of Minnesota , Rochester, Minnesota
| | - Lucas A Mutch
- 3 Department of Surgery, Preclinical Research Center, University of Minnesota , Minneapolis, Minnesota
| | - Jody Janecek
- 3 Department of Surgery, Preclinical Research Center, University of Minnesota , Minneapolis, Minnesota
| | - Timothy O'Brien
- 1 Stem Cell Institute, McGuire Translational Research Facility, University of Minnesota , Minneapolis, Minnesota.,4 Department of Veterinary Population Medicine, University of Minnesota , St. Paul, Minnesota
| | - Melanie L Graham
- 3 Department of Surgery, Preclinical Research Center, University of Minnesota , Minneapolis, Minnesota.,4 Department of Veterinary Population Medicine, University of Minnesota , St. Paul, Minnesota
| | - James R Dutton
- 1 Stem Cell Institute, McGuire Translational Research Facility, University of Minnesota , Minneapolis, Minnesota
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10
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AKINCI E, YILDIZ M, ÜNAL P, BADAKUL G. In vitro transcription and validation of human pancreatic transcription factors’ mRNAs. Turk J Biol 2017. [DOI: 10.3906/biy-1610-29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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11
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Zheng F, Zuo J. Cochlear hair cell regeneration after noise-induced hearing loss: Does regeneration follow development? Hear Res 2016; 349:182-196. [PMID: 28034617 DOI: 10.1016/j.heares.2016.12.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 11/22/2016] [Accepted: 12/20/2016] [Indexed: 12/14/2022]
Abstract
Noise-induced hearing loss (NIHL) affects a large number of military personnel and civilians. Regenerating inner-ear cochlear hair cells (HCs) is a promising strategy to restore hearing after NIHL. In this review, we first summarize recent transcriptome profile analysis of zebrafish lateral lines and chick utricles where spontaneous HC regeneration occurs after HC damage. We then discuss recent studies in other mammalian regenerative systems such as pancreas, heart and central nervous system. Both spontaneous and forced HC regeneration occurs in mammalian cochleae in vivo involving proliferation and direct lineage conversion. However, both processes are inefficient and incomplete, and decline with age. For direct lineage conversion in vivo in cochleae and in other systems, further improvement requires multiple factors, including transcription, epigenetic and trophic factors, with appropriate stoichiometry in appropriate architectural niche. Increasing evidence from other systems indicates that the molecular paths of direct lineage conversion may be different from those of normal developmental lineages. We therefore hypothesize that HC regeneration does not have to follow HC development and that epigenetic memory of supporting cells influences the HC regeneration, which may be a key to successful cochlear HC regeneration. Finally, we discuss recent efforts in viral gene therapy and drug discovery for HC regeneration. We hope that combination therapy targeting multiple factors and epigenetic signaling pathways will provide promising avenues for HC regeneration in humans with NIHL and other types of hearing loss.
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Affiliation(s)
- Fei Zheng
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS 322, Memphis, TN 38105, United States.
| | - Jian Zuo
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS 322, Memphis, TN 38105, United States.
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12
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Abstract
The nature of cells in early embryos may be respecified simply by exposure to inducing factors. In later stage embryos, determined cell populations do not respond to inducing factors but may be respecified by other stimuli, especially the introduction of specific transcription factors. Fully differentiated cell types are hard to respecify by any method, but some degree of success can be achieved using selected combinations of transcription factors, and this may have clinical significance in the future.
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13
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Abstract
Tissue replacement is a promising direction for the treatment of diabetes, which will become widely available only when islets or insulin-producing cells that will not be rejected by the diabetic recipients are available in unlimited amounts. The present review addresses the research in the field of generating functional insulin-producing cells by transdifferentiation of adult liver cells both in vitro and in vivo. It presents recent knowledge of the mechanisms which underlie the process and assesses the challenges which should be addressed for its efficient implementation as a cell based replacement therapy for diabetics.
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Affiliation(s)
- Irit Meivar-Levy
- Sheba Regenerative Medicine, Stem Cells and Tissue Engineering Center, Sheba Medical Center, Tel-Hashomer 52621, Israel.
| | - Sarah Ferber
- Sheba Regenerative Medicine, Stem Cells and Tissue Engineering Center, Sheba Medical Center, Tel-Hashomer 52621, Israel; Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel-Aviv University, 69978, Israel.
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14
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Cavelti-Weder C, Li W, Zumsteg A, Stemann M, Yamada T, Bonner-Weir S, Weir G, Zhou Q. Direct Reprogramming for Pancreatic Beta-Cells Using Key Developmental Genes. CURRENT PATHOBIOLOGY REPORTS 2015; 3:57-65. [PMID: 26998407 DOI: 10.1007/s40139-015-0068-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Direct reprogramming is a promising approach for regenerative medicine whereby one cell type is directly converted into another without going through a multipotent or pluripotent stage. This reprogramming approach has been extensively explored for the generation of functional insulin-secreting cells from non-beta-cells with the aim of developing novel cell therapies for the treatment of people with diabetes lacking sufficient endogenous beta-cells. A common approach for such conversion studies is the introduction of key regulators that are important in controlling beta-cell development and maintenance. In this review, we will summarize the recent advances in the field of beta-cell reprogramming and discuss the challenges of creating functional and long-lasting beta-cells.
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Affiliation(s)
- Claudia Cavelti-Weder
- Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA
| | - Weida Li
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Adrian Zumsteg
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Marianne Stemann
- Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA
| | - Takatsugu Yamada
- Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA
| | - Susan Bonner-Weir
- Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA
| | - Gordon Weir
- Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA
| | - Qiao Zhou
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
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