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Dai W, Wang H, Zhan Y, Li N, Li F, Wang J, Yan H, Zhang Y, Wang J, Wu L, Liu H, Fan Y, Tao Y, Mo X, Yang JJ, Sun K, Chen G, Yu Y. CCNK Gene Deficiency Influences Neural Progenitor Cells Via Wnt5a Signaling in CCNK-Related Syndrome. Ann Neurol 2023; 94:1136-1154. [PMID: 37597256 DOI: 10.1002/ana.26766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 08/07/2023] [Accepted: 08/11/2023] [Indexed: 08/21/2023]
Abstract
OBJECTIVE Rare variants of CCNK (cyclin K) give rise to a syndrome with intellectual disability. The purpose of this study was to describe the genotype-phenotype spectrum of CCNK-related syndrome and the underlying molecular mechanisms of pathogenesis. METHODS We identified a number of de novo CCNK variants in unrelated patients. We generated patient-induced pluripotent stem cells (iPSCs) and neural progenitor cells (NPCs) as disease models. In addition, we constructed NPC-specific Ccnk knockout (KO) mice and performed molecular and morphological analyses. RESULTS We identified 2 new patients harboring CCNK missense variants and followed-up 3 previous reported patients, which constitute the largest patient population analysis of the disease. We demonstrate that both the patient-derived NPC models and the Ccnk KO mouse displayed deficient NPC proliferation and enhanced apoptotic cell death. RNA sequencing analyses of these NPC models uncovered transcriptomic signatures unique to CCNK-related syndrome, revealing significant changes in genes, including WNT5A, critical for progenitor proliferation and cell death. Further, to confirm WNT5A's role, we conducted rescue experiments using NPC and mouse models. We found that a Wnt5a inhibitor significantly increased proliferation and reduced apoptosis in NPCs derived from patients with CCNK-related syndrome and NPCs in the developing cortex of Ccnk KO mice. INTERPRETATION We discussed the genotype-phenotype relationship of CCNK-related syndrome. Importantly, we demonstrated that CCNK plays critical roles in NPC proliferation and NPC apoptosis in vivo and in vitro. Together, our study highlights that Wnt5a may serve as a promising therapeutic target for the disease intervention. ANN NEUROL 2023;94:1136-1154.
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Affiliation(s)
- Weiqian Dai
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai, China
| | - He Wang
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yongkun Zhan
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Nan Li
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Fei Li
- Department of Developmental and Behavioral Pediatrics, Department of Child Primary Care, Brain and Behavioral Research Unit of Shanghai Institute for Pediatric Research and MOE-Shanghai Key Laboratory for Children's Environmental Health, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jingmin Wang
- Departmentof Pediatrics, Peking University First Hospital, Beijing, China
| | - Huifang Yan
- Departmentof Pediatrics, Peking University First Hospital, Beijing, China
| | - Yu Zhang
- Departmentof Pediatrics, Peking University First Hospital, Beijing, China
| | - Junyu Wang
- Departmentof Pediatrics, Peking University First Hospital, Beijing, China
| | - Lingqian Wu
- State Key Laboratory of Medical Genetics, Central South University, Changsha, China
| | - Huili Liu
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Yanjie Fan
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Yue Tao
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xi Mo
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jian-Jun Yang
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Kun Sun
- Department of Pediatric Cardiovascular, Center of Clinical Genetics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guiquan Chen
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Medical School, Nanjing University, Nanjing, China
| | - Yongguo Yu
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai, China
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Kumari K, Tandon S, Ghosh S, Baligar P. Gelatin scaffold ameliorates proliferation & stem cell differentiation into the hepatic like cell and support liver regeneration in partial-hepatectomized mice model. Biomed Mater 2023; 18:065022. [PMID: 37860885 DOI: 10.1088/1748-605x/ad04fd] [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: 05/14/2023] [Accepted: 10/19/2023] [Indexed: 10/21/2023]
Abstract
Stem cell-based tissue engineering is an emerging tool for developing functional tissues of choice. To understand pluripotency and hepatic differentiation of mouse embryonic stem cells (mESCs) on a three-dimensional (3D) scaffold, we established an efficient approach for generating hepatocyte-like cells (HLCs) from hepatoblast cells. We developed porous and biodegradable scaffold, which was stimulated with exogenous growth factors and investigated stemness and differentiation capacity of mESCs into HLCs on the scaffoldin-vitro. In animal studies, we had cultured mESCs-derived hepatoblast-like cells on the scaffold and then, transplanted them into the partially hepatectomized C57BL/6 male mice model to evaluate the effect of gelatin scaffold on hepatic regeneration. The 3D culture system allowed maintenance of stemness properties in mESCs. The step-wise induction of mESCs with differentiation factors leads to the formation of HLCs and expressed liver-specific genes, including albumin, hepatocyte nucleic factor 4 alpha, and cytokeratin 18. In addition, cells also expressed Ki67, indicating cells are proliferating. The secretome showed expression of albumin, urea, creatinine, alanine transaminase, and aspartate aminotransferase. However, the volume of the excised liver which aids regeneration has not been studied. Our results indicate that hepatoblast cells on the scaffold implanted in PH mouse indicates that these cells efficiently differentiate into HLCs and cholangiocytes, forming hepatic lobules with central and portal veins, and bile duct-like structures with neovascularization. The gelatin scaffold provides an efficient microenvironment for liver differentiation and regeneration bothin-vitroandin-vivo. These hepatoblasts cells would be a valuable source for 3D liver tissue engineering/transplantation in liver diseases.
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Affiliation(s)
- Kshama Kumari
- Amity Institute of Molecular Medicine & Stem Cell Research (AIMMSCR), Amity University, Noida, Uttar Pradesh, India
| | | | - Sourabh Ghosh
- Regenerative Engineering Laboratory, Department of Textile and Fibre Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Prakash Baligar
- Amity Institute of Molecular Medicine & Stem Cell Research (AIMMSCR), Amity University, Noida, Uttar Pradesh, India
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Smullen M, Olson MN, Reichert JM, Dawes P, Murray LF, Baer CE, Wang Q, Readhead B, Church GM, Lim ET, Chan Y. Reliable multiplex generation of pooled induced pluripotent stem cells. CELL REPORTS METHODS 2023; 3:100570. [PMID: 37751688 PMCID: PMC10545906 DOI: 10.1016/j.crmeth.2023.100570] [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: 06/28/2022] [Revised: 06/23/2023] [Accepted: 08/04/2023] [Indexed: 09/28/2023]
Abstract
Reprogramming somatic cells into pluripotent stem cells (iPSCs) enables the study of systems in vitro. To increase the throughput of reprogramming, we present induction of pluripotency from pooled cells (iPPC)-an efficient, scalable, and reliable reprogramming procedure. Using our deconvolution algorithm that employs pooled sequencing of single-nucleotide polymorphisms (SNPs), we accurately estimated individual donor proportions of the pooled iPSCs. With iPPC, we concurrently reprogrammed over one hundred donor lymphoblastoid cell lines (LCLs) into iPSCs and found strong correlations of individual donors' reprogramming ability across multiple experiments. Individual donors' reprogramming ability remains consistent across both same-day replicates and multiple experimental runs, and the expression of certain immunoglobulin precursor genes may impact reprogramming ability. The pooled iPSCs were also able to differentiate into cerebral organoids. Our procedure enables a multiplex framework of using pooled libraries of donor iPSCs for downstream research and investigation of in vitro phenotypes.
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Affiliation(s)
- Molly Smullen
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Meagan N Olson
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Julia M Reichert
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Pepper Dawes
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Liam F Murray
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Christina E Baer
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Qi Wang
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ 85281, USA
| | - Benjamin Readhead
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ 85281, USA
| | - George M Church
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Elaine T Lim
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Yingleong Chan
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
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Zheng H, Chen Y, Luo Q, Zhang J, Huang M, Xu Y, Huo D, Shan W, Tie R, Zhang M, Qian P, Huang H. Generating hematopoietic cells from human pluripotent stem cells: approaches, progress and challenges. CELL REGENERATION (LONDON, ENGLAND) 2023; 12:31. [PMID: 37656237 PMCID: PMC10474004 DOI: 10.1186/s13619-023-00175-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/13/2023] [Indexed: 09/02/2023]
Abstract
Human pluripotent stem cells (hPSCs) have been suggested as a potential source for the production of blood cells for clinical application. In two decades, almost all types of blood cells can be successfully generated from hPSCs through various differentiated strategies. Meanwhile, with a deeper understanding of hematopoiesis, higher efficiency of generating progenitors and precursors of blood cells from hPSCs is achieved. However, how to generate large-scale mature functional cells from hPSCs for clinical use is still difficult. In this review, we summarized recent approaches that generated both hematopoietic stem cells and mature lineage cells from hPSCs, and remarked their efficiency and mechanisms in producing mature functional cells. We also discussed the major challenges in hPSC-derived products of blood cells and provided some potential solutions. Our review summarized efficient, simple, and defined methodologies for developing good manufacturing practice standards for hPSC-derived blood cells, which will facilitate the translation of these products into the clinic.
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Affiliation(s)
- Haiqiong Zheng
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310012, China
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, 311121, China
- Institute of Hematology, Zhejiang University, Hangzhou, 310012, China
- Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou, 310012, China
| | - Yijin Chen
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310012, China
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, 311121, China
- Institute of Hematology, Zhejiang University, Hangzhou, 310012, China
- Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou, 310012, China
| | - Qian Luo
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310012, China
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, 311121, China
- Institute of Hematology, Zhejiang University, Hangzhou, 310012, China
- Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou, 310012, China
| | - Jie Zhang
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310012, China
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, 311121, China
- Institute of Hematology, Zhejiang University, Hangzhou, 310012, China
- Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou, 310012, China
| | - Mengmeng Huang
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310012, China
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, 311121, China
- Institute of Hematology, Zhejiang University, Hangzhou, 310012, China
- Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou, 310012, China
| | - Yulin Xu
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310012, China
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, 311121, China
- Institute of Hematology, Zhejiang University, Hangzhou, 310012, China
- Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou, 310012, China
| | - Dawei Huo
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310012, China
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, 311121, China
- Institute of Hematology, Zhejiang University, Hangzhou, 310012, China
- Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou, 310012, China
| | - Wei Shan
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310012, China
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, 311121, China
- Institute of Hematology, Zhejiang University, Hangzhou, 310012, China
- Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou, 310012, China
| | - Ruxiu Tie
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310012, China
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, 311121, China
- Institute of Hematology, Zhejiang University, Hangzhou, 310012, China
- Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou, 310012, China
| | - Meng Zhang
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310012, China.
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, 311121, China.
- Institute of Hematology, Zhejiang University, Hangzhou, 310012, China.
- Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou, 310012, China.
| | - Pengxu Qian
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, 311121, China.
- Institute of Hematology, Zhejiang University, Hangzhou, 310012, China.
- Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou, 310012, China.
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.
| | - He Huang
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310012, China.
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, 311121, China.
- Institute of Hematology, Zhejiang University, Hangzhou, 310012, China.
- Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou, 310012, China.
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Gao L, Wang F, Wang Y, Hu L, Mao J. A protocol for the generation of patient-specific iPSC lines from peripheral blood mononuclear cells. STAR Protoc 2022; 3:101530. [PMID: 35834385 PMCID: PMC9287807 DOI: 10.1016/j.xpro.2022.101530] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 04/06/2022] [Accepted: 06/13/2022] [Indexed: 11/24/2022] Open
Abstract
The current procedure thoroughly explains how to reprogram induced pluripotent stem cells (iPSCs) from the patient’s peripheral blood mononuclear cells (PBMCs), a less invasive source; e.g., somatic cells. We describe how to isolate PBMCs and reprogram them into iPSCs by electroporation. Furthermore, we provide an alternative approach to generating iPSC using Geltrex or Matrigel matrix to replace MEF-feeder. The challenge of this process is the relatively lower cell survival rates of PBMCs due to the damage of electroporation. For complete details on the use and execution of this protocol, please refer to Hu et al. (2021). Protocol to induce iPSC from patient-derived PBMCs Protocol to isolate PBMC from patients Alternative feeder approach to generating iPSC by Geltrex or Matrigel matrix
Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
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Ray A, Joshi JM, Sundaravadivelu PK, Raina K, Lenka N, Kaveeshwar V, Thummer RP. An Overview on Promising Somatic Cell Sources Utilized for the Efficient Generation of Induced Pluripotent Stem Cells. Stem Cell Rev Rep 2021; 17:1954-1974. [PMID: 34100193 DOI: 10.1007/s12015-021-10200-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/02/2021] [Indexed: 01/19/2023]
Abstract
Human induced Pluripotent Stem Cells (iPSCs) have enormous potential in understanding developmental biology, disease modeling, drug discovery, and regenerative medicine. The initial human iPSC studies used fibroblasts as a starting cell source to reprogram them; however, it has been identified to be a less appealing somatic cell source by numerous studies due to various reasons. One of the important criteria to achieve efficient reprogramming is determining an appropriate starting somatic cell type to induce pluripotency since the cellular source has a major influence on the reprogramming efficiency, kinetics, and quality of iPSCs. Therefore, numerous groups have explored various somatic cell sources to identify the promising sources for reprogramming into iPSCs with different reprogramming factor combinations. This review provides an overview of promising easily accessible somatic cell sources isolated in non-invasive or minimally invasive manner such as keratinocytes, urine cells, and peripheral blood mononuclear cells used for the generation of human iPSCs derived from healthy and diseased subjects. Notably, iPSCs generated from one of these cell types derived from the patient will offer ethical and clinical advantages. In addition, these promising somatic cell sources have the potential to efficiently generate bona fide iPSCs with improved reprogramming efficiency and faster kinetics. This knowledge will help in establishing strategies for safe and efficient reprogramming and the generation of patient-specific iPSCs from these cell types.
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Affiliation(s)
- Arnab Ray
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Jahnavy Madhukar Joshi
- Central Research Laboratory, SDM College of Medical Sciences and Hospital, Shri Dharmasthala Manjunatheshwara University, Dharwad, 580009, Karnataka, India
| | - Pradeep Kumar Sundaravadivelu
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Khyati Raina
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Nibedita Lenka
- National Centre for Cell Science, S. P. Pune University Campus, Pune - 411007, Ganeshkhind, Maharashtra, India
| | - Vishwas Kaveeshwar
- Central Research Laboratory, SDM College of Medical Sciences and Hospital, Shri Dharmasthala Manjunatheshwara University, Dharwad, 580009, Karnataka, India.
| | - Rajkumar P Thummer
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
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Walker SJ, Wagoner AL, Leavitt D, Mack DL. A simplified approach for derivation of induced pluripotent stem cells from Epstein-Barr virus immortalized B-lymphoblastoid cell lines. Heliyon 2021; 7:e06617. [PMID: 33869861 PMCID: PMC8047170 DOI: 10.1016/j.heliyon.2021.e06617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/06/2021] [Accepted: 03/24/2021] [Indexed: 11/26/2022] Open
Abstract
Given the limited availability of tissue, especially brain tissue, for neurological diseases and disorders research, the development of alternative biological tools for investigations of underlying molecular and genetic mechanisms is imperative. One important resource for this task is the large repositories that bank immortalized blood cells (i.e. lymphoblastoid cell lines; LCLs) from affected individuals and their unaffected family members. These repositories document demographic, phenotypic, and, in some cases, genotypic information about the donors and thus provide a ready-made sample source for hypothesis testing. Importantly, patient-specific LCLs can be used to generate induced pluripotent stem cells (iPSC) that, in turn, can be used to create specific cell types for use in mechanistic studies. To investigate this concept further, LCLs from two males (proband and sibling) were obtained from one such repository, the Autism Genetics Resource Exchange (AGRE), and iPSCs were generated by transfection with Epi5 Episomal iPSC reprogramming plasmids. Characterization of the resultant cell lines by PCR, RT-PCR, immunocytochemistry, karyotyping, and the Taqman® human pluripotent stem cell Scorecard™ Panel, was used to provide evidence of endogenous pluripotency and then to evaluate the trilineage potential of four representative clones. Results indicated that all four iPSC lines were initially pluripotent and displayed the trilineage potential predictive for successful differentiation to mesoderm, endoderm, or ectoderm-derived cell types. Compared to other published protocols, this study details a somewhat simplified approach, used here specifically for the generation and characterization of induced pluripotent stem cells from well-characterized and banked LCLs.
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Affiliation(s)
- Stephen J Walker
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Medical Center Blvd., Winston Salem, NC 27156, USA
| | - Ashley L Wagoner
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Medical Center Blvd., Winston Salem, NC 27156, USA
| | - Dana Leavitt
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Medical Center Blvd., Winston Salem, NC 27156, USA
| | - David L Mack
- Department of Rehabilitation Medicine and the Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
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Wang L, Ye Z, Jang YY. Convergence of human pluripotent stem cell, organoid, and genome editing technologies. Exp Biol Med (Maywood) 2021; 246:861-875. [PMID: 33467883 DOI: 10.1177/1535370220985808] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The last decade has seen many exciting technological breakthroughs that greatly expanded the toolboxes for biological and biomedical research, yet few have had more impact than induced pluripotent stem cells and modern-day genome editing. These technologies are providing unprecedented opportunities to improve physiological relevance of experimental models, further our understanding of developmental processes, and develop novel therapies. One of the research areas that benefit greatly from these technological advances is the three-dimensional human organoid culture systems that resemble human tissues morphologically and physiologically. Here we summarize the development of human pluripotent stem cells and their differentiation through organoid formation. We further discuss how genetic modifications, genome editing in particular, were applied to answer basic biological and biomedical questions using organoid cultures of both somatic and pluripotent stem cell origins. Finally, we discuss the potential challenges of applying human pluripotent stem cell and organoid technologies for safety and efficiency evaluation of emerging genome editing tools.
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Affiliation(s)
- Lin Wang
- Division of Cellular and Gene Therapies, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Zhaohui Ye
- Division of Cellular and Gene Therapies, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Yoon-Young Jang
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, John Hopkins University, Baltimore, MD 21218, USA
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9
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Induced pluripotency and spontaneous reversal of cellular aging in supercentenarian donor cells. Biochem Biophys Res Commun 2020; 525:563-569. [DOI: 10.1016/j.bbrc.2020.02.092] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 02/12/2020] [Indexed: 12/14/2022]
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Bulutoglu B, Rey-Bedón C, Mert S, Tian L, Jang YY, Yarmush ML, Usta OB. A comparison of hepato-cellular in vitro platforms to study CYP3A4 induction. PLoS One 2020; 15:e0229106. [PMID: 32106230 PMCID: PMC7046200 DOI: 10.1371/journal.pone.0229106] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 01/29/2020] [Indexed: 02/06/2023] Open
Abstract
In vitro studies of drug toxicity and drug-drug interactions are crucial for drug development efforts. Currently, the utilization of primary human hepatocytes (PHHs) is the de facto standard for this purpose, due to their functional xenobiotic response and drug metabolizing CYP450 enzyme metabolism. However, PHHs are scarce, expensive, require laborious maintenance, and exhibit lot-to-lot heterogeneity. Alternative human in vitro platforms include hepatic cell lines, which are easy to access and maintain, and induced pluripotent stem cell (iPSC) derived hepatocytes. In this study, we provide a direct comparison of drug induced CYP3A4 and PXR expression levels of PHHs, hepatic cell lines Huh7 and HepG2, and iPSC derived hepatocyte like cells. Confluently cultured Huh7s exhibited an improved CYP3A4 expression and were inducible by up to 4.9-fold, and hepatocytes differentiated from human iPSCs displayed a 3.3-fold CYP3A4 induction. In addition, an increase in PXR expression levels was observed in both hepatic cell lines and iPSC derived hepatocytes upon rifampicin treatment, whereas a reproducible increase in PXR expression was not achieved in PHHs. Our results indicate that both hepatoma originated cell lines and iPSCs may provide alternative sources to primary hepatocytes, providing reliable and reproducible results for CYP3A4/PXR metabolism, upon in vitro maturation. This study may serve as a guide for the selection of suitable and feasible in vitro platforms for drug-drug interaction and toxicology studies.
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Affiliation(s)
- Beyza Bulutoglu
- Center for Engineering in Medicine, Massachusetts General Hospital, Harvard Medical School and Shriners Hospitals for Children, Boston, Massachusetts, United States of America
| | - Camilo Rey-Bedón
- Center for Engineering in Medicine, Massachusetts General Hospital, Harvard Medical School and Shriners Hospitals for Children, Boston, Massachusetts, United States of America
| | - Safak Mert
- Center for Engineering in Medicine, Massachusetts General Hospital, Harvard Medical School and Shriners Hospitals for Children, Boston, Massachusetts, United States of America
| | - Lipeng Tian
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Institute for Cell Engineering, School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Yoon-Young Jang
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Institute for Cell Engineering, School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Martin L. Yarmush
- Center for Engineering in Medicine, Massachusetts General Hospital, Harvard Medical School and Shriners Hospitals for Children, Boston, Massachusetts, United States of America
- Department of Biomedical Engineering, Rutgers University, Piscataway, New Jersey, United States of America
| | - O. Berk Usta
- Center for Engineering in Medicine, Massachusetts General Hospital, Harvard Medical School and Shriners Hospitals for Children, Boston, Massachusetts, United States of America
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11
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Kumar S, Curran JE, Espinosa EC, Glahn DC, Blangero J. Highly efficient induced pluripotent stem cell reprogramming of cryopreserved lymphoblastoid cell lines. J Biol Methods 2020; 7:e124. [PMID: 31976351 PMCID: PMC6974695 DOI: 10.14440/jbm.2020.296] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 11/27/2019] [Accepted: 11/29/2019] [Indexed: 01/19/2023] Open
Abstract
Tissue culture based in-vitro experimental modeling of human inherited disorders provides insight into the cellular and molecular mechanisms involved and the underlying genetic component influencing the disease phenotype. The breakthrough development of induced pluripotent stem cell (iPSC) technology represents a quantum leap in experimental modeling of human diseases, providing investigators with a self-renewing and thus unlimited source of pluripotent cells for targeted differentiation into functionally relevant disease specific tissue/cell types. The existing rich bio-resource of Epstein-Barr virus (EBV) immortalized lymphoblastoid cell line (LCL) repositories generated from a wide array of patients in genetic and epidemiological studies worldwide, many of them with extensive genotypic, genomic and phenotypic data already existing, provides a great opportunity to reprogram iPSCs from any of these LCL donors in the context of their own genetic identity for disease modeling and disease gene identification. However, due to the low reprogramming efficiency and poor success rate of LCL to iPSC reprogramming, these LCL resources remain severely underused for this purpose. Here, we detailed step-by-step instructions to perform our highly efficient LCL-to-iPSC reprogramming protocol using EBNA1/OriP episomal plasmids encoding pluripotency transcription factors (i.e., OCT3/4, SOX2, KLF4, L-MYC, and LIN28), mouse p53DD (p53 carboxy-terminal dominant-negative fragment) and commercially available reprogramming media. We achieved a consistently high reprogramming efficiency and 100% success rate (> 200 reprogrammed iPSC lines) using this protocol.
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Affiliation(s)
- Satish Kumar
- Department of Human Genetics & South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Edinburg and Brownsville, TX 78541, USA
| | - Joanne E Curran
- Department of Human Genetics & South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Edinburg and Brownsville, TX 78541, USA
| | - Erika C Espinosa
- Department of Human Genetics & South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Edinburg and Brownsville, TX 78541, USA
| | - David C Glahn
- Olin Neuropsychiatry Research Center, The Institute of Living, Hartford, CT 06106, USA.,Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06510, USA
| | - John Blangero
- Department of Human Genetics & South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Edinburg and Brownsville, TX 78541, USA
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12
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Chen Y, Yi Y, Xu J, Chan WK, Loh YH. Re-entering the pluripotent state from blood lineage: promises and pitfalls of blood reprogramming. FEBS Lett 2019; 593:3244-3252. [PMID: 31691960 DOI: 10.1002/1873-3468.13659] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/27/2019] [Accepted: 11/01/2019] [Indexed: 12/22/2022]
Abstract
Blood reprogramming, in which induced pluripotent stem cells (iPSCs) are derived from haematopoietic lineages, has rapidly advanced over the past decade. Since the first report using human blood, haematopoietic cell types from various sources, such as the peripheral bone marrow and cord blood, have been successfully reprogrammed. The volume of blood required has also decreased, from around tens of millilitres to a single finger-prick drop. Besides, while early studies were limited to reprogramming methods relying on viral integration, nonintegrating reprogramming systems for blood lineages have been subsequently established. Together, these improvements have made feasible the future clinical applications of blood-derived iPSCs. Here, we review the progress in blood reprogramming from various perspectives, including the starting materials and subsequent reprogramming strategies. We also discuss the downstream applications of blood-derived iPSCs, highlighting their clinical value in terms of disease modelling and therapeutic development.
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Affiliation(s)
- Ying Chen
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore.,Epigenetics and Cell Fates Laboratory, Programme in Stem Cell, Regenerative Medicine and Aging, A*STAR Institute of Molecular and Cell Biology, Singapore, Singapore
| | - Yao Yi
- Department of Biological Sciences, National University of Singapore, Singapore.,Epigenetics and Cell Fates Laboratory, Programme in Stem Cell, Regenerative Medicine and Aging, A*STAR Institute of Molecular and Cell Biology, Singapore, Singapore
| | - Jian Xu
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore
| | - Woon-Khiong Chan
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore
| | - Yuin-Han Loh
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore.,Epigenetics and Cell Fates Laboratory, Programme in Stem Cell, Regenerative Medicine and Aging, A*STAR Institute of Molecular and Cell Biology, Singapore, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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13
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Wang AYL, Loh CYY. Episomal Induced Pluripotent Stem Cells: Functional and Potential Therapeutic Applications. Cell Transplant 2019; 28:112S-131S. [PMID: 31722555 PMCID: PMC7016470 DOI: 10.1177/0963689719886534] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The term episomal induced pluripotent stem cells (EiPSCs) refers to somatic cells that are reprogrammed into induced pluripotent stem cells (iPSCs) using non-integrative episomal vector methods. This reprogramming process has a better safety profile compared with integrative methods using viruses. There is a current trend toward using episomal plasmid reprogramming to generate iPSCs because of the improved safety profile. Clinical reports of potential human cell sources that have been successfully reprogrammed into EiPSCs are increasing, but no review or summary has been published. The functional applications of EiPSCs and their potential uses in various conditions have been described, and these may be applicable to clinical scenarios. This review summarizes the current direction of EiPSC research and the properties of these cells with the aim of explaining their potential role in clinical applications and functional restoration.
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Affiliation(s)
- Aline Yen Ling Wang
- Center for Vascularized Composite Allotransplantation, Chang Gung Memorial Hospital, Taoyuan, Taiwan.,*Both the authors contributed equally to this article
| | - Charles Yuen Yung Loh
- St Andrew's Center for Burns and Plastic Surgery, Chelmsford, United Kingdom.,*Both the authors contributed equally to this article
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14
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Kumar S, Espinosa EC, Leandro AC, Curran JE, Blangero J. microRNA and mRNA interactions in induced pluripotent stem cell reprogramming of lymphoblastoid cell lines. AMERICAN JOURNAL OF STEM CELLS 2019; 8:28-37. [PMID: 31523484 PMCID: PMC6737382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 07/23/2019] [Indexed: 06/10/2023]
Abstract
A large number of Epstein Barr virus (EBV) immortalized lymphoblastoid cell lines (LCLs) have been generated and maintained in genetic/epidemiological studies as a perpetual source of DNA and as a surrogate in vitro cell model. Recent successes in reprograming LCLs into induced pluripotent stem cells (iPSCs) has paved the way to generate more relevant in vitro disease models using this existing bioresource. However, the latent EBV infection in the LCLs make them a unique cell type by altering expression of many cellular genes and miRNAs. These EBV induced changes in the LCL miRNome and transcriptome are reversed upon reprogramming into iPSCs, which allows a unique opportunity to better understand the miRNA and mRNA interactions that are EBV induced in LCLs and the changes that takes place during iPSC reprogramming. To identify the potential miRNA-mRNA interactions and better understand their role in regulating the cellular transitions in LCLs and their reprogrammed iPSCs, we performed a parallel genome-wide miRNA and mRNA expression analysis in six LCLs and their reprogrammed iPSCs. A total of 85 miRNAs and 5,228 mRNAs were significantly differentially expressed (DE). The target prediction of the DE miRNAs using TargetScan-Human, TarBase and miRecords databases identified 1,842 mRNA targets that were DE between LCLs and their reprogrammed iPSCs. The functional annotation, upstream regulator and gene expression analysis of the predicted DE mRNA targets suggest the role of DE miRNAs in regulating EBV induced changes in LCLs and self-renewal, pluripotency and differentiation in iPSCs.
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Affiliation(s)
- Satish Kumar
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine Edinburg and Brownsville, TX, USA
| | - Erika C Espinosa
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine Edinburg and Brownsville, TX, USA
| | - Ana C Leandro
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine Edinburg and Brownsville, TX, USA
| | - Joanne E Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine Edinburg and Brownsville, TX, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine Edinburg and Brownsville, TX, USA
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15
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Chaudhari P, Tian L, Ye Z, Jang YY. Human-relevant preclinical in vitro models for studying hepatobiliary development and liver diseases using induced pluripotent stem cells. Exp Biol Med (Maywood) 2019; 244:702-708. [PMID: 30803263 DOI: 10.1177/1535370219834895] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
IMPACT STATEMENT In this review, we address the potential of human-induced pluripotent stem cell-based hepatobiliary differentiation technology as a means to study human liver development and cell fate determination, and to model liver diseases in an effort to develop a new human-relevant preclinical platform for drug development.
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Affiliation(s)
- Pooja Chaudhari
- 1 Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21205, USA.,2 Cellular and Molecular Medicine Graduate Program, Baltimore, MD 21205, USA
| | - Lipeng Tian
- 1 Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21205, USA
| | - Zhaohui Ye
- 3 Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yoon-Young Jang
- 1 Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21205, USA.,2 Cellular and Molecular Medicine Graduate Program, Baltimore, MD 21205, USA.,3 Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,4 Institute for Cell Engineering, Baltimore, MD 21205, USA
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16
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Abstract
Biliary atresia (BA) is the most common cause of pediatric end-stage liver disease and the etiology is poorly understood. There is no effective therapy for BA partly due to lack of human BA models. Towards developing in vitro human models of BA, disease-specific induced pluripotent stem cells (iPSCs) from 6 BA patients were generated using non-integrating episomal plasmids. In addition, to determine the functional significance of BA-susceptibility genes identified by genome-wide association studies (GWAS) in biliary development, a genome-editing approach was used to create iPSCs with defined mutations in these GWAS BA loci. Using the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 system, isogenic iPSCs deficient in BA-associated genes (GPC1 and ADD3) were created from healthy iPSCs. Both the BA patient-iPSCs and the knock out (KO) iPSCs were studied for their in vitro biliary differentiation potential. These BA-specific iPSCs demonstrated significantly decreased formation of ductal structures, decreased expression of biliary markers including CK7, EpCAM, SOX9, CK19, AE2, and CFTR and increased fibrosis markers such as alpha smooth muscle actin, Loxl2, and Collagen1 compared to controls. Both the patient- and the KO-iPSCs also showed increased yes-associated protein (YAP, a marker of bile duct proliferation/fibrosis). Collagen and YAP were reduced by treatment with the anti-fibrogenic drug pentoxifylline. In summary, these BA-specific human iPSCs showed deficiency in biliary differentiation along with increased fibrosis, the 2 key disease features of BA. These iPSCs can provide new human BA models for understanding the molecular basis of abnormal biliary development and opportunities to identify drugs that have therapeutic effects on BA.
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17
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Chaudhari P, Tian L, Kim A, Zhu Q, Anders R, Schwarz KB, Sharkis S, Ye Z, Jang YY. Transient c-Src Suppression During Endodermal Commitment of Human Induced Pluripotent Stem Cells Results in Abnormal Profibrotic Cholangiocyte-Like Cells. Stem Cells 2018; 37:306-317. [PMID: 30471152 DOI: 10.1002/stem.2950] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 10/05/2018] [Accepted: 10/25/2018] [Indexed: 12/18/2022]
Abstract
Directed differentiation of human induced pluripotent stem cells (iPSCs) toward hepatobiliary lineages has been increasingly used as models of human liver development/diseases. As protein kinases are important components of signaling pathways regulating cell fate changes, we sought to define the key molecular mediators regulating human liver development using inhibitors targeting tyrosine kinases during hepatic differentiation of human iPSCs. A library of tyrosine kinase inhibitors was used for initial screening during the multistage differentiation of human iPSCs to hepatic lineage. Among the 80 kinase inhibitors tested, only Src inhibitors suppressed endoderm formation while none had significant effect on later stages of hepatic differentiation. Transient inhibition of c-Src during endodermal induction of human iPSCs reduced endodermal commitment and expression of endodermal markers, including SOX17 and FOXA2, in a dose-dependent manner. Interestingly, the transiently treated cells later developed into profibrogenic cholangiocyte-like cells expressing both cholangiocyte markers, such as CK7 and CK19, and fibrosis markers, including Collagen1 and smooth muscle actin. Further analysis of these cells revealed colocalized expression of collagen and yes-associated protein (YAP; a marker associated with bile duct proliferation/fibrosis) and an increased production of interleukin-6 and tumor necrosis factor-α. Moreover, treatment with verteporfin, a YAP inhibitor, significantly reduced expression of fibrosis markers. In summary, these results suggest that c-Src has a critical role in cell fate determination during endodermal commitment of human iPSCs, and its alteration in early liver development in human may lead to increased production of abnormal YAP expressing profibrogenic proinflammatory cholangiocytes, similar to those seen in livers of patients with biliary fibrosis. Stem Cells 2019;37:306-317.
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Affiliation(s)
- Pooja Chaudhari
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Cellular and Molecular Medicine Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Lipeng Tian
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Amy Kim
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Qingfeng Zhu
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Robert Anders
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kathleen B Schwarz
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Saul Sharkis
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Cellular and Molecular Medicine Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Zhaohui Ye
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yoon-Young Jang
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Cellular and Molecular Medicine Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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18
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Skvortsova EV, Sinenko SA, Tomilin AN. Immortalized murine fibroblast cell lines are refractory to reprogramming to pluripotent state. Oncotarget 2018; 9:35241-35250. [PMID: 30443291 PMCID: PMC6219659 DOI: 10.18632/oncotarget.26235] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 10/06/2018] [Indexed: 12/21/2022] Open
Abstract
To date different cell types of various mammalian species have been reprogrammed to induced pluripotent stem cells (iPSCs) using Yamanaka's cocktail of transcription factors (Oct4, Klf4, Sox2, and cMyc). It has been shown that several primary human cancer cell lines could be reprogrammed to iPSCs. We sought if immortalized mouse fibroblast cell lines could also be reprogrammed to iPSCs. The approach of generating iPSCs from such cells should be valuable in different experimental settings as it allows clonally derive cell lines carrying mutations whose impact on reprogramming could be next evaluated. Therefore, we investigated reprogramming of widely used immortalized cell lines (NIH3T and STO), as well as of de novo immortalized fibroblast line (tKM) with the use of highly effective lentiviral polycistronic OKSM expression system. Our reprogramming experiments have shown that in contrast to mouse embryonic fibroblasts (MEFs), none of the immortalized cell lines can be reprogrammed to pluripotent state. Contrary to colonies derived from MEFs, those derived from the immortalized cells lines (1) developed much later, (2) contained large round cells, not typical for iPSCs, and (3) were negative for trusted markers of matured iPSCs, Nanog and SSEA1. Immortalized cell lines NIH3T and STO are known to be mostly aneuploid, whereas tKM population includes cells with normal karyotype, however, neither cell type can be reprogrammed. Thus our data argue that aneuploidy per se is not a reason for the observed refractoriness of mouse immortalized cells to reprogramming to pluripotent state.
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Affiliation(s)
- Elena V Skvortsova
- Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russian Federation
| | - Sergey A Sinenko
- Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russian Federation.,Division of Molecular and Radiation Biophysics, B.P. Konstantinov Petersburg Nuclear Physics Institute, NRC "Kurchatov Institute", Orlova Roscha, Gatchina, Russian Federation
| | - Alexey N Tomilin
- Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russian Federation.,St Petersburg State University, St Petersburg, Russian Federation
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19
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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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20
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Chao HM, Chern E. Patient-derived induced pluripotent stem cells for models of cancer and cancer stem cell research. J Formos Med Assoc 2018; 117:1046-1057. [PMID: 30172452 DOI: 10.1016/j.jfma.2018.06.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Revised: 05/28/2018] [Accepted: 06/15/2018] [Indexed: 02/06/2023] Open
Abstract
Induced pluripotent stem cells (iPSCs) are embryonic stem cell-like cells reprogrammed from somatic cells by four transcription factors, OCT4, SOX2, KLF4 and c-MYC. iPSCs derived from cancer cells (cancer-iPSCs) could be a novel strategy for studying cancer. During cancer cell reprogramming, the epigenetic status of the cancer cell may be altered, such that it acquires stemness and pluripotency. The cellular behavior of the reprogrammed cells exhibits dynamic changes during the different stages of reprogramming. The cells may acquire the properties of cancer stem cells (CSCs) during the process of reprogramming, and lose their carcinogenic properties during reprogramming into a cancer-iPSCs. Differentiation of cancer-iPSCs by teratoma formation or organoid culturing could mimic the process of tumorigenesis. Some of the molecular mechanisms associated with cancer progression could be elucidated using the cancer-iPSC model. Furthermore, cancer-iPSCs could be expanded in culture system or bioreactors, and serve as cell sources for research, and as personal disease models for therapy and drug screening. This article introduces cancer studies that used the cell reprogramming strategy.
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Affiliation(s)
- Hsiao-Mei Chao
- niChe Lab for Stem Cell and Regenerative Medicine, Department of Biochemical Science and Technology, National Taiwan University, Taiwan; Department of Pathology, Wan Fang Hospital, Taipei Medical University, Taiwan
| | - Edward Chern
- niChe Lab for Stem Cell and Regenerative Medicine, Department of Biochemical Science and Technology, National Taiwan University, Taiwan.
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21
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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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22
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Stern S, Santos R, Marchetto MC, Mendes APD, Rouleau GA, Biesmans S, Wang QW, Yao J, Charnay P, Bang AG, Alda M, Gage FH. Neurons derived from patients with bipolar disorder divide into intrinsically different sub-populations of neurons, predicting the patients' responsiveness to lithium. Mol Psychiatry 2018; 23:1453-1465. [PMID: 28242870 PMCID: PMC5573640 DOI: 10.1038/mp.2016.260] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 11/04/2016] [Accepted: 12/06/2016] [Indexed: 11/09/2022]
Abstract
Bipolar disorder (BD) is a progressive psychiatric disorder with more than 3% prevalence worldwide. Affected individuals experience recurrent episodes of depression and mania, disrupting normal life and increasing the risk of suicide greatly. The complexity and genetic heterogeneity of psychiatric disorders have challenged the development of animal and cellular models. We recently reported that hippocampal dentate gyrus (DG) neurons differentiated from induced pluripotent stem cell (iPSC)-derived fibroblasts of BD patients are electrophysiologically hyperexcitable. Here we used iPSCs derived from Epstein-Barr virus-immortalized B-lymphocytes to verify that the hyperexcitability of DG-like neurons is reproduced in this different cohort of patients and cells. Lymphocytes are readily available for research with a large number of banked lines with associated patient clinical description. We used whole-cell patch-clamp recordings of over 460 neurons to characterize neurons derived from control individuals and BD patients. Extensive functional analysis showed that intrinsic cell parameters are very different between the two groups of BD neurons, those derived from lithium (Li)-responsive (LR) patients and those derived from Li-non-responsive (NR) patients, which led us to partition our BD neurons into two sub-populations of cells and suggested two different subdisorders. Training a Naïve Bayes classifier with the electrophysiological features of patients whose responses to Li are known allows for accurate classification with more than 92% success rate for a new patient whose response to Li is unknown. Despite their very different functional profiles, both populations of neurons share a large, fast after-hyperpolarization (AHP). We therefore suggest that the large, fast AHP is a key feature of BD and a main contributor to the fast, sustained spiking abilities of BD neurons. Confirming our previous report with fibroblast-derived DG neurons, chronic Li treatment reduced the hyperexcitability in the lymphoblast-derived LR group but not in the NR group, strengthening the validity and utility of this new human cellular model of BD.
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Affiliation(s)
- S Stern
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - R Santos
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, USA,Ecole Normale Supérieure, PSL Research University, CNRS, Inserm, Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Paris, France
| | - MC Marchetto
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - APD Mendes
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - GA Rouleau
- Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
| | - S Biesmans
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Q-W Wang
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China
| | - J Yao
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China
| | - P Charnay
- Ecole Normale Supérieure, PSL Research University, CNRS, Inserm, Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Paris, France
| | - AG Bang
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - M Alda
- Department of Psychiatry, Dalhousie University, Halifax, NS, Canada. Correspondence: Professor FH Gage, Laboratory of Genetics, The Salk Institute for Biological Studies, The Salk Institute, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - FH Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, USA
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23
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Shioda S, Kasai F, Watanabe K, Kawakami K, Ohtani A, Iemura M, Ozawa M, Arakawa A, Hirayama N, Kawaguchi E, Tano T, Miyata S, Satoh M, Shimizu N, Kohara A. Screening for 15 pathogenic viruses in human cell lines registered at the JCRB Cell Bank: characterization of in vitro human cells by viral infection. ROYAL SOCIETY OPEN SCIENCE 2018; 5:172472. [PMID: 29892436 PMCID: PMC5990783 DOI: 10.1098/rsos.172472] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 03/23/2018] [Indexed: 05/04/2023]
Abstract
Human cell lines have been used in a variety of research fields as an in vitro model. These cells are all derived from human tissue samples, thus there is a possibility of virus infection. Virus tests are routinely performed in clinical practice, but are limited in cell lines. In this study, we investigated 15 kinds of viruses in 844 human cell lines registered at the Japanese Collection of Research Bioresources (JCRB) Cell Bank. Our real-time PCR analysis revealed that six viruses, EBV, HTLV-1, HBV, B19V, HHV-6 and HHV-7, were detected in 43 cell lines. Of them, 20 cell lines were transformed by intentional infection in vitro with EBV or HTLV-1. Viruses in the other 23 cell lines and one EBV transformed cell line are derived from an in vivo infection, including five de novo identifications of EBV, B19V or HHV-7 carriers. Among them, 17 cell lines were established from patients diagnosed with virus-associated diseases. However, the other seven cell lines originated from in vivo cells unrelated to disease or cellular tropism. Our approach to screen for a set of 15 viruses in each cell line has worked efficiently to identify these rare cases. Virus tests in cell lines contribute not only to safety assessments but also to investigation of in vivo viral infection which can be a characteristic feature of cell lines.
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Affiliation(s)
- Setsuko Shioda
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Fumio Kasai
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
- Author for correspondence: Fumio Kasai e-mail:
| | - Ken Watanabe
- Department of Virology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kohei Kawakami
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Azusa Ohtani
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Masashi Iemura
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Midori Ozawa
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Akemi Arakawa
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Noriko Hirayama
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Eiko Kawaguchi
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Tomoko Tano
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Sayaka Miyata
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Motonobu Satoh
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Norio Shimizu
- Department of Virology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Arihiro Kohara
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
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24
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Kasai F, Ferguson-Smith MA. A collection of XY female cell lines. Hum Cell 2018; 31:175-178. [PMID: 29330774 DOI: 10.1007/s13577-017-0195-5] [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] [Received: 10/30/2017] [Accepted: 12/08/2017] [Indexed: 10/18/2022]
Abstract
Discordance between sexual phenotype and the 46,XY sex chromosome complement may be found in certain disorders of sexual development (DSD). Many of these DSD patients with female external genitalia and secondary sex characteristics have undescended testes and male internal genitalia. Causative mutations involving genes of the sex determining pathway, including the androgen receptor, SRY and the 5-alpha-reductase genes, are well-known, but the origin of other cases remain unresolved. In this report, we introduce our collection of lymphoblastoid lines derived from female patients with a 46,XY karyotype. These cell lines have been deposited and registered with the JCRB Cell Bank. They are available for comparison with other DSD cases and for further characterization of genetic loci involved in the mammalian sex determining pathway.
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Affiliation(s)
- Fumio Kasai
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan. .,Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK.
| | - Malcolm A Ferguson-Smith
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK.
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25
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Kumar S, Blangero J, Curran JE. Induced Pluripotent Stem Cells in Disease Modeling and Gene Identification. Methods Mol Biol 2018; 1706:17-38. [PMID: 29423791 DOI: 10.1007/978-1-4939-7471-9_2] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Experimental modeling of human inherited disorders provides insight into the cellular and molecular mechanisms involved, and the underlying genetic component influencing, the disease phenotype. The breakthrough development of induced pluripotent stem cell (iPSC) technology represents a quantum leap in experimental modeling of human diseases, providing investigators with a self-renewing and, thus, unlimited source of pluripotent cells for targeted differentiation. In principle, the entire range of cell types found in the human body can be interrogated using an iPSC approach. Therefore, iPSC technology, and the increasingly refined abilities to differentiate iPSCs into disease-relevant target cells, has far-reaching implications for understanding disease pathophysiology, identifying disease-causing genes, and developing more precise therapeutics, including advances in regenerative medicine. In this chapter, we discuss the technological perspectives and recent developments in the application of patient-derived iPSC lines for human disease modeling and disease gene identification.
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Affiliation(s)
- Satish Kumar
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, School of Medicine, 1214 W Schunior St, Edinburg, TX, 78541, USA.
| | - John Blangero
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, School of Medicine, 1214 W Schunior St, Edinburg, TX, 78541, USA
| | - Joanne E Curran
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, School of Medicine, 1214 W Schunior St, Edinburg, TX, 78541, USA
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26
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Efficient and Controlled Generation of 2D and 3D Bile Duct Tissue from Human Pluripotent Stem Cell-Derived Spheroids. Stem Cell Rev Rep 2017; 12:500-8. [PMID: 27138846 DOI: 10.1007/s12015-016-9657-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
While in vitro liver tissue engineering has been increasingly studied during the last several years, presently engineered liver tissues lack the bile duct system. The lack of bile drainage not only hinders essential digestive functions of the liver, but also leads to accumulation of bile that is toxic to hepatocytes and known to cause liver cirrhosis. Clearly, generation of bile duct tissue is essential for engineering functional and healthy liver. Differentiation of human induced pluripotent stem cells (iPSCs) to bile duct tissue requires long and/or complex culture conditions, and has been inefficient so far. Towards generating a fully functional liver containing biliary system, we have developed defined and controlled conditions for efficient 2D and 3D bile duct epithelial tissue generation. A marker for multipotent liver progenitor in both adult human liver and ductal plate in human fetal liver, EpCAM, is highly expressed in hepatic spheroids generated from human iPSCs. The EpCAM high hepatic spheroids can, not only efficiently generate a monolayer of biliary epithelial cells (cholangiocytes), in a 2D differentiation condition, but also form functional ductal structures in a 3D condition. Importantly, this EpCAM high spheroid based biliary tissue generation is significantly faster than other existing methods and does not require cell sorting. In addition, we show that a knock-in CK7 reporter human iPSC line generated by CRISPR/Cas9 genome editing technology greatly facilitates the analysis of biliary differentiation. This new ductal differentiation method will provide a more efficient method of obtaining bile duct cells and tissues, which may facilitate engineering of complete and functional liver tissue in the future.
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27
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Chaterji S, Ahn EH, Kim DH. CRISPR Genome Engineering for Human Pluripotent Stem Cell Research. Theranostics 2017; 7:4445-4469. [PMID: 29158838 PMCID: PMC5695142 DOI: 10.7150/thno.18456] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 08/24/2017] [Indexed: 12/13/2022] Open
Abstract
The emergence of targeted and efficient genome editing technologies, such as repurposed bacterial programmable nucleases (e.g., CRISPR-Cas systems), has abetted the development of cell engineering approaches. Lessons learned from the development of RNA-interference (RNA-i) therapies can spur the translation of genome editing, such as those enabling the translation of human pluripotent stem cell engineering. In this review, we discuss the opportunities and the challenges of repurposing bacterial nucleases for genome editing, while appreciating their roles, primarily at the epigenomic granularity. First, we discuss the evolution of high-precision, genome editing technologies, highlighting CRISPR-Cas9. They exist in the form of programmable nucleases, engineered with sequence-specific localizing domains, and with the ability to revolutionize human stem cell technologies through precision targeting with greater on-target activities. Next, we highlight the major challenges that need to be met prior to bench-to-bedside translation, often learning from the path-to-clinic of complementary technologies, such as RNA-i. Finally, we suggest potential bioinformatics developments and CRISPR delivery vehicles that can be deployed to circumvent some of the challenges confronting genome editing technologies en route to the clinic.
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28
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Choudhury Y, Toh YC, Xing J, Qu Y, Poh J, Li H, Tan HS, Kanesvaran R, Yu H, Tan MH. Patient-specific hepatocyte-like cells derived from induced pluripotent stem cells model pazopanib-mediated hepatotoxicity. Sci Rep 2017; 7:41238. [PMID: 28120901 PMCID: PMC5264611 DOI: 10.1038/srep41238] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 12/19/2016] [Indexed: 12/18/2022] Open
Abstract
Idiosyncratic drug-induced hepatotoxicity is a major cause of liver damage and drug pipeline failure, and is difficult to study as patient-specific features are not readily incorporated in traditional hepatotoxicity testing approaches using population pooled cell sources. Here we demonstrate the use of patient-specific hepatocyte-like cells (HLCs) derived from induced pluripotent stem cells for modeling idiosyncratic hepatotoxicity to pazopanib (PZ), a tyrosine kinase inhibitor drug associated with significant hepatotoxicity of unknown mechanistic basis. In vitro cytotoxicity assays confirmed that HLCs from patients with clinically identified hepatotoxicity were more sensitive to PZ-induced toxicity than other individuals, while a prototype hepatotoxin acetaminophen was similarly toxic to all HLCs studied. Transcriptional analyses showed that PZ induces oxidative stress (OS) in HLCs in general, but in HLCs from susceptible individuals, PZ causes relative disruption of iron metabolism and higher burden of OS. Our study establishes the first patient-specific HLC-based platform for idiosyncratic hepatotoxicity testing, incorporating multiple potential causative factors and permitting the correlation of transcriptomic and cellular responses to clinical phenotypes. Establishment of patient-specific HLCs with clinical phenotypes representing population variations will be valuable for pharmaceutical drug testing.
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Affiliation(s)
- Yukti Choudhury
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, Nanos #04-01, Singapore 138669, Republic of Singapore
| | - Yi Chin Toh
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, Nanos #04-01, Singapore 138669, Republic of Singapore.,Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, 4 Engineering Drive 3, E4 #04-08, Singapore 117583, Republic of Singapore
| | - Jiangwa Xing
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, Nanos #04-01, Singapore 138669, Republic of Singapore
| | - Yinghua Qu
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, Nanos #04-01, Singapore 138669, Republic of Singapore
| | - Jonathan Poh
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, Nanos #04-01, Singapore 138669, Republic of Singapore
| | - Huan Li
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, Nanos #04-01, Singapore 138669, Republic of Singapore
| | - Hui Shan Tan
- Division of Medical Oncology, National Cancer Centre, Singapore 169610, Republic of Singapore
| | - Ravindran Kanesvaran
- Division of Medical Oncology, National Cancer Centre, Singapore 169610, Republic of Singapore
| | - Hanry Yu
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, Nanos #04-01, Singapore 138669, Republic of Singapore.,Yong Loo Lin School of Medicine and Mechanobiology Institute, National University of Singapore, Republic of Singapore.,Gastroenterology Department, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Min-Han Tan
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, Nanos #04-01, Singapore 138669, Republic of Singapore.,Division of Medical Oncology, National Cancer Centre, Singapore 169610, Republic of Singapore
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29
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Chaudhari P, Prasad N, Tian L, Jang YY. Determination of Functional Activity of Human iPSC-Derived Hepatocytes by Measurement of CYP Metabolism. Methods Mol Biol 2016; 1357:383-94. [PMID: 25410290 DOI: 10.1007/7651_2014_145] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The advent of induced pluripotent stem cell (iPSC) technology has enabled the modeling of an array of specific human disease phenotypes, aiding in the increasingly important and indispensable understanding of disease progression and pathogenesis. Pluripotent stem cell-derived hepatocytes present a new avenue for drug screening and personalized drug testing toward precision medicine. CYP450 microsomal enzymes play a critical role in drug metabolism. Hence, CYP activity measurement of iPSC-derived hepatocytes is a vital prerequisite, to ensure metabolic functionality before proceeding to drug testing. Herein, we describe the protocol for measurement of different CYP450 enzyme activities in human iPSC-derived hepatocytes.
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Affiliation(s)
- Pooja Chaudhari
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Neha Prasad
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Lipeng Tian
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Yoon-Young Jang
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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30
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Fujimori K, Tezuka T, Ishiura H, Mitsui J, Doi K, Yoshimura J, Tada H, Matsumoto T, Isoda M, Hashimoto R, Hattori N, Takahashi T, Morishita S, Tsuji S, Akamatsu W, Okano H. Modeling neurological diseases with induced pluripotent cells reprogrammed from immortalized lymphoblastoid cell lines. Mol Brain 2016; 9:88. [PMID: 27716287 PMCID: PMC5046991 DOI: 10.1186/s13041-016-0267-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 09/20/2016] [Indexed: 12/28/2022] Open
Abstract
Patient-specific induced pluripotent stem cells (iPSCs) facilitate understanding of the etiology of diseases, discovery of new drugs and development of novel therapeutic interventions. A frequently used starting source of cells for generating iPSCs has been dermal fibroblasts (DFs) isolated from skin biopsies. However, there are also numerous repositories containing lymphoblastoid B-cell lines (LCLs) generated from a variety of patients. To date, this rich bioresource of LCLs has been underused for generating iPSCs, and its use would greatly expand the range of targeted diseases that could be studied by using patient-specific iPSCs. However, it remains unclear whether patient’s LCL-derived iPSCs (LiPSCs) can function as a disease model. Therefore, we generated Parkinson’s disease patient-specific LiPSCs and evaluated their utility as tools for modeling neurological diseases. We established iPSCs from two LCL clones, which were derived from a healthy donor and a patient carrying PARK2 mutations, by using existing non-integrating episomal protocols. Whole genome sequencing (WGS) and comparative genomic hybridization (CGH) analyses showed that the appearance of somatic variations in the genomes of the iPSCs did not vary substantially according to the original cell types (LCLs, T-cells and fibroblasts). Furthermore, LiPSCs could be differentiated into functional neurons by using the direct neurosphere conversion method (dNS method), and they showed several Parkinson’s disease phenotypes that were similar to those of DF-iPSCs. These data indicate that the global LCL repositories can be used as a resource for generating iPSCs and disease models. Thus, LCLs are the powerful tools for generating iPSCs and modeling neurological diseases.
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Affiliation(s)
- Koki Fujimori
- Department of Physiology, Keio University, School of Medicine, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Toshiki Tezuka
- Department of Physiology, Keio University, School of Medicine, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Hiroyuki Ishiura
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Jun Mitsui
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Koichiro Doi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-0882, Japan
| | - Jun Yoshimura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-0882, Japan
| | - Hirobumi Tada
- Department of Physiology, Yokohama City University Graduate School of Medicine, Kanazawa-ku, Kanagawa, 236-0027, Japan.,Department of Integrative Aging Neuroscience, Section of Neuroendocrinology, National Center for Geriatrics and Gerontology, Obu, Aichi, 474-8511, Japan
| | - Takuya Matsumoto
- Department of Physiology, Keio University, School of Medicine, Shinjuku-ku, Tokyo, 160-8582, Japan.,Institute for Innovation, Ajinomoto Co., Inc., Kawasaki-ku, Kanagawa, 210-8681, Japan
| | - Miho Isoda
- Department of Physiology, Keio University, School of Medicine, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Ryota Hashimoto
- Molecular Research Center for Children's Mental Development, United Graduate School of Child Development, Osaka University, Suita-shi, Osaka, 565-0871, Japan.,Department of Psychiatry, Osaka University Graduate School of Medicine, Suita-shi, Osaka, 565-0871, Japan
| | - Nubutaka Hattori
- Department of Neurology, Juntendo University, School of Medicine, Bunkyo-ku, Tokyo, 113-8431, Japan
| | - Takuya Takahashi
- Department of Physiology, Yokohama City University Graduate School of Medicine, Kanazawa-ku, Kanagawa, 236-0027, Japan
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-0882, Japan.,Medical Genome Center, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Shoji Tsuji
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8655, Japan.,Medical Genome Center, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Wado Akamatsu
- Department of Physiology, Keio University, School of Medicine, Shinjuku-ku, Tokyo, 160-8582, Japan. .,Center for Genomic and Regenerative Medicine, Juntendo University, School of Medicine, Bunkyo-ku, Tokyo, 113-8431, Japan.
| | - Hideyuki Okano
- Department of Physiology, Keio University, School of Medicine, Shinjuku-ku, Tokyo, 160-8582, Japan.
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31
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Yu H, Hahn Y, Park SR, Chung SK, Jeong S, Yang I. Normalization of human RNA-seq experiments using chimpanzee RNA as a spike-in standard. Sci Rep 2016; 6:31923. [PMID: 27554056 PMCID: PMC4995400 DOI: 10.1038/srep31923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 07/29/2016] [Indexed: 11/25/2022] Open
Abstract
Normalization of human RNA-seq experiments employing chimpanzee RNA as a spike-in standard is reported. Human and chimpanzee RNAs exhibit single nucleotide variations (SNVs) in average 210-bp intervals. Spike-in chimpanzee RNA would behave the same as the human counterparts during the whole NGS procedures owing to the high sequence similarity. After discrimination of species origins of the NGS reads based on SNVs, the chimpanzee reads were used to read-by-read normalize biases and variations of human reads. By this approach, as many as 10,119 transcripts were simultaneously normalized for the entire NGS procedures leading to accurate and reproducible quantification of differential gene expression. In addition, incomparable data sets from different in-process degradations or from different library preparation methods were made well comparable by the normalization. Based on these results, we expect that the normalization approaches using near neighbor genomes as internal standards could be employed as a standard protocol, which will improve both accuracy and comparability of NGS results across different sample batches, laboratories and NGS platforms.
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Affiliation(s)
- Hannah Yu
- Center for Bioanalysis, Korea Research Institute of Standards and Science (KRISS), Korea.,Bioanalytical Science, University of Science and Technology (UST), Korea
| | - Yoonsoo Hahn
- Department of Life Science, Chung-Ang University, Korea
| | - Sang-Ryoul Park
- Center for Bioanalysis, Korea Research Institute of Standards and Science (KRISS), Korea.,Bioanalytical Science, University of Science and Technology (UST), Korea
| | - Sun-Ku Chung
- Medical Research Division, Korea Institute of Oriental Medicine (KIOM), Korea
| | - Sangkyun Jeong
- Medical Research Division, Korea Institute of Oriental Medicine (KIOM), Korea
| | - Inchul Yang
- Center for Bioanalysis, Korea Research Institute of Standards and Science (KRISS), Korea.,Bioanalytical Science, University of Science and Technology (UST), Korea
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32
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The Generation of Human Induced Pluripotent Stem Cells from Blood Cells: An Efficient Protocol Using Serial Plating of Reprogrammed Cells by Centrifugation. Stem Cells Int 2016; 2016:1329459. [PMID: 27579041 PMCID: PMC4989082 DOI: 10.1155/2016/1329459] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 06/08/2016] [Accepted: 07/03/2016] [Indexed: 12/26/2022] Open
Abstract
Human induced pluripotent stem cells (hiPSCs) have demonstrated great potential for differentiation into diverse tissues. We report a straightforward and highly efficient method for the generation of iPSCs from PBMCs. By plating the cells serially to a newly coated plate by centrifugation, this protocol provides multiple healthy iPSC colonies even from a small number of PBMCs. The generated iPSCs expressed pluripotent markers and differentiated into all three germ layer lineages. The protocol can also be used with umbilical cord blood mononuclear cells (CBMCs). In this study, we present a simple and efficient protocol that improved the yield of iPSCs from floating cells such as PBMCs and CBMCs by serial plating and centrifugation.
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Deficiency in Cardiolipin Reduces Doxorubicin-Induced Oxidative Stress and Mitochondrial Damage in Human B-Lymphocytes. PLoS One 2016; 11:e0158376. [PMID: 27434059 PMCID: PMC4951097 DOI: 10.1371/journal.pone.0158376] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 06/14/2016] [Indexed: 12/22/2022] Open
Abstract
Cardiolipin (CL) is an inner mitochondrial membrane phospholipid which plays an important role in mitochondrial function. Perturbation in CL biosynthesis alters mitochondrial bioenergetics causing a severe genetic disorder commonly known as Barth syndrome. Barth syndrome patients are known to have a reduced concentration and altered composition of CL. Cardiolipin is also known to have a high affinity for the chemotherapeutic agent doxorubicin (Dox), resulting in an extensive mitochondrial accumulation of the drug. Our results indicate that B-lymphocytes from healthy individuals are more sensitive to Dox-induced oxidative stress and cellular toxicity compared to the B-lymphocytes from Barth syndrome as indicated by greater cell death and greater level of cleaved caspase-3 following Dox treatment. Barth lymphocytes, when compared to healthy lymphocytes, showed a greater basal level of mitochondrial reactive oxygen species (mito-ROS), yet exhibited a lower level of induced mito-ROS production in response to Dox. Significantly less ATP content and slightly greater OXPHOS protein levels were detected in healthy cells compared to Barth cells after Dox treatment. Consistent with greater mitochondrial ROS, treatment with Dox induced a higher level of lipid peroxidation and protein carbonylation in healthy lymphocytes compared to Barth lymphocytes. The final remodeling of CL during CL synthesis is catalyzed by the tafazzin protein. Knockdown of tafazzin gene in H9c2 cardiomyocytes using siRNA showed decreased oxidant-induced damage, as observed in Barth lymphocytes. Our findings demonstrate that a deficiency in CL might provide a therapeutic advantage in favor of oxidant-induced anticancer activities.
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Tian L, Deshmukh A, Prasad N, Jang YY. Alcohol Increases Liver Progenitor Populations and Induces Disease Phenotypes in Human IPSC-Derived Mature Stage Hepatic Cells. Int J Biol Sci 2016; 12:1052-62. [PMID: 27570479 PMCID: PMC4997049 DOI: 10.7150/ijbs.15811] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 06/23/2016] [Indexed: 12/15/2022] Open
Abstract
Alcohol consumption has long been a global problem affecting human health, and has been found to influence both fetal and adult liver functions. However, how alcohol affects human liver development and liver progenitor cells remains largely unknown. Here, we used human induced pluripotent stem cells (iPSCs) as a model to examine the effects of alcohol, on multi-stage hepatic cells including hepatic progenitors, early and mature hepatocyte-like cells derived from human iPSCs. While alcohol has little effect on endoderm development from iPSCs, it reduces formation of hepatic progenitor cells during early hepatic specification. The proliferative activities of early and mature hepatocyte-like cells are significantly decreased after alcohol exposure. Importantly, at a mature stage of hepatocyte-like cells, alcohol treatment increases two liver progenitor subsets, causes oxidative mitochondrial injury and results in liver disease phenotypes (i.e., steatosis and hepatocellular carcinoma associated markers) in a dose dependent manner. Some of the phenotypes were significantly improved by antioxidant treatment. This report suggests that fetal alcohol exposure may impair generation of hepatic progenitors at early stage of hepatic specification and decrease proliferation of fetal hepatocytes; meanwhile alcohol injury in post-natal or mature stage human liver may contribute to disease phenotypes. This human iPSC model of alcohol-induced liver injury can be highly valuable for investigating alcoholic injury in the fetus as well as understanding the pathogenesis and ultimately developing effective treatment for alcoholic liver disease in adults.
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Affiliation(s)
- Lipeng Tian
- 1 Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center
| | - Abhijeet Deshmukh
- 1 Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center
| | - Neha Prasad
- 1 Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center
| | - Yoon-Young Jang
- 1 Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center; 2 Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Reprogramming of Notch1-induced acute lymphoblastic leukemia cells into pluripotent stem cells in mice. Blood Cancer J 2016; 6:e444. [PMID: 27391576 PMCID: PMC5030381 DOI: 10.1038/bcj.2016.57] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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Chaudhari P, Tian L, Deshmukh A, Jang YY. Expression kinetics of hepatic progenitor markers in cellular models of human liver development recapitulating hepatocyte and biliary cell fate commitment. Exp Biol Med (Maywood) 2016; 241:1653-62. [PMID: 27390263 DOI: 10.1177/1535370216657901] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Due to the limitations of research using human embryos and the lack of a biological model of human liver development, the roles of the various markers associated with liver stem or progenitor cell potential in humans are largely speculative, and based on studies utilizing animal models and certain patient tissues. Human pluripotent stem cell-based in vitro multistage hepatic differentiation systems may serve as good surrogate models for mimicking normal human liver development, pathogenesis and injury/regeneration studies. Here, we describe the implications of various liver stem or progenitor cell markers and their bipotency (i.e. hepatocytic- and biliary-epithelial cell differentiation), based on the pluripotent stem cell-derived model of human liver development. Future studies using the human cellular model(s) of liver and biliary development will provide more human relevant biological and/or pathological roles of distinct markers expressed in heterogeneous liver stem/progenitor cell populations.
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Affiliation(s)
- Pooja Chaudhari
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore 21205, USA Cellular and Molecular Medicine Graduate Program, Johns Hopkins University School of Medicine, Baltimore 21205, USA Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore 21205, USA
| | - Lipeng Tian
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore 21205, USA
| | - Abhijeet Deshmukh
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore 21205, USA
| | - Yoon-Young Jang
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore 21205, USA Cellular and Molecular Medicine Graduate Program, Johns Hopkins University School of Medicine, Baltimore 21205, USA Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore 21205, USA
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Saberi B, Dadabhai AS, Jang YY, Gurakar A, Mezey E. Current Management of Alcoholic Hepatitis and Future Therapies. J Clin Transl Hepatol 2016; 4:113-22. [PMID: 27350941 PMCID: PMC4913072 DOI: 10.14218/jcth.2016.00006] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Revised: 03/27/2016] [Accepted: 03/28/2016] [Indexed: 12/12/2022] Open
Abstract
Alcohol is one of the most common etiologies of liver disease, and alcoholic liver disease overall is the second most common indication for liver transplantation in the United States. It encompasses a spectrum of disease, including fatty liver disease, alcoholic hepatitis (AH), and alcoholic cirrhosis. AH can range from mild to severe disease, with severe disease being defined as: Discriminant Function (DF) ≥ 32, or Model for End-stage Liver Disease (MELD) ≥ 21, or presence of hepatic encephalopathy. Management of the mild disease consists mainly of abstinence and supportive care. Severe AH is associated with significant mortality. Currently, there is no ideal medical treatment for this condition. Besides alcohol cessation, corticosteroids have been used with conflicting results and are associated with an inherent risk of infection. Overall steroids have shown short term benefit when compared to placebo, but they have no obvious long term benefits. Pentoxifylline does not improve survival in patients with severe AH and is no longer recommended based on the results of the STOPAH (Steroid Or Pentoxifylline for Alcoholic Hepatitis) trial. Anti-tumor necrosis factor (TNF) agents are associated with increased risk of life threatening infections and death. Currently, early stage trials are underway, mainly targeting novel pathways based on disease pathogenesis, including modulation of innate immune system, inhibition of gut-liver axis and cell death pathways, and activation of transcription factor farnesyl X receptor (FXR). Future treatment may lie in human induced pluripotent stem cell (iPSC) technology, which is currently under investigation for the study of pathogenesis, drug discovery, and stem cell transplantation. Liver transplantation has been reported with good results in highly selected patients but is controversial due to limited organ supply.
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Affiliation(s)
- Behnam Saberi
- Division of Gastroenterology and Hepatology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- *Correspondence to: Behnam Saberi, Division of Gastroenterology and Hepatology, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA. Tel: +1-410-614-2543, Fax: +1-410-614-7340, E-mail:
| | - Alia S. Dadabhai
- Division of Gastroenterology and Hepatology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yoon-Young Jang
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ahmet Gurakar
- Division of Gastroenterology and Hepatology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Esteban Mezey
- Division of Gastroenterology and Hepatology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Utility of Lymphoblastoid Cell Lines for Induced Pluripotent Stem Cell Generation. Stem Cells Int 2016; 2016:2349261. [PMID: 27375745 PMCID: PMC4914736 DOI: 10.1155/2016/2349261] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 04/01/2016] [Accepted: 05/08/2016] [Indexed: 12/15/2022] Open
Abstract
A large number of EBV immortalized LCLs have been generated and maintained in genetic/epidemiological studies as a perpetual source of DNA and as a surrogate in vitro cell model. Recent successes in reprograming LCLs into iPSCs have paved the way for generating more relevant in vitro disease models using this existing bioresource. However, the overall reprogramming efficiency and success rate remain poor and very little is known about the mechanistic changes that take place at the transcriptome and cellular functional level during LCL-to-iPSC reprogramming. Here, we report a new optimized LCL-to-iPSC reprogramming protocol using episomal plasmids encoding pluripotency transcription factors and mouse p53DD (p53 carboxy-terminal dominant-negative fragment) and commercially available reprogramming media. We achieved a consistently high reprogramming efficiency and 100% success rate using this optimized protocol. Further, we investigated the transcriptional changes in mRNA and miRNA levels, using FC-abs ≥ 2.0 and FDR ≤ 0.05 cutoffs; 5,228 mRNAs and 77 miRNAs were differentially expressed during LCL-to-iPSC reprogramming. The functional enrichment analysis of the upregulated genes and activation of human pluripotency pathways in the reprogrammed iPSCs showed that the generated iPSCs possess transcriptional and functional profiles very similar to those of human ESCs.
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Shen Y, Huang J, Liu L, Xu X, Han C, Zhang G, Jiang H, Li J, Lin Z, Xiong N, Wang T. A Compendium of Preparation and Application of Stem Cells in Parkinson's Disease: Current Status and Future Prospects. Front Aging Neurosci 2016; 8:117. [PMID: 27303288 PMCID: PMC4885841 DOI: 10.3389/fnagi.2016.00117] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/09/2016] [Indexed: 12/22/2022] Open
Abstract
Parkinson's Disease (PD) is a progressively neurodegenerative disorder, implicitly characterized by a stepwise loss of dopaminergic (DA) neurons in the substantia nigra pars compacta (SNpc) and explicitly marked by bradykinesia, rigidity, resting tremor and postural instability. Currently, therapeutic approaches available are mainly palliative strategies, including L-3,4-dihydroxy-phenylalanine (L-DOPA) replacement therapy, DA receptor agonist and deep brain stimulation (DBS) procedures. As the disease proceeds, however, the pharmacotherapeutic efficacy is inevitably worn off, worse still, implicated by side effects of motor response oscillations as well as L-DOPA induced dyskinesia (LID). Therefore, the frustrating status above has propeled the shift to cell replacement therapy (CRT), a promising restorative therapy intending to secure a long-lasting relief of patients' symptoms. By far, stem cell lines of multifarious origins have been established, which can be further categorized into embryonic stem cells (ESCs), neural stem cells (NSCs), induced neural stem cells (iNSCs), mesenchymal stem cells (MSCs), and induced pluripotent stem cells (iPSCs). In this review, we intend to present a compendium of preparation and application of multifarious stem cells, especially in relation to PD research and therapy. In addition, the current status, potential challenges and future prospects for practical CRT in PD patients will be elaborated as well.
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Affiliation(s)
- Yan Shen
- Department of Neurology, Tongji Medical College, Union Hospital, Huazhong University of Science and Technology Wuhan, China
| | - Jinsha Huang
- Department of Neurology, Tongji Medical College, Union Hospital, Huazhong University of Science and Technology Wuhan, China
| | - Ling Liu
- Department of Neurology, Tongji Medical College, Union Hospital, Huazhong University of Science and Technology Wuhan, China
| | - Xiaoyun Xu
- Department of Neurology, Tongji Medical College, Union Hospital, Huazhong University of Science and Technology Wuhan, China
| | - Chao Han
- Department of Neurology, Tongji Medical College, Union Hospital, Huazhong University of Science and Technology Wuhan, China
| | - Guoxin Zhang
- Department of Neurology, Tongji Medical College, Union Hospital, Huazhong University of Science and Technology Wuhan, China
| | - Haiyang Jiang
- Department of Neurology, Tongji Medical College, Union Hospital, Huazhong University of Science and Technology Wuhan, China
| | - Jie Li
- Department of Neurology, Tongji Medical College, Union Hospital, Huazhong University of Science and Technology Wuhan, China
| | - Zhicheng Lin
- Department of Psychiatry, Harvard Medical School, Division of Alcohol and Drug Abuse, and Mailman Neuroscience Research Center, McLean Hospital Belmont, MA, USA
| | - Nian Xiong
- Department of Neurology, Tongji Medical College, Union Hospital, Huazhong University of Science and Technology Wuhan, China
| | - Tao Wang
- Department of Neurology, Tongji Medical College, Union Hospital, Huazhong University of Science and Technology Wuhan, China
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Tian L, Prasad N, Jang YY. In Vitro Modeling of Alcohol-Induced Liver Injury Using Human-Induced Pluripotent Stem Cells. Methods Mol Biol 2016; 1353:271-83. [PMID: 25520290 PMCID: PMC5881111 DOI: 10.1007/7651_2014_168] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Alcohol consumption has long been associated with a majority of liver diseases and has been found to influence both fetal and adult liver functions. In spite of being one of the major causes of morbidity and mortality in the world, currently, there are no effective strategies that can prevent or treat alcoholic liver disease (ALD), due to a lack of human-relevant research models. Recent success in generation of functionally active mature hepatocyte-like cells from human-induced pluripotent cells (iPSCs) enables us to better understand the effects of alcohol on liver functions. Here, we describe the method and effect of alcohol exposure on multistage hepatic cell types derived from human iPSCs, in an attempt to recapitulate the early stages of liver tissue injury associated with ALD. We exposed different stages of iPSC-induced hepatic cells to ethanol at a pathophysiological concentration. In addition to stage-specific molecular markers, we measured several key cellular parameters of hepatocyte injury, including apoptosis, proliferation, and lipid accumulation.
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Affiliation(s)
- Lipeng Tian
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Neha Prasad
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Yoon-Young Jang
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Cellular and Molecular Medicine Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, 1550 Orleans Street, CRB2 Rm552, Baltimore, MD, 21231, USA.
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41
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Esanov R, Belle KC, van Blitterswijk M, Belzil VV, Rademakers R, Dickson DW, Petrucelli L, Boylan KB, Dykxhoorn DM, Wuu J, Benatar M, Wahlestedt C, Zeier Z. C9orf72 promoter hypermethylation is reduced while hydroxymethylation is acquired during reprogramming of ALS patient cells. Exp Neurol 2015; 277:171-177. [PMID: 26746986 DOI: 10.1016/j.expneurol.2015.12.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 12/17/2015] [Accepted: 12/29/2015] [Indexed: 12/13/2022]
Abstract
Among several genetic mutations known to cause amyotrophic lateral sclerosis (ALS), a hexanucleotide repeat expansion in the C9orf72 gene is the most common. In approximately 30% of C9orf72-ALS cases, 5-methylcytosine (5mC) levels within the C9orf72 promoter are increased, resulting in a modestly attenuated phenotype. The developmental timing of C9orf72 promoter hypermethylation and the reason why it occurs in only a subset of patients remain unknown. In order to model the acquisition of C9orf72 hypermethylation and examine the potential role of 5-hydroxymethylcytosine (5hmC), we generated induced pluripotent stem cells (iPSCs) from an ALS patient with C9orf72 promoter hypermethylation. Our data show that 5mC levels are reduced by reprogramming and then re-acquired upon neuronal specification, while 5hmC levels increase following reprogramming and are highest in iPSCs and motor neurons. We confirmed the presence of 5hmC within the C9orf72 promoter in post-mortem brain tissues of hypermethylated patients. These findings show that iPSCs are a valuable model system for examining epigenetic perturbations caused by the C9orf72 mutation and reveal a potential role for cytosine demethylation.
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Affiliation(s)
- Rustam Esanov
- Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Psychiatry & Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Kinsley C Belle
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, USA; The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, USA
| | | | | | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | | | - Kevin B Boylan
- Department of Neurology, Mayo Clinic, Jacksonville, FL, USA
| | - Derek M Dykxhoorn
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, USA; The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, USA
| | - Joanne Wuu
- Department of Neurology, University of Miami Miller School of Medicine, USA
| | - Michael Benatar
- Department of Neurology, University of Miami Miller School of Medicine, USA
| | - Claes Wahlestedt
- Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Psychiatry & Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Zane Zeier
- Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Psychiatry & Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL, USA.
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42
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Freedman BS. Modeling Kidney Disease with iPS Cells. Biomark Insights 2015; 10:153-69. [PMID: 26740740 PMCID: PMC4689367 DOI: 10.4137/bmi.s20054] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 07/19/2015] [Accepted: 07/21/2015] [Indexed: 12/14/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) are somatic cells that have been transcriptionally reprogrammed to an embryonic stem cell (ESC)-like state. iPSCs are a renewable source of diverse somatic cell types and tissues matching the original patient, including nephron-like kidney organoids. iPSCs have been derived representing several kidney disorders, such as ADPKD, ARPKD, Alport syndrome, and lupus nephritis, with the goals of generating replacement tissue and ‘disease in a dish’ laboratory models. Cellular defects in iPSCs and derived kidney organoids provide functional, personalized biomarkers, which can be correlated with genetic and clinical information. In proof of principle, disease-specific phenotypes have been described in iPSCs and ESCs with mutations linked to polycystic kidney disease or focal segmental glomerulosclerosis. In addition, these cells can be used to model nephrotoxic chemical injury. Recent advances in directed differentiation and CRISPR genome editing enable more specific iPSC models and present new possibilities for diagnostics, disease modeling, therapeutic screens, and tissue regeneration using human cells. This review outlines growth opportunities and design strategies for this rapidly expanding and evolving field.
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Affiliation(s)
- Benjamin S Freedman
- Division of Nephrology, Kidney Research Institute, and Institute for Stem Cell and Regenerative Medicine, Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
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43
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Carpentieri A, Cozzoli E, Scimeca M, Bonanno E, Sardanelli AM, Gambacurta A. Differentiation of human neuroblastoma cells toward the osteogenic lineage by mTOR inhibitor. Cell Death Dis 2015; 6:e1974. [PMID: 26561783 PMCID: PMC4670915 DOI: 10.1038/cddis.2015.244] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 07/23/2015] [Accepted: 07/28/2015] [Indexed: 12/14/2022]
Abstract
Current hypothesis suggest that tumors can originate from adult cells after a process of 'reprogramming' driven by genetic and epigenetic alterations. These cancer cells, called cancer stem cells (CSCs), are responsible for the tumor growth and metastases. To date, the research effort has been directed to the identification, isolation and manipulation of this cell population. Independently of whether tumors were triggered by a reprogramming of gene expression or seeded by stem cells, their energetic metabolism is altered compared with a normal cell, resulting in a high aerobic glycolytic 'Warburg' phenotype and dysregulation of mitochondrial activity. This metabolic alteration is intricately linked to cancer progression.The aim of this work has been to demonstrate the possibility of differentiating a neoplastic cell toward different germ layer lineages, by evaluating the morphological, metabolic and functional changes occurring in this process. The cellular differentiation reported in this study brings to different conclusions from those present in the current literature. We demonstrate that 'in vitro' neuroblastoma cancer cells (chosen as experimental model) are able to differentiate directly into osteoblastic (by rapamycin, an mTOR inhibitor) and hepatic lineage without an intermediate 'stem' cell step. This process seems owing to a synergy among few master molecules, metabolic changes and scaffold presence acting in a concerted way to control the cell fate.
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Affiliation(s)
- A Carpentieri
- Biochemistry Laboratory, Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome 00133, Italy
| | - E Cozzoli
- Biochemistry Laboratory, Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome 00133, Italy
| | - M Scimeca
- Department of Biomedicine and Prevention, University of Rome 'Tor Vergata', Rome 00133, Italy
| | - E Bonanno
- Department of Biomedicine and Prevention, University of Rome 'Tor Vergata', Rome 00133, Italy
| | - A M Sardanelli
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari 'Aldo Moro', Bari, Italy.,Center of Integrated Research, Campus Bio-Medico, University of Rome, Rome 00128, Italy
| | - A Gambacurta
- Biochemistry Laboratory, Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome 00133, Italy.,NAST Centre for Nanoscience, University of Rome 'Tor Vergata', Rome 00133, Italy
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Poleganov MA, Eminli S, Beissert T, Herz S, Moon JI, Goldmann J, Beyer A, Heck R, Burkhart I, Barea Roldan D, Türeci Ö, Yi K, Hamilton B, Sahin U. Efficient Reprogramming of Human Fibroblasts and Blood-Derived Endothelial Progenitor Cells Using Nonmodified RNA for Reprogramming and Immune Evasion. Hum Gene Ther 2015; 26:751-66. [DOI: 10.1089/hum.2015.045] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Marco Alexander Poleganov
- TRON—Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- BioNTech RNA Pharmaceuticals GmbH, Mainz, Germany
| | | | - Tim Beissert
- TRON—Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Stephanie Herz
- TRON—Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- III. Department for Internal Medicine, Johannes Gutenberg University, Mainz, Germany
| | | | - Johanna Goldmann
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts
| | - Arianne Beyer
- TRON—Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- BioNTech RNA Pharmaceuticals GmbH, Mainz, Germany
| | - Rosario Heck
- TRON—Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- III. Department for Internal Medicine, Johannes Gutenberg University, Mainz, Germany
| | - Isabell Burkhart
- TRON—Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Diana Barea Roldan
- TRON—Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- III. Department for Internal Medicine, Johannes Gutenberg University, Mainz, Germany
| | - Özlem Türeci
- TRON—Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Kevin Yi
- Stemgent, Cambridge, Massachusetts
| | | | - Ugur Sahin
- TRON—Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- BioNTech RNA Pharmaceuticals GmbH, Mainz, Germany
- III. Department for Internal Medicine, Johannes Gutenberg University, Mainz, Germany
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45
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Reprogramming human B cells into induced pluripotent stem cells and its enhancement by C/EBPα. Leukemia 2015; 30:674-82. [PMID: 26500142 DOI: 10.1038/leu.2015.294] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 09/03/2015] [Accepted: 09/17/2015] [Indexed: 12/21/2022]
Abstract
B cells have been shown to be refractory to reprogramming and B-cell-derived induced pluripotent stem cells (iPSC) have only been generated from murine B cells engineered to carry doxycycline-inducible Oct4, Sox2, Klf4 and Myc (OSKM) cassette in every tissue and from EBV/SV40LT-immortalized lymphoblastoid cell lines. Here, we show for the first time that freshly isolated non-cultured human cord blood (CB)- and peripheral blood (PB)-derived CD19+CD20+ B cells can be reprogrammed to iPSCs carrying complete VDJH immunoglobulin (Ig) gene monoclonal rearrangements using non-integrative tetracistronic, but not monocistronic, OSKM-expressing Sendai Virus. Co-expression of C/EBPα with OSKM facilitates iPSC generation from both CB- and PB-derived B cells. We also demonstrate that myeloid cells are much easier to reprogram than B and T lymphocytes. Differentiation potential back into the cell type of their origin of B-cell-, T-cell-, myeloid- and fibroblast-iPSCs is not skewed, suggesting that their differentiation does not seem influenced by 'epigenetic memory'. Our data reflect the actual cell-autonomous reprogramming capacity of human primary B cells because biased reprogramming was avoided by using freshly isolated primary cells, not exposed to cytokine cocktails favoring proliferation, differentiation or survival. The ability to reprogram CB/PB-derived primary human B cells offers an unprecedented opportunity for studying developmental B lymphopoiesis and modeling B-cell malignancies.
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Oh SA, Yang I, Hahn Y, Kang YK, Chung SK, Jeong S. SiNG-PCRseq: Accurate inter-sequence quantification achieved by spiking-in a neighbor genome for competitive PCR amplicon sequencing. Sci Rep 2015; 5:11879. [PMID: 26144254 PMCID: PMC4491706 DOI: 10.1038/srep11879] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 04/10/2015] [Indexed: 01/04/2023] Open
Abstract
Despite the recent technological advances in DNA quantitation by sequencing, accurate delineation of the quantitative relationship among different DNA sequences is yet to be elaborated due to difficulties in correcting the sequence-specific quantitation biases. We here developed a novel DNA quantitation method via spiking-in a neighbor genome for competitive PCR amplicon sequencing (SiNG-PCRseq). This method utilizes genome-wide chemically equivalent but easily discriminable homologous sequences with a known copy arrangement in the neighbor genome. By comparing the amounts of selected human DNA sequences simultaneously to those of matched sequences in the orangutan genome, we could accurately draw the quantitative relationships for those sequences in the human genome (root-mean-square deviations <0.05). Technical replications of cDNA quantitation performed using different reagents at different time points also resulted in excellent correlations (R2 > 0.95). The cDNA quantitation using SiNG-PCRseq was highly concordant with the RNA-seq-derived version in inter-sample comparisons (R2 = 0.88), but relatively discordant in inter-sequence quantitation (R2 < 0.44), indicating considerable level of sequence-dependent quantitative biases in RNA-seq. Considering the measurement structure explicitly relating the amount of different sequences within a sample, SiNG-PCRseq will facilitate sharing and comparing the quantitation data generated under different spatio-temporal settings.
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Affiliation(s)
- Soo A Oh
- Medical Research Division, Korea Institute of Oriental Medicine (KIOM), Daejeon 305-811, Korea
| | - Inchul Yang
- Center for Bioanalysis, Korea Research Institute of Standards and Science (KRISS), Daejeon 305-340, Korea
| | - Yoonsoo Hahn
- Department of Life Science, Chung-Ang University, Seoul 156-756, Korea
| | - Yong-Kook Kang
- Development and Differentiation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 305-806, Korea
| | - Sun-Ku Chung
- Medical Research Division, Korea Institute of Oriental Medicine (KIOM), Daejeon 305-811, Korea
| | - Sangkyun Jeong
- Medical Research Division, Korea Institute of Oriental Medicine (KIOM), Daejeon 305-811, Korea
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Kurbanov F, Kim Y, Latanich R, Chaudhari P, El-Diwany R, Knabel M, Kandathil AJ, Cameron A, Cox A, Jang YY, Thomas DL, Balagopal A. IFNL3 genotype is associated with differential induction of IFNL3 in primary human hepatocytes. Antivir Ther 2015; 20:805-14. [PMID: 26109548 PMCID: PMC4821403 DOI: 10.3851/imp2974] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2015] [Indexed: 12/17/2022]
Abstract
BACKGROUND Lambda interferons (IFNLs) have potent antiviral activity against HCV, and polymorphisms within the IFNL gene cluster near the IFNL3 gene strongly predict spontaneous- and treatment-related HCV infection outcomes. The mechanism(s) linking IFNL polymorphisms and HCV control is currently elusive. METHODS IFNL induction was studied in primary human hepatocytes (PHH) from 18 human donors, peripheral blood mononuclear cells (PBMCs) from 18 human donors, multiple cell lines and induced pluripotent stem cell-derived hepatocyte-like cells (iPSC-hepatocytes) from 7 human donors. After stimulation with intracellular RNA and infectious HCV, quantitative PCR (qPCR) primers and probes were designed to distinguish and quantify closely related IFNL messenger (m)RNAs from IFNL1, IFNL2 and IFNL3. RESULTS PHH demonstrated the most potent induction of IFNLs, although had lower pre-stimulation levels compared to PBMCs, monocytes and cell lines. PHH stimulation with cytoplasmic poly I:C induced >1,000-fold expression of IFNL1, IFNL2 and IFNL3. PHH from donors who were homozygous for the favourable IFNL3 allele (IFNL3-CC) had higher IFNL3 induction compared to PHH from IFNL3-TT donors (P=0.03). Baseline IFNL mRNA expression and induction was also tested in iPSC-hepatocytes: iPSC-hepatocytes had significantly higher baseline expression of IFNLs compared to PHH (P<0.0001), and IFNL3 induction was marginally different in iPSC-hepatocytes by IFNL genotype (P=0.07). CONCLUSIONS Hepatocytes express IFNLs when stimulated by a synthetic viral RNA that signals the cell through the cytoplasm. IFNL induction may be greater in persons with the favourable IFNL3 allele. These data provide insight into the strong linkage between IFNL3 genetics and control of HCV infection.
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Affiliation(s)
- Fuat Kurbanov
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Yonghak Kim
- Stem Cell Biology Laboratory, Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Rachel Latanich
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Pooja Chaudhari
- Stem Cell Biology Laboratory, Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Ramy El-Diwany
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Matt Knabel
- Division of Transplant Surgery, Department of Surgery, Johns Hopkins School of Medicine, Baltimore, MD USA
| | - Abraham J Kandathil
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Andrew Cameron
- Division of Transplant Surgery, Department of Surgery, Johns Hopkins School of Medicine, Baltimore, MD USA
| | - Andrea Cox
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Yoon-Young Jang
- Stem Cell Biology Laboratory, Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - David L Thomas
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Ashwin Balagopal
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
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Cheng S, Li J, Liu W, Liu C, Su L, Liu X, Guo L, Ma Y, Song B, Liu J. LTA + 252A > G polymorphism is associated with risk of nasal NK/T-cell lymphoma in a Chinese population: a case-control study. BMC Cancer 2015; 15:480. [PMID: 26108796 PMCID: PMC4490687 DOI: 10.1186/s12885-015-1506-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 06/19/2015] [Indexed: 11/25/2022] Open
Abstract
Background Nasal NK/T-cell lymphoma is a rare type of lymphoma in Caucasian individuals, but is relatively common in Asian populations. Genetic variants in immune and inflammatory response genes may thus be associated with the risk of developing lymphoma. Here, we investigated the association between immuno-modulatory gene polymorphisms and risk for nasal NK/T-cell lymphoma in a Chinese population. Methods Analysis of 12 single nucleotide polymorphisms (SNPs) in IL-10, TNF-α, lymphotoxin-α (LTA), and CTLA-4 genes was performed for 125 patients with NK/T-cell lymphoma and 300 healthy controls by PCR-ligase detection reactions. Results The LTA +252 GA + AA genotypes were associated with increased risk for NK/T-cell lymphoma (OR = 2.96, 95 % CI = 1.42–6.19, P = 0.004 for GA + AA genotype). Haplotype C-G-G-A (TNF-α -857, -308, −238 and LTA +252) also conferred an increased risk (OR = 1.52, 95 % CI = 1.14–2.06, P = 0.005). Additionally, the LTA +252 GA + AA genotype was associated with an even higher risk in populations positive for Epstein–Barr virus (OR = 5.20, 95 % CI = 1.22–23.41, P = 0.03 for the GA + AA genotype). Conclusions Our data suggest that the LTA +252 A > G polymorphism is associated with the risk of developing NK/T-cell lymphoma, especially for Epstein–Barr virus-positive NK/T-cell lymphoma in the Chinese population.
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Affiliation(s)
- Sensen Cheng
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, 250117, China. .,School of Medicine and Life Sciences, University of Jinan, Shandong Academy of Medical Sciences, Jinan, China.
| | - Jianzhong Li
- Department of Oncology, General Hospital of Jinan Iron and Steel Group Limited Company, Jinan, China.
| | - Wenjian Liu
- Department of Oncology, Affiliated Hospital of Taishan Medical College, Taian, China.
| | - Chengxiang Liu
- Department of Oncology, General Hospital of Jinan Iron and Steel Group Limited Company, Jinan, China.
| | - Lei Su
- Department of Oncology, Zhangqiu People's Hospital of Shandong Province, Jinan, China.
| | - Xiuchun Liu
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, 250117, China.
| | - Liangjun Guo
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, 250117, China.
| | - Yuan Ma
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, 250117, China. .,School of Medicine and Life Sciences, University of Jinan, Shandong Academy of Medical Sciences, Jinan, China.
| | - Bao Song
- Basic Laboratory, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, 250117, China.
| | - Jie Liu
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, 250117, China.
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Thomas SM, Kagan C, Pavlovic BJ, Burnett J, Patterson K, Pritchard JK, Gilad Y. Reprogramming LCLs to iPSCs Results in Recovery of Donor-Specific Gene Expression Signature. PLoS Genet 2015; 11:e1005216. [PMID: 25950834 PMCID: PMC4423863 DOI: 10.1371/journal.pgen.1005216] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 04/13/2015] [Indexed: 11/18/2022] Open
Abstract
Renewable in vitro cell cultures, such as lymphoblastoid cell lines (LCLs), have facilitated studies that contributed to our understanding of genetic influence on human traits. However, the degree to which cell lines faithfully maintain differences in donor-specific phenotypes is still debated. We have previously reported that standard cell line maintenance practice results in a loss of donor-specific gene expression signatures in LCLs. An alternative to the LCL model is the induced pluripotent stem cell (iPSC) system, which carries the potential to model tissue-specific physiology through the use of differentiation protocols. Still, existing LCL banks represent an important source of starting material for iPSC generation, and it is possible that the disruptions in gene regulation associated with long-term LCL maintenance could persist through the reprogramming process. To address this concern, we studied the effect of reprogramming mature LCL cultures from six unrelated donors to iPSCs on the ensuing gene expression patterns within and between individuals. We show that the reprogramming process results in a recovery of donor-specific gene regulatory signatures, increasing the number of genes with a detectable donor effect by an order of magnitude. The proportion of variation in gene expression statistically attributed to donor increases from 6.9% in LCLs to 24.5% in iPSCs (P < 10-15). Since environmental contributions are unlikely to be a source of individual variation in our system of highly passaged cultured cell lines, our observations suggest that the effect of genotype on gene regulation is more pronounced in iPSCs than in LCLs. Our findings indicate that iPSCs can be a powerful model system for studies of phenotypic variation across individuals in general, and the genetic association with variation in gene regulation in particular. We further conclude that LCLs are an appropriate starting material for iPSC generation.
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Affiliation(s)
- Samantha M. Thomas
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Courtney Kagan
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Bryan J. Pavlovic
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Jonathan Burnett
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Kristen Patterson
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Jonathan K. Pritchard
- Departments of Genetics and Biology and Howard Hughes Medical Institute, Stanford University, Stanford, California, United States of America
| | - Yoav Gilad
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
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50
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Smith C, Abalde-Atristain L, He C, Brodsky BR, Braunstein EM, Chaudhari P, Jang YY, Cheng L, Ye Z. Efficient and allele-specific genome editing of disease loci in human iPSCs. Mol Ther 2015; 23:570-7. [PMID: 25418680 PMCID: PMC4351458 DOI: 10.1038/mt.2014.226] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Accepted: 11/17/2014] [Indexed: 12/26/2022] Open
Abstract
Efficient and precise genome editing is crucial for realizing the full research and therapeutic potential of human induced pluripotent stem cells (iPSCs). Engineered nucleases including CRISPR/Cas9 and transcription activator like effector nucleases (TALENs) provide powerful tools for enhancing gene-targeting efficiency. In this study, we investigated the relative efficiencies of CRISPR/Cas9 and TALENs in human iPSC lines for inducing both homologous donor-based precise genome editing and nonhomologous end joining (NHEJ)-mediated gene disruption. Significantly higher frequencies of NHEJ-mediated insertions/deletions were detected at several endogenous loci using CRISPR/Cas9 than using TALENs, especially at nonexpressed targets in iPSCs. In contrast, comparable efficiencies of inducing homologous donor-based genome editing were observed at disease-associated loci in iPSCs. In addition, we investigated the specificity of guide RNAs used in the CRISPR/Cas9 system in targeting disease-associated point mutations in patient-specific iPSCs. Using myeloproliferative neoplasm patient-derived iPSCs that carry an acquired JAK2-V617F point mutation and α1-antitrypsin (AAT) deficiency patient-derived iPSCs that carry an inherited Z-AAT point mutation, we demonstrate that Cas9 can specifically target either the mutant or the wild-type allele with little disruption at the other allele differing by a single nucleotide. Overall, our results demonstrate the advantages of the CRISPR/Cas9 system in allele-specific genome targeting and in NHEJ-mediated gene disruption.
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Affiliation(s)
- Cory Smith
- Division of Hematology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Predoctoral Training Program in Human Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Leire Abalde-Atristain
- Division of Hematology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Cellular and Molecular Medicine Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Chaoxia He
- Division of Hematology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Brett R Brodsky
- Division of Hematology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Evan M Braunstein
- Division of Hematology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Pooja Chaudhari
- Cellular and Molecular Medicine Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yoon-Young Jang
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Cellular and Molecular Medicine Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Linzhao Cheng
- Division of Hematology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Predoctoral Training Program in Human Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Cellular and Molecular Medicine Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Zhaohui Ye
- Division of Hematology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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