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Zeng J, Casirati G, Nguyen MA, Genovese P, Bauer DE. Base Editing of Human Hematopoietic Stem Cells. Methods Mol Biol 2023; 2606:43-62. [PMID: 36592307 DOI: 10.1007/978-1-0716-2879-9_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Base editing by nucleotide deaminases linked to programmable DNA-binding proteins represents a promising approach to remedy blood disorders. Here we describe the ex vivo base editing of human CD34+ hematopoietic stem and progenitor cells (HSPCs) by electroporation of base editor mRNA or protein.
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Affiliation(s)
- Jing Zeng
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Pediatrics, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, MA, USA
| | - Gabriele Casirati
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Pediatrics, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, MA, USA
| | - My Anh Nguyen
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Pediatrics, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, MA, USA
| | - Pietro Genovese
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Pediatrics, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, MA, USA
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA. .,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Pediatrics, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, MA, USA.
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2
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Mende N, Laurenti E, Göttgens B, Wilson NK. Simultaneous Analysis of Single-Cell Transcriptomes and Cell Surface Protein Expression of Human Hematopoietic Stem Cells and Progenitors Using the 10x Genomics Platform. Methods Mol Biol 2022; 2386:189-201. [PMID: 34766273 DOI: 10.1007/978-1-0716-1771-7_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
The CITE-seq workflow combines conventional single-cell transcriptomic analysis with simultaneous analysis of cell surface protein expression using oligonucleotide-conjugated antibodies. This addition of immunophenotyping to mRNA data allows for a more detailed characterization of single-cell heterogeneity and can help to identify markers for the prospective isolation of transcriptionally defined novel cell subsets. Here, we describe the workflow for the preparation of human cord blood mononuclear cells and CD34+-enriched hematopoietic progenitors for the simultaneous characterization of protein and RNA using the commercially available TotalSeq™ antibodies from BioLegend and the droplet-based single-cell RNA-seq commercial platform from 10x Genomics.
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Affiliation(s)
- Nicole Mende
- Department of Haematology, Wellcome and MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Elisa Laurenti
- Department of Haematology, Wellcome and MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Berthold Göttgens
- Department of Haematology, Wellcome and MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Nicola K Wilson
- Department of Haematology, Wellcome and MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK.
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Abstract
Cystinosis is an autosomal recessive metabolic disease that belongs to the family of lysosomal storage disorders. The gene involved is the CTNS gene that encodes cystinosin, a seven-transmembrane domain lysosomal protein, which is a proton-driven cystine transporter. Cystinosis is characterized by the lysosomal accumulation of cystine, a dimer of cysteine, in all the cells of the body leading to multi-organ failure, including the failure of the kidney, eye, thyroid, muscle, and pancreas, and eventually causing premature death in early adulthood. The current treatment is the drug cysteamine, which is onerous and expensive, and only delays the progression of the disease. Employing the mouse model of cystinosis, using Ctns-/- mice, we first showed that the transplantation of syngeneic wild-type murine hematopoietic stem and progenitor cells (HSPCs) led to abundant tissue integration of bone marrow-derived cells, a significant decrease in tissue cystine accumulation, and long-term kidney, eye and thyroid preservation. To translate this result to a potential human therapeutic treatment, given the risks of mortality and morbidity associated with allogeneic HSPC transplantation, we developed an autologous transplantation approach of HSPCs modified ex vivo using a self-inactivated lentiviral vector to introduce a functional version of the CTNS cDNA, pCCL-CTNS, and showed its efficacy in Ctns-/- mice. Based on these promising results, we held a pre-IND meeting with the Food and Drug Administration (FDA) to carry out the FDA agreed-upon pharmacological and toxicological studies for our therapeutic candidate, manufacturing development, production of the GMP lentiviral vector, design Phase 1/2 of the clinical trial, and filing of an IND application. Our IND was cleared by the FDA on 19 December 2018, to proceed to the clinical trial using CD34+ HSPCs from the G-CSF/plerixafor-mobilized peripheral blood stem cells of patients with cystinosis, modified by ex vivo transduction using the pCCL-CTNS vector (investigational product name: CTNS-RD-04). The clinical trial evaluated the safety and efficacy of CTNS-RD-04 and takes place at the University of California, San Diego (UCSD) and will include up to six patients affected with cystinosis. Following leukapheresis and cell manufacturing, the subjects undergo myeloablation before HSPC infusion. Patients also undergo comprehensive assessments before and after treatment to evaluate the impact of CTNS-RD-04 on the clinical outcomes and cystine and cystine crystal levels in the blood and tissues for 2 years. If successful, this treatment could be a one-time therapy that may eliminate or reduce renal deterioration as well as the long-term complications associated with cystinosis. In this review, we will describe the long path from bench-to-bedside for autologous HSPC gene therapy used to treat cystinosis.
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Affiliation(s)
- Stephanie Cherqui
- Department of Pediatrics, Division of Genetics, University of California, La Jolla, San Diego, CA 92093, USA
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Jäger P, Geyh S, Twarock S, Cadeddu RP, Rabes P, Koch A, Maus U, Hesper T, Zilkens C, Rautenberg C, Bormann F, Köhrer K, Petzsch P, Wieczorek D, Betz B, Surowy H, Hildebrandt B, Germing U, Kobbe G, Haas R, Schroeder T. Acute myeloid leukemia-induced functional inhibition of healthy CD34+ hematopoietic stem and progenitor cells. Stem Cells 2021; 39:1270-1284. [PMID: 34013984 DOI: 10.1002/stem.3387] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 03/01/2021] [Accepted: 03/21/2021] [Indexed: 11/11/2022]
Abstract
Acute myeloid leukemia (AML) is characterized by an expansion of leukemic cells and a simultaneous reduction of normal hematopoietic precursors in the bone marrow (BM) resulting in hematopoietic insufficiency, but the underlying mechanisms are poorly understood in humans. Assuming that leukemic cells functionally inhibit healthy CD34+ hematopoietic stem and progenitor cells (HSPC) via humoral factors, we exposed healthy BM-derived CD34+ HSPC to cell-free supernatants derived from AML cell lines as well as from 24 newly diagnosed AML patients. Exposure to AML-derived supernatants significantly inhibited proliferation, cell cycling, colony formation, and differentiation of healthy CD34+ HSPC. RNA sequencing of healthy CD34+ HSPC after exposure to leukemic conditions revealed a specific signature of genes related to proliferation, cell-cycle regulation, and differentiation, thereby reflecting their functional inhibition on a molecular level. Experiments with paired patient samples showed that these inhibitory effects are markedly related to the immunomagnetically enriched CD34+ leukemic cell population. Using PCR, ELISA, and RNA sequencing, we detected overexpression of TGFβ1 in leukemic cells on the transcriptional and protein level and, correspondingly, a molecular signature related to TGFβ1 signaling in healthy CD34+ HSPC. This inhibitory effect of TGFβ1 on healthy hematopoiesis was functionally corrobated and could be pharmacologically reverted by SD208, an inhibitor of TGFβ receptor 1 signaling. Overall, these data indicate that leukemic cells induce functional inhibition of healthy CD34+ HSPC, at least in part, through TGFβ1, suggesting that blockage of this pathway may improve hematopoiesis in AML.
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Affiliation(s)
- Paul Jäger
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Stefanie Geyh
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Sören Twarock
- Institute of Pharmacology and Clinical Pharmacology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Ron-Patrick Cadeddu
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Pablo Rabes
- Institute of Pharmacology and Clinical Pharmacology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Annemarie Koch
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Uwe Maus
- Department of Orthopaedies and Hand Surgery, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Tobias Hesper
- Department of Orthopaedies and Hand Surgery, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Christoph Zilkens
- Department of Orthopaedies and Hand Surgery, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Christina Rautenberg
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | | | - Karl Köhrer
- Biological and Medical Research Center (BMFZ), Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Patrick Petzsch
- Biological and Medical Research Center (BMFZ), Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Dagmar Wieczorek
- Institute of Human Genetics, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Beate Betz
- Institute of Human Genetics, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Harald Surowy
- Institute of Human Genetics, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Barbara Hildebrandt
- Institute of Human Genetics, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Ulrich Germing
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Guido Kobbe
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Rainer Haas
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Thomas Schroeder
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
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Shapiro J, Iancu O, Jacobi AM, McNeill MS, Turk R, Rettig GR, Amit I, Tovin-Recht A, Yakhini Z, Behlke MA, Hendel A. Increasing CRISPR Efficiency and Measuring Its Specificity in HSPCs Using a Clinically Relevant System. Mol Ther Methods Clin Dev 2020; 17:1097-1107. [PMID: 32478125 PMCID: PMC7251314 DOI: 10.1016/j.omtm.2020.04.027] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 04/29/2020] [Indexed: 12/26/2022]
Abstract
Genome editing of human cluster of differentiation 34+ (CD34+) hematopoietic stem and progenitor cells (HSPCs) holds great therapeutic potential. This study aimed to optimize on-target, ex vivo genome editing using the CRISPR-Cas9 system in CD34+ HSPCs and to create a clear workflow for precise identification of off-target effects. Modified synthetic guide RNAs (gRNAs), either 2-part gRNA or single-guide RNA (sgRNA), were delivered to CD34+ HSPCs as part of ribonucleoprotein (RNP) complexes, targeting therapeutically relevant genes. The addition of an Alt-R electroporation enhancer (EE), a short, single-stranded oligodeoxynucleotide (ssODN), significantly increased editing efficiency in CD34+ HSPCs. Notably, similar editing improvement was observed when excess gRNA over Cas9 protein was used, providing a DNA-free alternative suitable for therapeutic applications. Furthermore, we demonstrated that sgRNA may be preferable over 2-part gRNA in a locus-specific manner. Finally, we present a clear experimental framework suitable for the unbiased identification of bona fide off-target sites by Genome-Wide, Unbiased Identification of Double-Strand Breaks (DSBs) Enabled by Sequencing (GUIDE-seq), as well as subsequent editing quantification in CD34+ HSPCs using rhAmpSeq. These findings may facilitate the implementation of genome editing in CD34+ HSPCs for research and therapy and can be adapted for other hematopoietic cells.
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Affiliation(s)
- Jenny Shapiro
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Ortal Iancu
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | | | | | - Rolf Turk
- Integrated DNA Technologies, Coralville, IA 52241, USA
| | | | - Ido Amit
- Department of Computer Science, Interdisciplinary Center, Herzliya 4610101, Israel
| | - Adi Tovin-Recht
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Zohar Yakhini
- Department of Computer Science, Interdisciplinary Center, Herzliya 4610101, Israel.,Department of Computer Science, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Mark A Behlke
- Integrated DNA Technologies, Coralville, IA 52241, USA
| | - Ayal Hendel
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
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Okumura T, Horie Y, Lai CY, Lin HT, Shoda H, Natsumoto B, Fujio K, Kumaki E, Okano T, Ono S, Tanita K, Morio T, Kanegane H, Hasegawa H, Mizoguchi F, Kawahata K, Kohsaka H, Moritake H, Nunoi H, Waki H, Tamaru SI, Sasako T, Yamauchi T, Kadowaki T, Tanaka H, Kitanaka S, Nishimura K, Ohtaka M, Nakanishi M, Otsu M. Robust and highly efficient hiPSC generation from patient non-mobilized peripheral blood-derived CD34 + cells using the auto-erasable Sendai virus vector. Stem Cell Res Ther 2019; 10:185. [PMID: 31234949 PMCID: PMC6591940 DOI: 10.1186/s13287-019-1273-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 05/18/2019] [Accepted: 05/21/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Disease modeling with patient-derived induced pluripotent stem cells (iPSCs) is a powerful tool for elucidating the mechanisms underlying disease pathogenesis and developing safe and effective treatments. Patient peripheral blood (PB) cells are used for iPSC generation in many cases since they can be collected with minimum invasiveness. To derive iPSCs that lack immunoreceptor gene rearrangements, hematopoietic stem and progenitor cells (HSPCs) are often targeted as the reprogramming source. However, the current protocols generally require HSPC mobilization and/or ex vivo expansion owing to their sparsity at the steady state and low reprogramming efficiencies, making the overall procedure costly, laborious, and time-consuming. METHODS We have established a highly efficient method for generating iPSCs from non-mobilized PB-derived CD34+ HSPCs. The source PB mononuclear cells were obtained from 1 healthy donor and 15 patients and were kept frozen until the scheduled iPSC generation. CD34+ HSPC enrichment was done using immunomagnetic beads, with no ex vivo expansion culture. To reprogram the CD34+-rich cells to pluripotency, the Sendai virus vector SeVdp-302L was used to transfer four transcription factors: KLF4, OCT4, SOX2, and c-MYC. In this iPSC generation series, the reprogramming efficiencies, success rates of iPSC line establishment, and progression time were recorded. After generating the iPSC frozen stocks, the cell recovery and their residual transgenes, karyotypes, T cell receptor gene rearrangement, pluripotency markers, and differentiation capability were examined. RESULTS We succeeded in establishing 223 iPSC lines with high reprogramming efficiencies from 15 patients with 8 different disease types. Our method allowed the rapid appearance of primary colonies (~ 8 days), all of which were expandable under feeder-free conditions, enabling robust establishment steps with less workload. After thawing, the established iPSC lines were verified to be pluripotency marker-positive and of non-T cell origin. A majority of the iPSC lines were confirmed to be transgene-free, with normal karyotypes. Their trilineage differentiation capability was also verified in a defined in vitro assay. CONCLUSION This robust and highly efficient method enables the rapid and cost-effective establishment of transgene-free iPSC lines from a small volume of PB, thus facilitating the biobanking of patient-derived iPSCs and their use for the modeling of various diseases.
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Affiliation(s)
- Takashi Okumura
- Division of Stem Cell Processing/Stem Cell Bank, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639 Japan
| | - Yumi Horie
- Division of Stem Cell Processing/Stem Cell Bank, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639 Japan
| | - Chen-Yi Lai
- Division of Stem Cell Processing/Stem Cell Bank, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639 Japan
| | - Huan-Ting Lin
- Division of Stem Cell Processing/Stem Cell Bank, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639 Japan
| | - Hirofumi Shoda
- Department of Allergy and Rheumatology, Graduation School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Bunki Natsumoto
- Department of Allergy and Rheumatology, Graduation School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduation School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Eri Kumaki
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tsubasa Okano
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shintaro Ono
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kay Tanita
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tomohiro Morio
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hirokazu Kanegane
- Department of Child Health and Development, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hisanori Hasegawa
- Department of Rheumatology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Fumitaka Mizoguchi
- Department of Rheumatology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kimito Kawahata
- Department of Rheumatology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
- Division of Rheumatology and Allergy, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Kanagawa Japan
| | - Hitoshi Kohsaka
- Department of Rheumatology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroshi Moritake
- Division of Pediatrics, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Hiroyuki Nunoi
- Division of Pediatrics, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Hironori Waki
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shin-ichi Tamaru
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takayoshi Sasako
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Molecular Sciences on Diabetes, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Toshimasa Yamauchi
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takashi Kadowaki
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Prevention of Diabetes and Life-style Related Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Metabolism and Nutrition, Mizonokuchi Hospital, Teikyo University, Kawasaki, Kanagawa Japan
| | - Hiroyuki Tanaka
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Sachiko Kitanaka
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ken Nishimura
- Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Manami Ohtaka
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
- TOKIWA-Bio Inc., Tsukuba, Ibaraki, Japan
| | - Mahito Nakanishi
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
- TOKIWA-Bio Inc., Tsukuba, Ibaraki, Japan
| | - Makoto Otsu
- Division of Stem Cell Processing/Stem Cell Bank, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639 Japan
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7
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Luh T, Lucero K, Ma W, Lee J, Zhou YJ, Shen Y, Liu K. High Dimensional Functionomic Analysis of Human Hematopoietic Stem and Progenitor Cells at a Single Cell Level. Bio Protoc 2018; 8:e2851. [PMID: 34285968 DOI: 10.21769/bioprotoc.2851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/22/2018] [Accepted: 05/01/2018] [Indexed: 11/02/2022] Open
Abstract
The ability to conduct investigation of cellular transcription, signaling, and function at the single-cell level has opened opportunities to examine heterogeneous populations at unprecedented resolutions. Although methods have been developed to evaluate high-dimensional transcriptomic and proteomic data (relating to cellular mRNA and protein), there has not been a method to evaluate corresponding high-dimensional functionomic data (relating to cellular functions) from single cells. Here, we present a protocol to quantitatively measure the differentiation potentials of single human hematopoietic stem and progenitor cells, and then cluster the cells according to these measurements. High dimensional functionomic analysis of cell potential allows cell function to be linked to molecular mechanisms within the same progenitor population.
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Affiliation(s)
- Thomas Luh
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, New York, USA
| | - Kimberly Lucero
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, New York, USA
| | - Wenji Ma
- Department of Systems Biology and Department of Biomedical Informatics, Columbia University Medical Center, New York, New York, USA
| | - Jaeyop Lee
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, New York, USA
| | - Yu Jerry Zhou
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, New York, USA
| | - Yufeng Shen
- Department of Systems Biology and Department of Biomedical Informatics, Columbia University Medical Center, New York, New York, USA
| | - Kang Liu
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, New York, USA
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