1
|
Fansler MM, Mitschka S, Mayr C. Quantifying 3'UTR length from scRNA-seq data reveals changes independent of gene expression. Nat Commun 2024; 15:4050. [PMID: 38744866 PMCID: PMC11094166 DOI: 10.1038/s41467-024-48254-9] [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: 08/30/2023] [Accepted: 04/22/2024] [Indexed: 05/16/2024] Open
Abstract
Although more than half of all genes generate transcripts that differ in 3'UTR length, current analysis pipelines only quantify the amount but not the length of mRNA transcripts. 3'UTR length is determined by 3' end cleavage sites (CS). We map CS in more than 200 primary human and mouse cell types and increase CS annotations relative to the GENCODE database by 40%. Approximately half of all CS are used in few cell types, revealing that most genes only have one or two major 3' ends. We incorporate the CS annotations into a computational pipeline, called scUTRquant, for rapid, accurate, and simultaneous quantification of gene and 3'UTR isoform expression from single-cell RNA sequencing (scRNA-seq) data. When applying scUTRquant to data from 474 cell types and 2134 perturbations, we discover extensive 3'UTR length changes across cell types that are as widespread and coordinately regulated as gene expression changes but affect mostly different genes. Our data indicate that mRNA abundance and mRNA length are two largely independent axes of gene regulation that together determine the amount and spatial organization of protein synthesis.
Collapse
Affiliation(s)
- Mervin M Fansler
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Graduate College, New York, NY, 10021, USA
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Sibylle Mitschka
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Christine Mayr
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Graduate College, New York, NY, 10021, USA.
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
| |
Collapse
|
2
|
Zhu F, Yan N, Lu X, Xu J, Gu H, Liang J, Cheng K, Wang X, Ma X, Ma N, Zhao X, Chen C, Nie G. Cell-Reprogramming-Inspired Dynamically Responsive Hydrogel Boosts the Induction of Pluripotency via Phase-Separated Biomolecular Condensates. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2211609. [PMID: 36989141 DOI: 10.1002/adma.202211609] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/23/2023] [Indexed: 05/16/2023]
Abstract
Induced pluripotent stem cells (iPSCs) have wide applications in disease modeling, personalized medicine, and tissue engineering. The generation of iPSCs from somatic cells via transcriptional-factor- or chemical molecule-based approaches are time-consuming and inefficient. Here, a cell-reprogramming-inspired dynamically responsive hydrogel is fabricated via a synthetic-biology-based strategy. Human and mouse somatic cells (including senescent cells) are efficiently reprogrammed into iPSCs that exhibit key features of embryonic stem cells. The cell-reprogramming-responsive hydrogel possesses dynamic bioresponsiveness, and it faithfully senses metabolic remodeling and extracellular acidification during cell reprogramming, responding by changing its mechanical properties accordingly. Mechanistic study demonstrates that the autonomous change of the mechanical properties of the cell-reprogramming-responsive hydrogel elicits the formation of Yes-associated protein (YAP) biomolecular condensates with the appropriate timing during cell reprogramming, ensuring a faster and more efficient generation of iPSCs than conventional cell reprogramming approach. Taken together, this study reveals the robust induction of pluripotency by coordination of cell-reprogramming-inspired dynamically responsive hydrogel and phase-separated biomolecular condensates.
Collapse
Affiliation(s)
- Fei Zhu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, China
| | - Na Yan
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xukun Lu
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Junchao Xu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haiyan Gu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jie Liang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Keman Cheng
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, China
| | - Xiaona Wang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaotu Ma
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, China
| | - Nana Ma
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, China
| | - Xiao Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunying Chen
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
- The GBA National Institute for Nanotechnology Innovation, Guangdong, 510700, China
| | - Guangjun Nie
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
- The GBA National Institute for Nanotechnology Innovation, Guangdong, 510700, China
| |
Collapse
|
3
|
Cerneckis J, Cai H, Shi Y. Induced pluripotent stem cells (iPSCs): molecular mechanisms of induction and applications. Signal Transduct Target Ther 2024; 9:112. [PMID: 38670977 PMCID: PMC11053163 DOI: 10.1038/s41392-024-01809-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 03/09/2024] [Accepted: 03/17/2024] [Indexed: 04/28/2024] Open
Abstract
The induced pluripotent stem cell (iPSC) technology has transformed in vitro research and holds great promise to advance regenerative medicine. iPSCs have the capacity for an almost unlimited expansion, are amenable to genetic engineering, and can be differentiated into most somatic cell types. iPSCs have been widely applied to model human development and diseases, perform drug screening, and develop cell therapies. In this review, we outline key developments in the iPSC field and highlight the immense versatility of the iPSC technology for in vitro modeling and therapeutic applications. We begin by discussing the pivotal discoveries that revealed the potential of a somatic cell nucleus for reprogramming and led to successful generation of iPSCs. We consider the molecular mechanisms and dynamics of somatic cell reprogramming as well as the numerous methods available to induce pluripotency. Subsequently, we discuss various iPSC-based cellular models, from mono-cultures of a single cell type to complex three-dimensional organoids, and how these models can be applied to elucidate the mechanisms of human development and diseases. We use examples of neurological disorders, coronavirus disease 2019 (COVID-19), and cancer to highlight the diversity of disease-specific phenotypes that can be modeled using iPSC-derived cells. We also consider how iPSC-derived cellular models can be used in high-throughput drug screening and drug toxicity studies. Finally, we discuss the process of developing autologous and allogeneic iPSC-based cell therapies and their potential to alleviate human diseases.
Collapse
Affiliation(s)
- Jonas Cerneckis
- Department of Neurodegenerative Diseases, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
- Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Hongxia Cai
- Department of Neurodegenerative Diseases, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Yanhong Shi
- Department of Neurodegenerative Diseases, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA.
- Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA.
| |
Collapse
|
4
|
Huyghe A, Trajkova A, Lavial F. Cellular plasticity in reprogramming, rejuvenation and tumorigenesis: a pioneer TF perspective. Trends Cell Biol 2024; 34:255-267. [PMID: 37648593 DOI: 10.1016/j.tcb.2023.07.013] [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: 05/10/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 09/01/2023]
Abstract
The multistep process of in vivo reprogramming, mediated by the transcription factors (TFs) Oct4, Sox2, Klf4, and c-Myc (OSKM), holds great promise for the development of rejuvenating and regenerative strategies. However, most of the approaches developed so far are accompanied by a persistent risk of tumorigenicity. Here, we review the groundbreaking effects of in vivo reprogramming with a particular focus on rejuvenation and regeneration. We discuss how the activity of pioneer TFs generates cellular plasticity that may be critical for inducing not only reprogramming and regeneration, but also cancer initiation. Finally, we highlight how a better understanding of the uncoupled control of cellular identity, plasticity, and aging during reprogramming might pave the way to the development of rejuvenating/regenerating strategies in a nontumorigenic manner.
Collapse
Affiliation(s)
- Aurélia Huyghe
- Cellular Reprogramming, Stem Cells and Oncogenesis Laboratory, Equipe Labellisée la Ligue Contre le Cancer, Labex Dev2Can - Univeristy of Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France
| | - Aneta Trajkova
- Cellular Reprogramming, Stem Cells and Oncogenesis Laboratory, Equipe Labellisée la Ligue Contre le Cancer, Labex Dev2Can - Univeristy of Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France
| | - Fabrice Lavial
- Cellular Reprogramming, Stem Cells and Oncogenesis Laboratory, Equipe Labellisée la Ligue Contre le Cancer, Labex Dev2Can - Univeristy of Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France.
| |
Collapse
|
5
|
Jain N, Goyal Y, Dunagin MC, Cote CJ, Mellis IA, Emert B, Jiang CL, Dardani IP, Reffsin S, Arnett M, Yang W, Raj A. Retrospective identification of cell-intrinsic factors that mark pluripotency potential in rare somatic cells. Cell Syst 2024; 15:109-133.e10. [PMID: 38335955 PMCID: PMC10940218 DOI: 10.1016/j.cels.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/31/2023] [Accepted: 01/12/2024] [Indexed: 02/12/2024]
Abstract
Pluripotency can be induced in somatic cells by the expression of OCT4, KLF4, SOX2, and MYC. Usually only a rare subset of cells reprogram, and the molecular characteristics of this subset remain unknown. We apply retrospective clone tracing to identify and characterize the rare human fibroblasts primed for reprogramming. These fibroblasts showed markers of increased cell cycle speed and decreased fibroblast activation. Knockdown of a fibroblast activation factor identified by our analysis increased the reprogramming efficiency. We provide evidence for a unified model in which cells can move into and out of the primed state over time, explaining how reprogramming appears deterministic at short timescales and stochastic at long timescales. Furthermore, inhibiting the activity of LSD1 enlarged the pool of cells that were primed for reprogramming. Thus, even homogeneous cell populations can exhibit heritable molecular variability that can dictate whether individual rare cells will reprogram or not.
Collapse
Affiliation(s)
- Naveen Jain
- Genetics and Epigenetics Program, Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yogesh Goyal
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Center for Synthetic Biology, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Margaret C Dunagin
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christopher J Cote
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ian A Mellis
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Benjamin Emert
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Connie L Jiang
- Genetics and Epigenetics Program, Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ian P Dardani
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sam Reffsin
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Miles Arnett
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wenli Yang
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Arjun Raj
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
6
|
Sinenko SA, Tomilin AN. Metabolic control of induced pluripotency. Front Cell Dev Biol 2024; 11:1328522. [PMID: 38274274 PMCID: PMC10808704 DOI: 10.3389/fcell.2023.1328522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 12/13/2023] [Indexed: 01/27/2024] Open
Abstract
Pluripotent stem cells of the mammalian epiblast and their cultured counterparts-embryonic stem cells (ESCs) and epiblast stem cells (EpiSCs)-have the capacity to differentiate in all cell types of adult organisms. An artificial process of reactivation of the pluripotency program in terminally differentiated cells was established in 2006, which allowed for the generation of induced pluripotent stem cells (iPSCs). This iPSC technology has become an invaluable tool in investigating the molecular mechanisms of human diseases and therapeutic drug development, and it also holds tremendous promise for iPSC applications in regenerative medicine. Since the process of induced reprogramming of differentiated cells to a pluripotent state was discovered, many questions about the molecular mechanisms involved in this process have been clarified. Studies conducted over the past 2 decades have established that metabolic pathways and retrograde mitochondrial signals are involved in the regulation of various aspects of stem cell biology, including differentiation, pluripotency acquisition, and maintenance. During the reprogramming process, cells undergo major transformations, progressing through three distinct stages that are regulated by different signaling pathways, transcription factor networks, and inputs from metabolic pathways. Among the main metabolic features of this process, representing a switch from the dominance of oxidative phosphorylation to aerobic glycolysis and anabolic processes, are many critical stage-specific metabolic signals that control the path of differentiated cells toward a pluripotent state. In this review, we discuss the achievements in the current understanding of the molecular mechanisms of processes controlled by metabolic pathways, and vice versa, during the reprogramming process.
Collapse
Affiliation(s)
- Sergey A. Sinenko
- Institute of Cytology, Russian Academy of Sciences, Saint-Petersburg, Russia
| | | |
Collapse
|
7
|
Long C, Li H, Liang P, Chao L, Hong Y, Zhang J, Xi Q, Zuo Y. Deciphering the decisive factors driving fate bifurcations in somatic cell reprogramming. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 34:102044. [PMID: 37869261 PMCID: PMC10585637 DOI: 10.1016/j.omtn.2023.102044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/28/2023] [Indexed: 10/24/2023]
Abstract
Single-cell studies have demonstrated that somatic cell reprogramming is a continuous process of cell fates transition. Only partial reprogramming intermediates can overcome the molecular bottlenecks to acquire pluripotency. To decipher the underlying decisive factors driving cell fate, we identified induced pluripotent stem cells or stromal-like cells (iPSCs/SLCs) and iPSCs or trophoblast-like cells (iPSCs/TLCs) fate bifurcations by reconstructing cellular trajectory. The mesenchymal-epithelial transition and the activation of pluripotency networks are the main molecular series in successful reprogramming. Correspondingly, intermediates diverge into SLCs accompanied by the inhibition of cell cycle genes and the activation of extracellular matrix genes, whereas the TLCs fate is characterized by the up-regulation of placenta development genes. Combining putative gene regulatory networks, seven (Taf7, Ezh2, Klf2, etc.) and three key factors (Cdc5l, Klf4, and Nanog) were individually identified as drivers of the successful reprogramming by triggering downstream pluripotent networks during iPSCs/SLCs and iPSCs/TLCs fate bifurcation. Conversely, 11 factors (Cebpb, Sox4, Junb, etc.) and four factors (Gata2, Jund, Ctnnb1, etc.) drive SLCs fate and TLCs fate, respectively. Our study sheds new light on the understanding of decisive factors driving cell fate, which is helpful for improving reprogramming efficiency through manipulating cell fates to avoid alternative fates.
Collapse
Affiliation(s)
- Chunshen Long
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Hanshuang Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Pengfei Liang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Lemuge Chao
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Yan Hong
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Junping Zhang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
- School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Qilemuge Xi
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Yongchun Zuo
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| |
Collapse
|
8
|
Lasry R, Maoz N, Cheng AW, Yom Tov N, Kulenkampff E, Azagury M, Yang H, Ople C, Markoulaki S, Faddah DA, Makedonski K, Orzech D, Sabag O, Jaenisch R, Buganim Y. Complex haploinsufficiency in pluripotent cells yields somatic cells with DNA methylation abnormalities and pluripotency induction defects. Stem Cell Reports 2023; 18:2174-2189. [PMID: 37832543 PMCID: PMC10679652 DOI: 10.1016/j.stemcr.2023.09.009] [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: 04/13/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 10/15/2023] Open
Abstract
A complete knockout of a single key pluripotency gene may drastically affect embryonic stem cell function and epigenetic reprogramming. In contrast, elimination of only one allele of a single pluripotency gene is mostly considered harmless to the cell. To understand whether complex haploinsufficiency exists in pluripotent cells, we simultaneously eliminated a single allele in different combinations of two pluripotency genes (i.e., Nanog+/-;Sall4+/-, Nanog+/-;Utf1+/-, Nanog+/-;Esrrb+/- and Sox2+/-;Sall4+/-). Although these double heterozygous mutant lines similarly contribute to chimeras, fibroblasts derived from these systems show a significant decrease in their ability to induce pluripotency. Tracing the stochastic expression of Sall4 and Nanog at early phases of reprogramming could not explain the seen delay or blockage. Further exploration identifies abnormal methylation around pluripotent and developmental genes in the double heterozygous mutant fibroblasts, which could be rescued by hypomethylating agent or high OSKM levels. This study emphasizes the importance of maintaining two intact alleles for pluripotency induction.
Collapse
Affiliation(s)
- Rachel Lasry
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Noam Maoz
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Albert W Cheng
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Nataly Yom Tov
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Elisabeth Kulenkampff
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Meir Azagury
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Hui Yang
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Cora Ople
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Styliani Markoulaki
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Dina A Faddah
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kirill Makedonski
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Dana Orzech
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Ofra Sabag
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yosef Buganim
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel.
| |
Collapse
|
9
|
Park S, Lee J, Ahn KS, Shim HW, Yoon J, Hyun J, Lee JH, Jang S, Yoo KH, Jang Y, Kim T, Kim HK, Lee MR, Jang J, Shim H, Kim H. Cyclic Stretch Promotes Cellular Reprogramming Process through Cytoskeletal-Nuclear Mechano-Coupling and Epigenetic Modification. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303395. [PMID: 37727069 PMCID: PMC10646259 DOI: 10.1002/advs.202303395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/27/2023] [Indexed: 09/21/2023]
Abstract
Advancing the technologies for cellular reprogramming with high efficiency has significant impact on regenerative therapy, disease modeling, and drug discovery. Biophysical cues can tune the cell fate, yet the precise role of external physical forces during reprogramming remains elusive. Here the authors show that temporal cyclic-stretching of fibroblasts significantly enhances the efficiency of induced pluripotent stem cell (iPSC) production. Generated iPSCs are proven to express pluripotency markers and exhibit in vivo functionality. Bulk RNA-sequencing reveales that cyclic-stretching enhances biological characteristics required for pluripotency acquisition, including increased cell division and mesenchymal-epithelial transition. Of note, cyclic-stretching activates key mechanosensitive molecules (integrins, perinuclear actins, nesprin-2, and YAP), across the cytoskeletal-to-nuclear space. Furthermore, stretch-mediated cytoskeletal-nuclear mechano-coupling leads to altered epigenetic modifications, mainly downregulation in H3K9 methylation, and its global gene occupancy change, as revealed by genome-wide ChIP-sequencing and pharmacological inhibition tests. Single cell RNA-sequencing further identifies subcluster of mechano-responsive iPSCs and key epigenetic modifier in stretched cells. Collectively, cyclic-stretching activates iPSC reprogramming through mechanotransduction process and epigenetic changes accompanied by altered occupancy of mechanosensitive genes. This study highlights the strong link between external physical forces with subsequent mechanotransduction process and the epigenetic changes with expression of related genes in cellular reprogramming, holding substantial implications in the field of cell biology, tissue engineering, and regenerative medicine.
Collapse
|
10
|
Nair S, Ameen M, Sundaram L, Pampari A, Schreiber J, Balsubramani A, Wang YX, Burns D, Blau HM, Karakikes I, Wang KC, Kundaje A. Transcription factor stoichiometry, motif affinity and syntax regulate single-cell chromatin dynamics during fibroblast reprogramming to pluripotency. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.04.560808. [PMID: 37873116 PMCID: PMC10592962 DOI: 10.1101/2023.10.04.560808] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Ectopic expression of OCT4, SOX2, KLF4 and MYC (OSKM) transforms differentiated cells into induced pluripotent stem cells. To refine our mechanistic understanding of reprogramming, especially during the early stages, we profiled chromatin accessibility and gene expression at single-cell resolution across a densely sampled time course of human fibroblast reprogramming. Using neural networks that map DNA sequence to ATAC-seq profiles at base-resolution, we annotated cell-state-specific predictive transcription factor (TF) motif syntax in regulatory elements, inferred affinity- and concentration-dependent dynamics of Tn5-bias corrected TF footprints, linked peaks to putative target genes, and elucidated rewiring of TF-to-gene cis-regulatory networks. Our models reveal that early in reprogramming, OSK, at supraphysiological concentrations, rapidly open transient regulatory elements by occupying non-canonical low-affinity binding sites. As OSK concentration falls, the accessibility of these transient elements decays as a function of motif affinity. We find that these OSK-dependent transient elements sequester the somatic TF AP-1. This redistribution is strongly associated with the silencing of fibroblast-specific genes within individual nuclei. Together, our integrated single-cell resource and models reveal insights into the cis-regulatory code of reprogramming at unprecedented resolution, connect TF stoichiometry and motif syntax to diversification of cell fate trajectories, and provide new perspectives on the dynamics and role of transient regulatory elements in somatic silencing.
Collapse
Affiliation(s)
- Surag Nair
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Mohamed Ameen
- Department of Cancer Biology, Stanford University, Stanford, CA, USA
- Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Dermatology, Stanford University, Stanford, CA, USA
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA
| | | | - Anusri Pampari
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Jacob Schreiber
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Yu Xin Wang
- Baxter Laboratory for Stem Cell Biology, Stanford University, Stanford, CA, USA
| | - David Burns
- Baxter Laboratory for Stem Cell Biology, Stanford University, Stanford, CA, USA
| | - Helen M Blau
- Baxter Laboratory for Stem Cell Biology, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Ioannis Karakikes
- Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | - Kevin C Wang
- Department of Dermatology, Stanford University, Stanford, CA, USA
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA
- Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA
| | - Anshul Kundaje
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| |
Collapse
|
11
|
Han L, Song B, Zhang P, Zhong Z, Zhang Y, Bo X, Wang H, Zhang Y, Cui X, Zhou W. PC3T: a signature-driven predictor of chemical compounds for cellular transition. Commun Biol 2023; 6:989. [PMID: 37758874 PMCID: PMC10533498 DOI: 10.1038/s42003-023-05225-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 08/07/2023] [Indexed: 09/29/2023] Open
Abstract
Cellular transitions hold great promise in translational medicine research. However, therapeutic applications are limited by the low efficiency and safety concerns of using transcription factors. Small molecules provide a temporal and highly tunable approach to overcome these issues. Here, we present PC3T, a computational framework to enrich molecules that induce desired cellular transitions, and PC3T was able to consistently enrich small molecules that had been experimentally validated in both bulk and single-cell datasets. We then predicted small molecule reprogramming of fibroblasts into hepatic progenitor-like cells (HPLCs). The converted cells exhibited epithelial cell-like morphology and HPLC-like gene expression pattern. Hepatic functions were also observed, such as glycogen storage and lipid accumulation. Finally, we collected and manually curated a cell state transition resource containing 224 time-course gene expression datasets and 153 cell types. Our framework, together with the data resource, is freely available at http://pc3t.idrug.net.cn/ . We believe that PC3T is a powerful tool to promote chemical-induced cell state transitions.
Collapse
Affiliation(s)
- Lu Han
- Beijing Institute of Pharmacology and Toxicology, 100850, Beijing, China
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing, China
| | - Bin Song
- Department of Pancreatic Surgery, Changhai Hospital, Second Military Medical University, 200438, Shanghai, China
| | - Peilin Zhang
- National Center for Liver Cancer, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, 200438, Shanghai, China
| | - Zhi Zhong
- Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, 200032, Shanghai, China
| | - Yongxiang Zhang
- Beijing Institute of Pharmacology and Toxicology, 100850, Beijing, China
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing, China
| | - Xiaochen Bo
- Department of Bioinformatics, Institute of Health Service and Transfusion Medicine, 100850, Beijing, China
| | - Hongyang Wang
- National Center for Liver Cancer, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, 200438, Shanghai, China
| | - Yong Zhang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China.
| | - Xiuliang Cui
- National Center for Liver Cancer, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, 200438, Shanghai, China.
| | - Wenxia Zhou
- Beijing Institute of Pharmacology and Toxicology, 100850, Beijing, China.
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing, China.
| |
Collapse
|
12
|
Wang J, Sun S, Deng H. Chemical reprogramming for cell fate manipulation: Methods, applications, and perspectives. Cell Stem Cell 2023; 30:1130-1147. [PMID: 37625410 DOI: 10.1016/j.stem.2023.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 08/27/2023]
Abstract
Chemical reprogramming offers an unprecedented opportunity to control somatic cell fate and generate desired cell types including pluripotent stem cells for applications in biomedicine in a precise, flexible, and controllable manner. Recent success in the chemical reprogramming of human somatic cells by activating a regeneration-like program provides an alternative way of producing stem cells for clinical translation. Likewise, chemical manipulation enables the capture of multiple (stem) cell states, ranging from totipotency to the stabilization of somatic fates in vitro. Here, we review progress in using chemical approaches for cell fate manipulation in addition to future opportunities in this promising field.
Collapse
Affiliation(s)
- Jinlin Wang
- MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China; Department of Rheumatology and Immunology, Peking University Third Hospital, Beijing, China
| | - Shicheng Sun
- Changping Laboratory, 28 Life Science Park Road, Beijing, China; Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC, Australia.
| | - Hongkui Deng
- MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China; Changping Laboratory, 28 Life Science Park Road, Beijing, China.
| |
Collapse
|
13
|
Fu X, Zhuang Q, Babarinde IA, Shi L, Ma G, Hu H, Li Y, Chen J, Xiao Z, Deng B, Sun L, Jauch R, Hutchins AP. Restricting epigenetic activity promotes the reprogramming of transformed cells to pluripotency in a line-specific manner. Cell Death Discov 2023; 9:245. [PMID: 37452056 PMCID: PMC10349098 DOI: 10.1038/s41420-023-01533-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 06/15/2023] [Accepted: 06/28/2023] [Indexed: 07/18/2023] Open
Abstract
Somatic cell reprogramming and oncogenic transformation share surprisingly similar features, yet transformed cells are resistant to reprogramming. Epigenetic barriers must block transformed cells from reprogramming, but the nature of those barriers is unclear. In this study, we generated a systematic panel of transformed mouse embryonic fibroblasts (MEFs) using oncogenic transgenes and discovered transformed cell lines compatible with reprogramming when transfected with Oct4/Sox2/Klf4/Myc. By comparing the reprogramming-capable and incapable transformed lines we identified multiple stages of failure in the reprogramming process. Some transformed lines failed at an early stage, whilst other lines seemed to progress through a conventional reprogramming process. Finally, we show that MEK inhibition overcomes one critical reprogramming barrier by indirectly suppressing a hyperacetylated active epigenetic state. This study reveals that diverse epigenetic barriers underly resistance to reprogramming of transformed cells.
Collapse
Affiliation(s)
- Xiuling Fu
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Qiang Zhuang
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Isaac A Babarinde
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Liyang Shi
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Gang Ma
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Haoqing Hu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Yuhao Li
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jiao Chen
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Zhen Xiao
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Boping Deng
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Li Sun
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Ralf Jauch
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Translational Stem Cell Biology, Hong Kong SAR, China
| | - Andrew P Hutchins
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
| |
Collapse
|
14
|
Lv T, Jiang S, Wang X, Hou Y. Profiling A-to-I RNA editing during mouse somatic reprogramming at the single-cell level. Heliyon 2023; 9:e18133. [PMID: 37519753 PMCID: PMC10375800 DOI: 10.1016/j.heliyon.2023.e18133] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 08/01/2023] Open
Abstract
Mouse somatic cells can be reprogrammed into induced pluripotent stem cells through a highly heterogeneous process regulated by numerous biological factors, including adenosine-to-inosine (A-to-I) RNA editing. In this study, we analyzed A-to-I RNA editing sites using a single-cell RNA sequencing (scRNA-seq) dataset with high-depth and full-length coverage. Our method revealed that A-to-I RNA editing frequency varied widely at the single-cell level and underwent dynamic changes. We also found that A-to-I RNA editing level was correlated with the expression of the RNA editing enzyme ADAR1. The analysis combined with gene ontology (GO) enrichment revealed that ADAR1-dependent A-to-I editing may downregulate the expression levels of Igtp, Irgm2, Mndal, Ifi202b, and Tapbp in the early stage, to inhibit the pathways of cellular response to interferon-beta and regulation of protein complex stability to promote mesenchymal-epithelial transition (MET). Notably, we identified a negative correlation between A-to-I RNA editing frequency and the expression of certain genes, such as Nras, Ube2l6, Zfp987, and Adsl.
Collapse
Affiliation(s)
- Tianhang Lv
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Siyuan Jiang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Yong Hou
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Shenzhen, Shenzhen, 518083, China
| |
Collapse
|
15
|
Sun Y, Shim WJ, Shen S, Sinniah E, Pham D, Su Z, Mizikovsky D, White MD, Ho JK, Nguyen Q, Bodén M, Palpant N. Inferring cell diversity in single cell data using consortium-scale epigenetic data as a biological anchor for cell identity. Nucleic Acids Res 2023; 51:e62. [PMID: 37125641 PMCID: PMC10287941 DOI: 10.1093/nar/gkad307] [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: 10/26/2022] [Accepted: 04/28/2023] [Indexed: 05/02/2023] Open
Abstract
Methods for cell clustering and gene expression from single-cell RNA sequencing (scRNA-seq) data are essential for biological interpretation of cell processes. Here, we present TRIAGE-Cluster which uses genome-wide epigenetic data from diverse bio-samples to identify genes demarcating cell diversity in scRNA-seq data. By integrating patterns of repressive chromatin deposited across diverse cell types with weighted density estimation, TRIAGE-Cluster determines cell type clusters in a 2D UMAP space. We then present TRIAGE-ParseR, a machine learning method which evaluates gene expression rank lists to define gene groups governing the identity and function of cell types. We demonstrate the utility of this two-step approach using atlases of in vivo and in vitro cell diversification and organogenesis. We also provide a web accessible dashboard for analysis and download of data and software. Collectively, genome-wide epigenetic repression provides a versatile strategy to define cell diversity and study gene regulation of scRNA-seq data.
Collapse
Affiliation(s)
- Yuliangzi Sun
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Woo Jun Shim
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Sophie Shen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Enakshi Sinniah
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Duy Pham
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Zezhuo Su
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, Hong Kong SAR, China
| | - Dalia Mizikovsky
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Melanie D White
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Joshua W K Ho
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, Hong Kong SAR, China
| | - Quan Nguyen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Mikael Bodén
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Nathan J Palpant
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| |
Collapse
|
16
|
Jin Y, Lu Y, Lin L, Liu C, Ma X, Chen X, Zhou Z, Hu Z, Pu J, Chen G, Deng Q, Jiang L, Li Y, Zhao Y, Wang H, Fu J, Li W, Zhu S. Harnessing endogenous transcription factors directly by small molecules for chemically induced pluripotency inception. Proc Natl Acad Sci U S A 2023; 120:e2215155120. [PMID: 37192170 PMCID: PMC10214147 DOI: 10.1073/pnas.2215155120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 03/27/2023] [Indexed: 05/18/2023] Open
Abstract
Chemistry-alone approach has recently been applied for incepting pluripotency in somatic cells, representing a breakthrough in biology. However, chemical reprogramming is hampered by low efficiency, and the underlying molecular mechanisms remain unclear. Particularly, chemical compounds do not have specific DNA-recognition domains or transcription regulatory domains, and then how do small molecules work as a driving force for reinstating pluripotency in somatic cells? Furthermore, how to efficiently clear materials and structures of an old cell to prepare the rebuilding of a new one? Here, we show that small molecule CD3254 activates endogenous existing transcription factor RXRα to significantly promote mouse chemical reprogramming. Mechanistically, CD3254-RXRα axis can directly activate all the 11 RNA exosome component genes (Exosc1-10 and Dis3) at transcriptional level. Unexpectedly, rather than degrading mRNAs as its substrates, RNA exosome mainly modulates the degradation of transposable element (TE)-associated RNAs, particularly MMVL30, which is identified as a new barrier for cell-fate determination. In turn, MMVL30-mediated inflammation (IFN-γ and TNF-α pathways) is reduced, contributing to the promotion of successful reprogramming. Collectively, our study provides conceptual advances for translating environmental cues into pluripotency inception, particularly, identifies that CD3254-RXRα-RNA exosome axis can promote chemical reprogramming, and suggests modulation of TE-mediated inflammation via CD3254-inducible RNA exosome as important opportunities for controlling cell fates and regenerative medicine.
Collapse
Affiliation(s)
- Yan Jin
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The Ministry of Education Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou310058, China
| | - Yunkun Lu
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The Ministry of Education Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou310058, China
| | - Lianyu Lin
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The Ministry of Education Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou310058, China
| | - Chao Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing100101, China
| | - Xiaojie Ma
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The Ministry of Education Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou310058, China
| | - Xi Chen
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The Ministry of Education Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou310058, China
| | - Ziyu Zhou
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The Ministry of Education Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou310058, China
| | - Zhensheng Hu
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The Ministry of Education Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou310058, China
| | - Jiaqi Pu
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The Ministry of Education Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou310058, China
- Department of Endocrinology, Children's Hospital of Zhejiang University School of Medicine, Hangzhou310052, China
| | - Guo Chen
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The Ministry of Education Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou310058, China
| | - Qian Deng
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The Ministry of Education Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou310058, China
| | - Liling Jiang
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The Ministry of Education Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou310058, China
| | - Yuhan Li
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The Ministry of Education Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou310058, China
| | - Yulong Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing100101, China
| | - Hao Wang
- Hangzhou Women’s Hospital, Prenatal Diagnosis Center, Zhejiang University, Hangzhou310008, China
| | - Junfen Fu
- Department of Endocrinology, Children's Hospital of Zhejiang University School of Medicine, Hangzhou310052, China
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing100101, China
| | - Saiyong Zhu
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The Ministry of Education Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou310058, China
| |
Collapse
|
17
|
Cheng Y, Fan X, Zhang J, Li Y. A scalable sparse neural network framework for rare cell type annotation of single-cell transcriptome data. Commun Biol 2023; 6:545. [PMID: 37210444 DOI: 10.1038/s42003-023-04928-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 05/11/2023] [Indexed: 05/22/2023] Open
Abstract
Automatic cell type annotation methods are increasingly used in single-cell RNA sequencing (scRNA-seq) analysis due to their fast and precise advantages. However, current methods often fail to account for the imbalance of scRNA-seq datasets and ignore information from smaller populations, leading to significant biological analysis errors. Here, we introduce scBalance, an integrated sparse neural network framework that incorporates adaptive weight sampling and dropout techniques for auto-annotation tasks. Using 20 scRNA-seq datasets with varying scales and degrees of imbalance, we demonstrate that scBalance outperforms current methods in both intra- and inter-dataset annotation tasks. Additionally, scBalance displays impressive scalability in identifying rare cell types in million-level datasets, as shown in the bronchoalveolar cell landscape. scBalance is also significantly faster than commonly used tools and comes in a user-friendly format, making it a superior tool for scRNA-seq analysis on the Python-based platform.
Collapse
Affiliation(s)
- Yuqi Cheng
- Department of Computer Science and Engineering (CSE), The Chinese University of Hong Kong (CUHK), Hong Kong SAR, China
- School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Xingyu Fan
- School of Information and Software Engineering, University of Electronic Science and Technology of China, 610054, Chengdu, China
| | - Jianing Zhang
- Department of Computer Science and Engineering (CSE), The Chinese University of Hong Kong (CUHK), Hong Kong SAR, China
| | - Yu Li
- Department of Computer Science and Engineering (CSE), The Chinese University of Hong Kong (CUHK), Hong Kong SAR, China.
- The CUHK Shenzhen Research Institute, Hi-Tech Park, Nanshan, 518057, Shenzhen, China.
| |
Collapse
|
18
|
Panariello F, Gagliano O, Luni C, Grimaldi A, Angiolillo S, Qin W, Manfredi A, Annunziata P, Slovin S, Vaccaro L, Riccardo S, Bouche V, Dionisi M, Salvi M, Martewicz S, Hu M, Cui M, Stuart H, Laterza C, Baruzzo G, Schiebinger G, Di Camillo B, Cacchiarelli D, Elvassore N. Cellular population dynamics shape the route to human pluripotency. Nat Commun 2023; 14:2829. [PMID: 37198156 DOI: 10.1038/s41467-023-37270-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/09/2023] [Indexed: 05/19/2023] Open
Abstract
Human cellular reprogramming to induced pluripotency is still an inefficient process, which has hindered studying the role of critical intermediate stages. Here we take advantage of high efficiency reprogramming in microfluidics and temporal multi-omics to identify and resolve distinct sub-populations and their interactions. We perform secretome analysis and single-cell transcriptomics to show functional extrinsic pathways of protein communication between reprogramming sub-populations and the re-shaping of a permissive extracellular environment. We pinpoint the HGF/MET/STAT3 axis as a potent enhancer of reprogramming, which acts via HGF accumulation within the confined system of microfluidics, and in conventional dishes needs to be supplied exogenously to enhance efficiency. Our data suggest that human cellular reprogramming is a transcription factor-driven process that it is deeply dependent on extracellular context and cell population determinants.
Collapse
Affiliation(s)
- Francesco Panariello
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Onelia Gagliano
- Department of Industrial Engineering, University of Padova, Padova, Italy
- Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
- Stem Cell and Regenerative Medicine Section, GOS Institute of Child Health, University College London, London, UK
| | - Camilla Luni
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai, China
- Department of Civil, Chemical, Environmental and Materials Engineering (DICAM), University of Bologna, Bologna, Italy
| | - Antonio Grimaldi
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Silvia Angiolillo
- Department of Industrial Engineering, University of Padova, Padova, Italy
- Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Wei Qin
- Department of Industrial Engineering, University of Padova, Padova, Italy
- Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai, China
| | - Anna Manfredi
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
- NEGEDIA (Next Generation Diagnostic srl), Pozzuoli, Italy
| | - Patrizia Annunziata
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
- NEGEDIA (Next Generation Diagnostic srl), Pozzuoli, Italy
| | - Shaked Slovin
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Lorenzo Vaccaro
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Sara Riccardo
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
- NEGEDIA (Next Generation Diagnostic srl), Pozzuoli, Italy
| | - Valentina Bouche
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Manuela Dionisi
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Marcello Salvi
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Sebastian Martewicz
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai, China
| | - Manli Hu
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai, China
| | - Meihua Cui
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai, China
| | - Hannah Stuart
- Department of Industrial Engineering, University of Padova, Padova, Italy
- Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Cecilia Laterza
- Department of Industrial Engineering, University of Padova, Padova, Italy
- Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Giacomo Baruzzo
- Department of Information Engineering, University of Padova, Padova, Italy
| | | | - Barbara Di Camillo
- Department of Information Engineering, University of Padova, Padova, Italy
- Department of Comparative Biomedicine and Food Science, University of Padova, Padova, Italy
- CRIBI Biotechnology Center, University of Padova, Padova, Italy
| | - Davide Cacchiarelli
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy.
- Department of Translational Medicine, University of Naples "Federico II", Naples, Italy.
- School for Advanced Studies, Genomics and Experimental Medicine Program, University of Naples "Federico II", Naples, Italy.
| | - Nicola Elvassore
- Department of Industrial Engineering, University of Padova, Padova, Italy.
- Veneto Institute of Molecular Medicine (VIMM), Padova, Italy.
- Stem Cell and Regenerative Medicine Section, GOS Institute of Child Health, University College London, London, UK.
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai, China.
| |
Collapse
|
19
|
Li H, Long C, Hong Y, Luo L, Zuo Y. Characterizing Cellular Differentiation Potency and Waddington Landscape via Energy Indicator. RESEARCH (WASHINGTON, D.C.) 2023; 6:0118. [PMID: 37223479 PMCID: PMC10202187 DOI: 10.34133/research.0118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 03/20/2023] [Indexed: 05/25/2023]
Abstract
The precise characterization of cellular differentiation potency remains an open question, which is fundamentally important for deciphering the dynamics mechanism related to cell fate transition. We quantitatively evaluated the differentiation potency of different stem cells based on the Hopfield neural network (HNN). The results emphasized that cellular differentiation potency can be approximated by Hopfield energy values. We then profiled the Waddington energy landscape of embryogenesis and cell reprogramming processes. The energy landscape at single-cell resolution further confirmed that cell fate decision is progressively specified in a continuous process. Moreover, the transition of cells from one steady state to another in embryogenesis and cell reprogramming processes was dynamically simulated on the energy ladder. These two processes can be metaphorized as the motion of descending and ascending ladders, respectively. We further deciphered the dynamics of the gene regulatory network (GRN) for driving cell fate transition. Our study proposes a new energy indicator to quantitatively characterize cellular differentiation potency without prior knowledge, facilitating the further exploration of the potential mechanism of cellular plasticity.
Collapse
Affiliation(s)
- Hanshuang Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences,
Inner Mongolia University, Hohhot 010070, China
| | - Chunshen Long
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences,
Inner Mongolia University, Hohhot 010070, China
| | - Yan Hong
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences,
Inner Mongolia University, Hohhot 010070, China
| | - Liaofu Luo
- Department of Physics,
Inner Mongolia University, Hohhot 010070, China
| | - Yongchun Zuo
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences,
Inner Mongolia University, Hohhot 010070, China
| |
Collapse
|
20
|
Bonefas KM, Vallianatos CN, Raines B, Tronson NC, Iwase S. Sexually Dimorphic Alterations in the Transcriptome and Behavior with Loss of Histone Demethylase KDM5C. Cells 2023; 12:cells12040637. [PMID: 36831303 PMCID: PMC9954040 DOI: 10.3390/cells12040637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/08/2023] [Accepted: 02/15/2023] [Indexed: 02/18/2023] Open
Abstract
Chromatin dysregulation has emerged as a major hallmark of neurodevelopmental disorders such as intellectual disability (ID) and autism spectrum disorders (ASD). The prevalence of ID and ASD is higher in males compared to females, with unknown mechanisms. Intellectual developmental disorder, X-linked syndromic, Claes-Jensen type (MRXSCJ), is caused by loss-of-function mutations of lysine demethylase 5C (KDM5C), a histone H3K4 demethylase gene. KDM5C escapes X-inactivation, thereby presenting at a higher level in females. Initially, MRXSCJ was exclusively reported in males, while it is increasingly evident that females with heterozygous KDM5C mutations can show cognitive deficits. The mouse model of MRXSCJ, male Kdm5c-hemizygous knockout animals, recapitulates key features of human male patients. However, the behavioral and molecular traits of Kdm5c-heterozygous female mice remain incompletely characterized. Here, we report that gene expression and behavioral abnormalities are readily detectable in Kdm5c-heterozygous female mice, demonstrating the requirement for a higher KDM5C dose in females. Furthermore, we found both shared and sex-specific consequences of a reduced KDM5C dose in social behavior, gene expression, and genetic interaction with the counteracting enzyme KMT2A. These observations provide an essential insight into the sex-biased manifestation of neurodevelopmental disorders and sex chromosome evolution.
Collapse
Affiliation(s)
- Katherine M. Bonefas
- Department of Human Genetics, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Christina N. Vallianatos
- Department of Human Genetics, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Genetics and Genomics Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Brynne Raines
- Department of Psychology, College of LS&A, University of Michigan, Ann Arbor, MI 48109, USA
| | - Natalie C. Tronson
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Psychology, College of LS&A, University of Michigan, Ann Arbor, MI 48109, USA
- Correspondence: (N.C.T.); (S.I.)
| | - Shigeki Iwase
- Department of Human Genetics, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
- Genetics and Genomics Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
- Correspondence: (N.C.T.); (S.I.)
| |
Collapse
|
21
|
Jain N, Goyal Y, Dunagin MC, Cote CJ, Mellis IA, Emert B, Jiang CL, Dardani IP, Reffsin S, Raj A. Retrospective identification of intrinsic factors that mark pluripotency potential in rare somatic cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.10.527870. [PMID: 36798299 PMCID: PMC9934612 DOI: 10.1101/2023.02.10.527870] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
Pluripotency can be induced in somatic cells by the expression of the four "Yamanaka" factors OCT4, KLF4, SOX2, and MYC. However, even in homogeneous conditions, usually only a rare subset of cells admit reprogramming, and the molecular characteristics of this subset remain unknown. Here, we apply retrospective clone tracing to identify and characterize the individual human fibroblast cells that are primed for reprogramming. These fibroblasts showed markers of increased cell cycle speed and decreased fibroblast activation. Knockdown of a fibroblast activation factor identified by our analysis led to increased reprogramming efficiency, identifying it as a barrier to reprogramming. Changing the frequency of reprogramming by inhibiting the activity of LSD1 led to an enlarging of the pool of cells that were primed for reprogramming. Our results show that even homogeneous cell populations can exhibit heritable molecular variability that can dictate whether individual rare cells will reprogram or not.
Collapse
Affiliation(s)
- Naveen Jain
- Genetics and Epigenetics Program, Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yogesh Goyal
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Margaret C Dunagin
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Christopher J Cote
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Ian A Mellis
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin Emert
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Connie L Jiang
- Genetics and Epigenetics Program, Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ian P Dardani
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Sam Reffsin
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Arjun Raj
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| |
Collapse
|
22
|
Durand S, Bruelle M, Bourdelais F, Bennychen B, Blin-Gonthier J, Isaac C, Huyghe A, Martel S, Seyve A, Vanbelle C, Adrait A, Couté Y, Meyronet D, Catez F, Diaz JJ, Lavial F, Ricci EP, Ducray F, Gabut M. RSL24D1 sustains steady-state ribosome biogenesis and pluripotency translational programs in embryonic stem cells. Nat Commun 2023; 14:356. [PMID: 36690642 PMCID: PMC9870888 DOI: 10.1038/s41467-023-36037-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 01/13/2023] [Indexed: 01/24/2023] Open
Abstract
Embryonic stem cell (ESC) fate decisions are regulated by a complex circuitry that coordinates gene expression at multiple levels from chromatin to mRNA processing. Recently, ribosome biogenesis and translation have emerged as key pathways that efficiently control stem cell homeostasis, yet the underlying molecular mechanisms remain largely unknown. Here, we identified RSL24D1 as highly expressed in both mouse and human pluripotent stem cells. RSL24D1 is associated with nuclear pre-ribosomes and is required for the biogenesis of 60S subunits in mouse ESCs. Interestingly, RSL24D1 depletion significantly impairs global translation, particularly of key pluripotency factors and of components from the Polycomb Repressive Complex 2 (PRC2). While having a moderate impact on differentiation, RSL24D1 depletion significantly alters ESC self-renewal and lineage commitment choices. Altogether, these results demonstrate that RSL24D1-dependant ribosome biogenesis is both required to sustain the expression of pluripotent transcriptional programs and to silence PRC2-regulated developmental programs, which concertedly dictate ESC homeostasis.
Collapse
Affiliation(s)
- Sébastien Durand
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Labex Dev2Can, Lyon, France
| | - Marion Bruelle
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
| | - Fleur Bourdelais
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Labex Dev2Can, Lyon, France
- Inovarion, 75005, Paris, France
| | - Bigitha Bennychen
- Dept. of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, K1A 0R6, Canada
| | - Juliana Blin-Gonthier
- Laboratoire de Biologie et de Modélisation de la Cellule, ENS de Lyon, CNRS UMR 5239, Inserm U1293, Lyon, France
| | - Caroline Isaac
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Labex Dev2Can, Lyon, France
| | - Aurélia Huyghe
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Labex Dev2Can, Lyon, France
- Equipe labellisée la Ligue contre le cancer, Lyon, France
| | - Sylvie Martel
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
| | - Antoine Seyve
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Neuro-oncology department, Hospices Civils de Lyon, Lyon, France
| | - Christophe Vanbelle
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
| | - Annie Adrait
- University Grenoble Alpes, INSERM, CEA, UA13 BGE, CNRS, CEA, FR2048, 38000, Grenoble, France
| | - Yohann Couté
- University Grenoble Alpes, INSERM, CEA, UA13 BGE, CNRS, CEA, FR2048, 38000, Grenoble, France
| | - David Meyronet
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Institut de Pathologie Est, Hospices Civils de Lyon, Lyon, France
| | - Frédéric Catez
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Labex Dev2Can, Lyon, France
| | - Jean-Jacques Diaz
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Labex Dev2Can, Lyon, France
| | - Fabrice Lavial
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Labex Dev2Can, Lyon, France
- Equipe labellisée la Ligue contre le cancer, Lyon, France
| | - Emiliano P Ricci
- Laboratoire de Biologie et de Modélisation de la Cellule, ENS de Lyon, CNRS UMR 5239, Inserm U1293, Lyon, France
| | - François Ducray
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Neuro-oncology department, Hospices Civils de Lyon, Lyon, France
| | - Mathieu Gabut
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France.
- Institut Convergence Plascan, Lyon, France.
| |
Collapse
|
23
|
Comparative roadmaps of reprogramming and oncogenic transformation identify Bcl11b and Atoh8 as broad regulators of cellular plasticity. Nat Cell Biol 2022; 24:1350-1363. [PMID: 36075976 PMCID: PMC9481462 DOI: 10.1038/s41556-022-00986-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 07/27/2022] [Indexed: 12/22/2022]
Abstract
Coordinated changes of cellular plasticity and identity are critical for pluripotent reprogramming and oncogenic transformation. However, the sequences of events that orchestrate these intermingled modifications have never been comparatively dissected. Here, we deconvolute the cellular trajectories of reprogramming (via Oct4/Sox2/Klf4/c-Myc) and transformation (via Ras/c-Myc) at the single-cell resolution and reveal how the two processes intersect before they bifurcate. This approach led us to identify the transcription factor Bcl11b as a broad-range regulator of cell fate changes, as well as a pertinent marker to capture early cellular intermediates that emerge simultaneously during reprogramming and transformation. Multiomics characterization of these intermediates unveiled a c-Myc/Atoh8/Sfrp1 regulatory axis that constrains reprogramming, transformation and transdifferentiation. Mechanistically, we found that Atoh8 restrains cellular plasticity, independent of cellular identity, by binding a specific enhancer network. This study provides insights into the partitioned control of cellular plasticity and identity for both regenerative and cancer biology. Huyghe, Furlan et al. compare pluripotent reprogramming with oncogenic transformation and identify Bcl11b and Atoh8 as regulators of cellular plasticity in both processes, thus offering a unifying theory on the factors constraining cell fate changes.
Collapse
|
24
|
Mettl14-driven senescence-associated secretory phenotype facilitates somatic cell reprogramming. Stem Cell Reports 2022; 17:1799-1809. [PMID: 35947961 PMCID: PMC9391510 DOI: 10.1016/j.stemcr.2022.06.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 11/24/2022] Open
Abstract
The METTL3-METTL14 complex, the “writer” of N6-methyladenosine (m6A), plays an important role in many biological processes. Previous studies have shown that Mettl3 overexpression can increase the level of m6A and promote somatic cell reprogramming. Here, we demonstrate that Mettl14, another component of the methyltransferase complex, can significantly enhance the generation of induced pluripotent stem cells (iPSCs) in an m6A-independent manner. In cooperation with Oct4, Sox2, Klf4, and c-Myc, overexpressed Mettl14 transiently promoted senescence-associated secretory phenotype (SASP) gene expression in non-reprogrammed cells in the late stage of reprogramming. Subsequently, we demonstrated that interleukin-6 (IL-6), a component of the SASP, significantly enhanced somatic cell reprogramming. In contrast, blocking the SASP using a senolytic agent or a nuclear factor κB (NF-κB) inhibitor impaired the effect of Mettl14 on reprogramming. Our results highlight the m6A-independent function of Mettl14 in reprogramming and provide new insight into the interplay between senescence and reprogramming in vitro. Mettl14 can facilitate somatic cell reprogramming in an m6A-independent manner Mettl14 transcriptionally drives the senescence-associated secretory phenotype (SASP) Mettl14-driven SASPs are mainly secreted from non-reprogramming cells Blocking of SASP impairs the effect of Mettl14 on reprogramming
Collapse
|
25
|
Roux AE, Zhang C, Paw J, Zavala-Solorio J, Malahias E, Vijay T, Kolumam G, Kenyon C, Kimmel JC. Diverse partial reprogramming strategies restore youthful gene expression and transiently suppress cell identity. Cell Syst 2022; 13:574-587.e11. [PMID: 35690067 DOI: 10.1016/j.cels.2022.05.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 02/15/2022] [Accepted: 05/10/2022] [Indexed: 01/25/2023]
Abstract
Partial pluripotent reprogramming can reverse features of aging in mammalian cells, but the impact on somatic identity and the necessity of individual reprogramming factors remain unknown. Here, we used single-cell genomics to map the identity trajectory induced by partial reprogramming in multiple murine cell types and dissected the influence of each factor by screening all Yamanaka Factor subsets with pooled single-cell screens. We found that partial reprogramming restored youthful expression in adipogenic and mesenchymal stem cells but also temporarily suppressed somatic identity programs. Our pooled screens revealed that many subsets of the Yamanaka Factors both restore youthful expression and suppress somatic identity, but these effects were not tightly entangled. We also found that a multipotent reprogramming strategy inspired by amphibian regeneration restored youthful expression in myogenic cells. Our results suggest that various sets of reprogramming factors can restore youthful expression with varying degrees of somatic identity suppression. A record of this paper's Transparent Peer Review process is included in the supplemental information.
Collapse
Affiliation(s)
- Antoine E Roux
- Calico Life Sciences, LLC, 1170 Veterans Blvd, South San Francisco, CA 94080, USA
| | - Chunlian Zhang
- Calico Life Sciences, LLC, 1170 Veterans Blvd, South San Francisco, CA 94080, USA
| | - Jonathan Paw
- Calico Life Sciences, LLC, 1170 Veterans Blvd, South San Francisco, CA 94080, USA
| | - José Zavala-Solorio
- Calico Life Sciences, LLC, 1170 Veterans Blvd, South San Francisco, CA 94080, USA
| | - Evangelia Malahias
- Calico Life Sciences, LLC, 1170 Veterans Blvd, South San Francisco, CA 94080, USA
| | - Twaritha Vijay
- Calico Life Sciences, LLC, 1170 Veterans Blvd, South San Francisco, CA 94080, USA
| | - Ganesh Kolumam
- Calico Life Sciences, LLC, 1170 Veterans Blvd, South San Francisco, CA 94080, USA
| | - Cynthia Kenyon
- Calico Life Sciences, LLC, 1170 Veterans Blvd, South San Francisco, CA 94080, USA
| | - Jacob C Kimmel
- Calico Life Sciences, LLC, 1170 Veterans Blvd, South San Francisco, CA 94080, USA.
| |
Collapse
|
26
|
He J, Lin L, Chen J. Practical bioinformatics pipelines for single-cell RNA-seq data analysis. BIOPHYSICS REPORTS 2022; 8:158-169. [PMID: 37288243 PMCID: PMC10189648 DOI: 10.52601/bpr.2022.210041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 03/01/2022] [Indexed: 11/05/2022] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) is a revolutionary tool to explore cells. With an increasing number of scRNA-seq data analysis tools that have been developed, it is challenging for users to choose and compare their performance. Here, we present an overview of the workflow for computational analysis of scRNA-seq data. We detail the steps of a typical scRNA-seq analysis, including experimental design, pre-processing and quality control, feature selection, dimensionality reduction, cell clustering and annotation, and downstream analysis including batch correction, trajectory inference and cell-cell communication. We provide guidelines according to our best practice. This review will be helpful for the experimentalists interested in analyzing their data, and will aid the users seeking to update their analysis pipelines.
Collapse
Affiliation(s)
- Jiangping He
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510320, China
| | - Lihui Lin
- Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Jiekai Chen
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510320, China
- Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| |
Collapse
|
27
|
Comparative parallel multi-omics analysis during the induction of pluripotent and trophectoderm states. Nat Commun 2022; 13:3475. [PMID: 35715410 PMCID: PMC9205865 DOI: 10.1038/s41467-022-31131-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/31/2022] [Indexed: 11/09/2022] Open
Abstract
Following fertilization, it is only at the 32-64-cell stage when a clear segregation between cells of the inner cell mass and trophectoderm is observed, suggesting a 'T'-shaped model of specification. Here, we examine whether the acquisition of these two states in vitro, by nuclear reprogramming, share similar dynamics/trajectories. Using a comparative parallel multi-omics analysis (i.e., bulk RNA-seq, scRNA-seq, ATAC-seq, ChIP-seq, RRBS and CNVs) on cells undergoing reprogramming to pluripotency and TSC state we show that each reprogramming system exhibits specific trajectories from the onset of the process, suggesting 'V'-shaped model. We describe in detail the various trajectories toward the two states and illuminate reprogramming stage-specific markers, blockers, facilitators and TSC subpopulations. Finally, we show that while the acquisition of the TSC state involves the silencing of embryonic programs by DNA methylation, during the acquisition of pluripotency these regions are initially defined but retain inactive by the elimination of H3K27ac.
Collapse
|
28
|
Sun J, Wu G, Pastor F, Rahman N, Wang WH, Zhang Z, Merle P, Hui L, Salvetti A, Durantel D, Yang D, Andrisani O. RNA helicase DDX5 enables STAT1 mRNA translation and interferon signalling in hepatitis B virus replicating hepatocytes. Gut 2022; 71:991-1005. [PMID: 34021034 PMCID: PMC8606016 DOI: 10.1136/gutjnl-2020-323126] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 05/09/2021] [Indexed: 12/18/2022]
Abstract
OBJECTIVE RNA helicase DDX5 is downregulated during HBV replication and poor prognosis HBV-related hepatocellular carcinoma (HCC). The objective of this study is to investigate the role of DDX5 in interferon (IFN) signalling. We provide evidence of a novel mechanism involving DDX5 that enables translation of transcription factor STAT1 mediating the IFN response. DESIGN AND RESULTS Molecular, pharmacological and biophysical assays were used together with cellular models of HBV replication, HCC cell lines and liver tumours. We demonstrate that DDX5 regulates STAT1 mRNA translation by resolving a G-quadruplex (rG4) RNA structure, proximal to the 5' end of STAT1 5'UTR. We employed luciferase reporter assays comparing wild type (WT) versus mutant rG4 sequence, rG4-stabilising compounds, CRISPR/Cas9 editing of the STAT1-rG4 sequence and circular dichroism determination of the rG4 structure. STAT1-rG4 edited cell lines were resistant to the effect of rG4-stabilising compounds in response to IFN-α, while HCC cell lines expressing low DDX5 exhibited reduced IFN response. Ribonucleoprotein and electrophoretic mobility assays demonstrated direct and selective binding of RNA helicase-active DDX5 to the WT STAT1-rG4 sequence. Immunohistochemistry of normal liver and liver tumours demonstrated that absence of DDX5 corresponded to absence of STAT1. Significantly, knockdown of DDX5 in HBV infected HepaRG cells reduced the anti-viral effect of IFN-α. CONCLUSION RNA helicase DDX5 resolves a G-quadruplex structure in 5'UTR of STAT1 mRNA, enabling STAT1 translation. We propose that DDX5 is a key regulator of the dynamic range of IFN response during innate immunity and adjuvant IFN-α therapy.
Collapse
Affiliation(s)
- Jiazeng Sun
- Basic Medical Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Guanhui Wu
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA
| | - Florentin Pastor
- International Center for Infectiology Research (CIRI), INSERM U1111-CNRS UMR5308, Lyon, France
| | - Naimur Rahman
- Basic Medical Sciences, Purdue University System, West Lafayette, Indiana, USA
| | - Wen-Hung Wang
- Gene Editing Core, Bindley Biosciences Center, Purdue University, West Lafayette, Indiana, USA
| | - Zhengtao Zhang
- Department of Biochemistry and Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Shanghai, China
| | - Philippe Merle
- Service d'Hépatologie, Hôpital de La Croix-Rousse Centre Livet, Lyon, Rhône-Alpes, France
| | - Lijian Hui
- Department of Biochemistry and Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Shanghai, China
| | - Anna Salvetti
- International Center for Infectiology Research (CIRI), INSERM U1111-CNRS UMR5308, Lyon, France
| | - David Durantel
- INSERM U1111-CNRS UMR5308 International Center for Infectiology Research (CIRI), Lyon, France
| | - Danzhou Yang
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA
| | - Ourania Andrisani
- Basic Medical Sciences, Purdue University, West Lafayette, Indiana, USA
| |
Collapse
|
29
|
Hörnblad A, Remeseiro S. Epigenetics, Enhancer Function and 3D Chromatin Organization in Reprogramming to Pluripotency. Cells 2022; 11:cells11091404. [PMID: 35563711 PMCID: PMC9105757 DOI: 10.3390/cells11091404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/13/2022] [Accepted: 04/19/2022] [Indexed: 12/22/2022] Open
Abstract
Genome architecture, epigenetics and enhancer function control the fate and identity of cells. Reprogramming to induced pluripotent stem cells (iPSCs) changes the transcriptional profile and chromatin landscape of the starting somatic cell to that of the pluripotent cell in a stepwise manner. Changes in the regulatory networks are tightly regulated during normal embryonic development to determine cell fate, and similarly need to function in cell fate control during reprogramming. Switching off the somatic program and turning on the pluripotent program involves a dynamic reorganization of the epigenetic landscape, enhancer function, chromatin accessibility and 3D chromatin topology. Within this context, we will review here the current knowledge on the processes that control the establishment and maintenance of pluripotency during somatic cell reprogramming.
Collapse
Affiliation(s)
- Andreas Hörnblad
- Umeå Centre for Molecular Medicine (UCMM), Umeå University, 901 87 Umeå, Sweden
- Correspondence: (A.H.); (S.R.)
| | - Silvia Remeseiro
- Umeå Centre for Molecular Medicine (UCMM), Umeå University, 901 87 Umeå, Sweden
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, 901 87 Umeå, Sweden
- Correspondence: (A.H.); (S.R.)
| |
Collapse
|
30
|
Bae J, Kim JE, Perumalsamy H, Park S, Kim Y, Jun DW, Yoon TH. Mass Cytometry Study on Hepatic Fibrosis and Its Drug-Induced Recovery Using Mouse Peripheral Blood Mononuclear Cells. Front Immunol 2022; 13:814030. [PMID: 35222390 PMCID: PMC8863676 DOI: 10.3389/fimmu.2022.814030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 01/03/2022] [Indexed: 01/10/2023] Open
Abstract
The number of patients with liver diseases has increased significantly with the progress of global industrialization. Hepatic fibrosis, one of the most common liver diseases diagnosed in many developed countries, occurs in response to chronic liver injury and is primarily driven by the development of inflammation. Earlier immunological studies have been focused on the importance of the innate immune response in the pathophysiology of steatohepatitis and fibrosis, but recently, it has also been reported that adaptive immunity, particularly B cells, plays an essential role in hepatic inflammation and fibrosis. However, despite recent data showing the importance of adaptive immunity, relatively little is known about the role of B cells in the pathogenesis of steatohepatitis fibrosis. In this study, a single-cell-based, high-dimensional mass cytometric investigation of the peripheral blood mononuclear cells collected from mice belonging to three groups [normal chow (NC), thioacetamide (TAA), and 11beta-HSD inhibitor drug] was conducted to further understand the pathogenesis of liver fibrosis through reliable noninvasive biomarkers. Firstly, major immune cell types and their population changes were qualitatively analyzed using UMAP dimensionality reduction and two-dimensional visualization technique combined with a conventional manual gating strategy. The population of B cells displayed a twofold increase in the TAA group compared to that in the NC group, which was recovered slightly after treatment with the 11beta-HSD inhibitor drug. In contrast, the populations of NK cells, effector CD4+ T cells, and memory CD8+ T cells were significantly reduced in the TAA group compared with those in the NC group. Further identification and quantification of the major immune cell types and their subsets were conducted based on automated clustering approaches [PhenoGraph (PG) and FlowSOM]. The B-cell subset corresponding to PhenoGraph cluster PG#2 (CD62LhighCD44highLy6chigh B cells) and PG#3 (CD62LhighCD44highLy6clow B cell) appears to play a major role in both the development of hepatic fibrosis and recovery via treatment, whereas PG#1 (CD62LlowCD44highLy6clow B cell) seems to play a dominant role in the development of hepatic fibrosis. These findings provide insights into the roles of cellular subsets of B cells during the progression of, and recovery from, hepatic fibrosis.
Collapse
Affiliation(s)
- Jiwon Bae
- Department of Chemistry, College of Natural Sciences, Hanyang University, Seoul, South Korea
| | - Ji Eun Kim
- Department of Internal Medicine, Hanyang University Hospital, Seoul, South Korea
| | - Haribalan Perumalsamy
- Research Institute for Convergence of Basic Science, Hanyang University, Seoul, South Korea
| | - Sehee Park
- Department of Chemistry, College of Natural Sciences, Hanyang University, Seoul, South Korea
| | - Yun Kim
- Hanyang Medicine-Engineering-Bio Collaborative & Comprehensive Center for Drug Development, Hanyang University, Seoul, South Korea.,Department of Clinical Pharmacology and Therapeutics, Hanyang University Hospital, Seoul, South Korea
| | - Dae Won Jun
- Department of Internal Medicine, Hanyang University Hospital, Seoul, South Korea.,Hanyang Medicine-Engineering-Bio Collaborative & Comprehensive Center for Drug Development, Hanyang University, Seoul, South Korea.,Department of Medical and Digital Engineering, College of Engineering, Hanyang University, Seoul, South Korea
| | - Tae Hyun Yoon
- Department of Chemistry, College of Natural Sciences, Hanyang University, Seoul, South Korea.,Research Institute for Convergence of Basic Science, Hanyang University, Seoul, South Korea.,Institute of Next Generation Material Design, Hanyang University, Seoul, South Korea.,Yoon Idea Lab. Co. Ltd, Seoul, South Korea
| |
Collapse
|
31
|
Jiang Z, Qin L, Tang Y, Liao R, Shi J, He B, Li S, Zheng D, Cui Y, Wu Q, Long Y, Yao Y, Wei Z, Hong Q, Wu Y, Mai Y, Gou S, Li X, Weinkove R, Norton S, Luo W, Feng W, Zhou H, Liu Q, Chen J, Lai L, Chen X, Pei D, Graf T, Liu X, Li Y, Liu P, Zhang Z, Li P. Human induced-T-to-natural killer cells have potent anti-tumour activities. Biomark Res 2022; 10:13. [PMID: 35331335 PMCID: PMC8943975 DOI: 10.1186/s40364-022-00358-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 02/16/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Adoptive cell therapy (ACT) is a particularly promising area of cancer immunotherapy, engineered T and NK cells that express chimeric antigen receptors (CAR) are being explored for treating hematopoietic malignancies but exhibit limited clinical benefits for solid tumour patients, successful cellular immunotherapy of solid tumors demands new strategies. METHODS Inactivation of BCL11B were performed by CRISPR/Cas9 in human T cells. Immunophenotypic and transcriptional profiles of sgBCL11B T cells were characterized by cytometer and transcriptomics, respectively. sgBCL11B T cells are further engineered with chimeric antigen receptor. Anti-tumor activity of ITNK or CAR-ITNK cells were evaluated in preclinical and clinical studies. RESULTS We report that inactivation of BCL11B in human CD8+ and CD4+ T cells induced their reprogramming into induced T-to-natural killer cells (ITNKs). ITNKs contained a diverse TCR repertoire; downregulated T cell-associated genes such as TCF7 and LEF1; and expressed high levels of NK cell lineage-associated genes. ITNKs and chimeric antigen receptor (CAR)-transduced ITNKs selectively lysed a variety of cancer cells in culture and suppressed the growth of solid tumors in xenograft models. In a preliminary clinical study, autologous administration of ITNKs in patients with advanced solid tumors was well tolerated, and tumor stabilization was seen in six out nine patients, with one partial remission. CONCLUSIONS The novel ITNKs thus may be a promising novel cell source for cancer immunotherapy. TRIAL REGISTRATION ClinicalTrials.gov, NCT03882840 . Registered 20 March 2019-Retrospectively registered.
Collapse
Affiliation(s)
- Zhiwu Jiang
- China-New Zealand Joint Laboratory of Biomedine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Chinese Academy of Sciences Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Le Qin
- China-New Zealand Joint Laboratory of Biomedine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Chinese Academy of Sciences Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yuou Tang
- Department of Radiology; Guangdong Provincial Education Department Key Laboratory of Nano-Immunoregulation Tumour Microenvironment; Guangzhou Key Laboratory for Research and Development of Nano-Biomedical Technology for Diagnosis and Therapy, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Rui Liao
- China-New Zealand Joint Laboratory of Biomedine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Chinese Academy of Sciences Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jingxuan Shi
- China-New Zealand Joint Laboratory of Biomedine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Chinese Academy of Sciences Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Bingjia He
- Department of Radiology; Guangdong Provincial Education Department Key Laboratory of Nano-Immunoregulation Tumour Microenvironment; Guangzhou Key Laboratory for Research and Development of Nano-Biomedical Technology for Diagnosis and Therapy, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shanglin Li
- China-New Zealand Joint Laboratory of Biomedine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Chinese Academy of Sciences Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Diwei Zheng
- China-New Zealand Joint Laboratory of Biomedine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Chinese Academy of Sciences Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yuanbin Cui
- China-New Zealand Joint Laboratory of Biomedine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Chinese Academy of Sciences Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Qiting Wu
- China-New Zealand Joint Laboratory of Biomedine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Chinese Academy of Sciences Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Youguo Long
- China-New Zealand Joint Laboratory of Biomedine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Chinese Academy of Sciences Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yao Yao
- China-New Zealand Joint Laboratory of Biomedine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Chinese Academy of Sciences Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Zhihui Wei
- Guangdong Zhaotai InVivo Biomedicine Co. Ltd., Guangzhou, China
| | - Qilan Hong
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China.,Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Yi Wu
- China-New Zealand Joint Laboratory of Biomedine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Chinese Academy of Sciences Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Yuanbang Mai
- China-New Zealand Joint Laboratory of Biomedine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Chinese Academy of Sciences Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Shixue Gou
- China-New Zealand Joint Laboratory of Biomedine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Chinese Academy of Sciences Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xiaoping Li
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Robert Weinkove
- Cancer Immunotherapy Programme, Malaghan Institute of Medical Research, Wellington, New Zealand
| | | | - Wei Luo
- Clinical Research Institute, The First People's Hospital of Foshan, Foshan, China
| | - Weineng Feng
- Department of Head and Neck/Thoracic Medical Oncology, The First People's Hospital of Foshan, Foshan, Guangdong, China
| | - Hongsheng Zhou
- Department of Hematology, Nanfang Hospital, Guangzhou, China
| | - Qifa Liu
- Department of Hematology, Nanfang Hospital, Guangzhou, China
| | - Jiekai Chen
- China-New Zealand Joint Laboratory of Biomedine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Chinese Academy of Sciences Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Liangxue Lai
- China-New Zealand Joint Laboratory of Biomedine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Chinese Academy of Sciences Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xinwen Chen
- China-New Zealand Joint Laboratory of Biomedine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Chinese Academy of Sciences Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Duanqing Pei
- School of Life Sciences, Westlake University, Hangzhou, China
| | - Thomas Graf
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China.,Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Xingguo Liu
- China-New Zealand Joint Laboratory of Biomedine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Chinese Academy of Sciences Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Yangqiu Li
- Institute of Hematology, Medical College, Jinan University, Guangzhou, China
| | - Pentao Liu
- School of Biomedical Sciences, Stem Cell and Regenerative Medicine Consortium, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China.
| | - Zhenfeng Zhang
- Department of Radiology; Guangdong Provincial Education Department Key Laboratory of Nano-Immunoregulation Tumour Microenvironment; Guangzhou Key Laboratory for Research and Development of Nano-Biomedical Technology for Diagnosis and Therapy, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Peng Li
- China-New Zealand Joint Laboratory of Biomedine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Chinese Academy of Sciences Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China. .,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China. .,Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong, SAR, China.
| |
Collapse
|
32
|
Borisova E, Nishimura K, An Y, Takami M, Li J, Song D, Matsuo-Takasaki M, Luijkx D, Aizawa S, Kuno A, Sugihara E, Sato TA, Yumoto F, Terada T, Hisatake K, Hayashi Y. Structurally-discovered KLF4 variants accelerate and stabilize reprogramming to pluripotency. iScience 2022; 25:103525. [PMID: 35106457 PMCID: PMC8786646 DOI: 10.1016/j.isci.2021.103525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 09/14/2021] [Accepted: 11/23/2021] [Indexed: 02/07/2023] Open
Abstract
Non-genetically modified somatic cells can only be inefficiently and stochastically reprogrammed to pluripotency by exogenous expression of reprogramming factors. Low competence of natural reprogramming factors may prevent the majority of cells to successfully and synchronously reprogram. Here we screened DNA-interacting amino acid residues in the zinc-finger domain of KLF4 for enhanced reprogramming efficiency using alanine-substitution scanning methods. Identified KLF4 L507A mutant accelerated and stabilized reprogramming to pluripotency in both mouse and human somatic cells. By testing all the variants of L507 position, variants with smaller amino acid residues in the KLF4 L507 position showed higher reprogramming efficiency. L507A bound more to promoters or enhancers of pluripotency genes, such as KLF5, and drove gene expression of these genes during reprogramming. Molecular dynamics simulations predicted that L507A formed additional interactions with DNA. Our study demonstrates how modifications in amino acid residues of DNA-binding domains enable next-generation reprogramming technology with engineered reprogramming factors. KLF4 L507A variant accelerates and stabilizes reprogramming to pluripotency KLF4 L507A has distinctive features of transcriptional binding and activation KLF4 L507A may acquire a unique conformation with additional DNA interaction Smaller amino acid residues in L507 position cause higher reprogramming efficiency
Collapse
Affiliation(s)
- Evgeniia Borisova
- iPS Cell Advanced Characterization and Development Team, BioResource Research Center, RIKEN, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan.,Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Ken Nishimura
- Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Yuri An
- iPS Cell Advanced Characterization and Development Team, BioResource Research Center, RIKEN, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Miho Takami
- iPS Cell Advanced Characterization and Development Team, BioResource Research Center, RIKEN, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan.,Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Jingyue Li
- iPS Cell Advanced Characterization and Development Team, BioResource Research Center, RIKEN, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan.,Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Dan Song
- iPS Cell Advanced Characterization and Development Team, BioResource Research Center, RIKEN, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Mami Matsuo-Takasaki
- iPS Cell Advanced Characterization and Development Team, BioResource Research Center, RIKEN, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Dorian Luijkx
- iPS Cell Advanced Characterization and Development Team, BioResource Research Center, RIKEN, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Shiho Aizawa
- Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Akihiro Kuno
- Laboratory of Animal Resource Center, Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan.,Ph.D. Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Eiji Sugihara
- Research and Development Center for Precision Medicine, University of Tsukuba, 1-2 Kasuga, Tsukuba, Ibaraki 305-8550, Japan.,The Center for Joint Research Facilities Support, Research Promotion and Support Headquarters, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Taka-Aki Sato
- Research and Development Center for Precision Medicine, University of Tsukuba, 1-2 Kasuga, Tsukuba, Ibaraki 305-8550, Japan
| | - Fumiaki Yumoto
- Institute of Materials Structure Science, High Energy Accelerator Research Organization in Tsukuba, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Tohru Terada
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Koji Hisatake
- Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Yohei Hayashi
- iPS Cell Advanced Characterization and Development Team, BioResource Research Center, RIKEN, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| |
Collapse
|
33
|
Zhou R, Xiao X, He P, Zhao Y, Xu M, Zheng X, Yang R, Chen S, Zhou L, Zhang D, Yang Q, Song J, Tang C, Zhang Y, Lin JW, Cheng L, Chen L. OUP accepted manuscript. Nucleic Acids Res 2022; 50:e66. [PMID: 35288753 PMCID: PMC9226526 DOI: 10.1093/nar/gkac167] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/26/2022] [Accepted: 03/09/2022] [Indexed: 11/14/2022] Open
Abstract
Alternative polyadenylation increases transcript diversities at the 3’ end, regulating biological processes including cell differentiation, embryonic development and cancer progression. Here, we present a Bayesian method SCAPE, which enables de novo identification and quantification of polyadenylation (pA) sites at single-cell level by utilizing insert size information. We demonstrated its accuracy and robustness and identified 31 558 sites from 36 mouse organs, 43.8% (13 807) of which were novel. We illustrated that APA isoforms were associated with miRNAs binding and regulated in tissue-, cell type-and tumor-specific manners where no difference was found at gene expression level, providing an extra layer of information for cell clustering. Furthermore, we found genome-wide dynamic changes of APA usage during erythropoiesis and induced pluripotent stem cell (iPSC) differentiation, suggesting APA contributes to the functional flexibility and diversity of single cells. We expect SCAPE to aid the analyses of cellular dynamics and diversities in health and disease.
Collapse
Affiliation(s)
- Ran Zhou
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xia Xiao
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Ping He
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yuancun Zhao
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Mengying Xu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xiuran Zheng
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Ruirui Yang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Shasha Chen
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Lifang Zhou
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Dan Zhang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Qingxin Yang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Junwei Song
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Chao Tang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yiming Zhang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jing-wen Lin
- To whom correspondence should be addressed. Tel: +86 028 8546 8389;
| | - Lu Cheng
- Correspondence may also be addressed to Lu Cheng.
| | - Lu Chen
- Correspondence may also be addressed to Lu Chen.
| |
Collapse
|
34
|
Talon I, Janiszewski A, Theeuwes B, Lefevre T, Song J, Bervoets G, Vanheer L, De Geest N, Poovathingal S, Allsop R, Marine JC, Rambow F, Voet T, Pasque V. Enhanced chromatin accessibility contributes to X chromosome dosage compensation in mammals. Genome Biol 2021; 22:302. [PMID: 34724962 PMCID: PMC8558763 DOI: 10.1186/s13059-021-02518-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 10/13/2021] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Precise gene dosage of the X chromosomes is critical for normal development and cellular function. In mice, XX female somatic cells show transcriptional X chromosome upregulation of their single active X chromosome, while the other X chromosome is inactive. Moreover, the inactive X chromosome is reactivated during development in the inner cell mass and in germ cells through X chromosome reactivation, which can be studied in vitro by reprogramming of somatic cells to pluripotency. How chromatin processes and gene regulatory networks evolved to regulate X chromosome dosage in the somatic state and during X chromosome reactivation remains unclear. RESULTS Using genome-wide approaches, allele-specific ATAC-seq and single-cell RNA-seq, in female embryonic fibroblasts and during reprogramming to pluripotency, we show that chromatin accessibility on the upregulated mammalian active X chromosome is increased compared to autosomes. We further show that increased accessibility on the active X chromosome is erased by reprogramming, accompanied by erasure of transcriptional X chromosome upregulation and the loss of increased transcriptional burst frequency. In addition, we characterize gene regulatory networks during reprogramming and X chromosome reactivation, revealing changes in regulatory states. Our data show that ZFP42/REX1, a pluripotency-associated gene that evolved specifically in placental mammals, targets multiple X-linked genes, suggesting an evolutionary link between ZFP42/REX1, X chromosome reactivation, and pluripotency. CONCLUSIONS Our data reveal the existence of intrinsic compensatory mechanisms that involve modulation of chromatin accessibility to counteract X-to-Autosome gene dosage imbalances caused by evolutionary or in vitro X chromosome loss and X chromosome inactivation in mammalian cells.
Collapse
Affiliation(s)
- Irene Talon
- Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven – University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- Leuven Stem Cell Institute (SCIL), 3000 Leuven, Belgium
| | - Adrian Janiszewski
- Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven – University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- Leuven Stem Cell Institute (SCIL), 3000 Leuven, Belgium
| | - Bart Theeuwes
- Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven – University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- Leuven Stem Cell Institute (SCIL), 3000 Leuven, Belgium
| | - Thomas Lefevre
- Laboratory of Reproductive Genomics, Centre for Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Juan Song
- Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven – University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- Leuven Stem Cell Institute (SCIL), 3000 Leuven, Belgium
| | - Greet Bervoets
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, VIB, 3000 Leuven, Belgium
- Department of Oncology, Laboratory for Molecular Cancer Biology, KU Leuven, 3000 Leuven, Belgium
| | - Lotte Vanheer
- Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven – University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- Leuven Stem Cell Institute (SCIL), 3000 Leuven, Belgium
| | - Natalie De Geest
- Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven – University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- Leuven Stem Cell Institute (SCIL), 3000 Leuven, Belgium
| | - Suresh Poovathingal
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium
| | - Ryan Allsop
- Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven – University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- Leuven Stem Cell Institute (SCIL), 3000 Leuven, Belgium
| | - Jean-Christophe Marine
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, VIB, 3000 Leuven, Belgium
- Department of Oncology, Laboratory for Molecular Cancer Biology, KU Leuven, 3000 Leuven, Belgium
| | - Florian Rambow
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, VIB, 3000 Leuven, Belgium
| | - Thierry Voet
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- Laboratory of Reproductive Genomics, Centre for Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Vincent Pasque
- Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven – University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- Leuven Stem Cell Institute (SCIL), 3000 Leuven, Belgium
| |
Collapse
|
35
|
Distinct human Langerhans cell subsets orchestrate reciprocal functions and require different developmental regulation. Immunity 2021; 54:2305-2320.e11. [PMID: 34508661 DOI: 10.1016/j.immuni.2021.08.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 05/19/2021] [Accepted: 08/11/2021] [Indexed: 12/22/2022]
Abstract
Langerhans cells (LCs) play a pivotal role in skin homeostasis, and the heterogeneity of LCs has long been considered. In this study, we have identified two steady-state (LC1 and LC2) and two activated LC subsets in the epidermis of human skin and in LCs derived from CD34+ hemopoietic stem cells (HSC-LCs) by utilizing single-cell RNA sequencing and mass cytometry. Analysis of HSC-LCs at multiple time-points during differentiation revealed that EGR1 and Notch signaling were among the top pathways regulating the bifurcation of LC1 and LC2. LC1 were characterized as classical LCs, mainly related to innate immunity and antigen processing. LC2 were similar to monocytes or myeloid dendritic cells, involving in immune responses and leukocyte activation. LC1 remained stable under inflammatory microenvironment, whereas LC2 were prone to being activated and demonstrated elevated expression of immuno-suppressive molecules. We revealed distinct human LC subsets that require different developmental regulation and orchestrate reciprocal functions.
Collapse
|
36
|
Qin J, Hu Y, Yao JC, Leung RWT, Zhou Y, Qin Y, Wang J. Cell fate conversion prediction by group sparse optimization method utilizing single-cell and bulk OMICs data. Brief Bioinform 2021; 22:6347206. [PMID: 34374760 DOI: 10.1093/bib/bbab311] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/06/2021] [Accepted: 07/19/2021] [Indexed: 01/09/2023] Open
Abstract
Cell fate conversion by overexpressing defined factors is a powerful tool in regenerative medicine. However, identifying key factors for cell fate conversion requires laborious experimental efforts; thus, many of such conversions have not been achieved yet. Nevertheless, cell fate conversions found in many published studies were incomplete as the expression of important gene sets could not be manipulated thoroughly. Therefore, the identification of master transcription factors for complete and efficient conversion is crucial to render this technology more applicable clinically. In the past decade, systematic analyses on various single-cell and bulk OMICs data have uncovered numerous gene regulatory mechanisms, and made it possible to predict master gene regulators during cell fate conversion. By virtue of the sparse structure of master transcription factors and the group structure of their simultaneous regulatory effects on the cell fate conversion process, this study introduces a novel computational method predicting master transcription factors based on group sparse optimization technique integrating data from multi-OMICs levels, which can be applicable to both single-cell and bulk OMICs data with a high tolerance of data sparsity. When it is compared with current prediction methods by cross-referencing published and validated master transcription factors, it possesses superior performance. In short, this method facilitates fast identification of key regulators, give raise to the possibility of higher successful conversion rate and in the hope of reducing experimental cost.
Collapse
Affiliation(s)
- Jing Qin
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Yaohua Hu
- Shenzhen Key Laboratory of Advanced Machine Learning and Applications, College of Mathematics and Statistics, Shenzhen University, Shenzhen 518060, China
| | - Jen-Chih Yao
- Research Center for Interneural Computing, China Medical University, Taichung 40402, Taiwan
| | - Ricky Wai Tak Leung
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Yongqiang Zhou
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Yiming Qin
- Center for Genomic Sciences & School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Junwen Wang
- Department of Quantitative Health Sciences and Center for Individualized Medicine, Mayo Clinic, Scottsdale, AZ 85259, USA.,Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA
| |
Collapse
|
37
|
Long C, Li H, Li X, Yang W, Zuo Y. Nuclear Transfer Arrest Embryos Show Massive Dysregulation of Genes Involved in Transcription Pathways. Int J Mol Sci 2021; 22:ijms22158187. [PMID: 34360962 PMCID: PMC8347363 DOI: 10.3390/ijms22158187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 11/28/2022] Open
Abstract
Somatic cell nuclear transfer (SCNT) technology can reprogram terminally differentiated cell nuclei into a totipotent state. However, the underlying molecular barriers of SCNT embryo development remain incompletely elucidated. Here, we observed that transcription-related pathways were incompletely activated in nuclear transfer arrest (NTA) embryos compared to normal SCNT embryos and in vivo fertilized (WT) embryos, which hinders the development of SCNT embryos. We further revealed the transcription pathway associated gene regulatory networks (GRNs) and found the aberrant transcription pathways can lead to the massive dysregulation of genes in NTA embryos. The predicted target genes of transcription pathways contain a series of crucial factors in WT embryos, which play an important role in catabolic process, pluripotency regulation, epigenetic modification and signal transduction. In NTA embryos, however, these genes were varying degrees of inhibition and show a defect in synergy. Overall, our research found that the incomplete activation of transcription pathways is another potential molecular barrier for SCNT embryos besides the incomplete reprogramming of epigenetic modifications, broadening the understanding of molecular mechanism of SCNT embryonic development.
Collapse
|
38
|
Deng W, Jacobson EC, Collier AJ, Plath K. The transcription factor code in iPSC reprogramming. Curr Opin Genet Dev 2021; 70:89-96. [PMID: 34246082 DOI: 10.1016/j.gde.2021.06.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 06/11/2021] [Indexed: 01/10/2023]
Abstract
Transcription factor (TF)-induced reprogramming of somatic cells across lineages and to induced pluripotent stem cells (iPSCs) has revealed a remarkable plasticity of differentiated cells and presents great opportunities for generating clinically relevant cell types for disease modeling and regenerative medicine. The understanding of iPSC reprogramming provides insights into the mechanisms that safeguard somatic cell identity, drive epigenetic reprogramming, and underlie cell fate specification in vivo. The combinatorial action of TFs has emerged as the key mechanism for the direct and indirect effects of reprogramming factors that induce the remodelling of the enhancer landscape. The interplay of TFs in iPSC reprogramming also yields trophectoderm- and extraembryonic endoderm-like cell populations, uncovering an intriguing plasticity of cell states and opening new avenues for exploring cell fate decisions during early embryogenesis.
Collapse
Affiliation(s)
- Weixian Deng
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Interdepartmental Graduate Program, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Elsie C Jacobson
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Amanda J Collier
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Kathrin Plath
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Interdepartmental Graduate Program, University of California Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, Jonsson Comprehensive Cancer Center, Brain Research Institute, Graduate Program in the Biosciences, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA 90095, USA.
| |
Collapse
|
39
|
Fu M, Chen H, Cai Z, Yang Y, Feng Z, Zeng M, Chen L, Qin Y, Cai B, Zhu P, Zhou C, Yu S, Guo J, Liu J, Cao S, Pei D. Forkhead box family transcription factors as versatile regulators for cellular reprogramming to pluripotency. CELL REGENERATION (LONDON, ENGLAND) 2021; 10:17. [PMID: 34212295 PMCID: PMC8249537 DOI: 10.1186/s13619-021-00078-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/01/2021] [Indexed: 11/24/2022]
Abstract
Forkhead box (Fox) transcription factors play important roles in mammalian development and disease. However, their function in mouse somatic cell reprogramming remains unclear. Here, we report that FoxD subfamily and FoxG1 accelerate induced pluripotent stem cells (iPSCs) generation from mouse fibroblasts as early as day4 while FoxA and FoxO subfamily impede this process obviously. More importantly, FoxD3, FoxD4 and FoxG1 can replace Oct4 respectively and generate iPSCs with germline transmission together with Sox2 and Klf4. On the contrary, FoxO6 almost totally blocks reprogramming through inhibiting cell proliferation, suppressing the expression of pluripotent genes and hindering the process of mesenchymal to epithelial transition (MET). Thus, our study uncovers unexpected roles of Fox transcription factors in reprogramming and offers new insights into cell fate transition.
Collapse
Affiliation(s)
- Meijun Fu
- Joint School of Life Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academic and Sciences, Guangzhou Medical School, Guangzhou, 511436, China.,CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Science, Chinese Academic and Sciences, Guangzhou, 510530, China.,University of Chinese Academy of Science, Beijing, 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Science, Chinese Academic and Sciences, Guangzhou, 510530, China
| | - Huan Chen
- Joint School of Life Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academic and Sciences, Guangzhou Medical School, Guangzhou, 511436, China.,CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Science, Chinese Academic and Sciences, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Science, Chinese Academic and Sciences, Guangzhou, 510530, China
| | - Zepo Cai
- Joint School of Life Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academic and Sciences, Guangzhou Medical School, Guangzhou, 511436, China.,CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Science, Chinese Academic and Sciences, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Science, Chinese Academic and Sciences, Guangzhou, 510530, China
| | - Yihang Yang
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Science, Chinese Academic and Sciences, Guangzhou, 510530, China.,University of Chinese Academy of Science, Beijing, 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Science, Chinese Academic and Sciences, Guangzhou, 510530, China
| | - Ziyu Feng
- Center for Cell Lineage and Atlas, Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China
| | - Mengying Zeng
- Center for Cell Lineage and Atlas, Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China
| | - Lijun Chen
- Joint School of Life Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academic and Sciences, Guangzhou Medical School, Guangzhou, 511436, China.,CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Science, Chinese Academic and Sciences, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Science, Chinese Academic and Sciences, Guangzhou, 510530, China
| | - Yue Qin
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Science, Chinese Academic and Sciences, Guangzhou, 510530, China.,University of Chinese Academy of Science, Beijing, 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Science, Chinese Academic and Sciences, Guangzhou, 510530, China
| | - Baomei Cai
- Center for Cell Lineage and Atlas, Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China
| | - Pinghui Zhu
- Center for Cell Lineage and Atlas, Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China
| | - Chunhua Zhou
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Science, Chinese Academic and Sciences, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Science, Chinese Academic and Sciences, Guangzhou, 510530, China
| | - Shengyong Yu
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Science, Chinese Academic and Sciences, Guangzhou, 510530, China.,University of Chinese Academy of Science, Beijing, 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Science, Chinese Academic and Sciences, Guangzhou, 510530, China
| | - Jing Guo
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Science, Chinese Academic and Sciences, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Science, Chinese Academic and Sciences, Guangzhou, 510530, China
| | - Jing Liu
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Science, Chinese Academic and Sciences, Guangzhou, 510530, China. .,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Science, Chinese Academic and Sciences, Guangzhou, 510530, China. .,Center for Cell Lineage and Atlas, Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China.
| | - Shangtao Cao
- Center for Cell Lineage and Atlas, Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China.
| | - Duanqing Pei
- Joint School of Life Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academic and Sciences, Guangzhou Medical School, Guangzhou, 511436, China. .,CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Science, Chinese Academic and Sciences, Guangzhou, 510530, China. .,University of Chinese Academy of Science, Beijing, 100049, China. .,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Science, Chinese Academic and Sciences, Guangzhou, 510530, China. .,Center for Cell Lineage and Atlas, Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China.
| |
Collapse
|
40
|
Bessi BW, Botigelli RC, Pieri NCG, Machado LS, Cruz JB, de Moraes P, de Souza AF, Recchia K, Barbosa G, de Castro RVG, Nogueira MFG, Bressan FF. Cattle In Vitro Induced Pluripotent Stem Cells Generated and Maintained in 5 or 20% Oxygen and Different Supplementation. Cells 2021; 10:cells10061531. [PMID: 34204517 PMCID: PMC8234940 DOI: 10.3390/cells10061531] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/07/2021] [Accepted: 06/15/2021] [Indexed: 12/11/2022] Open
Abstract
The event of cellular reprogramming into pluripotency is influenced by several factors, such as in vitro culture conditions (e.g., culture medium and oxygen concentration). Herein, bovine iPSCs (biPSCs) were generated in different levels of oxygen tension (5% or 20% of oxygen) and supplementation (bFGF or bFGF + LIF + 2i-bFL2i) to evaluate the efficiency of pluripotency induction and maintenance in vitro. Initial reprogramming was observed in all groups and bFL2i supplementation initially resulted in a superior number of colonies. However, bFL2i supplementation in low oxygen led to a loss of self-renewal and pluripotency maintenance. All clonal lines were positive for alkaline phosphatase; they expressed endogenous pluripotency-related genes SOX2, OCT4 and STELLA. However, expression was decreased throughout the passages without the influence of oxygen tension. GLUT1 and GLUT3 were upregulated by low oxygen. The biPSCs were immunofluorescence-positive stained for OCT4 and SOX2 and they formed embryoid bodies which differentiated in ectoderm and mesoderm (all groups), as well as endoderm (one line from bFL2i in high oxygen). Our study is the first to compare high and low oxygen environments during and after induced reprogramming in cattle. In our conditions, a low oxygen environment did not favor the pluripotency maintenance of biPSCs.
Collapse
Affiliation(s)
- Brendon Willian Bessi
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo (USP), Pirassununga 13635-000, Brazil; (B.W.B.); (N.C.G.P.); (L.S.M.); (J.B.C.); (P.d.M.); (A.F.d.S.); (K.R.); (G.B.); (R.V.G.d.C.)
| | - Ramon Cesar Botigelli
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo (USP), Pirassununga 13635-000, Brazil; (B.W.B.); (N.C.G.P.); (L.S.M.); (J.B.C.); (P.d.M.); (A.F.d.S.); (K.R.); (G.B.); (R.V.G.d.C.)
- Department of Pharmacology, Institute of Biosciences (IBB), São Paulo State University (UNESP), Botucatu 18618-689, Brazil
- Correspondence: (R.C.B.); (F.F.B.)
| | - Naira Caroline Godoy Pieri
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo (USP), Pirassununga 13635-000, Brazil; (B.W.B.); (N.C.G.P.); (L.S.M.); (J.B.C.); (P.d.M.); (A.F.d.S.); (K.R.); (G.B.); (R.V.G.d.C.)
- Department of Animal Reproduction, Faculty of Veterinary Medicine and Animal Sciences, University of São Paulo (USP), São Paulo 05508-270, Brazil
| | - Lucas Simões Machado
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo (USP), Pirassununga 13635-000, Brazil; (B.W.B.); (N.C.G.P.); (L.S.M.); (J.B.C.); (P.d.M.); (A.F.d.S.); (K.R.); (G.B.); (R.V.G.d.C.)
| | - Jessica Brunhara Cruz
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo (USP), Pirassununga 13635-000, Brazil; (B.W.B.); (N.C.G.P.); (L.S.M.); (J.B.C.); (P.d.M.); (A.F.d.S.); (K.R.); (G.B.); (R.V.G.d.C.)
| | - Pamela de Moraes
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo (USP), Pirassununga 13635-000, Brazil; (B.W.B.); (N.C.G.P.); (L.S.M.); (J.B.C.); (P.d.M.); (A.F.d.S.); (K.R.); (G.B.); (R.V.G.d.C.)
| | - Aline Fernanda de Souza
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo (USP), Pirassununga 13635-000, Brazil; (B.W.B.); (N.C.G.P.); (L.S.M.); (J.B.C.); (P.d.M.); (A.F.d.S.); (K.R.); (G.B.); (R.V.G.d.C.)
| | - Kaiana Recchia
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo (USP), Pirassununga 13635-000, Brazil; (B.W.B.); (N.C.G.P.); (L.S.M.); (J.B.C.); (P.d.M.); (A.F.d.S.); (K.R.); (G.B.); (R.V.G.d.C.)
| | - Gabriela Barbosa
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo (USP), Pirassununga 13635-000, Brazil; (B.W.B.); (N.C.G.P.); (L.S.M.); (J.B.C.); (P.d.M.); (A.F.d.S.); (K.R.); (G.B.); (R.V.G.d.C.)
| | - Raquel Vasconcelos Guimarães de Castro
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo (USP), Pirassununga 13635-000, Brazil; (B.W.B.); (N.C.G.P.); (L.S.M.); (J.B.C.); (P.d.M.); (A.F.d.S.); (K.R.); (G.B.); (R.V.G.d.C.)
- Department of Pathology, Reproduction and One Health, Faculty of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Botucatu 14884-900, Brazil
| | - Marcelo Fábio Gouveia Nogueira
- Department of Biological Science, School of Sciences, Humanities and Languages, São Paulo State University (UNESP), Assis 19806-900, Brazil;
| | - Fabiana Fernandes Bressan
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo (USP), Pirassununga 13635-000, Brazil; (B.W.B.); (N.C.G.P.); (L.S.M.); (J.B.C.); (P.d.M.); (A.F.d.S.); (K.R.); (G.B.); (R.V.G.d.C.)
- Correspondence: (R.C.B.); (F.F.B.)
| |
Collapse
|
41
|
Kim HK, Ha TW, Lee MR. Single-Cell Transcriptome Analysis as a Promising Tool to Study Pluripotent Stem Cell Reprogramming. Int J Mol Sci 2021; 22:ijms22115988. [PMID: 34206025 PMCID: PMC8198005 DOI: 10.3390/ijms22115988] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/26/2021] [Accepted: 05/31/2021] [Indexed: 12/15/2022] Open
Abstract
Cells are the basic units of all organisms and are involved in all vital activities, such as proliferation, differentiation, senescence, and apoptosis. A human body consists of more than 30 trillion cells generated through repeated division and differentiation from a single-cell fertilized egg in a highly organized programmatic fashion. Since the recent formation of the Human Cell Atlas consortium, establishing the Human Cell Atlas at the single-cell level has been an ongoing activity with the goal of understanding the mechanisms underlying diseases and vital cellular activities at the level of the single cell. In particular, transcriptome analysis of embryonic stem cells at the single-cell level is of great importance, as these cells are responsible for determining cell fate. Here, we review single-cell analysis techniques that have been actively used in recent years, introduce the single-cell analysis studies currently in progress in pluripotent stem cells and reprogramming, and forecast future studies.
Collapse
|
42
|
Brown KE, Fisher AG. Reprogramming lineage identity through cell-cell fusion. Curr Opin Genet Dev 2021; 70:15-23. [PMID: 34087754 DOI: 10.1016/j.gde.2021.04.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/12/2021] [Accepted: 04/23/2021] [Indexed: 12/23/2022]
Abstract
The conversion of differentiated cells to a pluripotent state through somatic cell nuclear transfer provided the first unequivocal evidence that differentiation was reversible. In more recent times, introducing a combination of key transcription factors into terminally differentiated mammalian cells was shown to drive their conversion to induced pluripotent stem cells (iPSCs). These discoveries were transformative, but the relatively slow speed (2-3 weeks) and low efficiency of reprogramming (0.1-1%) made deciphering the underlying molecular mechanisms difficult and complex. Cell fusion provides an alternative reprogramming approach that is both efficient and tractable, particularly when combined with modern multi-omics analysis of individual cells. Here we review the history and the recent advances in cell-cell fusion that are enabling a better understanding cell fate conversion, and we discuss how this knowledge could be used to shape improved strategies for regenerative medicine.
Collapse
Affiliation(s)
- Karen E Brown
- Epigenetic Memory Group, MRC London Institute of Medical Sciences (LMS), Imperial College London, Du Cane Road, London W12 0NN, UK.
| | - Amanda G Fisher
- Epigenetic Memory Group, MRC London Institute of Medical Sciences (LMS), Imperial College London, Du Cane Road, London W12 0NN, UK
| |
Collapse
|
43
|
Modular, efficient and constant-memory single-cell RNA-seq preprocessing. Nat Biotechnol 2021; 39:813-818. [PMID: 33795888 DOI: 10.1038/s41587-021-00870-2] [Citation(s) in RCA: 171] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 02/09/2021] [Indexed: 11/08/2022]
Abstract
We describe a workflow for preprocessing of single-cell RNA-sequencing data that balances efficiency and accuracy. Our workflow is based on the kallisto and bustools programs, and is near optimal in speed with a constant memory requirement providing scalability for arbitrarily large datasets. The workflow is modular, and we demonstrate its flexibility by showing how it can be used for RNA velocity analyses.
Collapse
|
44
|
He J, Babarinde IA, Sun L, Xu S, Chen R, Shi J, Wei Y, Li Y, Ma G, Zhuang Q, Hutchins AP, Chen J. Identifying transposable element expression dynamics and heterogeneity during development at the single-cell level with a processing pipeline scTE. Nat Commun 2021; 12:1456. [PMID: 33674594 PMCID: PMC7935913 DOI: 10.1038/s41467-021-21808-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 02/04/2021] [Indexed: 12/16/2022] Open
Abstract
Transposable elements (TEs) make up a majority of a typical eukaryote’s genome, and contribute to cell heterogeneity in unclear ways. Single-cell sequencing technologies are powerful tools to explore cells, however analysis is typically gene-centric and TE expression has not been addressed. Here, we develop a single-cell TE processing pipeline, scTE, and report the expression of TEs in single cells in a range of biological contexts. Specific TE types are expressed in subpopulations of embryonic stem cells and are dynamically regulated during pluripotency reprogramming, differentiation, and embryogenesis. Unexpectedly, TEs are expressed in somatic cells, including human disease-specific TEs that are undetectable in bulk analyses. Finally, we apply scTE to single-cell ATAC-seq data, and demonstrate that scTE can discriminate cell type using chromatin accessibly of TEs alone. Overall, our results classify the dynamic patterns of TEs in single cells and their contributions to cell heterogeneity. How transposable elements (TE) contribute to cell fate changes is unclear. Here, the authors generate a pipeline to quantify TE expression from single cell data. They show the dynamic expression of TEs from gastrulation to somatic cell reprogramming and human disease
Collapse
Affiliation(s)
- Jiangping He
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Isaac A Babarinde
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Li Sun
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Shuyang Xu
- Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Ruhai Chen
- Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Junjie Shi
- Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yuanjie Wei
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Yuhao Li
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Gang Ma
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Qiang Zhuang
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Andrew P Hutchins
- Department of Biology, Southern University of Science and Technology, Shenzhen, China.
| | - Jiekai Chen
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China. .,Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China. .,Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
| |
Collapse
|
45
|
Tobias IC, Kao MMC, Parmentier T, Hunter H, LaMarre J, Betts DH. Targeted expression profiling reveals distinct stages of early canine fibroblast reprogramming are regulated by 2-oxoglutarate hydroxylases. Stem Cell Res Ther 2020; 11:528. [PMID: 33298190 PMCID: PMC7725121 DOI: 10.1186/s13287-020-02047-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 11/24/2020] [Indexed: 02/06/2023] Open
Abstract
Background Ectopic expression of a defined set of transcription factors allows the reprogramming of mammalian somatic cells to pluripotency. Despite continuous progress in primate and rodent reprogramming, limited attention has been paid to cell reprogramming in domestic and companion species. Previous studies attempting to reprogram canine cells have mostly assessed a small number of presumptive canine induced pluripotent stem cell (iPSC) lines for generic pluripotency attributes. However, why canine cell reprogramming remains extremely inefficient is poorly understood. Methods To better characterize the initial steps of pluripotency induction in canine somatic cells, we optimized an experimental system where canine fetal fibroblasts (cFFs) are transduced with the Yamanaka reprogramming factors by Sendai virus vectors. We use quantitative PCR arrays to measure the expression of 80 target genes at various stages of canine cell reprogramming. We ask how cFF reprogramming is influenced by small molecules affecting the epigenomic modification 5-hydroxymethylcytosine, specifically L-ascorbic acid and retinoic acid (AA/RA). Results We found that the expression and catalytic output of a class of 2-oxoglutarate-dependent (2-OG) hydroxylases, known as ten-eleven translocation (TET) enzymes, can be modulated in canine cells treated with AA/RA. We further show that AA/RA treatment induces TET1 expression and facilitates early canine reprogramming, evidenced by upregulation of epithelial and pluripotency markers. Using a chemical inhibitor of 2-OG hydroxylases, we demonstrate that 2-OG hydroxylase activity regulates the expression of a subset of genes involved in mesenchymal-to-epithelial transition (MET) and pluripotency in early canine reprogramming. We identify a set of transcription factors depleted in maturing reprogramming intermediates compared to pluripotent canine embryonic stem cells. Conclusions Our findings highlight 2-OG hydroxylases have evolutionarily conserved and divergent functions regulating the early reprogramming of canine somatic cells and show reprogramming conditions can be rationally optimized for the generation of maturing canine iPSC.
Collapse
Affiliation(s)
- Ian C Tobias
- Department of Physiology and Pharmacology, Schulich School of Medicine & Dentistry, Western University, Dental Sciences Building, Room DSB 2022, London, Ontario, N6A 5C1, Canada.,Present Affiliation: Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Mian-Mian C Kao
- Department of Physiology and Pharmacology, Schulich School of Medicine & Dentistry, Western University, Dental Sciences Building, Room DSB 2022, London, Ontario, N6A 5C1, Canada
| | - Thomas Parmentier
- Department of Biomedical Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Hailey Hunter
- Department of Physiology and Pharmacology, Schulich School of Medicine & Dentistry, Western University, Dental Sciences Building, Room DSB 2022, London, Ontario, N6A 5C1, Canada
| | - Jonathan LaMarre
- Department of Biomedical Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Dean H Betts
- Department of Physiology and Pharmacology, Schulich School of Medicine & Dentistry, Western University, Dental Sciences Building, Room DSB 2022, London, Ontario, N6A 5C1, Canada. .,Children's Health Research Institute, Lawson Health Research Institute, London, Ontario, Canada.
| |
Collapse
|
46
|
Shi B, Gao D, Zhong L, Zhi M, Weng X, Xu J, Li J, Du X, Xin Y, Gao J, Zhu Q, Cao S, Liu Z, Han J. IRF-1 expressed in the inner cell mass of the porcine early blastocyst enhances the pluripotency of induced pluripotent stem cells. Stem Cell Res Ther 2020; 11:505. [PMID: 33246502 PMCID: PMC7694439 DOI: 10.1186/s13287-020-01983-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 10/20/2020] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Despite years of research, porcine-induced pluripotent stem cells (piPSCs) with germline chimeric capacity have not been established. Furthermore, the key transcription factors (TFs) defining the naïve state in piPSCs also remain elusive, even though TFs in the inner cell mass (ICM) are believed to be key molecular determinants of naïve pluripotency. In this study, interferon regulatory factor 1 (IRF-1) was screened to express higher in ICM than trophectoderm (TE). But the impact of IRF-1 on maintenance of pluripotency in piPSCs was not determined. METHODS Transcriptome profiles of the early ICM were analyzed to determine highly interconnected TFs. Cells carrying these TFs' reporter were used to as donor cells for somatic cell nuclear transfer to detect expression patterns in blastocysts. Next, IRF1-Flag was overexpressed in DOX-hLIF-2i piPSCs and AP staining, qRT-PCR, and RNA-seq were conducted to examine the effect of IRF-1 on pluripotency. Then, the expression of IRF-1 in DOX-hLIF-2i piPSCs was labeled by GFP and qRT-PCR was conducted to determine the difference between GFP-positive and GFP-negative cells. Next, ChIP-Seq was conducted to identify genes target by IRF-1. Treatment with IL7 in wild-type piPSCs and STAT3 phosphorylation inhibitor in IRF-1 overexpressing piPSCs was conducted to confirm the roles of JAK-STAT3 signaling pathway in IRF-1's regulation of pluripotency. Moreover, during reprogramming, IRF-1 was overexpressed and knocked down to determine the change of reprogramming efficiency. RESULTS IRF-1 was screened to be expressed higher in porcine ICM than TE of d6~7 SCNT blastocysts. First, overexpression of IRF-1 in the piPSCs was observed to promote the morphology, AP staining, and expression profiles of pluripotency genes as would be expected when cells approach the naïve state. Genes, KEGG pathways, and GO terms related to the process of differentiation were also downregulated. Next, in the wild-type piPSCs, high-level fluorescence activated by the IRF-1 promoter was associated with higher expression of naïve related genes in piPSCs. Analysis by ChIP-Seq indicated that genes related to the JAK-STAT pathway, and expression of IL7 and STAT3 were activated by IRF-1. The inhibitor of STAT3 phosphorylation was observed could revert the expression of primed genes in IRF-1 overexpressing cells, but the addition of IL7 in culture medium had no apparent change in the cell morphology, AP staining results, or expression of pluripotency related genes. In addition, knockdown of IRF-1 during reprogramming appeared to reduce reprogramming efficiency, whereas overexpression exerted the converse effect. CONCLUSION The IRF-1 expressed in the ICM of pigs' early blastocyst enhances the pluripotency of piPSCs, in part through promoting the JAK-STAT pathway.
Collapse
Affiliation(s)
- Bingbo Shi
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Dengfeng Gao
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Liang Zhong
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- Hebei Provincial Key Laboratory of Basic Medicine for Diabetes, The Shijiazhuang Second Hospital, Shijiazhuang, 050051, Hebei, China
| | - Minglei Zhi
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xiaogang Weng
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Junjun Xu
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Junhong Li
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xuguang Du
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yanli Xin
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jie Gao
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Qianqian Zhu
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Suying Cao
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China
| | - Zhonghua Liu
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Jianyong Han
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
47
|
Bisogno LS, Yang J, Bennett BD, Ward JM, Mackey LC, Annab LA, Bushel PR, Singhal S, Schurman SH, Byun JS, Nápoles AM, Pérez-Stable EJ, Fargo DC, Gardner K, Archer TK. Ancestry-dependent gene expression correlates with reprogramming to pluripotency and multiple dynamic biological processes. SCIENCE ADVANCES 2020; 6:6/47/eabc3851. [PMID: 33219026 PMCID: PMC7679169 DOI: 10.1126/sciadv.abc3851] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 10/02/2020] [Indexed: 05/10/2023]
Abstract
Induced pluripotent stem cells (iPSCs) can be derived from differentiated cells, enabling the generation of personalized disease models by differentiating patient-derived iPSCs into disease-relevant cell lines. While genetic variability between different iPSC lines affects differentiation potential, how this variability in somatic cells affects pluripotent potential is less understood. We generated and compared transcriptomic data from 72 dermal fibroblast-iPSC pairs with consistent variation in reprogramming efficiency. By considering equal numbers of samples from self-reported African Americans and White Americans, we identified both ancestry-dependent and ancestry-independent transcripts associated with reprogramming efficiency, suggesting that transcriptomic heterogeneity can substantially affect reprogramming. Moreover, reprogramming efficiency-associated genes are involved in diverse dynamic biological processes, including cancer and wound healing, and are predictive of 5-year breast cancer survival in an independent cohort. Candidate genes may provide insight into mechanisms of ancestry-dependent regulation of cell fate transitions and motivate additional studies for improvement of reprogramming.
Collapse
Affiliation(s)
- Laura S Bisogno
- Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Jun Yang
- Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Brian D Bennett
- Integrative Bioinformatics, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - James M Ward
- Integrative Bioinformatics, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Lantz C Mackey
- Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Lois A Annab
- Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Pierre R Bushel
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Sandeep Singhal
- Department of Pathology, Department of Computer Science, University of North Dakota, Grand Forks, ND, USA
| | - Shepherd H Schurman
- Clinical Research Unit, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Jung S Byun
- Division of Intramural Research, Office of the Scientific Director, National Institute on Minority Health and Health Disparities, Bethesda, MD, USA
| | - Anna María Nápoles
- Division of Intramural Research, Office of the Scientific Director, National Institute on Minority Health and Health Disparities, Bethesda, MD, USA
| | - Eliseo J Pérez-Stable
- Division of Intramural Research, Office of the Scientific Director, National Institute on Minority Health and Health Disparities, Bethesda, MD, USA
- Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD, USA
| | - David C Fargo
- Office of Scientific Computing, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Kevin Gardner
- Division of Intramural Research, Office of the Scientific Director, National Institute on Minority Health and Health Disparities, Bethesda, MD, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, Columbia University, New York, NY, USA
| | - Trevor K Archer
- Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA.
| |
Collapse
|
48
|
Huang Y, Zhang H, Wang L, Tang C, Qin X, Wu X, Pan M, Tang Y, Yang Z, Babarinde IA, Lin R, Ji G, Lai Y, Xu X, Su J, Wen X, Satoh T, Ahmed T, Malik V, Ward C, Volpe G, Guo L, Chen J, Sun L, Li Y, Huang X, Bao X, Gao F, Liu B, Zheng H, Jauch R, Lai L, Pan G, Chen J, Testa G, Akira S, Hu J, Pei D, Hutchins AP, Esteban MA, Qin B. JMJD3 acts in tandem with KLF4 to facilitate reprogramming to pluripotency. Nat Commun 2020; 11:5061. [PMID: 33033262 PMCID: PMC7545202 DOI: 10.1038/s41467-020-18900-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 09/16/2020] [Indexed: 12/13/2022] Open
Abstract
The interplay between the Yamanaka factors (OCT4, SOX2, KLF4 and c-MYC) and transcriptional/epigenetic co-regulators in somatic cell reprogramming is incompletely understood. Here, we demonstrate that the histone H3 lysine 27 trimethylation (H3K27me3) demethylase JMJD3 plays conflicting roles in mouse reprogramming. On one side, JMJD3 induces the pro-senescence factor Ink4a and degrades the pluripotency regulator PHF20 in a reprogramming factor-independent manner. On the other side, JMJD3 is specifically recruited by KLF4 to reduce H3K27me3 at both enhancers and promoters of epithelial and pluripotency genes. JMJD3 also promotes enhancer-promoter looping through the cohesin loading factor NIPBL and ultimately transcriptional elongation. This competition of forces can be shifted towards improved reprogramming by using early passage fibroblasts or boosting JMJD3’s catalytic activity with vitamin C. Our work, thus, establishes a multifaceted role for JMJD3, placing it as a key partner of KLF4 and a scaffold that assists chromatin interactions and activates gene transcription. Previous work suggested that histone demethylase JMJD3 is detrimental to somatic cell reprogramming. Here, the authors show that while JMJD3 has a context-independent detrimental effect on early stages of reprogramming, during late stages it activates epithelial and pluripotency genes together with Klf4.
Collapse
Affiliation(s)
- Yinghua Huang
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Laboratory of Metabolism and Cell Fate, GIBH, CAS, 510530, Guangzhou, China
| | - Hui Zhang
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), 510005, Guangzhou, China
| | - Lulu Wang
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Laboratory of Metabolism and Cell Fate, GIBH, CAS, 510530, Guangzhou, China
| | - Chuanqing Tang
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Laboratory of Metabolism and Cell Fate, GIBH, CAS, 510530, Guangzhou, China
| | - Xiaogan Qin
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Laboratory of Metabolism and Cell Fate, GIBH, CAS, 510530, Guangzhou, China
| | - Xinyu Wu
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Laboratory of Metabolism and Cell Fate, GIBH, CAS, 510530, Guangzhou, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Meifang Pan
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Laboratory of Metabolism and Cell Fate, GIBH, CAS, 510530, Guangzhou, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yujia Tang
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Laboratory of Metabolism and Cell Fate, GIBH, CAS, 510530, Guangzhou, China
| | - Zhongzhou Yang
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China
| | - Isaac A Babarinde
- Department of Biology, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Runxia Lin
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Laboratory of Metabolism and Cell Fate, GIBH, CAS, 510530, Guangzhou, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Guanyu Ji
- Science and Technology Department, E-GENE, 518118, Shenzhen, China
| | - Yiwei Lai
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Laboratory of Integrative Biology, GIBH, CAS, 510530, Guangzhou, China
| | - Xueting Xu
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Laboratory of Metabolism and Cell Fate, GIBH, CAS, 510530, Guangzhou, China.,School of Life Sciences, University of Science and Technology of China, 230027, Hefei, China
| | - Jianbin Su
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Laboratory of Metabolism and Cell Fate, GIBH, CAS, 510530, Guangzhou, China
| | - Xue Wen
- Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, 130061, Changchun, China
| | - Takashi Satoh
- Department of Host Defense, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871, Japan
| | - Tanveer Ahmed
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Laboratory of Metabolism and Cell Fate, GIBH, CAS, 510530, Guangzhou, China
| | - Vikas Malik
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Laboratory of Integrative Biology, GIBH, CAS, 510530, Guangzhou, China
| | - Carl Ward
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Laboratory of Integrative Biology, GIBH, CAS, 510530, Guangzhou, China
| | - Giacomo Volpe
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Laboratory of Integrative Biology, GIBH, CAS, 510530, Guangzhou, China
| | - Lin Guo
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China
| | - Jinlong Chen
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China
| | - Li Sun
- Department of Biology, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Yingying Li
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), 510005, Guangzhou, China
| | - Xiaofen Huang
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China
| | - Xichen Bao
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), 510005, Guangzhou, China.,Joint School of Life Sciences, GIBH and Guangzhou Medical University, 511436, Guangzhou, China
| | - Fei Gao
- Science and Technology Department, E-GENE, 518118, Shenzhen, China.,Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Baohua Liu
- Health Science Center, Shenzhen University, 518060, Shenzhen, China
| | - Hui Zheng
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), 510005, Guangzhou, China.,Joint School of Life Sciences, GIBH and Guangzhou Medical University, 511436, Guangzhou, China
| | - Ralf Jauch
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Liangxue Lai
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), 510005, Guangzhou, China.,Joint School of Life Sciences, GIBH and Guangzhou Medical University, 511436, Guangzhou, China
| | - Guangjin Pan
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), 510005, Guangzhou, China.,Joint School of Life Sciences, GIBH and Guangzhou Medical University, 511436, Guangzhou, China
| | - Jiekai Chen
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), 510005, Guangzhou, China.,Joint School of Life Sciences, GIBH and Guangzhou Medical University, 511436, Guangzhou, China
| | - Giuseppe Testa
- Department of Experimental Oncology, European Institute of Oncology, Milan, 20139, Italy
| | - Shizuo Akira
- Department of Host Defense, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871, Japan
| | - Jifan Hu
- Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, 130061, Changchun, China
| | - Duanqing Pei
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), 510005, Guangzhou, China
| | - Andrew P Hutchins
- Department of Biology, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Miguel A Esteban
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China. .,Laboratory of Integrative Biology, GIBH, CAS, 510530, Guangzhou, China. .,Joint School of Life Sciences, GIBH and Guangzhou Medical University, 511436, Guangzhou, China. .,Institute for Stem Cells and Regeneration, CAS, 100101, Beijing, China.
| | - Baoming Qin
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China. .,Laboratory of Metabolism and Cell Fate, GIBH, CAS, 510530, Guangzhou, China. .,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), 510005, Guangzhou, China. .,Joint School of Life Sciences, GIBH and Guangzhou Medical University, 511436, Guangzhou, China.
| |
Collapse
|
49
|
Liu J, Gao M, Xu S, Chen Y, Wu K, Liu H, Wang J, Yang X, Wang J, Liu W, Bao X, Chen J. YTHDF2/3 Are Required for Somatic Reprogramming through Different RNA Deadenylation Pathways. Cell Rep 2020; 32:108120. [DOI: 10.1016/j.celrep.2020.108120] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 07/12/2020] [Accepted: 08/17/2020] [Indexed: 12/18/2022] Open
|
50
|
Minchington TG, Griffiths-Jones S, Papalopulu N. Dynamical gene regulatory networks are tuned by transcriptional autoregulation with microRNA feedback. Sci Rep 2020; 10:12960. [PMID: 32737375 PMCID: PMC7395740 DOI: 10.1038/s41598-020-69791-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 07/06/2020] [Indexed: 01/06/2023] Open
Abstract
Concepts from dynamical systems theory, including multi-stability, oscillations, robustness and stochasticity, are critical for understanding gene regulation during cell fate decisions, inflammation and stem cell heterogeneity. However, the prevalence of the structures within gene networks that drive these dynamical behaviours, such as autoregulation or feedback by microRNAs, is unknown. We integrate transcription factor binding site (TFBS) and microRNA target data to generate a gene interaction network across 28 human tissues. This network was analysed for motifs capable of driving dynamical gene expression, including oscillations. Identified autoregulatory motifs involve 56% of transcription factors (TFs) studied. TFs that autoregulate have more interactions with microRNAs than non-autoregulatory genes and 89% of autoregulatory TFs were found in dual feedback motifs with a microRNA. Both autoregulatory and dual feedback motifs were enriched in the network. TFs that autoregulate were highly conserved between tissues. Dual feedback motifs with microRNAs were also conserved between tissues, but less so, and TFs regulate different combinations of microRNAs in a tissue-dependent manner. The study of these motifs highlights ever more genes that have complex regulatory dynamics. These data provide a resource for the identification of TFs which regulate the dynamical properties of human gene expression.
Collapse
Affiliation(s)
- Thomas G Minchington
- School of Medical Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Sam Griffiths-Jones
- School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
| | - Nancy Papalopulu
- School of Medical Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
| |
Collapse
|