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Choi J, Kang S, An HI, Kim CE, Lee S, Pack CG, Yoon YI, Jin H, Cho YP, Kim CJ, Namgoong JM, Kim JK, Tak E. Fasudil and viscosity of gelatin promote hepatic differentiation by regulating organelles in human umbilical cord matrix-mesenchymal stem cells. Stem Cell Res Ther 2024; 15:229. [PMID: 39075621 PMCID: PMC11288082 DOI: 10.1186/s13287-024-03851-9] [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: 04/29/2024] [Accepted: 07/14/2024] [Indexed: 07/31/2024] Open
Abstract
BACKGROUND Human mesenchymal stem cells originating from umbilical cord matrix are a promising therapeutic resource, and their differentiated cells are spotlighted as a tissue regeneration treatment. However, there are limitations to the medical use of differentiated cells from human umbilical cord matrix-mesenchymal stem cells (hUCM-MSCs), such as efficient differentiation methods. METHODS To effectively differentiate hUCM-MSCs into hepatocyte-like cells (HLCs), we used the ROCK inhibitor, fasudil, which is known to induce endoderm formation, and gelatin, which provides extracellular matrix to the differentiated cells. To estimate a differentiation efficiency of early stage according to combination of gelatin and fasudil, transcription analysis was conducted. Moreover, to demonstrate that organelle states affect differentiation, we performed transcription, tomographic, and mitochondrial function analysis at each stage of hepatic differentiation. Finally, we evaluated hepatocyte function based on the expression of mRNA and protein, secretion of albumin, and activity of CYP3A4 in mature HLCs. RESULTS Fasudil induced endoderm-related genes (GATA4, SOX17, and FOXA2) in hUCM-MSCs, and it also induced lipid droplets (LDs) inside the differentiated cells. However, the excessive induction of LDs caused by fasudil inhibited mitochondrial function and prevented differentiation into hepatoblasts. To prevent the excessive LDs formation, we used gelatin as a coating material. When hUCM-MSCs were induced into hepatoblasts with fasudil on high-viscosity (1%) gelatin-coated dishes, hepatoblast-related genes (AFP and HNF4A) showed significant upregulation on high-viscosity gelatin-coated dishes compared to those treated with low-viscosity (0.1%) gelatin. Moreover, other germline cell fates, such as ectoderm and mesoderm, were repressed under these conditions. In addition, LDs abundance was also reduced, whereas mitochondrial function was increased. On the other hand, unlike early stage of the differentiation, low viscosity gelatin was more effective in generating mature HLCs. In this condition, the accumulation of LDs was inhibited in the cells, and mitochondria were activated. Consequently, HLCs originated from hUCM-MSCs were genetically and functionally more matured in low-viscosity gelatin. CONCLUSIONS This study demonstrated an effective method for differentiating hUCM-MSCs into hepatic cells using fasudil and gelatin of varying viscosities. Moreover, we suggest that efficient hepatic differentiation and the function of hepatic cells differentiated from hUCM-MSCs depend not only on genetic changes but also on the regulation of organelle states.
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Affiliation(s)
- Jiwan Choi
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
- Asan Medical Institute of Convergence Science and Technology (AMIST), Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Seoon Kang
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
- Asan Medical Institute of Convergence Science and Technology (AMIST), Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Hye-In An
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
- Asan Medical Institute of Convergence Science and Technology (AMIST), Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Chae-Eun Kim
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
- Asan Medical Institute of Convergence Science and Technology (AMIST), Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Sanghwa Lee
- Biomedical Engineering Research Center, Asan Medical Center, Seoul, Republic of Korea
| | - Chan-Gi Pack
- Department of Biomedical Engineering, College of Medicine, University of Ulsan, Seoul, Republic of Korea
| | - Young-In Yoon
- Division of Hepatobiliary Surgery and Liver Transplantation, Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Hana Jin
- Division of Vascular Surgery, Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Yong-Pil Cho
- Division of Vascular Surgery, Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Chong Jai Kim
- Department of Pathology, Asan Medical Center, Asan-Minnesota Institute for Innovating Transplantation (AMIT), University of Ulsan College of Medicine, Seoul, Korea
| | - Jung-Man Namgoong
- Department of Pediatric Surgery, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Republic of Korea.
| | - Jun Ki Kim
- Biomedical Engineering Research Center, Asan Medical Center, Seoul, Republic of Korea.
- Department of Biomedical Engineering, College of Medicine, University of Ulsan, Seoul, Republic of Korea.
| | - Eunyoung Tak
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
- Asan Medical Institute of Convergence Science and Technology (AMIST), Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
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Mehlferber MM, Kuyumcu-Martinez M, Miller CL, Sheynkman GM. Transcription factors and splice factors - interconnected regulators of stem cell differentiation. CURRENT STEM CELL REPORTS 2023; 9:31-41. [PMID: 38939410 PMCID: PMC11210451 DOI: 10.1007/s40778-023-00227-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/12/2023] [Indexed: 06/29/2024]
Abstract
Purpose of review The underlying molecular mechanisms that direct stem cell differentiation into fully functional, mature cells remain an area of ongoing investigation. Cell state is the product of the combinatorial effect of individual factors operating within a coordinated regulatory network. Here, we discuss the contribution of both gene regulatory and splicing regulatory networks in defining stem cell fate during differentiation and the critical role of protein isoforms in this process. Recent findings We review recent experimental and computational approaches that characterize gene regulatory networks, splice regulatory networks, and the resulting transcriptome and proteome they mediate during differentiation. Such approaches include long-read RNA sequencing, which has demonstrated high-resolution profiling of mRNA isoforms, and Cas13-based CRISPR, which could make possible high-throughput isoform screening. Collectively, these developments enable systems-level profiling of factors contributing to cell state. Summary Overall, gene and splice regulatory networks are important in defining cell state. The emerging high-throughput systems-level approaches will characterize the gene regulatory network components necessary in driving stem cell differentiation.
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Affiliation(s)
- Madison M Mehlferber
- Department of Biochemistry and Molecular Genetics, University Virginia, Charlottesville, VA 22903
| | - Muge Kuyumcu-Martinez
- Department of Molecular Physiology and Biological Physics, University of Virginia, School of Medicine, Fontaine Medical Office Building 1, 415 Ray C. Hunt Dr, Charlottesville, VA 22903
| | - Clint L Miller
- Department of Public Health Sciences, Department of Biochemistry and Molecular Genetics, and Department of Biomedical Engineering, University of Virginia, Multistory Building, West Complex, 1335 Lee St, Charlottesville, VA 22908, PO Box 800717, Charlottesville, Virginia 22908
| | - Gloria M Sheynkman
- Department of Molecular Physiology and Biological Physics, Center for Public Health Genomics, UVA Comprehensive Cancer Center, Department of Biochemistry and Molecular Genetics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22903
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3
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Lummertz da Rocha E, Kubaczka C, Sugden WW, Najia MA, Jing R, Markel A, LeBlanc ZC, Dos Santos Peixoto R, Falchetti M, Collins JJ, North TE, Daley GQ. CellComm infers cellular crosstalk that drives haematopoietic stem and progenitor cell development. Nat Cell Biol 2022; 24:579-589. [PMID: 35414020 PMCID: PMC10123873 DOI: 10.1038/s41556-022-00884-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/01/2022] [Indexed: 01/05/2023]
Abstract
Intercellular communication orchestrates a multitude of physiologic and pathologic conditions. Algorithms to infer cell-cell communication and predict downstream signalling and regulatory networks are needed to illuminate mechanisms of stem cell differentiation and tissue development. Here, to fill this gap, we developed and applied CellComm to investigate how the aorta-gonad-mesonephros microenvironment dictates haematopoietic stem and progenitor cell emergence. We identified key microenvironmental signals and transcriptional networks that regulate haematopoietic development, including Stat3, Nr0b2, Ybx1 and App, and confirmed their roles using zebrafish, mouse and human models. Notably, CellComm revealed extensive crosstalk among signalling pathways and convergence on common transcriptional regulators, indicating a resilient developmental programme that ensures dynamic adaptation to changes in the embryonic environment. Our work provides an algorithm and data resource for the scientific community.
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Affiliation(s)
- Edroaldo Lummertz da Rocha
- Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Caroline Kubaczka
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Wade W Sugden
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA, USA
| | - Mohamad Ali Najia
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard-MIT Health Sciences & Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ran Jing
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Arianna Markel
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Zachary C LeBlanc
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA, USA
| | - Rafael Dos Santos Peixoto
- Undergraduate program in Automation and Control Engineering, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Marcelo Falchetti
- Graduate Program of Pharmacology, Center for Biological Sciences, Federal University of Santa Catarina, Florianópolis, Brazil
| | - James J Collins
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard-MIT Health Sciences & Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Trista E North
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA.
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA, USA.
| | - George Q Daley
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA.
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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4
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Korn D, Thieme AJ, Alves VM, Yeakey M, V V B Borba J, Capuzzi SJ, Fecho K, Bizon C, Edwards SW, Chirkova R, Colvis CM, Southall NT, Austin CP, Muratov EN, Tropsha A. Defining clinical outcome pathways. Drug Discov Today 2022; 27:1671-1678. [PMID: 35182735 DOI: 10.1016/j.drudis.2022.02.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 01/07/2022] [Accepted: 02/14/2022] [Indexed: 12/23/2022]
Abstract
Here, we propose a broad concept of 'Clinical Outcome Pathways' (COPs), which are defined as a series of key molecular and cellular events that underlie therapeutic effects of drug molecules. We formalize COPs as a chain of the following events: molecular initiating event (MIE) → intermediate event(s) → clinical outcome. We illustrate the concept with COP examples both for primary and alternative (i.e., drug repurposing) therapeutic applications. We also describe the elucidation of COPs for several drugs of interest using the publicly accessible Reasoning Over Biomedical Objects linked in Knowledge-Oriented Pathways (ROBOKOP) biomedical knowledge graph-mining tool. We propose that broader use of COP uncovered with the help of biomedical knowledge graph mining will likely accelerate drug discovery and repurposing efforts.
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Affiliation(s)
- Daniel Korn
- Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA; UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Andrew J Thieme
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Vinicius M Alves
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Michael Yeakey
- Massachusetts College of Pharmacy and Health Sciences, Boston, MA, USA
| | - Joyce V V B Borba
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Stephen J Capuzzi
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Karamarie Fecho
- Renaissance Computing Institute, University of North Carolina, Chapel Hill, NC, USA
| | - Chris Bizon
- Renaissance Computing Institute, University of North Carolina, Chapel Hill, NC, USA
| | | | - Rada Chirkova
- Department of Computer Science, North Carolina State University, Raleigh, NC, USA
| | - Christine M Colvis
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Noel T Southall
- Department of Computer Science, North Carolina State University, Raleigh, NC, USA
| | - Christopher P Austin
- Department of Computer Science, North Carolina State University, Raleigh, NC, USA
| | - Eugene N Muratov
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA.
| | - Alexander Tropsha
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA.
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5
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Lucas LM, Dwivedi V, Senfeld JI, Cullum RL, Mill CP, Piazza JT, Bryant IN, Cook LJ, Miller ST, Lott JH, Kelley CM, Knerr EL, Markham JA, Kaufmann DP, Jacobi MA, Shen J, Riese DJ. The Yin and Yang of ERBB4: Tumor Suppressor and Oncoprotein. Pharmacol Rev 2022; 74:18-47. [PMID: 34987087 PMCID: PMC11060329 DOI: 10.1124/pharmrev.121.000381] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/15/2021] [Indexed: 12/11/2022] Open
Abstract
ERBB4 (HER4) is a member of the ERBB family of receptor tyrosine kinases, a family that includes the epidermal growth factor receptor (EGFR/ERBB1/HER1), ERBB2 (Neu/HER2), and ERBB3 (HER3). EGFR and ERBB2 are oncoproteins and validated targets for therapeutic intervention in a variety of solid tumors. In contrast, the role that ERBB4 plays in human malignancies is ambiguous. Thus, here we review the literature regarding ERBB4 function in human malignancies. We review the mechanisms of ERBB4 signaling with an emphasis on mechanisms of signaling specificity. In the context of this signaling specificity, we discuss the hypothesis that ERBB4 appears to function as a tumor suppressor protein and as an oncoprotein. Next, we review the literature that describes the role of ERBB4 in tumors of the bladder, liver, prostate, brain, colon, stomach, lung, bone, ovary, thyroid, hematopoietic tissues, pancreas, breast, skin, head, and neck. Whenever possible, we discuss the possibility that ERBB4 mutants function as biomarkers in these tumors. Finally, we discuss the potential roles of ERBB4 mutants in the staging of human tumors and how ERBB4 function may dictate the treatment of human tumors. SIGNIFICANCE STATEMENT: This articles reviews ERBB4 function in the context of the mechanistic model that ERBB4 homodimers function as tumor suppressors, whereas ERBB4-EGFR or ERBB4-ERBB2 heterodimers act as oncogenes. Thus, this review serves as a mechanistic framework for clinicians and scientists to consider the role of ERBB4 and ERBB4 mutants in staging and treating human tumors.
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Affiliation(s)
- Lauren M Lucas
- Department of Drug Discovery and Development, Harrison School of Pharmacy (L.M.L., V.D., J.I.S., R.L.C., C.P.M., J.T.P., L.J.C., S.T.M., J.H.L., C.M.K., E.L.K., J.A.M., D.P.K., M.A.J., J.S., D.J.R.), and Department of Chemical Engineering, Samuel Ginn College of Engineering (R.L.C.), Auburn University, Auburn, Alabama; The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.P.M.); Office of the Executive Vice President for Research and Partnerships, Purdue University, West Lafayette, Indiana (I.N.B.); and Cancer Biology and Immunology Program, O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham, Birmingham, Alabama (D.J.R.)
| | - Vipasha Dwivedi
- Department of Drug Discovery and Development, Harrison School of Pharmacy (L.M.L., V.D., J.I.S., R.L.C., C.P.M., J.T.P., L.J.C., S.T.M., J.H.L., C.M.K., E.L.K., J.A.M., D.P.K., M.A.J., J.S., D.J.R.), and Department of Chemical Engineering, Samuel Ginn College of Engineering (R.L.C.), Auburn University, Auburn, Alabama; The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.P.M.); Office of the Executive Vice President for Research and Partnerships, Purdue University, West Lafayette, Indiana (I.N.B.); and Cancer Biology and Immunology Program, O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham, Birmingham, Alabama (D.J.R.)
| | - Jared I Senfeld
- Department of Drug Discovery and Development, Harrison School of Pharmacy (L.M.L., V.D., J.I.S., R.L.C., C.P.M., J.T.P., L.J.C., S.T.M., J.H.L., C.M.K., E.L.K., J.A.M., D.P.K., M.A.J., J.S., D.J.R.), and Department of Chemical Engineering, Samuel Ginn College of Engineering (R.L.C.), Auburn University, Auburn, Alabama; The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.P.M.); Office of the Executive Vice President for Research and Partnerships, Purdue University, West Lafayette, Indiana (I.N.B.); and Cancer Biology and Immunology Program, O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham, Birmingham, Alabama (D.J.R.)
| | - Richard L Cullum
- Department of Drug Discovery and Development, Harrison School of Pharmacy (L.M.L., V.D., J.I.S., R.L.C., C.P.M., J.T.P., L.J.C., S.T.M., J.H.L., C.M.K., E.L.K., J.A.M., D.P.K., M.A.J., J.S., D.J.R.), and Department of Chemical Engineering, Samuel Ginn College of Engineering (R.L.C.), Auburn University, Auburn, Alabama; The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.P.M.); Office of the Executive Vice President for Research and Partnerships, Purdue University, West Lafayette, Indiana (I.N.B.); and Cancer Biology and Immunology Program, O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham, Birmingham, Alabama (D.J.R.)
| | - Christopher P Mill
- Department of Drug Discovery and Development, Harrison School of Pharmacy (L.M.L., V.D., J.I.S., R.L.C., C.P.M., J.T.P., L.J.C., S.T.M., J.H.L., C.M.K., E.L.K., J.A.M., D.P.K., M.A.J., J.S., D.J.R.), and Department of Chemical Engineering, Samuel Ginn College of Engineering (R.L.C.), Auburn University, Auburn, Alabama; The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.P.M.); Office of the Executive Vice President for Research and Partnerships, Purdue University, West Lafayette, Indiana (I.N.B.); and Cancer Biology and Immunology Program, O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham, Birmingham, Alabama (D.J.R.)
| | - J Tyler Piazza
- Department of Drug Discovery and Development, Harrison School of Pharmacy (L.M.L., V.D., J.I.S., R.L.C., C.P.M., J.T.P., L.J.C., S.T.M., J.H.L., C.M.K., E.L.K., J.A.M., D.P.K., M.A.J., J.S., D.J.R.), and Department of Chemical Engineering, Samuel Ginn College of Engineering (R.L.C.), Auburn University, Auburn, Alabama; The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.P.M.); Office of the Executive Vice President for Research and Partnerships, Purdue University, West Lafayette, Indiana (I.N.B.); and Cancer Biology and Immunology Program, O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham, Birmingham, Alabama (D.J.R.)
| | - Ianthe N Bryant
- Department of Drug Discovery and Development, Harrison School of Pharmacy (L.M.L., V.D., J.I.S., R.L.C., C.P.M., J.T.P., L.J.C., S.T.M., J.H.L., C.M.K., E.L.K., J.A.M., D.P.K., M.A.J., J.S., D.J.R.), and Department of Chemical Engineering, Samuel Ginn College of Engineering (R.L.C.), Auburn University, Auburn, Alabama; The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.P.M.); Office of the Executive Vice President for Research and Partnerships, Purdue University, West Lafayette, Indiana (I.N.B.); and Cancer Biology and Immunology Program, O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham, Birmingham, Alabama (D.J.R.)
| | - Laura J Cook
- Department of Drug Discovery and Development, Harrison School of Pharmacy (L.M.L., V.D., J.I.S., R.L.C., C.P.M., J.T.P., L.J.C., S.T.M., J.H.L., C.M.K., E.L.K., J.A.M., D.P.K., M.A.J., J.S., D.J.R.), and Department of Chemical Engineering, Samuel Ginn College of Engineering (R.L.C.), Auburn University, Auburn, Alabama; The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.P.M.); Office of the Executive Vice President for Research and Partnerships, Purdue University, West Lafayette, Indiana (I.N.B.); and Cancer Biology and Immunology Program, O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham, Birmingham, Alabama (D.J.R.)
| | - S Tyler Miller
- Department of Drug Discovery and Development, Harrison School of Pharmacy (L.M.L., V.D., J.I.S., R.L.C., C.P.M., J.T.P., L.J.C., S.T.M., J.H.L., C.M.K., E.L.K., J.A.M., D.P.K., M.A.J., J.S., D.J.R.), and Department of Chemical Engineering, Samuel Ginn College of Engineering (R.L.C.), Auburn University, Auburn, Alabama; The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.P.M.); Office of the Executive Vice President for Research and Partnerships, Purdue University, West Lafayette, Indiana (I.N.B.); and Cancer Biology and Immunology Program, O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham, Birmingham, Alabama (D.J.R.)
| | - James H Lott
- Department of Drug Discovery and Development, Harrison School of Pharmacy (L.M.L., V.D., J.I.S., R.L.C., C.P.M., J.T.P., L.J.C., S.T.M., J.H.L., C.M.K., E.L.K., J.A.M., D.P.K., M.A.J., J.S., D.J.R.), and Department of Chemical Engineering, Samuel Ginn College of Engineering (R.L.C.), Auburn University, Auburn, Alabama; The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.P.M.); Office of the Executive Vice President for Research and Partnerships, Purdue University, West Lafayette, Indiana (I.N.B.); and Cancer Biology and Immunology Program, O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham, Birmingham, Alabama (D.J.R.)
| | - Connor M Kelley
- Department of Drug Discovery and Development, Harrison School of Pharmacy (L.M.L., V.D., J.I.S., R.L.C., C.P.M., J.T.P., L.J.C., S.T.M., J.H.L., C.M.K., E.L.K., J.A.M., D.P.K., M.A.J., J.S., D.J.R.), and Department of Chemical Engineering, Samuel Ginn College of Engineering (R.L.C.), Auburn University, Auburn, Alabama; The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.P.M.); Office of the Executive Vice President for Research and Partnerships, Purdue University, West Lafayette, Indiana (I.N.B.); and Cancer Biology and Immunology Program, O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham, Birmingham, Alabama (D.J.R.)
| | - Elizabeth L Knerr
- Department of Drug Discovery and Development, Harrison School of Pharmacy (L.M.L., V.D., J.I.S., R.L.C., C.P.M., J.T.P., L.J.C., S.T.M., J.H.L., C.M.K., E.L.K., J.A.M., D.P.K., M.A.J., J.S., D.J.R.), and Department of Chemical Engineering, Samuel Ginn College of Engineering (R.L.C.), Auburn University, Auburn, Alabama; The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.P.M.); Office of the Executive Vice President for Research and Partnerships, Purdue University, West Lafayette, Indiana (I.N.B.); and Cancer Biology and Immunology Program, O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham, Birmingham, Alabama (D.J.R.)
| | - Jessica A Markham
- Department of Drug Discovery and Development, Harrison School of Pharmacy (L.M.L., V.D., J.I.S., R.L.C., C.P.M., J.T.P., L.J.C., S.T.M., J.H.L., C.M.K., E.L.K., J.A.M., D.P.K., M.A.J., J.S., D.J.R.), and Department of Chemical Engineering, Samuel Ginn College of Engineering (R.L.C.), Auburn University, Auburn, Alabama; The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.P.M.); Office of the Executive Vice President for Research and Partnerships, Purdue University, West Lafayette, Indiana (I.N.B.); and Cancer Biology and Immunology Program, O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham, Birmingham, Alabama (D.J.R.)
| | - David P Kaufmann
- Department of Drug Discovery and Development, Harrison School of Pharmacy (L.M.L., V.D., J.I.S., R.L.C., C.P.M., J.T.P., L.J.C., S.T.M., J.H.L., C.M.K., E.L.K., J.A.M., D.P.K., M.A.J., J.S., D.J.R.), and Department of Chemical Engineering, Samuel Ginn College of Engineering (R.L.C.), Auburn University, Auburn, Alabama; The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.P.M.); Office of the Executive Vice President for Research and Partnerships, Purdue University, West Lafayette, Indiana (I.N.B.); and Cancer Biology and Immunology Program, O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham, Birmingham, Alabama (D.J.R.)
| | - Megan A Jacobi
- Department of Drug Discovery and Development, Harrison School of Pharmacy (L.M.L., V.D., J.I.S., R.L.C., C.P.M., J.T.P., L.J.C., S.T.M., J.H.L., C.M.K., E.L.K., J.A.M., D.P.K., M.A.J., J.S., D.J.R.), and Department of Chemical Engineering, Samuel Ginn College of Engineering (R.L.C.), Auburn University, Auburn, Alabama; The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.P.M.); Office of the Executive Vice President for Research and Partnerships, Purdue University, West Lafayette, Indiana (I.N.B.); and Cancer Biology and Immunology Program, O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham, Birmingham, Alabama (D.J.R.)
| | - Jianzhong Shen
- Department of Drug Discovery and Development, Harrison School of Pharmacy (L.M.L., V.D., J.I.S., R.L.C., C.P.M., J.T.P., L.J.C., S.T.M., J.H.L., C.M.K., E.L.K., J.A.M., D.P.K., M.A.J., J.S., D.J.R.), and Department of Chemical Engineering, Samuel Ginn College of Engineering (R.L.C.), Auburn University, Auburn, Alabama; The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.P.M.); Office of the Executive Vice President for Research and Partnerships, Purdue University, West Lafayette, Indiana (I.N.B.); and Cancer Biology and Immunology Program, O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham, Birmingham, Alabama (D.J.R.)
| | - David J Riese
- Department of Drug Discovery and Development, Harrison School of Pharmacy (L.M.L., V.D., J.I.S., R.L.C., C.P.M., J.T.P., L.J.C., S.T.M., J.H.L., C.M.K., E.L.K., J.A.M., D.P.K., M.A.J., J.S., D.J.R.), and Department of Chemical Engineering, Samuel Ginn College of Engineering (R.L.C.), Auburn University, Auburn, Alabama; The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.P.M.); Office of the Executive Vice President for Research and Partnerships, Purdue University, West Lafayette, Indiana (I.N.B.); and Cancer Biology and Immunology Program, O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham, Birmingham, Alabama (D.J.R.)
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6
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Zhang H, Qin Z, Yue X, Liu Y, Sun X, Feng J, Xu Z, Zhao J, Li K, Qiu J, Yang W, He F, Ding C. Proteome-wide profiling of transcriptional machinery on accessible chromatin with biotinylated transposons. SCIENCE ADVANCES 2021; 7:eabh1022. [PMID: 34678055 PMCID: PMC10763760 DOI: 10.1126/sciadv.abh1022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 08/31/2021] [Indexed: 06/13/2023]
Abstract
To directly and quantitatively identify the transcriptional protein complexes assembled on accessible chromatin, we develop an assay for transposase-accessible chromatin using mass spectrum (ATAC-MS) based on direct transposition of biotinylated adaptors into open chromatin. Coupling with activated gene sequence information by ATAC-seq, ATAC-MS can profile the accessible chromatin-protein machinery. ATAC-MS, combined with fractionation strategies (fATAC-MS), can provide a high-resolution chromatin-transcriptional machinery atlas. ATAC-MS with a novel Tn5-dCas9 fusion protein [dCas9-targeted ATAC-MS (ctATAC-MS)] further facilitates systematic pinpointing of the transcriptional machinery at specific open chromatin regions. We used ATAC-MS and ATAC-seq to investigate transcriptional regulation during C2C12 cell differentiation and demonstrated the role of RFX1 in regulating the proliferation and differentiation of C2C12 cells. Our strategy provides a universal toolbox including ATAC-MS, fATAC-MS, and ctATAC-MS, which enables us to portray the transcriptional regulation machinery atlas in genome scale and investigate the protein-DNA complex at a specific genomic locus.
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Affiliation(s)
- Haizhu Zhang
- State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Zhaoyu Qin
- State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Xuetong Yue
- State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Yang Liu
- State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Xiaogang Sun
- State Key Laboratory Cell Differentiation and Regulation, Overseas Expertise Introduction Center for Discipline Innovation of Pulmonary Fibrosis, (111 Project), College of Life Science, Henan Normal University, Xinxiang, Henan 453007, China
| | - Jinwen Feng
- State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Ziyan Xu
- State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Jiangyan Zhao
- State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Kai Li
- State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Jiange Qiu
- Cell Signaling and Proteomics Research Center, Academy of Medical Science, Zhengzhou University, Zhengzhou 450000, China
| | - Wenjun Yang
- Department of Pediatric Orthopedics, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Fuchu He
- State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200433, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing 102206, China
| | - Chen Ding
- State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200433, China
- State Key Laboratory Cell Differentiation and Regulation, Overseas Expertise Introduction Center for Discipline Innovation of Pulmonary Fibrosis, (111 Project), College of Life Science, Henan Normal University, Xinxiang, Henan 453007, China
- Cell Signaling and Proteomics Research Center, Academy of Medical Science, Zhengzhou University, Zhengzhou 450000, China
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7
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Kim MH, Kino-Oka M. Mechanobiological conceptual framework for assessing stem cell bioprocess effectiveness. Biotechnol Bioeng 2021; 118:4537-4549. [PMID: 34460101 DOI: 10.1002/bit.27929] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 08/22/2021] [Accepted: 08/27/2021] [Indexed: 12/12/2022]
Abstract
Fully realizing the enormous potential of stem cells requires developing efficient bioprocesses and optimizations founded in mechanobiological considerations. Here, we emphasize the importance of mechanotransduction as one of the governing principles of stem cell bioprocesses, underscoring the need to further explore the behavioral mechanisms involved in sensing mechanical cues and coordinating transcriptional responses. We identify the sources of intrinsic, extrinsic, and external noise in bioprocesses requiring further study, and discuss the criteria and indicators that may be used to assess and predict cell-to-cell variability resulting from environmental fluctuations. Specifically, we propose a conceptual framework to explain the impact of mechanical forces within the cellular environment, identify key cell state determinants in bioprocesses, and discuss downstream implementation challenges.
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Affiliation(s)
- Mee-Hae Kim
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan
| | - Masahiro Kino-Oka
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan
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8
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Smith K, Mercuri J. Microgravity and Radiation Effects on Astronaut Intervertebral Disc Health. Aerosp Med Hum Perform 2021; 92:342-352. [PMID: 33875067 DOI: 10.3357/amhp.5713.2021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
INTRODUCTION: The effects of spaceflight on the intervertebral disc (IVD) have not been thoroughly studied, despite the knowledge that spaceflight increases the risk of herniation of IVDs in astronauts upon return to Earth. However, as long duration missions become more common, fully characterizing the mechanisms behind space-induced IVD degeneration becomes increasingly imperative for mission success. This review therefore surveys current literature to outline the results of human, animal, and cell-level studies investigating the effect of microgravity and radiation exposure on IVD health. Overall, recurring study findings include increases in IVD height in microgravity conditions, upregulation of catabolic proteases leading to a weakening extracellular matrix (ECM), and both nucleus pulposus (NP) swelling and loss of annulus fibrosus (AF) fiber alignment which are hypothesized to contribute to the increased risk of herniation when reloading is experienced. However, the limitations of current studies are also discussed. For example, human studies do not allow for invasive measures of the underpinning biochemical mechanisms, correlating animal model results to the human condition may be difficult, and cellular studies lack incorporation of ECM and other complexities that mimic the native IVD microarchitecture and environment. Moving forward, the use of three-dimensional organoid culture models that incorporate IVD-specific human cells, ECM, and signals as well as the development of cell- and ECM-level computational models may further improve our understanding of the impacts that spaceflight has on astronaut IVD health.Smith K, Mercuri J. Microgravity and radiation effects on astronaut intervertebral disc health. Aerosp Med Hum Perform. 2021; 92(5):342352.
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Papantoniou I, Nilsson Hall G, Loverdou N, Lesage R, Herpelinck T, Mendes L, Geris L. Turning Nature's own processes into design strategies for living bone implant biomanufacturing: a decade of Developmental Engineering. Adv Drug Deliv Rev 2021; 169:22-39. [PMID: 33290762 PMCID: PMC7839840 DOI: 10.1016/j.addr.2020.11.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 11/20/2020] [Accepted: 11/29/2020] [Indexed: 12/14/2022]
Abstract
A decade after the term developmental engineering (DE) was coined to indicate the use of developmental processes as blueprints for the design and development of engineered living implants, a myriad of proof-of-concept studies demonstrate the potential of this approach in small animal models. This review provides an overview of DE work, focusing on applications in bone regeneration. Enabling technologies allow to quantify the distance between in vitro processes and their developmental counterpart, as well as to design strategies to reduce that distance. By embedding Nature's robust mechanisms of action in engineered constructs, predictive large animal data and subsequent positive clinical outcomes can be gradually achieved. To this end, the development of next generation biofabrication technologies should provide the necessary scale and precision for robust living bone implant biomanufacturing.
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Affiliation(s)
- Ioannis Papantoniou
- Institute of Chemical Engineering Sciences, Foundation for Research and Technology - Hellas (FORTH), Stadiou street, 26504 Patras, Greece; Skeletal Biology & Engineering Research Center, KU Leuven, Herestraat 49 (813), 3000 Leuven, Belgium; Prometheus, The KU Leuven R&D Division for Skeletal Tissue Engineering, Herestraat 49 (813), 3000 Leuven, Belgium.
| | - Gabriella Nilsson Hall
- Skeletal Biology & Engineering Research Center, KU Leuven, Herestraat 49 (813), 3000 Leuven, Belgium; Prometheus, The KU Leuven R&D Division for Skeletal Tissue Engineering, Herestraat 49 (813), 3000 Leuven, Belgium.
| | - Niki Loverdou
- Prometheus, The KU Leuven R&D Division for Skeletal Tissue Engineering, Herestraat 49 (813), 3000 Leuven, Belgium; GIGA in silico medicine, University of Liège, Avenue de l'Hôpital 11 (B34), 4000 Liège, Belgium; Biomechanics Section, KU Leuven, Celestijnenlaan 300C (2419), 3001 Leuven, Belgium.
| | - Raphaelle Lesage
- Prometheus, The KU Leuven R&D Division for Skeletal Tissue Engineering, Herestraat 49 (813), 3000 Leuven, Belgium; Biomechanics Section, KU Leuven, Celestijnenlaan 300C (2419), 3001 Leuven, Belgium.
| | - Tim Herpelinck
- Skeletal Biology & Engineering Research Center, KU Leuven, Herestraat 49 (813), 3000 Leuven, Belgium; Prometheus, The KU Leuven R&D Division for Skeletal Tissue Engineering, Herestraat 49 (813), 3000 Leuven, Belgium.
| | - Luis Mendes
- Skeletal Biology & Engineering Research Center, KU Leuven, Herestraat 49 (813), 3000 Leuven, Belgium; Prometheus, The KU Leuven R&D Division for Skeletal Tissue Engineering, Herestraat 49 (813), 3000 Leuven, Belgium.
| | - Liesbet Geris
- Skeletal Biology & Engineering Research Center, KU Leuven, Herestraat 49 (813), 3000 Leuven, Belgium; GIGA in silico medicine, University of Liège, Avenue de l'Hôpital 11 (B34), 4000 Liège, Belgium; Prometheus, The KU Leuven R&D Division for Skeletal Tissue Engineering, Herestraat 49 (813), 3000 Leuven, Belgium; Biomechanics Section, KU Leuven, Celestijnenlaan 300C (2419), 3001 Leuven, Belgium.
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10
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Jashnsaz H, Fox ZR, Hughes JJ, Li G, Munsky B, Neuert G. Diverse Cell Stimulation Kinetics Identify Predictive Signal Transduction Models. iScience 2020; 23:101565. [PMID: 33083733 PMCID: PMC7549069 DOI: 10.1016/j.isci.2020.101565] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 08/18/2020] [Accepted: 09/11/2020] [Indexed: 11/28/2022] Open
Abstract
Computationally understanding the molecular mechanisms that give rise to cell signaling responses upon different environmental, chemical, and genetic perturbations is a long-standing challenge that requires models that fit and predict quantitative responses for new biological conditions. Overcoming this challenge depends not only on good models and detailed experimental data but also on the rigorous integration of both. We propose a quantitative framework to perturb and model generic signaling networks using multiple and diverse changing environments (hereafter "kinetic stimulations") resulting in distinct pathway activation dynamics. We demonstrate that utilizing multiple diverse kinetic stimulations better constrains model parameters and enables predictions of signaling dynamics that would be impossible using traditional dose-response or individual kinetic stimulations. To demonstrate our approach, we use experimentally identified models to predict signaling dynamics in normal, mutated, and drug-treated conditions upon multitudes of kinetic stimulations and quantify which proteins and reaction rates are most sensitive to which extracellular stimulations.
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Affiliation(s)
- Hossein Jashnsaz
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | - Zachary R. Fox
- Inria Saclay Ile-de-France, Palaiseau 91120, France
- Institut Pasteur, USR 3756 IP CNRS, Paris 75015, France
- Keck Scholars, School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523, USA
| | - Jason J. Hughes
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | - Guoliang Li
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | - Brian Munsky
- Keck Scholars, School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523, USA
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523, USA
| | - Gregor Neuert
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
- Department of Biomedical Engineering, School of Engineering, Vanderbilt University, Nashville, TN 37232, USA
- Department of Pharmacology, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
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11
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Bogdanova A, Kaestner L. Early Career Scientists' Guide to the Red Blood Cell - Don't Panic! Front Physiol 2020; 11:588. [PMID: 32903637 PMCID: PMC7438720 DOI: 10.3389/fphys.2020.00588] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 05/11/2020] [Indexed: 12/15/2022] Open
Abstract
Why should we take interest in studying red blood cells? This mini review attempts to answer this question and highlights the problems that authors find most appealing in this dynamic research area. It addresses the early career scientists who are just starting their independent journey and facing tough times. Despite unlimited access to information, the exponential development of computational and intellectual powers, and the seemingly endless possibilities open to talented and ambitious early career researchers, they soon realize that the pressure of imminent competition for financial support is hard. They have to hit deadlines, produce data, publish, report, teach, manage, lead groups, and remain loving family members at the same time. Are these countless hardships worth it? We think they are. Despite centuries of research, red blood cells remain a mysterious and fascinating study objects. These cells bring together experts within the family of the European Red Cell Society and beyond. We all share our joy for the unknown and excitement in understanding how red cells function and what they tell us about the microenvironments and macroenvironments they live in. This review is an invitation to our colleagues to join us on our quest.
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Affiliation(s)
- Anna Bogdanova
- Red Blood Cell Research Group, Institute of Veterinary Physiology, Vetsuisse Faculty and the Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, Zurich, Switzerland
| | - Lars Kaestner
- Theoretical Medicine and Biosciences, Saarland University, Homburg, Germany.,Experimental Physics, Saarland University, Saarbrücken, Germany
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12
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Gilchrist AE, Harley BA. Connecting secretome to hematopoietic stem cell phenotype shifts in an engineered bone marrow niche. Integr Biol (Camb) 2020; 12:175-187. [PMID: 32556172 PMCID: PMC7384206 DOI: 10.1093/intbio/zyaa013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 04/21/2020] [Accepted: 05/08/2020] [Indexed: 01/06/2023]
Abstract
Hematopoietic stem cells (HSCs) primarily reside in the bone marrow, where they receive external cues from their local microenvironment. The complex milieu of biophysical cues, cellular components and cell-secreted factors regulates the process by which HSC produce the blood and immune system. We previously showed direct coculture of primary murine hematopoietic stem and progenitor cells with a population of marrow-derived mesenchymal stromal and progenitor cells (MSPCs) in a methacrylamide-functionalized gelatin (GelMA) hydrogel improves hematopoietic progenitor maintenance. However, the mechanism by which MSPCs influenced HSC fate decisions remained unknown. Herein, we report the use of proteomic analysis to correlate HSC phenotype to a broad candidate pool of 200 soluble factors produced by combined mesenchymal and hematopoietic progeny. Partial least squares regression (PLSR), along with an iterative filter method, identified TGFβ-1, MMP-3, c-RP and TROY as positively correlated with HSC maintenance. Experimentally, we then observe exogenous stimulation of HSC monocultures in GelMA hydrogels with these combined cytokines increases the ratio of hematopoietic progenitors to committed progeny after a 7-day culture 7.52 ± 3.65-fold compared to non-stimulated monocultures. Findings suggest a cocktail of the downselected cytokines amplifies hematopoietic maintenance potential of HSCs beyond that of MSPC-secreted factors alone. This work integrates empirical and computation methods to identify cytokine combinations to improve HSC maintenance within an engineered HSC niche, suggesting a route toward identifying feeder-free culture platforms for HSC expansion. Insight Hematopoietic stem cells within an artificial niche receive maintenance cues in the form of soluble factors from hematopoietic and mesenchymal progeny. Applying a proteomic regression analysis, we identify a reduced set of soluble factors correlated to maintenance of a hematopoietic phenotype during culture in a biomaterial model of the bone marrow niche. We identify a minimum factor cocktail that promotes hematopoietic maintenance potential in a gelatin-based culture, regardless of the presence of mesenchymal feeder cells. By combining empirical and computational methods, we report an experimentally feasible number of factors from a large dataset, enabling exogenous integration of soluble factors into an engineered hematopoietic stem cell for enhanced maintenance potential of a quiescent stem cell population.
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Affiliation(s)
- Aidan E. Gilchrist
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Brendan A.C. Harley
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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13
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Julian LM, Stanford WL. Organelle Cooperation in Stem Cell Fate: Lysosomes as Emerging Regulators of Cell Identity. Front Cell Dev Biol 2020; 8:591. [PMID: 32733892 PMCID: PMC7358313 DOI: 10.3389/fcell.2020.00591] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 06/17/2020] [Indexed: 12/26/2022] Open
Abstract
Regulation of stem cell fate is best understood at the level of gene and protein regulatory networks, though it is now clear that multiple cellular organelles also have critical impacts. A growing appreciation for the functional interconnectedness of organelles suggests that an orchestration of integrated biological networks functions to drive stem cell fate decisions and regulate metabolism. Metabolic signaling itself has emerged as an integral regulator of cell fate including the determination of identity, activation state, survival, and differentiation potential of many developmental, adult, disease, and cancer-associated stem cell populations and their progeny. As the primary adenosine triphosphate-generating organelles, mitochondria are well-known regulators of stem cell fate decisions, yet it is now becoming apparent that additional organelles such as the lysosome are important players in mediating these dynamic decisions. In this review, we will focus on the emerging role of organelles, in particular lysosomes, in the reprogramming of both metabolic networks and stem cell fate decisions, especially those that impact the determination of cell identity. We will discuss the inter-organelle interactions, cell signaling pathways, and transcriptional regulatory mechanisms with which lysosomes engage and how these activities impact metabolic signaling. We will further review recent data that position lysosomes as critical regulators of cell identity determination programs and discuss the known or putative biological mechanisms. Finally, we will briefly highlight the potential impact of elucidating mechanisms by which lysosomes regulate stem cell identity on our understanding of disease pathogenesis, as well as the development of refined regenerative medicine, biomarker, and therapeutic strategies.
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Affiliation(s)
- Lisa M. Julian
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - William L. Stanford
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
- Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
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14
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Kalev-Zylinska ML, Hearn JI, Makhro A, Bogdanova A. N-Methyl-D-Aspartate Receptors in Hematopoietic Cells: What Have We Learned? Front Physiol 2020; 11:577. [PMID: 32625106 PMCID: PMC7311790 DOI: 10.3389/fphys.2020.00577] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 05/08/2020] [Indexed: 12/24/2022] Open
Abstract
The N-methyl-D-aspartate receptor (NMDAR) provides a pathway for glutamate-mediated inter-cellular communication, best known for its role in the brain but with multiple examples of functionality in non-neuronal cells. Data previously published by others and us provided ex vivo evidence that NMDARs regulate platelet and red blood cell (RBC) production. Here, we summarize what is known about these hematopoietic roles of the NMDAR. Types of NMDAR subunits expressed in megakaryocytes (platelet precursors) and erythroid cells are more commonly found in the developing rather than adult brain, suggesting trophic functions. Nevertheless, similar to their neuronal counterparts, hematopoietic NMDARs function as ion channels, and are permeable to calcium ions (Ca2+). Inhibitors that block open NMDAR (memantine and MK-801) interfere with megakaryocytic maturation and proplatelet formation in primary culture. The effect on proplatelet formation appears to involve Ca2+ influx-dependent regulation of the cytoskeletal remodeling. In contrast to normal megakaryocytes, NMDAR effects in leukemic Meg-01 cells are diverted away from differentiation to increase proliferation. NMDAR hypofunction triggers differentiation of Meg-01 cells with the bias toward erythropoiesis. The underlying mechanism involves changes in the intracellular Ca2+ homeostasis, cell stress pathways, and hematopoietic transcription factors that upon NMDAR inhibition shift from the predominance of megakaryocytic toward erythroid regulators. This ability of NMDAR to balance both megakaryocytic and erythroid cell fates suggests receptor involvement at the level of a bipotential megakaryocyte-erythroid progenitor. In human erythroid precursors and circulating RBCs, NMDAR regulates intracellular Ca2+ homeostasis. NMDAR activity supports survival of early proerythroblasts, and in mature RBCs NMDARs impact cellular hydration state, hemoglobin oxygen affinity, and nitric oxide synthase activity. Overexcitation of NMDAR in mature RBCs leads to Ca2+ overload, K+ loss, RBC dehydration, and oxidative stress, which may contribute to the pathogenesis of sickle cell disease. In summary, there is growing evidence that glutamate-NMDAR signaling regulates megakaryocytic and erythroid cells at different stages of maturation, with some intriguing differences emerging in NMDAR expression and function between normal and diseased cells. NMDAR signaling may provide new therapeutic opportunities in hematological disease, but in vivo applicability needs to be confirmed.
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Affiliation(s)
- Maggie L. Kalev-Zylinska
- Blood and Cancer Biology Laboratory, Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
- Department of Pathology and Laboratory Medicine, LabPlus Haematology, Auckland City Hospital, Auckland, New Zealand
| | - James I. Hearn
- Blood and Cancer Biology Laboratory, Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Asya Makhro
- Red Blood Cell Research Group, Institute of Veterinary Physiology, Vetsuisse Faculty, University of Zurich, Zürich, Switzerland
- Zurich Center for Integrative Human Physiology, University of Zurich, Zürich, Switzerland
| | - Anna Bogdanova
- Red Blood Cell Research Group, Institute of Veterinary Physiology, Vetsuisse Faculty, University of Zurich, Zürich, Switzerland
- Zurich Center for Integrative Human Physiology, University of Zurich, Zürich, Switzerland
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15
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Wells CA, Choi J. Transcriptional Profiling of Stem Cells: Moving from Descriptive to Predictive Paradigms. Stem Cell Reports 2020; 13:237-246. [PMID: 31412285 PMCID: PMC6700522 DOI: 10.1016/j.stemcr.2019.07.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/09/2019] [Accepted: 07/10/2019] [Indexed: 12/24/2022] Open
Abstract
Transcriptional profiling is a powerful tool commonly used to benchmark stem cells and their differentiated progeny. As the wealth of stem cell data builds in public repositories, we highlight common data traps, and review approaches to combine and mine this data for new cell classification and cell prediction tools. We touch on future trends for stem cell profiling, such as single-cell profiling, long-read sequencing, and improved methods for measuring molecular modifications on chromatin and RNA that bring new challenges and opportunities for stem cell analysis.
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Affiliation(s)
- Christine A Wells
- Centre for Stem Cell Systems, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville 3010, Australia.
| | - Jarny Choi
- Centre for Stem Cell Systems, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville 3010, Australia
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Hearn JI, Green TN, Chopra M, Nursalim YNS, Ladvanszky L, Knowlton N, Blenkiron C, Poulsen RC, Singleton DC, Bohlander SK, Kalev-Zylinska ML. N-Methyl-D-Aspartate Receptor Hypofunction in Meg-01 Cells Reveals a Role for Intracellular Calcium Homeostasis in Balancing Megakaryocytic-Erythroid Differentiation. Thromb Haemost 2020; 120:671-686. [PMID: 32289863 PMCID: PMC7286128 DOI: 10.1055/s-0040-1708483] [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] [Indexed: 01/18/2023]
Abstract
The release of calcium ions (Ca
2+
) from the endoplasmic reticulum (ER) and related store-operated calcium entry (SOCE) regulate maturation of normal megakaryocytes. The
N
-methyl-D-aspartate (NMDA) receptor (NMDAR) provides an additional mechanism for Ca
2+
influx in megakaryocytic cells, but its role remains unclear. We created a model of NMDAR hypofunction in Meg-01 cells using CRISPR-Cas9 mediated knockout of the
GRIN1
gene, which encodes an obligate, GluN1 subunit of the NMDAR. We found that compared with unmodified Meg-01 cells, Meg-01-
GRIN1−/−
cells underwent atypical differentiation biased toward erythropoiesis, associated with increased basal ER stress and cell death. Resting cytoplasmic Ca
2+
levels were higher in Meg-01-
GRIN1−/−
cells, but ER Ca
2+
release and SOCE were lower after activation. Lysosome-related organelles accumulated including immature dense granules that may have contributed an alternative source of intracellular Ca
2+
. Microarray analysis revealed that Meg-01-
GRIN1−/−
cells had deregulated expression of transcripts involved in Ca
2+
metabolism, together with a shift in the pattern of hematopoietic transcription factors toward erythropoiesis. In keeping with the observed pro-cell death phenotype induced by
GRIN1
deletion, memantine (NMDAR inhibitor) increased cytotoxic effects of cytarabine in unmodified Meg-01 cells. In conclusion, NMDARs comprise an integral component of the Ca
2+
regulatory network in Meg-01 cells that help balance ER stress and megakaryocytic-erythroid differentiation. We also provide the first evidence that megakaryocytic NMDARs regulate biogenesis of lysosome-related organelles, including dense granules. Our results argue that intracellular Ca
2+
homeostasis may be more important for normal megakaryocytic and erythroid differentiation than currently recognized; thus, modulation may offer therapeutic opportunities.
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Affiliation(s)
- James I Hearn
- Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland, Auckland, New Zealand
| | - Taryn N Green
- Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland, Auckland, New Zealand
| | - Martin Chopra
- Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland, Auckland, New Zealand
| | - Yohanes N S Nursalim
- Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland, Auckland, New Zealand
| | - Leandro Ladvanszky
- Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland, Auckland, New Zealand
| | - Nicholas Knowlton
- Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland, Auckland, New Zealand
| | - Cherie Blenkiron
- Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland, Auckland, New Zealand
| | - Raewyn C Poulsen
- Department of Medicine, School of Medicine, University of Auckland, Auckland, New Zealand.,Department of Pharmacology and Clinical Pharmacology, School of Medical Sciences, University of Auckland, Auckland, New Zealand
| | - Dean C Singleton
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand
| | - Stefan K Bohlander
- Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland, Auckland, New Zealand
| | - Maggie L Kalev-Zylinska
- Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland, Auckland, New Zealand.,LabPlus Haematology, Auckland City Hospital, Auckland, New Zealand
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