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Mitchell W, Goeminne LJE, Tyshkovskiy A, Zhang S, Chen JY, Paulo JA, Pierce KA, Choy AH, Clish CB, Gygi SP, Gladyshev VN. Multi-omics characterization of partial chemical reprogramming reveals evidence of cell rejuvenation. eLife 2024; 12:RP90579. [PMID: 38517750 PMCID: PMC10959535 DOI: 10.7554/elife.90579] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2024] Open
Abstract
Partial reprogramming by cyclic short-term expression of Yamanaka factors holds promise for shifting cells to younger states and consequently delaying the onset of many diseases of aging. However, the delivery of transgenes and potential risk of teratoma formation present challenges for in vivo applications. Recent advances include the use of cocktails of compounds to reprogram somatic cells, but the characteristics and mechanisms of partial cellular reprogramming by chemicals remain unclear. Here, we report a multi-omics characterization of partial chemical reprogramming in fibroblasts from young and aged mice. We measured the effects of partial chemical reprogramming on the epigenome, transcriptome, proteome, phosphoproteome, and metabolome. At the transcriptome, proteome, and phosphoproteome levels, we saw widescale changes induced by this treatment, with the most notable signature being an upregulation of mitochondrial oxidative phosphorylation. Furthermore, at the metabolome level, we observed a reduction in the accumulation of aging-related metabolites. Using both transcriptomic and epigenetic clock-based analyses, we show that partial chemical reprogramming reduces the biological age of mouse fibroblasts. We demonstrate that these changes have functional impacts, as evidenced by changes in cellular respiration and mitochondrial membrane potential. Taken together, these results illuminate the potential for chemical reprogramming reagents to rejuvenate aged biological systems and warrant further investigation into adapting these approaches for in vivo age reversal.
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Affiliation(s)
- Wayne Mitchell
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Ludger JE Goeminne
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Alexander Tyshkovskiy
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Sirui Zhang
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Julie Y Chen
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical SchoolBostonUnited States
| | - Kerry A Pierce
- Broad Institute of MIT and HarvardCambridgeUnited States
| | | | - Clary B Clish
- Broad Institute of MIT and HarvardCambridgeUnited States
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical SchoolBostonUnited States
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
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Mitchell W, Goeminne LJ, Tyshkovskiy A, Zhang S, Chen JY, Paulo JA, Pierce KA, Choy AH, Clish CB, Gygi SP, Gladyshev VN. Multi-omics characterization of partial chemical reprogramming reveals evidence of cell rejuvenation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.30.546730. [PMID: 37425825 PMCID: PMC10327104 DOI: 10.1101/2023.06.30.546730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Partial reprogramming by cyclic short-term expression of Yamanaka factors holds promise for shifting cells to younger states and consequently delaying the onset of many diseases of aging. However, the delivery of transgenes and potential risk of teratoma formation present challenges for in vivo applications. Recent advances include the use of cocktails of compounds to reprogram somatic cells, but the characteristics and mechanisms of partial cellular reprogramming by chemicals remain unclear. Here, we report a multi-omics characterization of partial chemical reprogramming in fibroblasts from young and aged mice. We measured the effects of partial chemical reprogramming on the epigenome, transcriptome, proteome, phosphoproteome, and metabolome. At the transcriptome, proteome, and phosphoproteome levels, we saw widescale changes induced by this treatment, with the most notable signature being an upregulation of mitochondrial oxidative phosphorylation. Furthermore, at the metabolome level, we observed a reduction in the accumulation of aging-related metabolites. Using both transcriptomic and epigenetic clock-based analyses, we show that partial chemical reprogramming reduces the biological age of mouse fibroblasts. We demonstrate that these changes have functional impacts, as evidenced by changes in cellular respiration and mitochondrial membrane potential. Taken together, these results illuminate the potential for chemical reprogramming reagents to rejuvenate aged biological systems and warrant further investigation into adapting these approaches for in vivo age reversal.
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Affiliation(s)
- Wayne Mitchell
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 United States
| | - Ludger J.E. Goeminne
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 United States
| | - Alexander Tyshkovskiy
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 United States
| | - Sirui Zhang
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 United States
| | - Julie Y. Chen
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 United States
| | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115 United States
| | - Kerry A. Pierce
- Broad Institute of MIT and Harvard, Cambridge, MA 01241 United States
| | - Angelina H. Choy
- Broad Institute of MIT and Harvard, Cambridge, MA 01241 United States
| | - Clary B. Clish
- Broad Institute of MIT and Harvard, Cambridge, MA 01241 United States
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115 United States
| | - Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 United States
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McCoy DE, Schwiebert EM, Karlson KH, Spielman WS, Stanton BA. Identification and function of A1 adenosine receptors in normal and cystic fibrosis human airway epithelial cells. THE AMERICAN JOURNAL OF PHYSIOLOGY 1995; 268:C1520-7. [PMID: 7611373 DOI: 10.1152/ajpcell.1995.268.6.c1520] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A role for adenosine in the regulation of ion transport in pulmonary epithelial cells has recently been proposed. Although evidence exists documenting the presence and function of adenosine A2 receptors in airway epithelia, the presence of adenosine A1 receptors remains controversial. The present study used reverse transcriptase-polymerase chain reaction (PCR) and whole cell patch-clamp analysis to investigate A1 receptor presence and function in normal and cystic fibrosis (CF) human airway epithelial cells. Oligonucleotide primers complementary to the human brain A1 receptor sequence generated a PCR product of the predicted size (311 bp) in normal tracheal (9HTEo-) and CF submucosal (2CFSMEo-) airway cell lines and in primary cultures of CF nasal polyp epithelial cells. An oligonucleotide probe internal to the PCR primers hybridized with the 311-bp cDNAs by Southern blot analysis. cDNA sequencing demonstrated that the normal and CF airway cell PCR products are 100% identical to the corresponding sequence of the human brain adenosine A1 receptor. Northern blot analysis of 9HTEo-and 2CFSMEo- poly(A)+ RNA revealed the presence of two bands of approximately 3.0 and approximately 5.5 kb corresponding to the A1 receptor. Whole cell patch-clamp analyses demonstrated that 8-cyclopentyl-1,3-dipropylxanthine, a specific A1 receptor antagonist, increases adenosine 3',5'-cyclic monophosphate (cAMP)-activated Cl- conductance in 9HTEo-airway cells and allows cAMP to increase Cl- conductance in 2CFSMEo- CF airway cells and CF nasal polyp epithelial cells in primary culture. These results provide evidence for the presence and function of A1 receptors in normal and CF airway epithelial cells and provide support for a role of adenosine A1 receptors in modulating airway epithelial cell Cl- transport.
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Affiliation(s)
- D E McCoy
- Department of Physiology, Dartmouth Medical School, Hanover, New Hampshire 03755, USA
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Klewes L, Prehm P. Intracellular signal transduction for serum activation of the hyaluronan synthase in eukaryotic cell lines. J Cell Physiol 1994; 160:539-44. [PMID: 8077292 DOI: 10.1002/jcp.1041600317] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Hyaluronan synthase was activated in B6 cells or 3T3 fibroblasts by foetal calf serum with maximal activity after 6 h. Activation was inhibited by cycloheximide or by the protein kinase inhibitors H-7 or H-8, indicating that transcription as well as phosphorylation was required for activation. The activation by serum was markedly prolonged, when serum was added together with cholera toxin or theophylline. Without serum stimulation the hyaluronan synthase could also be activated by phorbol-12-myristate-13-acetate, by dibutyryl-c-AMP, or by forskolin. Increasing the intracellular Ca-ion concentration with a Ca-ionophore also led to an activation. The activation of the drugs was not synergistic. In isolated plasma membranes the synthase activity could be decreased by phosphatase treatment and enhanced by ATP in B6 cells and by ATP in the presence of phorbol-12-myristate-13-acetate in 3T3 fibroblasts. Stimulation correlated with increased transcription and phosphorylation of the 52 kD hyaluronan synthase at serine residues. The results led to the conclusion that hyaluronan synthase is induced by transcription and activated by phosphorylation by protein kinase C, c-AMP-dependent protein kinases, or Ca-ion-dependent protein kinases.
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Affiliation(s)
- L Klewes
- Institut für Physiologische Chemie und Pathobiochemie, Münster, Germany
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Tamura RN, Cox GS. Enhancement by theophylline of the butyrate-mediated induction of choriogonadotropin alpha-subunit in HeLa cells. I. Lack of correlation with cAMP. Arch Biochem Biophys 1990; 280:87-94. [PMID: 1693836 DOI: 10.1016/0003-9861(90)90522-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The glycoprotein hormone common alpha-subunit can be induced in HeLa and other nontrophoblastic tumor cell lines by sodium butyrate. This report demonstrates that production of alpha-subunit can be further modulated by theophylline, especially in conjunction with butyrate. This synergism was not observed with other phosphodiesterase inhibitors such as xanthine, caffeine, theobromine, or methylisobutylxanthine. Induction by a combination of the short chain fatty acid plus the methylxanthine results from a decrease in the lag time after effector addition as well as a change in the rate of subunit accumulation. The increase in alpha-subunit is correlated with an increase in the levels of alpha-subunit mRNA, suggesting that induction is manifest at a pretranslational stage. The production of alpha-subunit was only marginally affected in cultures treated with 8-Br-cAMP or forskolin. Intracellular levels of cAMP were increased approximately threefold by methylisobutylxanthine, twofold by theophylline, fourfold by forskolin, and about 50% by butyrate, yet significant induction was achieved only by butyrate and theophylline. Taken together, these data suggest that the synergism between butyrate and theophylline is not mediated by cAMP.
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Affiliation(s)
- R N Tamura
- Department of Biochemistry, University of Nebraska Medical Center, Omaha 68198-4525
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