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Zhou S, Hui X, Wang W, Zhao C, Jin M, Qin Y, Chen M. SARS-CoV-2 and HCoV-OC43 regulate host m6A modification via activation of the mTORC1 signalling pathway to facilitate viral replication. Emerg Microbes Infect 2025; 14:2447620. [PMID: 39745173 PMCID: PMC11852242 DOI: 10.1080/22221751.2024.2447620] [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: 09/27/2024] [Revised: 12/08/2024] [Accepted: 12/22/2024] [Indexed: 02/25/2025]
Abstract
N6-methyladenosine (m6A) is the most prevalent post-transcriptional modification in eukaryotic RNA and is also present in various viral RNAs, where it plays a crucial role in regulating the viral life cycle. However, the molecular mechanisms through which viruses regulate host RNA m6A methylation are not fully understood. In this study, we reveal that SARS-CoV-2 and HCoV-OC43 infection enhance host m6A modification by activating the mTORC1 signalling pathway. Specifically, the viral non-structural protein nsp14 upregulates the expression of S-adenosylmethionine synthase MAT2A in an mTORC1-dependent manner. This mTORC1-MAT2A axis subsequently stimulates the synthesis of S-adenosylmethionine (SAM). The increase of SAM then enhances the m6A methylation of host RNA and facilitates viral replication. Our findings uncover a molecular mechanism by which viruses regulate host m6A methylation and provide insights into how SARS-CoV-2 hijacks host cellular epitranscriptomic modifications to promote its replication.
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Affiliation(s)
- Shixiong Zhou
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Xianfeng Hui
- National key laboratory of agricultural microbiology, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Weiwei Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Chunbei Zhao
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Meilin Jin
- National key laboratory of agricultural microbiology, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Yali Qin
- School of Life Sciences, Hubei University, Wuhan, People’s Republic of China
| | - Mingzhou Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
- School of Life Sciences, Hubei University, Wuhan, People’s Republic of China
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2
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Hamadmad S, Heisler‐Taylor T, Goswami S, Hawthorn E, Chaurasia S, Martini D, Summitt D, Zatari A, Shalash R, Sohail M, Urbanski EG, Bernstein K, Racine J, Satoskar A, El‐Hodiri HM, Fischer AJ, Cebulla CM. Ibudilast Protects Retinal Bipolar Cells From Excitotoxic Retinal Damage and Activates the mTOR Pathway. Glia 2025; 73:905-927. [PMID: 39916387 PMCID: PMC11920683 DOI: 10.1002/glia.24657] [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: 03/04/2024] [Revised: 10/09/2024] [Accepted: 11/24/2024] [Indexed: 02/12/2025]
Abstract
Ibudilast, an inhibitor of macrophage migration inhibitory factor (MIF) and phosphodiesterase (PDE), has been recently shown to have neuroprotective effects in a variety of neurologic diseases. We utilize a chick excitotoxic retinal damage model to investigate ibudilast's potential to protect retinal neurons. Using single cell RNA-sequencing (scRNA-seq), we find that MIF, putative MIF receptors CD74 and CD44, and several PDEs are upregulated in different retinal cells during damage. Intravitreal ibudilast is well tolerated in the eye and causes no evidence of toxicity. Ibudilast effectively protects neurons in the inner nuclear layer from NMDA-induced cell death, restores retinal layer thickness on spectral domain optical coherence tomography (SD-OCT), and preserves retinal neuron function, particularly for the ON bipolar cells, as assessed by electroretinography. PDE inhibition seems essential for ibudilast's neuroprotection, as AV1013, the analogue that lacks PDE inhibitor activity, is ineffective. scRNA-seq analysis reveals upregulation of multiple signaling pathways, including mTOR, in damaged Müller glia (MG) with ibudilast treatment compared to AV1013. Components of mTORC1 and mTORC2 are upregulated in both bipolar cells and MG with ibudilast. The mTOR inhibitor rapamycin blocked accumulation of pS6 but did not reduce TUNEL positive dying cells. Additionally, through ligand-receptor interaction analysis, crosstalk between bipolar cells and MG may be important for neuroprotection. We have identified several paracrine signaling pathways that are known to contribute to cell survival and neuroprotection and might play essential roles in ibudilast function. These findings highlight ibudilast's potential to protect inner retinal neurons during damage and show promise for future clinical translation.
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Affiliation(s)
- Sumaya Hamadmad
- Department of Ophthalmology and Visual Sciences, Havener Eye InstituteThe Ohio State University, Wexner Medical CenterColumbusOhioUSA
| | - Tyler Heisler‐Taylor
- Department of Ophthalmology and Visual Sciences, Havener Eye InstituteThe Ohio State University, Wexner Medical CenterColumbusOhioUSA
| | - Sandeep Goswami
- Department of Ophthalmology and Visual Sciences, Havener Eye InstituteThe Ohio State University, Wexner Medical CenterColumbusOhioUSA
| | - Evan Hawthorn
- Department of Ophthalmology and Visual Sciences, Havener Eye InstituteThe Ohio State University, Wexner Medical CenterColumbusOhioUSA
| | - Sameer Chaurasia
- Department of Ophthalmology and Visual Sciences, Havener Eye InstituteThe Ohio State University, Wexner Medical CenterColumbusOhioUSA
| | - Dena Martini
- Department of Ophthalmology and Visual Sciences, Havener Eye InstituteThe Ohio State University, Wexner Medical CenterColumbusOhioUSA
| | - Diana Summitt
- Department of Ophthalmology and Visual Sciences, Havener Eye InstituteThe Ohio State University, Wexner Medical CenterColumbusOhioUSA
| | - Ali Zatari
- Department of Ophthalmology and Visual Sciences, Havener Eye InstituteThe Ohio State University, Wexner Medical CenterColumbusOhioUSA
| | - Rahaf Shalash
- Department of Ophthalmology and Visual Sciences, Havener Eye InstituteThe Ohio State University, Wexner Medical CenterColumbusOhioUSA
| | - Misha Sohail
- Department of Ophthalmology and Visual Sciences, Havener Eye InstituteThe Ohio State University, Wexner Medical CenterColumbusOhioUSA
| | - Elizabeth G. Urbanski
- Department of Ophthalmology and Visual Sciences, Havener Eye InstituteThe Ohio State University, Wexner Medical CenterColumbusOhioUSA
| | - Kayla Bernstein
- Department of Ophthalmology and Visual Sciences, Havener Eye InstituteThe Ohio State University, Wexner Medical CenterColumbusOhioUSA
| | | | - Abhay Satoskar
- Department of PathologyThe Ohio State University, Wexner Medical CenterColumbusOhioUSA
| | - Heithem M. El‐Hodiri
- Department of Neuroscience, College of MedicineThe Ohio State UniversityColumbusOhioUSA
| | - Andy J. Fischer
- Department of Neuroscience, College of MedicineThe Ohio State UniversityColumbusOhioUSA
| | - Colleen M. Cebulla
- Department of Ophthalmology and Visual Sciences, Havener Eye InstituteThe Ohio State University, Wexner Medical CenterColumbusOhioUSA
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3
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Boff MO, Xavier FAC, Diz FM, Gonçalves JB, Ferreira LM, Zambeli J, Pazzin DB, Previato TTR, Erwig HS, Gonçalves JIB, Bruzzo FTK, Marinowic D, da Costa JC, Zanirati G. mTORopathies in Epilepsy and Neurodevelopmental Disorders: The Future of Therapeutics and the Role of Gene Editing. Cells 2025; 14:662. [PMID: 40358185 PMCID: PMC12071303 DOI: 10.3390/cells14090662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2025] [Revised: 02/06/2025] [Accepted: 02/06/2025] [Indexed: 05/15/2025] Open
Abstract
mTORopathies represent a group of neurodevelopmental disorders linked to dysregulated mTOR signaling, resulting in conditions such as tuberous sclerosis complex, focal cortical dysplasia, hemimegalencephaly, and Smith-Kingsmore Syndrome. These disorders often manifest with epilepsy, cognitive impairments, and, in some cases, structural brain anomalies. The mTOR pathway, a central regulator of cell growth and metabolism, plays a crucial role in brain development, where its hyperactivation leads to abnormal neuroplasticity, tumor formation, and heightened neuronal excitability. Current treatments primarily rely on mTOR inhibitors, such as rapamycin, which reduce seizure frequency and tumor size but fail to address underlying genetic causes. Advances in gene editing, particularly via CRISPR/Cas9, offer promising avenues for precision therapies targeting the genetic mutations driving mTORopathies. New delivery systems, including viral and non-viral vectors, aim to enhance the specificity and efficacy of these therapies, potentially transforming the management of these disorders. While gene editing holds curative potential, challenges remain concerning delivery, long-term safety, and ethical considerations. Continued research into mTOR mechanisms and innovative gene therapies may pave the way for transformative, personalized treatments for patients affected by these complex neurodevelopmental conditions.
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Affiliation(s)
- Marina Ottmann Boff
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre 90610-000, RS, Brazil; (M.O.B.); (F.A.C.X.); (F.M.D.); (J.B.G.); (L.M.F.); (J.Z.); (D.B.P.); (T.T.R.P.); (H.S.E.); (J.I.B.G.); (F.T.K.B.); (D.M.); (J.C.d.C.)
- School of Medicine, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre 90619-900, RS, Brazil
| | - Fernando Antônio Costa Xavier
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre 90610-000, RS, Brazil; (M.O.B.); (F.A.C.X.); (F.M.D.); (J.B.G.); (L.M.F.); (J.Z.); (D.B.P.); (T.T.R.P.); (H.S.E.); (J.I.B.G.); (F.T.K.B.); (D.M.); (J.C.d.C.)
- Graduate Program in Medicine and Health Sciences, School of Medicine, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre 90619-900, RS, Brazil
| | - Fernando Mendonça Diz
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre 90610-000, RS, Brazil; (M.O.B.); (F.A.C.X.); (F.M.D.); (J.B.G.); (L.M.F.); (J.Z.); (D.B.P.); (T.T.R.P.); (H.S.E.); (J.I.B.G.); (F.T.K.B.); (D.M.); (J.C.d.C.)
| | - Júlia Budelon Gonçalves
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre 90610-000, RS, Brazil; (M.O.B.); (F.A.C.X.); (F.M.D.); (J.B.G.); (L.M.F.); (J.Z.); (D.B.P.); (T.T.R.P.); (H.S.E.); (J.I.B.G.); (F.T.K.B.); (D.M.); (J.C.d.C.)
| | - Laura Meireles Ferreira
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre 90610-000, RS, Brazil; (M.O.B.); (F.A.C.X.); (F.M.D.); (J.B.G.); (L.M.F.); (J.Z.); (D.B.P.); (T.T.R.P.); (H.S.E.); (J.I.B.G.); (F.T.K.B.); (D.M.); (J.C.d.C.)
- School of Medicine, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre 90619-900, RS, Brazil
| | - Jean Zambeli
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre 90610-000, RS, Brazil; (M.O.B.); (F.A.C.X.); (F.M.D.); (J.B.G.); (L.M.F.); (J.Z.); (D.B.P.); (T.T.R.P.); (H.S.E.); (J.I.B.G.); (F.T.K.B.); (D.M.); (J.C.d.C.)
- School of Medicine, University of the Valley of the Rio dos Sinos (UNISINOS), São Leopoldo 93022-750, RS, Brazil
| | - Douglas Bottega Pazzin
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre 90610-000, RS, Brazil; (M.O.B.); (F.A.C.X.); (F.M.D.); (J.B.G.); (L.M.F.); (J.Z.); (D.B.P.); (T.T.R.P.); (H.S.E.); (J.I.B.G.); (F.T.K.B.); (D.M.); (J.C.d.C.)
- Graduate Program in Pediatrics and Child Health, School of Medicine, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre 90619-900, RS, Brazil
| | - Thales Thor Ramos Previato
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre 90610-000, RS, Brazil; (M.O.B.); (F.A.C.X.); (F.M.D.); (J.B.G.); (L.M.F.); (J.Z.); (D.B.P.); (T.T.R.P.); (H.S.E.); (J.I.B.G.); (F.T.K.B.); (D.M.); (J.C.d.C.)
- Graduate Program in Biomedical Gerontology, School of Medicine, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre 90619-900, RS, Brazil
| | - Helena Scartassini Erwig
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre 90610-000, RS, Brazil; (M.O.B.); (F.A.C.X.); (F.M.D.); (J.B.G.); (L.M.F.); (J.Z.); (D.B.P.); (T.T.R.P.); (H.S.E.); (J.I.B.G.); (F.T.K.B.); (D.M.); (J.C.d.C.)
- School of Health and Life, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre 90619-900, RS, Brazil
| | - João Ismael Budelon Gonçalves
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre 90610-000, RS, Brazil; (M.O.B.); (F.A.C.X.); (F.M.D.); (J.B.G.); (L.M.F.); (J.Z.); (D.B.P.); (T.T.R.P.); (H.S.E.); (J.I.B.G.); (F.T.K.B.); (D.M.); (J.C.d.C.)
| | - Fernanda Thays Konat Bruzzo
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre 90610-000, RS, Brazil; (M.O.B.); (F.A.C.X.); (F.M.D.); (J.B.G.); (L.M.F.); (J.Z.); (D.B.P.); (T.T.R.P.); (H.S.E.); (J.I.B.G.); (F.T.K.B.); (D.M.); (J.C.d.C.)
| | - Daniel Marinowic
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre 90610-000, RS, Brazil; (M.O.B.); (F.A.C.X.); (F.M.D.); (J.B.G.); (L.M.F.); (J.Z.); (D.B.P.); (T.T.R.P.); (H.S.E.); (J.I.B.G.); (F.T.K.B.); (D.M.); (J.C.d.C.)
- School of Health and Life, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre 90619-900, RS, Brazil
| | - Jaderson Costa da Costa
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre 90610-000, RS, Brazil; (M.O.B.); (F.A.C.X.); (F.M.D.); (J.B.G.); (L.M.F.); (J.Z.); (D.B.P.); (T.T.R.P.); (H.S.E.); (J.I.B.G.); (F.T.K.B.); (D.M.); (J.C.d.C.)
| | - Gabriele Zanirati
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre 90610-000, RS, Brazil; (M.O.B.); (F.A.C.X.); (F.M.D.); (J.B.G.); (L.M.F.); (J.Z.); (D.B.P.); (T.T.R.P.); (H.S.E.); (J.I.B.G.); (F.T.K.B.); (D.M.); (J.C.d.C.)
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4
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Wang J, Huang Y, Wang Z, Liu J, Liu Z, Yang J, He Z. The mTOR Signaling Pathway: Key Regulator and Therapeutic Target for Heart Disease. Biomedicines 2025; 13:397. [PMID: 40002810 PMCID: PMC11853667 DOI: 10.3390/biomedicines13020397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2024] [Revised: 01/25/2025] [Accepted: 02/04/2025] [Indexed: 02/27/2025] Open
Abstract
Heart disease, including myocardial infarction, heart failure, cardiac hypertrophy, and cardiomyopathy, remains a leading cause of mortality worldwide. The mammalian target of rapamycin (mTOR) is a centrally regulated kinase that governs key cellular processes, including growth, proliferation, metabolism, and survival. Notably, mTOR plays a pivotal role in cardiovascular health and disease, particularly in the onset and progression of cardiac conditions. In this review, we discuss mTOR's structure and function as well as the regulatory mechanisms of its associated signaling pathways. We focus on the molecular mechanisms by which mTOR signaling regulates cardiac diseases and the potential of mTOR inhibitors and related regulatory drugs in preventing these conditions. We conclude that the mTOR signaling pathway is a promising therapeutic target for heart disease.
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Affiliation(s)
- Jieyu Wang
- Department of Basic Medicine, School of Medicine, Hunan Normal University, Changsha 410013, China; (J.W.); (Y.H.); (Z.W.); (J.L.)
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, Hunan Normal University, Changsha 410013, China
| | - Yuxuan Huang
- Department of Basic Medicine, School of Medicine, Hunan Normal University, Changsha 410013, China; (J.W.); (Y.H.); (Z.W.); (J.L.)
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, Hunan Normal University, Changsha 410013, China
| | - Zhaoxia Wang
- Department of Basic Medicine, School of Medicine, Hunan Normal University, Changsha 410013, China; (J.W.); (Y.H.); (Z.W.); (J.L.)
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, Hunan Normal University, Changsha 410013, China
| | - Jing Liu
- Department of Basic Medicine, School of Medicine, Hunan Normal University, Changsha 410013, China; (J.W.); (Y.H.); (Z.W.); (J.L.)
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, Hunan Normal University, Changsha 410013, China
| | - Zhijian Liu
- Department of Anesthesiology, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya, School of Medicine, Central South University, Changsha 410013, China;
| | - Jinfeng Yang
- Department of Anesthesiology, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya, School of Medicine, Central South University, Changsha 410013, China;
| | - Zuping He
- Department of Basic Medicine, School of Medicine, Hunan Normal University, Changsha 410013, China; (J.W.); (Y.H.); (Z.W.); (J.L.)
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, Hunan Normal University, Changsha 410013, China
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Zou J, Wu B, Tao Y, Liu Z, Zhao H, Wang P, Liang Y, Qu J, Zhang S. Inhibition of the rapamycin-insensitive mTORC1 /4E-BP1 axis attenuates TGF-β1-induced fibrotic response in human Tenon's fibroblasts. Exp Eye Res 2024; 244:109927. [PMID: 38750784 DOI: 10.1016/j.exer.2024.109927] [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: 02/02/2024] [Revised: 04/26/2024] [Accepted: 05/12/2024] [Indexed: 05/20/2024]
Abstract
Subconjunctival fibrosis is the major cause of failure in both conventional and modern minimally invasive glaucoma surgeries (MIGSs) with subconjunctival filtration. The search for safe and effective anti-fibrotic agents is critical for improving long-term surgical outcomes. In this study, we investigated the effect of inhibiting the rapamycin-insensitive mTORC1/4E-BP1 axis on the transforming growth factor-beta 1(TGF-β1)-induced fibrotic responses in human Tenon's fibroblasts (HTFs), as well as in a rat model of glaucoma filtration surgery (GFS). Primary cultured HTFs were treated with 3 ng/mL TGF-β1 for 24 h, followed by treatment with 10 μM CZ415 for additional 24 h. Rapamycin (10 μM) was utilized as a control for mTORC1/4E-BP1 signaling insensitivity. The expression levels of fibrosis-associated molecules were measured using quantitative real-time PCR, Western blotting, and immunofluorescence analysis. Cell migration was assessed through the scratch wound assay. Additionally, a rat model of GFS was employed to evaluate the anti-fibrotic effect of CZ415 in vivo. Our findings indicated that both rapamycin and CZ415 treatment significantly reduced the TGF-β1-induced cell proliferation, migration, and the expression of pro-fibrotic factors in HTFs. CZ415 also more effectively inhibited TGF-β1-mediated collagen synthesis in HTFs compared to rapamycin. Activation of mTORC1/4E-BP signaling following TGF-β1 exposure was highly suppressed by CZ415 but was only modestly inhibited by rapamycin. Furthermore, CZ415 was found to decrease subconjunctival collagen deposition in rats post GFS. Our results suggest that rapamycin-insensitive mTORC1/4E-BP1 signaling plays a critical role in TGF-β1-driven collagen synthesis in HTFs. This study demonstrated that inhibition of the mTORC1/4E-BP1 axis offers superior anti-fibrotic efficacy compared to rapamycin and represents a promising target for improving the success rate of both traditional and modern GFSs.
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Affiliation(s)
- Jiayu Zou
- The Eye Hospital, School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, China
| | - Binrong Wu
- The Eye Hospital, School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, China
| | - Yan Tao
- The Eye Hospital, School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, China
| | - Zuimeng Liu
- The Eye Hospital, School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, China
| | - Huanyu Zhao
- The Eye Hospital, School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, China
| | - Pin Wang
- The Eye Hospital, School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, China
| | - Yuanbo Liang
- The Eye Hospital, School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, China; National Clinical Research Center for Ocular Diseases, Wenzhou, China; Glaucoma Research Institute, Wenzhou Medical University, Wenzhou, China
| | - Jia Qu
- The Eye Hospital, School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, China; National Clinical Research Center for Ocular Diseases, Wenzhou, China.
| | - Shaodan Zhang
- The Eye Hospital, School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, China; National Clinical Research Center for Ocular Diseases, Wenzhou, China; Glaucoma Research Institute, Wenzhou Medical University, Wenzhou, China.
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6
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Hamadmad S, Heisler-Taylor T, Goswami S, Hawthorn E, Chaurasia S, Martini D, Summitt D, Zaatari A, Urbanski EG, Bernstein K, Racine J, Satoskar A, El-Hodiri HM, Fischer AJ, Cebulla CM. Ibudilast Protects Retinal Bipolar Cells from Excitotoxic Retinal Damage and Activates the mTOR Pathway. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585556. [PMID: 38562805 PMCID: PMC10983953 DOI: 10.1101/2024.03.18.585556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Ibudilast, an inhibitor of macrophage migration inhibitory factor (MIF) and phosphodiesterase (PDE), has been recently shown to have neuroprotective effects in a variety of neurologic diseases. We utilize a chick excitotoxic retinal damage model to investigate ibudilast's potential to protect retinal neurons. Using single cell RNA-sequencing (scRNA-seq), we find that MIF, putative MIF receptors CD74 and CD44, and several PDEs are upregulated in different retinal cells during damage. Intravitreal ibudilast is well tolerated in the eye and causes no evidence of toxicity. Ibudilast effectively protects neurons in the inner nuclear layer from NMDA-induced cell death, restores retinal layer thickness on spectral domain optical coherence tomography, and preserves retinal neuron function, particularly for the ON bipolar cells, as assessed by electroretinography. PDE inhibition seems essential for ibudilast's neuroprotection, as AV1013, the analogue that lacks PDE inhibitor activity, is ineffective. scRNA-seq analysis reveals upregulation of multiple signaling pathways, including mTOR, in damaged Müller glia (MG) with ibudilast treatment compared to AV1013. Components of mTORC1 and mTORC2 are upregulated in both bipolar cells and MG with ibudilast. The mTOR inhibitor rapamycin blocked accumulation of pS6 but did not reduce TUNEL positive dying cells. Additionally, through ligand-receptor interaction analysis, crosstalk between bipolar cells and MG may be important for neuroprotection. We have identified several paracrine signaling pathways that are known to contribute to cell survival and neuroprotection and might play essential roles in ibudilast function. These findings highlight ibudilast's potential to protect inner retinal neurons during damage and show promise for future clinical translation.
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Ankrah PK, Mensah ED, Dabie K, Mensah C, Akangbe B, Essuman J. Harnessing Genetics to Extend Lifespan and Healthspan: Current Progress and Future Directions. Cureus 2024; 16:e55495. [PMID: 38571872 PMCID: PMC10990068 DOI: 10.7759/cureus.55495] [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] [Accepted: 03/04/2024] [Indexed: 04/05/2024] Open
Abstract
Aging is inevitable, but the lifespan (duration of life) and healthspan (healthy aging) vary greatly among individuals and across species. Unlocking the secrets behind these differences has captivated scientific curiosity for ages. This review presents relevant recent advances in genetics and cell biology that are shedding new light by untangling how subtle changes in conserved genes, pathways, and epigenetic factors influence organismal senescence and associated declines. Biogerontology is a complex and rapidly growing field aimed at elucidating genetic modifications that extend lifespan and healthspan. This review explores gerontogenes, genes influencing lifespan and healthspan across species. Though subtle differences exist, long-lived individuals such as centenarians demonstrate extended healthspans, and numerous studies confirm the heritability of longevity/healthspan genes. Importantly, genes and gerontogenes are directly and indirectly involved in DNA repair, insulin/IGF-1 and mTOR signaling pathways, long non-coding RNAs, sirtuins, and heat shock proteins. The complex interactions between genetics and epigenetics are teased apart. While more research into optimizing healthspan is needed, conserved gerontogenes offer synergistic potential to forestall aging and age-related diseases. Understanding complex longevity genetics brings closer the goal of extending not only lifespan but quality years of life. The primary aim of human Biogerontology is to enhance lifespan and healthspan, but the question remains: are current genetic modifications effectively promoting healthy aging? This article collates the advancements in gerontogenes that enhance lifespan and improve healthspan alongside their potential challenges.
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Affiliation(s)
| | - Enock D Mensah
- Chemistry, Virginia Polytechnic Institute and State University, Blacksburg, USA
| | - Kwabena Dabie
- Chemistry and Chemical Biology, University of New Mexico, Albuquerque, USA
| | - Caleb Mensah
- Translational Biology, Medicine and Health, Virginia Polytechnic Institute and State University, Blacksburg, USA
| | | | - Jonathan Essuman
- School of Molecular Sciences, Arizona State University, Tempe, USA
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8
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Wang N, Zhou K, Liang Z, Sun R, Tang H, Yang Z, Zhao W, Peng Y, Song P, Zheng S, Xie H. RapaLink-1 outperforms rapamycin in alleviating allogeneic graft rejection by inhibiting the mTORC1-4E-BP1 pathway in mice. Int Immunopharmacol 2023; 125:111172. [PMID: 37951193 DOI: 10.1016/j.intimp.2023.111172] [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: 08/18/2023] [Revised: 10/16/2023] [Accepted: 10/31/2023] [Indexed: 11/13/2023]
Abstract
Inhibition of mammalian target of rapamycin (mTOR), which is a component of both mTORC1 and mTORC2, leads to clinical benefits for organ transplant recipients. Pathways to inhibit mTOR include strengthening the association of FKBP12-mTOR or competing with ATP at the active site of mTOR, which have been applied to the design of first- and second-generation mTOR inhibitors, respectively. However, the clinical efficacy of these mTOR inhibitors may be limited by side effects, compensatory activation of kinases and attenuation of feedback inhibition of receptor expression. A new generation of mTOR inhibitors possess a core structure similar to rapamycin and covalently link to mTOR kinase inhibitors, resulting in moderate selectivity and potent inhibition of mTORC1. Since the immunosuppressive potential of this class of compounds remains unknown, our goal is to examine the therapeutic efficacy of a third-generation mTOR inhibitor in organ transplantation. In this study, RapaLink-1 outperformed rapamycin in inhibiting T-cell proliferation and significantly prolonged graft survival time. Mechanistically, the ameliorated rejection induced by RapaLink-1 is associated with a reduction in p-4E-BP1 in T cells, resulting in an elevation in Treg cells alongside a decline in Th1 and Th17 cells. For the first time, these studies demonstrate the effectiveness of third-generation mTOR inhibitors in inhibiting allograft rejection, highlighting the potential of this novel class of mTOR inhibitors for further investigation.
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Affiliation(s)
- Ning Wang
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Ke Zhou
- Division of Lung Transplantation and Thoracic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Zhi Liang
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Ruiqi Sun
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Hong Tang
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Zhentao Yang
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Wentao Zhao
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Yiyang Peng
- College of Pharmaceutical Sciences, Zhejiang University, 310058 Hangzhou, China
| | - Penghong Song
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Shusen Zheng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China; Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment for Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019), Hangzhou 310003, China; NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou 310003, China; Key Laboratory of Organ Transplantation, State Key Laboratory for The Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang Province 310003, China.
| | - Haiyang Xie
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China; Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment for Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019), Hangzhou 310003, China; NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou 310003, China; Key Laboratory of Organ Transplantation, State Key Laboratory for The Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang Province 310003, China.
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9
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Sawada D, Kato H, Kaneko H, Kinoshita D, Funayama S, Minamizuka T, Takasaki A, Igarashi K, Koshizaka M, Takada-Watanabe A, Nakamura R, Aono K, Yamaguchi A, Teramoto N, Maeda Y, Ohno T, Hayashi A, Ide K, Ide S, Shoji M, Kitamoto T, Endo Y, Ogata H, Kubota Y, Mitsukawa N, Iwama A, Ouchi Y, Takayama N, Eto K, Fujii K, Takatani T, Shiohama T, Hamada H, Maezawa Y, Yokote K. Senescence-associated inflammation and inhibition of adipogenesis in subcutaneous fat in Werner syndrome. Aging (Albany NY) 2023; 15:9948-9964. [PMID: 37793000 PMCID: PMC10599740 DOI: 10.18632/aging.205078] [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: 12/07/2022] [Accepted: 09/06/2023] [Indexed: 10/06/2023]
Abstract
Werner syndrome (WS) is a hereditary premature aging disorder characterized by visceral fat accumulation and subcutaneous lipoatrophy, resulting in severe insulin resistance. However, its underlying mechanism remains unclear. In this study, we show that senescence-associated inflammation and suppressed adipogenesis play a role in subcutaneous adipose tissue reduction and dysfunction in WS. Clinical data from four Japanese patients with WS revealed significant associations between the decrease of areas of subcutaneous fat and increased insulin resistance measured by the glucose clamp. Adipose-derived stem cells from the stromal vascular fraction derived from WS subcutaneous adipose tissues (WSVF) showed early replicative senescence and a significant increase in the expression of senescence-associated secretory phenotype (SASP) markers. Additionally, adipogenesis and insulin signaling were suppressed in WSVF, and the expression of adipogenesis suppressor genes and SASP-related genes was increased. Rapamycin, an inhibitor of the mammalian target of rapamycin (mTOR), alleviated premature cellular senescence, rescued the decrease in insulin signaling, and extended the lifespan of WS model of C. elegans. To the best of our knowledge, this study is the first to reveal the critical role of cellular senescence in subcutaneous lipoatrophy and severe insulin resistance in WS, highlighting the therapeutic potential of rapamycin for this disease.
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Affiliation(s)
- Daisuke Sawada
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
- Department of Pediatrics, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Hisaya Kato
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
- Division of Diabetes, Metabolism and Endocrinology, Chiba University Hospital, Chiba, Japan
| | - Hiyori Kaneko
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
- Division of Diabetes, Metabolism and Endocrinology, Chiba University Hospital, Chiba, Japan
| | - Daisuke Kinoshita
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Shinichiro Funayama
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Takuya Minamizuka
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
- Division of Diabetes, Metabolism and Endocrinology, Chiba University Hospital, Chiba, Japan
| | - Atsushi Takasaki
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
- Division of Diabetes, Metabolism and Endocrinology, Chiba University Hospital, Chiba, Japan
| | - Katsushi Igarashi
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
- Division of Diabetes, Metabolism and Endocrinology, Chiba University Hospital, Chiba, Japan
| | - Masaya Koshizaka
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
- Division of Diabetes, Metabolism and Endocrinology, Chiba University Hospital, Chiba, Japan
| | - Aki Takada-Watanabe
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Rito Nakamura
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Kazuto Aono
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
- Division of Diabetes, Metabolism and Endocrinology, Chiba University Hospital, Chiba, Japan
| | - Ayano Yamaguchi
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
- Division of Diabetes, Metabolism and Endocrinology, Chiba University Hospital, Chiba, Japan
| | - Naoya Teramoto
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
- Division of Diabetes, Metabolism and Endocrinology, Chiba University Hospital, Chiba, Japan
| | - Yukari Maeda
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
- Division of Diabetes, Metabolism and Endocrinology, Chiba University Hospital, Chiba, Japan
| | - Tomohiro Ohno
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
- Division of Diabetes, Metabolism and Endocrinology, Chiba University Hospital, Chiba, Japan
| | - Aiko Hayashi
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
- Division of Diabetes, Metabolism and Endocrinology, Chiba University Hospital, Chiba, Japan
| | - Kana Ide
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
- Division of Diabetes, Metabolism and Endocrinology, Chiba University Hospital, Chiba, Japan
| | - Shintaro Ide
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
- Division of Diabetes, Metabolism and Endocrinology, Chiba University Hospital, Chiba, Japan
| | - Mayumi Shoji
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
- Division of Diabetes, Metabolism and Endocrinology, Chiba University Hospital, Chiba, Japan
| | - Takumi Kitamoto
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
- Division of Diabetes, Metabolism and Endocrinology, Chiba University Hospital, Chiba, Japan
| | - Yusuke Endo
- Laboratory of Medical Omics Research, Kazusa DNA Research Institute, Kisarazu, Japan
- Department of Omics Medicine, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Hideyuki Ogata
- Department of Plastic, Reconstructive, And Aesthetic Surgery, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Yoshitaka Kubota
- Department of Plastic, Reconstructive, And Aesthetic Surgery, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Nobuyuki Mitsukawa
- Department of Plastic, Reconstructive, And Aesthetic Surgery, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Atsushi Iwama
- Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yasuo Ouchi
- Department of Regenerative Medicine, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Naoya Takayama
- Department of Regenerative Medicine, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Koji Eto
- Department of Regenerative Medicine, Chiba University Graduate School of Medicine, Chiba, Japan
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Katsunori Fujii
- Department of Pediatrics, Chiba University Graduate School of Medicine, Chiba, Japan
- Department of Pediatrics, International University of Welfare and Health School of Medicine, Narita, Japan
| | - Tomozumi Takatani
- Department of Pediatrics, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Tadashi Shiohama
- Department of Pediatrics, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Hiromichi Hamada
- Department of Pediatrics, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Yoshiro Maezawa
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
- Division of Diabetes, Metabolism and Endocrinology, Chiba University Hospital, Chiba, Japan
| | - Koutaro Yokote
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
- Division of Diabetes, Metabolism and Endocrinology, Chiba University Hospital, Chiba, Japan
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10
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Steinbüchel M, Menne J, Schröter R, Neugebauer U, Schlatter E, Ciarimboli G. Regulation of Transporters for Organic Cations by High Glucose. Int J Mol Sci 2023; 24:14051. [PMID: 37762353 PMCID: PMC10531077 DOI: 10.3390/ijms241814051] [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: 08/01/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Endogenous positively charged organic substances, including neurotransmitters and cationic uremic toxins, as well as exogenous organic cations such as the anti-diabetic medication metformin, serve as substrates for organic cation transporters (OCTs) and multidrug and toxin extrusion proteins (MATEs). These proteins facilitate their transport across cell membranes. Vectorial transport through the OCT/MATE axis mediates the hepatic and renal excretion of organic cations, regulating their systemic and local concentrations. Organic cation transporters are part of the remote sensing and signaling system, whose activity can be regulated to cope with changes in the composition of extra- and intracellular fluids. Glucose, as a source of energy, can also function as a crucial signaling molecule, regulating gene expression in various organs and tissues. Its concentration in the blood may fluctuate in specific physiological and pathophysiological conditions. In this work, the regulation of the activity of organic cation transporters was measured by incubating human embryonic kidney cells stably expressing human OCT1 (hOCT1), hOCT2, or hMATE1 with high glucose concentrations (16.7 mM). Incubation with this high glucose concentration for 48 h significantly stimulated the activity of hOCT1, hOCT2, and hMATE1 by increasing their maximal velocity (Vmax), but without significantly changing their affinity for the substrates. These effects were independent of changes in osmolarity, as the addition of equimolar concentrations of mannitol did not alter transporter activity. The stimulation of transporter activity was associated with a significant increase in transporter mRNA expression. Inhibition of the mechanistic target of rapamycin (mTOR) kinase with Torin-1 suppressed the transporter stimulation induced by incubation with 16.7 mM glucose. Focusing on hOCT2, it was shown that incubation with 16.7 mM glucose increased hOCT2 protein expression in the plasma membrane. Interestingly, an apparent trend towards higher hOCT2 mRNA expression was observed in kidneys from diabetic patients, a pathology characterized by high serum glucose levels. Due to the small number of samples from diabetic patients (three), this observation must be interpreted with caution. In conclusion, incubation for 48 h with a high glucose concentration of 16.7 mM stimulated the activity and expression of organic cation transporters compared to those measured in the presence of 5.6 mM glucose. This stimulation by a diabetic environment could increase cellular uptake of the anti-diabetic drug metformin and increase renal tubular secretion of organic cations in an early stage of diabetes.
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Affiliation(s)
| | | | | | | | | | - Giuliano Ciarimboli
- Experimental Nephrology, Department of Internal Medicine D, University Hospital Münster, 48149 Münster, Germany; (M.S.); (J.M.); (R.S.); (U.N.); (E.S.)
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11
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Phillips NJ, Vinaithirthan BM, Oses-Prieto JA, Chalkley RJ, Burlingame AL. Capture, Release, and Identification of Newly Synthesized Proteins for Improved Profiling of Functional Translatomes. Mol Cell Proteomics 2023; 22:100497. [PMID: 36642223 PMCID: PMC9971285 DOI: 10.1016/j.mcpro.2023.100497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 12/17/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
New protein synthesis is regulated both at the level of mRNA transcription and translation. RNA-Seq is effective at measuring levels of mRNA expression, but techniques to monitor mRNA translation are much more limited. Previously, we reported results from O-propargyl-puromycin (OPP) labeling of proteins undergoing active translation in a 2-h time frame, followed by biotinylation using click chemistry, affinity purification, and on-bead digestion to identify nascent proteins by mass spectrometry (OPP-ID). As with any on-bead digestion protocol, the problem of nonspecific binders complicated the rigorous categorization of nascent proteins by OPP-ID. Here, we incorporate a chemically cleavable linker, Dde biotin-azide, into the protocol (OPP-IDCL) to provide specific release of modified proteins from the streptavidin beads. Following capture, the Dde moiety is readily cleaved with 2% hydrazine, releasing nascent polypeptides bearing OPP plus a residual C3H8N4 tag. When results are compared side by side with the original OPP-ID method, change to a cleavable linker led to a dramatic reduction in the number of background proteins detected in controls and a concomitant increase in the number of proteins that could be characterized as newly synthesized. We evaluated the method's ability to detect nascent proteins at various submilligram protein input levels and showed that, when starting with only 100 μg of protein, ∼1500 nascent proteins could be identified with low background. Upon treatment of K562 cells with MLN128, a potent inhibitor of the mammalian target of rapamycin, prior to OPP treatment, we identified 1915 nascent proteins, the majority of which were downregulated upon inhibitor treatment. Repressed proteins with log2 FC <-1 revealed a complex network of functionally interacting proteins, with the largest cluster associated with translational initiation. Overall, incorporation of the Dde biotin-azide cleavable linker into our protocol has increased the depth and accuracy of profiling of nascent protein networks.
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Affiliation(s)
- Nancy J Phillips
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Bala M Vinaithirthan
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Juan A Oses-Prieto
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Robert J Chalkley
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA.
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12
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Lin H. Substrate-selective small-molecule modulators of enzymes: Mechanisms and opportunities. Curr Opin Chem Biol 2023; 72:102231. [PMID: 36455490 PMCID: PMC9870951 DOI: 10.1016/j.cbpa.2022.102231] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/19/2022] [Accepted: 10/22/2022] [Indexed: 11/29/2022]
Abstract
Small-molecule inhibitors of enzymes are widely used tools in reverse chemical genetics to probe biology and explore therapeutic opportunities. They are often compared with genetic knockdown or knockout and are expected to produce phenotypes similar to the genetic perturbations. This review aims to highlight that small molecule inhibitors of enzymes and genetic perturbations may not necessarily produce the same phenotype due to the possibility of substrate-selective or substrate-dependent effects of the inhibitors. Examples of substrate-selective inhibitors and the mechanisms for the substrate-selective effects are discussed. Substrate-selective modulators of enzymes have distinct advantages and cannot be easily replaced with biologics. Thus, they present an exciting opportunity for chemical biologists and medicinal chemists.
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Affiliation(s)
- Hening Lin
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
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13
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Brüggenthies JB, Fiore A, Russier M, Bitsina C, Brötzmann J, Kordes S, Menninger S, Wolf A, Conti E, Eickhoff JE, Murray PJ. A cell-based chemical-genetic screen for amino acid stress response inhibitors reveals torins reverse stress kinase GCN2 signaling. J Biol Chem 2022; 298:102629. [PMID: 36273589 PMCID: PMC9668732 DOI: 10.1016/j.jbc.2022.102629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
Abstract
mTORC1 and GCN2 are serine/threonine kinases that control how cells adapt to amino acid availability. mTORC1 responds to amino acids to promote translation and cell growth while GCN2 senses limiting amino acids to hinder translation via eIF2α phosphorylation. GCN2 is an appealing target for cancer therapies because malignant cells can harness the GCN2 pathway to temper the rate of translation during rapid amino acid consumption. To isolate new GCN2 inhibitors, we created cell-based, amino acid limitation reporters via genetic manipulation of Ddit3 (encoding the transcription factor CHOP). CHOP is strongly induced by limiting amino acids and in this context, GCN2-dependent. Using leucine starvation as a model for essential amino acid sensing, we unexpectedly discovered ATP-competitive PI3 kinase-related kinase inhibitors, including ATR and mTOR inhibitors like torins, completely reversed GCN2 activation in a time-dependent way. Mechanistically, via inhibiting mTORC1-dependent translation, torins increased intracellular leucine, which was sufficient to reverse GCN2 activation and the downstream integrated stress response including stress-induced transcriptional factor ATF4 expression. Strikingly, we found that general translation inhibitors mirrored the effects of torins. Therefore, we propose that mTOR kinase inhibitors concurrently inhibit different branches of amino acid sensing by a dual mechanism involving direct inhibition of mTOR and indirect suppression of GCN2 that are connected by effects on the translation machinery. Collectively, our results highlight distinct ways of regulating GCN2 activity.
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Affiliation(s)
| | | | - Marion Russier
- Max Planck Institute for Biochemistry, Martinsried, Germany
| | | | | | | | | | | | - Elena Conti
- Max Planck Institute for Biochemistry, Martinsried, Germany
| | | | - Peter J. Murray
- Max Planck Institute for Biochemistry, Martinsried, Germany,For correspondence: Peter J. Murray
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14
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Blazev R, Carl CS, Ng YK, Molendijk J, Voldstedlund CT, Zhao Y, Xiao D, Kueh AJ, Miotto PM, Haynes VR, Hardee JP, Chung JD, McNamara JW, Qian H, Gregorevic P, Oakhill JS, Herold MJ, Jensen TE, Lisowski L, Lynch GS, Dodd GT, Watt MJ, Yang P, Kiens B, Richter EA, Parker BL. Phosphoproteomics of three exercise modalities identifies canonical signaling and C18ORF25 as an AMPK substrate regulating skeletal muscle function. Cell Metab 2022; 34:1561-1577.e9. [PMID: 35882232 DOI: 10.1016/j.cmet.2022.07.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/31/2022] [Accepted: 07/08/2022] [Indexed: 11/03/2022]
Abstract
Exercise induces signaling networks to improve muscle function and confer health benefits. To identify divergent and common signaling networks during and after different exercise modalities, we performed a phosphoproteomic analysis of human skeletal muscle from a cross-over intervention of endurance, sprint, and resistance exercise. This identified 5,486 phosphosites regulated during or after at least one type of exercise modality and only 420 core phosphosites common to all exercise. One of these core phosphosites was S67 on the uncharacterized protein C18ORF25, which we validated as an AMPK substrate. Mice lacking C18ORF25 have reduced skeletal muscle fiber size, exercise capacity, and muscle contractile function, and this was associated with reduced phosphorylation of contractile and Ca2+ handling proteins. Expression of C18ORF25 S66/67D phospho-mimetic reversed the decreased muscle force production. This work defines the divergent and canonical exercise phosphoproteome across different modalities and identifies C18ORF25 as a regulator of exercise signaling and muscle function.
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Affiliation(s)
- Ronnie Blazev
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia; Centre for Muscle Research, The University of Melbourne, Parkville, VIC, Australia
| | - Christian S Carl
- August Krogh Section for Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark
| | - Yaan-Kit Ng
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia; Centre for Muscle Research, The University of Melbourne, Parkville, VIC, Australia
| | - Jeffrey Molendijk
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia; Centre for Muscle Research, The University of Melbourne, Parkville, VIC, Australia
| | - Christian T Voldstedlund
- August Krogh Section for Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark
| | - Yuanyuan Zhao
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia
| | - Di Xiao
- Children's Medical Research Institute, The University of Sydney, Camperdown, NSW, Australia; School of Mathematics and Statistics, The University of Sydney, Camperdown, NSW, Australia
| | - Andrew J Kueh
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Paula M Miotto
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia
| | - Vanessa R Haynes
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia
| | - Justin P Hardee
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia; Centre for Muscle Research, The University of Melbourne, Parkville, VIC, Australia
| | - Jin D Chung
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia; Centre for Muscle Research, The University of Melbourne, Parkville, VIC, Australia
| | - James W McNamara
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia; Centre for Muscle Research, The University of Melbourne, Parkville, VIC, Australia; Murdoch Children's Research Institute and Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine, The Royal Children's Hospital, Parkville, VIC, Australia
| | - Hongwei Qian
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia; Centre for Muscle Research, The University of Melbourne, Parkville, VIC, Australia
| | - Paul Gregorevic
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia; Centre for Muscle Research, The University of Melbourne, Parkville, VIC, Australia
| | | | - Marco J Herold
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Thomas E Jensen
- August Krogh Section for Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark
| | - Leszek Lisowski
- Children's Medical Research Institute, The University of Sydney, Camperdown, NSW, Australia; Military Institute of Medicine, Warsaw, Poland
| | - Gordon S Lynch
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia; Centre for Muscle Research, The University of Melbourne, Parkville, VIC, Australia
| | - Garron T Dodd
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia
| | - Matthew J Watt
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia
| | - Pengyi Yang
- Children's Medical Research Institute, The University of Sydney, Camperdown, NSW, Australia; The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Bente Kiens
- August Krogh Section for Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark.
| | - Erik A Richter
- August Krogh Section for Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark.
| | - Benjamin L Parker
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia; Centre for Muscle Research, The University of Melbourne, Parkville, VIC, Australia.
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Zatulovskiy E, Lanz MC, Zhang S, McCarthy F, Elias JE, Skotheim JM. Delineation of proteome changes driven by cell size and growth rate. Front Cell Dev Biol 2022; 10:980721. [PMID: 36133920 PMCID: PMC9483106 DOI: 10.3389/fcell.2022.980721] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/09/2022] [Indexed: 01/10/2023] Open
Abstract
Increasing cell size drives changes to the proteome, which affects cell physiology. As cell size increases, some proteins become more concentrated while others are diluted. As a result, the state of the cell changes continuously with increasing size. In addition to these proteomic changes, large cells have a lower growth rate (protein synthesis rate per unit volume). That both the cell's proteome and growth rate change with cell size suggests they may be interdependent. To test this, we used quantitative mass spectrometry to measure how the proteome changes in response to the mTOR inhibitor rapamycin, which decreases the cellular growth rate and has only a minimal effect on cell size. We found that large cell size and mTOR inhibition, both of which lower the growth rate of a cell, remodel the proteome in similar ways. This suggests that many of the effects of cell size are mediated by the size-dependent slowdown of the cellular growth rate. For example, the previously reported size-dependent expression of some senescence markers could reflect a cell's declining growth rate rather than its size per se. In contrast, histones and other chromatin components are diluted in large cells independently of the growth rate, likely so that they remain in proportion with the genome. Finally, size-dependent changes to the cell's growth rate and proteome composition are still apparent in cells continually exposed to a saturating dose of rapamycin, which indicates that cell size can affect the proteome independently of mTORC1 signaling. Taken together, our results clarify the dependencies between cell size, growth, mTOR activity, and the proteome remodeling that ultimately controls many aspects of cell physiology.
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Affiliation(s)
| | - Michael C. Lanz
- Department of Biology, Stanford University, Stanford, CA, United States
- Chan Zuckerberg Biohub, Stanford, CA, United States
| | - Shuyuan Zhang
- Department of Biology, Stanford University, Stanford, CA, United States
| | | | | | - Jan M. Skotheim
- Department of Biology, Stanford University, Stanford, CA, United States
- Chan Zuckerberg Biohub, Stanford, CA, United States
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