1
|
Kedlian VR, Wang Y, Liu T, Chen X, Bolt L, Tudor C, Shen Z, Fasouli ES, Prigmore E, Kleshchevnikov V, Pett JP, Li T, Lawrence JEG, Perera S, Prete M, Huang N, Guo Q, Zeng X, Yang L, Polański K, Chipampe NJ, Dabrowska M, Li X, Bayraktar OA, Patel M, Kumasaka N, Mahbubani KT, Xiang AP, Meyer KB, Saeb-Parsy K, Teichmann SA, Zhang H. Human skeletal muscle aging atlas. NATURE AGING 2024; 4:727-744. [PMID: 38622407 PMCID: PMC11108788 DOI: 10.1038/s43587-024-00613-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 03/19/2024] [Indexed: 04/17/2024]
Abstract
Skeletal muscle aging is a key contributor to age-related frailty and sarcopenia with substantial implications for global health. Here we profiled 90,902 single cells and 92,259 single nuclei from 17 donors to map the aging process in the adult human intercostal muscle, identifying cellular changes in each muscle compartment. We found that distinct subsets of muscle stem cells exhibit decreased ribosome biogenesis genes and increased CCL2 expression, causing different aging phenotypes. Our atlas also highlights an expansion of nuclei associated with the neuromuscular junction, which may reflect re-innervation, and outlines how the loss of fast-twitch myofibers is mitigated through regeneration and upregulation of fast-type markers in slow-twitch myofibers with age. Furthermore, we document the function of aging muscle microenvironment in immune cell attraction. Overall, we present a comprehensive human skeletal muscle aging resource ( https://www.muscleageingcellatlas.org/ ) together with an in-house mouse muscle atlas to study common features of muscle aging across species.
Collapse
Affiliation(s)
- Veronika R Kedlian
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Yaning Wang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Tianliang Liu
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xiaoping Chen
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Liam Bolt
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Catherine Tudor
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Zhuojian Shen
- Department of Thoracic Surgery, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Eirini S Fasouli
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Elena Prigmore
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Jan Patrick Pett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Tong Li
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - John E G Lawrence
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Shani Perera
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Martin Prete
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ni Huang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Qin Guo
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xinrui Zeng
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Lu Yang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Krzysztof Polański
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Nana-Jane Chipampe
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Monika Dabrowska
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Xiaobo Li
- Core Facilities for Medical Science, Sun Yat-sen University, Guangzhou, China
| | - Omer Ali Bayraktar
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Minal Patel
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Natsuhiko Kumasaka
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Krishnaa T Mahbubani
- Department of Surgery, University of Cambridge, Cambridge, UK
- Collaborative Biorepository for Translational Medicine (CBTM), NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Andy Peng Xiang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, Cambridge, UK.
- Collaborative Biorepository for Translational Medicine (CBTM), NIHR Cambridge Biomedical Research Centre, Cambridge, UK.
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
- Cavendish Laboratory, University of Cambridge, Cambridge, UK.
| | - Hongbo Zhang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
| |
Collapse
|
2
|
Raynor JL, Chi H. Nutrients: Signal 4 in T cell immunity. J Exp Med 2024; 221:e20221839. [PMID: 38411744 PMCID: PMC10899091 DOI: 10.1084/jem.20221839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/30/2024] [Accepted: 02/02/2024] [Indexed: 02/28/2024] Open
Abstract
T cells are integral in mediating adaptive immunity to infection, autoimmunity, and cancer. Upon immune challenge, T cells exit from a quiescent state, followed by clonal expansion and effector differentiation. These processes are shaped by three established immune signals, namely antigen stimulation (Signal 1), costimulation (Signal 2), and cytokines (Signal 3). Emerging findings reveal that nutrients, including glucose, amino acids, and lipids, are crucial regulators of T cell responses and interplay with Signals 1-3, highlighting nutrients as Signal 4 to license T cell immunity. Here, we first summarize the functional importance of Signal 4 and the underlying mechanisms of nutrient transport, sensing, and signaling in orchestrating T cell activation and quiescence exit. We also discuss the roles of nutrients in programming T cell differentiation and functional fitness and how nutrients can be targeted to improve disease therapy. Understanding how T cells respond to Signal 4 nutrients in microenvironments will provide insights into context-dependent functions of adaptive immunity and therapeutic interventions.
Collapse
Affiliation(s)
- Jana L Raynor
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hongbo Chi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| |
Collapse
|
3
|
Xia L, Nie T, Lu F, Huang L, Shi X, Ren D, Lu J, Li X, Xu T, Cui B, Wang Q, Gao G, Yang Q. Direct regulation of FNIP1 and FNIP2 by MEF2 sustains MTORC1 activation and tumor progression in pancreatic cancer. Autophagy 2024; 20:505-524. [PMID: 37772772 PMCID: PMC10936626 DOI: 10.1080/15548627.2023.2259735] [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: 01/12/2023] [Accepted: 09/12/2023] [Indexed: 09/30/2023] Open
Abstract
MTOR (mechanistic target of rapamycin kinase) complex 1 (MTORC1) orchestrates diverse environmental signals to facilitate cell growth and is frequently activated in cancer. Translocation of MTORC1 from the cytosol to the lysosomal surface by the RRAG GTPases is the key step in MTORC1 activation. Here, we demonstrated that transcription factors MEF2A and MEF2D synergistically regulated MTORC1 activation via modulating its cyto-lysosome shutting. Mechanically, MEF2A and MEF2D controlled the transcription of FNIP1 and FNIP2, the components of the FLCN-FNIP1 or FNIP2 complex that acts as a RRAGC-RRAGD GTPase-activating element to promote the recruitment of MTORC1 to lysosome and its activation. Furthermore, we determined that the pro-oncogenic protein kinase SRC/c-Src directly phosphorylated MEF2D at three conserved tyrosine residues. The tyrosine phosphorylation enhanced MEF2D transcriptional activity and was indispensable for MTORC1 activation. Finally, both the protein and tyrosine phosphorylation levels of MEF2D are elevated in human pancreatic cancers, positively correlating with MTORC1 activity. Depletion of both MEF2A and MEF2D or expressing the unphosphorylatable MEF2D mutant suppressed tumor cell growth. Thus, our study revealed a transcriptional regulatory mechanism of MTORC1 that promoted cell anabolism and proliferation and uncovered its critical role in pancreatic cancer progression.Abbreviation: ACTB: actin beta; ChIP: chromatin immunoprecipitation; EGF: epidermal growth factor; EIF4EBP1: eukaryotic translation initiation factor 4E binding protein 1; FLCN: folliculin; FNIP1: folliculin interacting protein 1; FNIP2: folliculin interacting protein 2; GAP: GTPase activator protein; GEF: guanine nucleotide exchange factors; GTPase: guanosine triphosphatase; LAMP2: lysosomal associated membrane protein 2; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; MEF2: myocyte enhancer factor 2; MEF2A: myocyte enhancer factor 2A; MEF2D: myocyte enhancer factor 2D; MEF2D-3YF: Y131F, Y333F, Y337F mutant; MTOR: mechanistic target of rapamycin kinase; MTORC1: MTOR complex 1; NR4A1: nuclear receptor subfamily 4 group A member 1; RPTOR: regulatory associated protein of MTOR complex 1; RHEB: Ras homolog, mTORC1 binding; RPS6KB1: ribosomal protein S6 kinase B1; RRAG: Ras related GTP binding; RT-qPCR: real time-quantitative PCR; SRC: SRC proto-oncogene, non-receptor tyrosine kinase; TMEM192: transmembrane protein 192; WT: wild-type.
Collapse
Affiliation(s)
- Li Xia
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
- Department of Neurosurgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Tiejian Nie
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Fangfang Lu
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Lu Huang
- Department of Anesthesiology, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Xiaolong Shi
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Dongni Ren
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Jianjun Lu
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Xiaobin Li
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Tuo Xu
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Bozhou Cui
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Qing Wang
- Department of General Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Guodong Gao
- Department of Neurosurgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Qian Yang
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
| |
Collapse
|
4
|
Settembre C, Perera RM. Lysosomes as coordinators of cellular catabolism, metabolic signalling and organ physiology. Nat Rev Mol Cell Biol 2024; 25:223-245. [PMID: 38001393 DOI: 10.1038/s41580-023-00676-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2023] [Indexed: 11/26/2023]
Abstract
Every cell must satisfy basic requirements for nutrient sensing, utilization and recycling through macromolecular breakdown to coordinate programmes for growth, repair and stress adaptation. The lysosome orchestrates these key functions through the synchronised interplay between hydrolytic enzymes, nutrient transporters and signalling factors, which together enable metabolic coordination with other organelles and regulation of specific gene expression programmes. In this Review, we discuss recent findings on lysosome-dependent signalling pathways, focusing on how the lysosome senses nutrient availability through its physical and functional association with mechanistic target of rapamycin complex 1 (mTORC1) and how, in response, the microphthalmia/transcription factor E (MiT/TFE) transcription factors exert feedback regulation on lysosome biogenesis. We also highlight the emerging interactions of lysosomes with other organelles, which contribute to cellular homeostasis. Lastly, we discuss how lysosome dysfunction contributes to diverse disease pathologies and how inherited mutations that compromise lysosomal hydrolysis, transport or signalling components lead to multi-organ disorders with severe metabolic and neurological impact. A deeper comprehension of lysosomal composition and function, at both the cellular and organismal level, may uncover fundamental insights into human physiology and disease.
Collapse
Affiliation(s)
- Carmine Settembre
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy.
- Department of Clinical Medicine and Surgery, Federico II University, Naples, Italy.
| | - Rushika M Perera
- Department of Anatomy, University of California at San Francisco, San Francisco, CA, USA.
- Department of Pathology, University of California at San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA.
| |
Collapse
|
5
|
Yang S, Ting CY, Lilly MA. The GATOR2 complex maintains lysosomal-autophagic function by inhibiting the protein degradation of MiT/TFEs. Mol Cell 2024; 84:727-743.e8. [PMID: 38325378 PMCID: PMC10940221 DOI: 10.1016/j.molcel.2024.01.012] [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: 01/12/2023] [Revised: 07/31/2023] [Accepted: 01/17/2024] [Indexed: 02/09/2024]
Abstract
Lysosomes are central to metabolic homeostasis. The microphthalmia bHLH-LZ transcription factors (MiT/TFEs) family members MITF, TFEB, and TFE3 promote the transcription of lysosomal and autophagic genes and are often deregulated in cancer. Here, we show that the GATOR2 complex, an activator of the metabolic regulator TORC1, maintains lysosomal function by protecting MiT/TFEs from proteasomal degradation independent of TORC1, GATOR1, and the RAG GTPase. We determine that in GATOR2 knockout HeLa cells, members of the MiT/TFEs family are ubiquitylated by a trio of E3 ligases and are degraded, resulting in lysosome dysfunction. Additionally, we demonstrate that GATOR2 protects MiT/TFE proteins in pancreatic ductal adenocarcinoma and Xp11 translocation renal cell carcinoma, two cancers that are driven by MiT/TFE hyperactivation. In summary, we find that the GATOR2 complex has independent roles in TORC1 regulation and MiT/TFE protein protection and thus is central to coordinating cellular metabolism with control of the lysosomal-autophagic system.
Collapse
Affiliation(s)
- Shu Yang
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chun-Yuan Ting
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mary A Lilly
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
| |
Collapse
|
6
|
Xiao L, Yin Y, Sun Z, Liu J, Jia Y, Yang L, Mao Y, Peng S, Xie Z, Fang L, Li J, Xie X, Gan Z. AMPK phosphorylation of FNIP1 (S220) controls mitochondrial function and muscle fuel utilization during exercise. SCIENCE ADVANCES 2024; 10:eadj2752. [PMID: 38324677 PMCID: PMC10849678 DOI: 10.1126/sciadv.adj2752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 01/08/2024] [Indexed: 02/09/2024]
Abstract
Exercise-induced activation of adenosine monophosphate-activated protein kinase (AMPK) and substrate phosphorylation modulate the metabolic capacity of mitochondria in skeletal muscle. However, the key effector(s) of AMPK and the regulatory mechanisms remain unclear. Here, we showed that AMPK phosphorylation of the folliculin interacting protein 1 (FNIP1) serine-220 (S220) controls mitochondrial function and muscle fuel utilization during exercise. Loss of FNIP1 in skeletal muscle resulted in increased mitochondrial content and augmented metabolic capacity, leading to enhanced exercise endurance in mice. Using skeletal muscle-specific nonphosphorylatable FNIP1 (S220A) and phosphomimic (S220D) transgenic mouse models as well as biochemical analysis in primary skeletal muscle cells, we demonstrated that exercise-induced FNIP1 (S220) phosphorylation by AMPK in muscle regulates mitochondrial electron transfer chain complex assembly, fuel utilization, and exercise performance without affecting mechanistic target of rapamycin complex 1-transcription factor EB signaling. Therefore, FNIP1 is a multifunctional AMPK effector for mitochondrial adaptation to exercise, implicating a mechanism for exercise tolerance in health and disease.
Collapse
Affiliation(s)
- Liwei Xiao
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Division of Spine Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation Center (ChemBIC), Medical School of Nanjing University, Nanjing University, Nanjing, China
| | - Yujing Yin
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Division of Spine Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation Center (ChemBIC), Medical School of Nanjing University, Nanjing University, Nanjing, China
| | - Zongchao Sun
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Division of Spine Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation Center (ChemBIC), Medical School of Nanjing University, Nanjing University, Nanjing, China
| | - Jing Liu
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Division of Spine Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation Center (ChemBIC), Medical School of Nanjing University, Nanjing University, Nanjing, China
| | - Yuhuan Jia
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Division of Spine Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation Center (ChemBIC), Medical School of Nanjing University, Nanjing University, Nanjing, China
| | - Likun Yang
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Division of Spine Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation Center (ChemBIC), Medical School of Nanjing University, Nanjing University, Nanjing, China
| | - Yan Mao
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Division of Spine Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation Center (ChemBIC), Medical School of Nanjing University, Nanjing University, Nanjing, China
| | - Shujun Peng
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Zhifu Xie
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Lei Fang
- Jiangsu Key Laboratory of Molecular Medicine & Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing, China
| | - Jingya Li
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Xiaoduo Xie
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Zhenji Gan
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Division of Spine Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation Center (ChemBIC), Medical School of Nanjing University, Nanjing University, Nanjing, China
| |
Collapse
|
7
|
Baer SB, Dorn AD, Osborne DM. Sex differences in response to obesity and caloric restriction on cognition and hippocampal measures of autophagic-lysosomal transcripts and signaling pathways. BMC Neurosci 2024; 25:1. [PMID: 38166559 PMCID: PMC10759648 DOI: 10.1186/s12868-023-00840-1] [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: 04/20/2023] [Accepted: 12/18/2023] [Indexed: 01/04/2024] Open
Abstract
BACKGROUND Obesity rates in the U.S. continue to increase, with nearly 50% of the population being either obese or morbidly obese. Obesity, along with female sex, are leading risk factors for sporadic Alzheimer's Disease (AD) necessitating the need to better understand how these variables impact cellular function independent of age or genetic mutations. Animal and clinical studies both indicate that autophagy-lysosomal pathway (ALP) dysfunction is among the earliest known cellular systems to become perturbed in AD, preceding cognitive decline, yet little is known about how obesity and sex affects these cellular functions in the hippocampus, a brain region uniquely susceptible to the negative effects of obesity. We hypothesized that obesity would negatively affect key markers of ALP in the hippocampus, effects would vary based on sex, and that caloric restriction would counteract obesity effects. METHODS Female and male mice were placed on an obesogenic diet for 10 months, at which point half were switched to caloric restriction for three months, followed by cognitive testing in the Morris watermaze. Hippocampus was analyzed by western blot and qPCR. RESULTS Cognitive function in female mice responded differently to caloric restriction based on whether they were on a normal or obesogenic diet; male cognition was only mildly affected by caloric restriction and not obesity. Significant male-specific changes occurred in cellular markers of autophagy, including obesity increasing pAkt, Slc38a9, and Atg12, while caloric restriction reduced pRPS6 and increased Atg7. In contrast females experienced changes due to diet/caloric restriction predominately in lysosomal markers including increased TFE3, FLCN, FNIP2, and pAMPK. CONCLUSIONS Results support that hippocampal ALP is a target of obesity and that sex shapes molecular responses, while providing insight into how dietary manipulations affect learning and memory based on sex.
Collapse
Affiliation(s)
- Sadie B Baer
- R.S. Dow Neurobiology, Legacy Research Institute, Portland, OR, USA
| | - Adrianah D Dorn
- R.S. Dow Neurobiology, Legacy Research Institute, Portland, OR, USA
| | | |
Collapse
|
8
|
Jeong E, Willett R, Rissone A, La Spina M, Puertollano R. TMEM55B links autophagy flux, lysosomal repair, and TFE3 activation in response to oxidative stress. Nat Commun 2024; 15:93. [PMID: 38168055 PMCID: PMC10761734 DOI: 10.1038/s41467-023-44316-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024] Open
Abstract
Lysosomes have emerged as critical regulators of cellular homeostasis. Here we show that the lysosomal protein TMEM55B contributes to restore cellular homeostasis in response to oxidative stress by three different mechanisms: (1) TMEM55B mediates NEDD4-dependent PLEKHM1 ubiquitination, causing PLEKHM1 proteasomal degradation and halting autophagosome/lysosome fusion; (2) TMEM55B promotes recruitment of components of the ESCRT machinery to lysosomal membranes to stimulate lysosomal repair; and (3) TMEM55B sequesters the FLCN/FNIP complex to facilitate translocation of the transcription factor TFE3 to the nucleus, allowing expression of transcriptional programs that enable cellular adaptation to stress. Knockout of tmem55 genes in zebrafish embryos increases their susceptibility to oxidative stress, causing early death of tmem55-KO animals in response to arsenite toxicity. Altogether, our work identifies a role for TMEM55B as a molecular sensor that coordinates autophagosome degradation, lysosomal repair, and activation of stress responses.
Collapse
Affiliation(s)
- Eutteum Jeong
- Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rose Willett
- Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alberto Rissone
- Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Martina La Spina
- Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rosa Puertollano
- Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
9
|
Diesler R, Ahmad K, Chalabreysse L, Glérant JC, Harzallah I, Touraine R, Si-Mohamed S, Cottin V. [Genetic diffuse cystic lung disease in adults]. Rev Mal Respir 2024; 41:69-88. [PMID: 37951745 DOI: 10.1016/j.rmr.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 08/31/2023] [Indexed: 11/14/2023]
Abstract
Multiple cystic lung diseases comprise a wide range of various diseases, some of them of genetic origin. Lymphangioleiomyomatosis (LAM) is a disease occurring almost exclusively in women, sporadically or in association with tuberous sclerosis complex (TSC). Patients with LAM present with lymphatic complications, renal angiomyolipomas and cystic lung disease responsible for spontaneous pneumothoraces and progressive respiratory insufficiency. TSC and LAM have been ascribed to mutations in TSC1 or TSC2 genes. Patients with TSC are variably affected by cutaneous, cognitive and neuropsychiatric manifestations, epilepsy, cerebral and renal tumors, usually of benign nature. Birt-Hogg-Dubé syndrome is caused by mutations in FLCN encoding folliculin. This syndrome includes lung cysts of basal predominance, cutaneous fibrofolliculomas and various renal tumors. The main complications are spontaneous pneumothoraces and renal tumors requiring systematic screening. The mammalian target of rapamycin (mTOR) pathway is involved in the pathophysiology of TSC, sporadic LAM and Birt-Hogg-Dubé syndrome. MTOR inhibitors are used in LAM and in TSC while Birt-Hogg-Dubé syndrome does not progress towards chronic respiratory failure. Future challenges in these often under-recognized diseases include the need to reduce the delay to diagnosis, and to develop potentially curative treatments. In France, physicians can seek help from the network of reference centers for the diagnosis and management of rare pulmonary diseases.
Collapse
Affiliation(s)
- R Diesler
- UMR754, INRAE, ERN-LUNG, service de pneumologie, centre de référence coordonnateur des maladies pulmonaires rares (OrphaLung), hôpital Louis-Pradel, Hospices civils de Lyon, université Lyon 1, Lyon, France
| | - K Ahmad
- ERN-LUNG, service de pneumologie, centre de référence coordonnateur des maladies pulmonaires Rares (OrphaLung), hôpital Louis-Pradel, Hospices civils de Lyon, université Lyon 1, Lyon, France
| | - L Chalabreysse
- Service de pathologie, groupe hospitalier Est, Hospices civils de Lyon, université Lyon 1, Lyon, France
| | - J-C Glérant
- Service d'explorations fonctionnelles respiratoires, hôpital Louis-Pradel, Hospices civils de Lyon, Lyon, France
| | - I Harzallah
- Service de génétique clinique, chromosomique et moléculaire, CHU-hôpital Nord, Saint-Étienne, France
| | - R Touraine
- Service de génétique clinique, chromosomique et moléculaire, CHU-hôpital Nord, Saint-Étienne, France
| | - S Si-Mohamed
- Service d'imagerie, hôpital Louis-Pradel, Hospices civils de Lyon, université Lyon 1, Lyon, France
| | - V Cottin
- UMR754, INRAE, ERN-LUNG, service de pneumologie, centre de référence coordonnateur des maladies pulmonaires rares (OrphaLung), hôpital Louis-Pradel, Hospices civils de Lyon, université Lyon 1, Lyon, France.
| |
Collapse
|
10
|
Alchoueiry M, Cornejo K, Henske EP. Kidney cancer: Links between hereditary syndromes and sporadic tumorigenesis. Semin Diagn Pathol 2024; 41:1-7. [PMID: 38008653 DOI: 10.1053/j.semdp.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/06/2023] [Indexed: 11/28/2023]
Abstract
Multiple hereditary syndromes predispose to kidney cancer, including Von Hippel-Lindau syndrome, BAP1-Tumor Predisposition Syndrome, Hereditary Papillary Renal Cell Carcinoma, Tuberous Sclerosis Complex, Birt-Hogg-Dubé syndrome, Hereditary Paraganglioma-Pheochromocytoma Syndrome, Fumarate Hydratase Tumor Predisposition Syndrome, and Cowden syndrome. In some cases, mutations in the genes that cause hereditary kidney cancer are tightly linked to similar histologic features in sporadic RCC. For example, clear cell RCC occurs in the hereditary syndrome VHL, and sporadic ccRCC usually has inactivation of the VHL gene. In contrast, mutations in FLCN, the causative gene for Birt-Hogg-Dube syndrome, are rarely found in sporadic RCC. Here, we focus on the genes and pathways that link hereditary and sporadic RCC.
Collapse
Affiliation(s)
- Michel Alchoueiry
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kristine Cornejo
- Pathology Department, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Elizabeth P Henske
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
11
|
Talaia G, Bentley-DeSousa A, Ferguson SM. Lysosomal TBK1 Responds to Amino Acid Availability to Relieve Rab7-Dependent mTORC1 Inhibition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.16.571979. [PMID: 38168426 PMCID: PMC10760094 DOI: 10.1101/2023.12.16.571979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Lysosomes play a pivotal role in coordinating macromolecule degradation and regulating cell growth and metabolism. Despite substantial progress in identifying lysosomal signaling proteins, understanding the pathways that synchronize lysosome functions with changing cellular demands remains incomplete. This study uncovers a role for TANK-binding kinase 1 (TBK1), well known for its role in innate immunity and organelle quality control, in modulating lysosomal responsiveness to nutrients. Specifically, we identify a pool of TBK1 that is recruited to lysosomes in response to elevated amino acid levels. At lysosomes, this TBK1 phosphorylates Rab7 on serine 72. This is critical for alleviating Rab7-mediated inhibition of amino acid-dependent mTORC1 activation. Furthermore, a TBK1 mutant (E696K) associated with amyotrophic lateral sclerosis and frontotemporal dementia constitutively accumulates at lysosomes, resulting in elevated Rab7 phosphorylation and increased mTORC1 activation. This data establishes the lysosome as a site of amino acid regulated TBK1 signaling that is crucial for efficient mTORC1 activation. This lysosomal pool of TBK1 has broader implications for lysosome homeostasis, and its dysregulation could contribute to the pathogenesis of ALS-FTD.
Collapse
Affiliation(s)
- Gabriel Talaia
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Wu Tsai Institute, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Amanda Bentley-DeSousa
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Wu Tsai Institute, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Shawn M. Ferguson
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Wu Tsai Institute, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| |
Collapse
|
12
|
Takla M, Keshri S, Rubinsztein DC. The post-translational regulation of transcription factor EB (TFEB) in health and disease. EMBO Rep 2023; 24:e57574. [PMID: 37728021 PMCID: PMC10626434 DOI: 10.15252/embr.202357574] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/10/2023] [Accepted: 08/25/2023] [Indexed: 09/21/2023] Open
Abstract
Transcription factor EB (TFEB) is a basic helix-loop-helix leucine zipper transcription factor that acts as a master regulator of lysosomal biogenesis, lysosomal exocytosis, and macro-autophagy. TFEB contributes to a wide range of physiological functions, including mitochondrial biogenesis and innate and adaptive immunity. As such, TFEB is an essential component of cellular adaptation to stressors, ranging from nutrient deprivation to pathogenic invasion. The activity of TFEB depends on its subcellular localisation, turnover, and DNA-binding capacity, all of which are regulated at the post-translational level. Pathological states are characterised by a specific set of stressors, which elicit post-translational modifications that promote gain or loss of TFEB function in the affected tissue. In turn, the resulting increase or decrease in survival of the tissue in which TFEB is more or less active, respectively, may either benefit or harm the organism as a whole. In this way, the post-translational modifications of TFEB account for its otherwise paradoxical protective and deleterious effects on organismal fitness in diseases ranging from neurodegeneration to cancer. In this review, we describe how the intracellular environment characteristic of different diseases alters the post-translational modification profile of TFEB, enabling cellular adaptation to a particular pathological state.
Collapse
Affiliation(s)
- Michael Takla
- Department of Medical Genetics, Cambridge Institute for Medical Research (CIMR)University of CambridgeCambridgeUK
- UK Dementia Research Institute, Cambridge Institute for Medical Research (CIMR)University of CambridgeCambridgeUK
| | - Swati Keshri
- Department of Medical Genetics, Cambridge Institute for Medical Research (CIMR)University of CambridgeCambridgeUK
- UK Dementia Research Institute, Cambridge Institute for Medical Research (CIMR)University of CambridgeCambridgeUK
| | - David C Rubinsztein
- Department of Medical Genetics, Cambridge Institute for Medical Research (CIMR)University of CambridgeCambridgeUK
- UK Dementia Research Institute, Cambridge Institute for Medical Research (CIMR)University of CambridgeCambridgeUK
| |
Collapse
|
13
|
Sun Z, Yang L, Kiram A, Yang J, Yang Z, Xiao L, Yin Y, Liu J, Mao Y, Zhou D, Yu H, Zhou Z, Xu D, Jia Y, Ding C, Guo Q, Wang H, Li Y, Wang L, Fu T, Hu S, Gan Z. FNIP1 abrogation promotes functional revascularization of ischemic skeletal muscle by driving macrophage recruitment. Nat Commun 2023; 14:7136. [PMID: 37932296 PMCID: PMC10628247 DOI: 10.1038/s41467-023-42690-9] [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: 02/07/2023] [Accepted: 10/18/2023] [Indexed: 11/08/2023] Open
Abstract
Ischaemia of the heart and limbs attributable to compromised blood supply is a major cause of mortality and morbidity. The mechanisms of functional angiogenesis remain poorly understood, however. Here we show that FNIP1 plays a critical role in controlling skeletal muscle functional angiogenesis, a process pivotal for muscle revascularization during ischemia. Muscle FNIP1 expression is down-regulated by exercise. Genetic overexpression of FNIP1 in myofiber causes limited angiogenesis in mice, whereas its myofiber-specific ablation markedly promotes the formation of functional blood vessels. Interestingly, the increased muscle angiogenesis is independent of AMPK but due to enhanced macrophage recruitment in FNIP1-depleted muscles. Mechanistically, myofiber FNIP1 deficiency induces PGC-1α to activate chemokine gene transcription, thereby driving macrophage recruitment and muscle angiogenesis program. Furthermore, in a mouse hindlimb ischemia model of peripheral artery disease, the loss of myofiber FNIP1 significantly improved the recovery of blood flow. Thus, these results reveal a pivotal role of FNIP1 as a negative regulator of functional angiogenesis in muscle, offering insight into potential therapeutic strategies for ischemic diseases.
Collapse
Affiliation(s)
- Zongchao Sun
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Division of Spine Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Medical School of Nanjing University, Nanjing University, Nanjing, China
| | - Likun Yang
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Division of Spine Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Medical School of Nanjing University, Nanjing University, Nanjing, China
| | - Abdukahar Kiram
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Division of Spine Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Medical School of Nanjing University, Nanjing University, Nanjing, China
| | - Jing Yang
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Division of Spine Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Medical School of Nanjing University, Nanjing University, Nanjing, China
| | - Zhuangzhuang Yang
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College, Soochow University, Suzhou, China
| | - Liwei Xiao
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Division of Spine Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Medical School of Nanjing University, Nanjing University, Nanjing, China
| | - Yujing Yin
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Division of Spine Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Medical School of Nanjing University, Nanjing University, Nanjing, China
| | - Jing Liu
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Division of Spine Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Medical School of Nanjing University, Nanjing University, Nanjing, China
| | - Yan Mao
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Division of Spine Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Medical School of Nanjing University, Nanjing University, Nanjing, China
| | - Danxia Zhou
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Division of Spine Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Medical School of Nanjing University, Nanjing University, Nanjing, China
| | - Hao Yu
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Division of Spine Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Medical School of Nanjing University, Nanjing University, Nanjing, China
| | - Zheng Zhou
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Division of Spine Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Medical School of Nanjing University, Nanjing University, Nanjing, China
| | - Dengqiu Xu
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Division of Spine Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Medical School of Nanjing University, Nanjing University, Nanjing, China
| | - Yuhuan Jia
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Division of Spine Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Medical School of Nanjing University, Nanjing University, Nanjing, China
| | - Chenyun Ding
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Division of Spine Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Medical School of Nanjing University, Nanjing University, Nanjing, China
| | - Qiqi Guo
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Division of Spine Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Medical School of Nanjing University, Nanjing University, Nanjing, China
| | - Hongwei Wang
- Center for Translational Medicine and Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, China
| | - Yan Li
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Li Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Tingting Fu
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Division of Spine Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Medical School of Nanjing University, Nanjing University, Nanjing, China.
| | - Shijun Hu
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College, Soochow University, Suzhou, China.
| | - Zhenji Gan
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Division of Spine Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Medical School of Nanjing University, Nanjing University, Nanjing, China.
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing University, Nanjing, China.
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China.
| |
Collapse
|
14
|
Panwar V, Singh A, Bhatt M, Tonk RK, Azizov S, Raza AS, Sengupta S, Kumar D, Garg M. Multifaceted role of mTOR (mammalian target of rapamycin) signaling pathway in human health and disease. Signal Transduct Target Ther 2023; 8:375. [PMID: 37779156 PMCID: PMC10543444 DOI: 10.1038/s41392-023-01608-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/25/2023] [Accepted: 08/14/2023] [Indexed: 10/03/2023] Open
Abstract
The mammalian target of rapamycin (mTOR) is a protein kinase that controls cellular metabolism, catabolism, immune responses, autophagy, survival, proliferation, and migration, to maintain cellular homeostasis. The mTOR signaling cascade consists of two distinct multi-subunit complexes named mTOR complex 1/2 (mTORC1/2). mTOR catalyzes the phosphorylation of several critical proteins like AKT, protein kinase C, insulin growth factor receptor (IGF-1R), 4E binding protein 1 (4E-BP1), ribosomal protein S6 kinase (S6K), transcription factor EB (TFEB), sterol-responsive element-binding proteins (SREBPs), Lipin-1, and Unc-51-like autophagy-activating kinases. mTOR signaling plays a central role in regulating translation, lipid synthesis, nucleotide synthesis, biogenesis of lysosomes, nutrient sensing, and growth factor signaling. The emerging pieces of evidence have revealed that the constitutive activation of the mTOR pathway due to mutations/amplification/deletion in either mTOR and its complexes (mTORC1 and mTORC2) or upstream targets is responsible for aging, neurological diseases, and human malignancies. Here, we provide the detailed structure of mTOR, its complexes, and the comprehensive role of upstream regulators, as well as downstream effectors of mTOR signaling cascades in the metabolism, biogenesis of biomolecules, immune responses, and autophagy. Additionally, we summarize the potential of long noncoding RNAs (lncRNAs) as an important modulator of mTOR signaling. Importantly, we have highlighted the potential of mTOR signaling in aging, neurological disorders, human cancers, cancer stem cells, and drug resistance. Here, we discuss the developments for the therapeutic targeting of mTOR signaling with improved anticancer efficacy for the benefit of cancer patients in clinics.
Collapse
Affiliation(s)
- Vivek Panwar
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Aishwarya Singh
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University Uttar Pradesh, Sector-125, Noida, Uttar Pradesh, 201313, India
| | - Manini Bhatt
- Department of Biomedical Engineering, Indian Institute of Technology, Ropar, Punjab, 140001, India
| | - Rajiv K Tonk
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Delhi Pharmaceutical Sciences and Research University (DPSRU), New Delhi, 110017, India
| | - Shavkatjon Azizov
- Laboratory of Biological Active Macromolecular Systems, Institute of Bioorganic Chemistry, Academy of Sciences Uzbekistan, Tashkent, 100125, Uzbekistan
- Faculty of Life Sciences, Pharmaceutical Technical University, 100084, Tashkent, Uzbekistan
| | - Agha Saquib Raza
- Rajive Gandhi Super Speciality Hospital, Tahirpur, New Delhi, 110093, India
| | - Shinjinee Sengupta
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University Uttar Pradesh, Sector-125, Noida, Uttar Pradesh, 201313, India.
| | - Deepak Kumar
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Shoolini University, Solan, Himachal Pradesh, 173229, India.
| | - Manoj Garg
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University Uttar Pradesh, Sector-125, Noida, Uttar Pradesh, 201313, India.
| |
Collapse
|
15
|
Zoncu R, Perera RM. Emerging roles of the MiT/TFE factors in cancer. Trends Cancer 2023; 9:817-827. [PMID: 37400313 DOI: 10.1016/j.trecan.2023.06.005] [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: 04/13/2023] [Revised: 06/04/2023] [Accepted: 06/06/2023] [Indexed: 07/05/2023]
Abstract
The microphthalmia/transcription factor E (MiT/TFE) transcription factors (TFs; TFEB, TFE3, MITF, and TFEC) play a central role in cellular catabolism and quality control and are subject to extensive layers of regulation that influence their localization, stability, and activity. Recent studies have highlighted a broader role for these TFs in driving diverse stress-adaptation pathways, which manifest in a context- and tissue-dependent manner. Several human cancers upregulate the MiT/TFE factors to survive extreme fluctuations in nutrients, energy, and pharmacological challenges. Emerging data suggest that reduced activity of the MiT/TFE factors can also promote tumorigenesis. Here, we outline recent findings relating to novel mechanisms of regulation and activity of MiT/TFE proteins across some of the most aggressive human cancers.
Collapse
Affiliation(s)
- Roberto Zoncu
- Department of Molecular and Cellular Biology, University of California at Berkeley, Berkeley, CA 94720, USA.
| | - Rushika M Perera
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA; Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA.
| |
Collapse
|
16
|
Tu W, Cao YW, Sun M, Liu Q, Zhao HG. mTOR signaling in hair follicle and hair diseases: recent progress. Front Med (Lausanne) 2023; 10:1209439. [PMID: 37727765 PMCID: PMC10506410 DOI: 10.3389/fmed.2023.1209439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 08/23/2023] [Indexed: 09/21/2023] Open
Abstract
Mammalian target of rapamycin (mTOR) signaling pathway is a major regulator of cell proliferation and metabolism, playing significant roles in proliferation, apoptosis, inflammation, and illness. More and more evidences showed that the mTOR signaling pathway affects hair follicle circulation and maintains the stability of hair follicle stem cells. mTOR signaling may be a critical cog in Vitamin D receptor (VDR) deficiency-mediated hair follicle damage and degeneration and related alopecia disorders. This review examines the function of mTOR signaling in hair follicles and hair diseases, and talks about the underlying molecular mechanisms that mTOR signaling regulates.
Collapse
Affiliation(s)
| | | | | | | | - Heng-Guang Zhao
- Department of Dermatology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| |
Collapse
|
17
|
Yang H, Tan JX. Lysosomal quality control: molecular mechanisms and therapeutic implications. Trends Cell Biol 2023; 33:749-764. [PMID: 36717330 PMCID: PMC10374877 DOI: 10.1016/j.tcb.2023.01.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/08/2023] [Accepted: 01/10/2023] [Indexed: 01/29/2023]
Abstract
Lysosomes are essential catabolic organelles with an acidic lumen and dozens of hydrolytic enzymes. The detrimental consequences of lysosomal leakage have been well known since lysosomes were discovered during the 1950s. However, detailed knowledge of lysosomal quality control mechanisms has only emerged relatively recently. It is now clear that lysosomal leakage triggers multiple lysosomal quality control pathways that replace, remove, or directly repair damaged lysosomes. Here, we review how lysosomal damage is sensed and resolved in mammalian cells, with a focus on the molecular mechanisms underlying different lysosomal quality control pathways. We also discuss the clinical implications and therapeutic potential of these pathways.
Collapse
Affiliation(s)
- Haoxiang Yang
- Aging Institute, University of Pittsburgh School of Medicine/University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA
| | - Jay Xiaojun Tan
- Aging Institute, University of Pittsburgh School of Medicine/University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA; Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA.
| |
Collapse
|
18
|
Hu JH, Li SY, Yu LH, Guan ZR, Jiang YP, Hu D, Wang HJ, Zhao LP, Zhou ZH, Yan YX, Xie T, Huang ZH, Lou JS. TFEB: a double-edged sword for tumor metastasis. J Mol Med (Berl) 2023; 101:917-929. [PMID: 37328669 DOI: 10.1007/s00109-023-02337-0] [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: 02/18/2023] [Revised: 05/14/2023] [Accepted: 05/31/2023] [Indexed: 06/18/2023]
Abstract
Transcription factor EB, a member of the microphthalmia-associated transcription factor (MiTF/TFE) family, is a master regulator of autophagy, lysosome biogenesis, and TAMs. Metastasis is one of the main reasons for the failure of tumor therapy. Studies on the relationship between TFEB and tumor metastasis are contradictory. On the positive side, TFEB mainly affects tumor cell metastasis via five aspects, including autophagy, epithelial-mesenchymal transition (EMT), lysosomal biogenesis, lipid metabolism, and oncogenic signaling pathways; on the negative side, TFEB mainly affects tumor cell metastasis in two aspects, including tumor-associated macrophages (TAMs) and EMT. In this review, we described the detailed mechanism of TFEB-mediated regulation of metastasis. In addition, we also described the activation and inactivation of TFEB in several aspects, including the mTORC1 and Rag GTPase systems, ERK2, and AKT. However, the exact process by which TFEB regulates tumor metastasis remains unclear in some pathways, which requires further studies.
Collapse
Affiliation(s)
- Jun-Hu Hu
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines; Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
| | - Shou-Ye Li
- College of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, 311300, China
- Zhejiang Eyoung Pharmaceutical Research and Development Center, Hangzhou, Zhejiang, 311258, China
| | - Li-Hua Yu
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines; Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
| | - Zhen-Rong Guan
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines; Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
| | - Ya-Ping Jiang
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines; Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
| | - Die Hu
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines; Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
| | - Hao-Jie Wang
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines; Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
| | - Li-Ping Zhao
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines; Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
| | - Zhao-Huang Zhou
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines; Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
| | - Ya-Xin Yan
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines; Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
| | - Tian Xie
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China.
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines; Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China.
| | - Zhi-Hui Huang
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China.
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines; Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China.
| | - Jian-Shu Lou
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China.
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines; Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China.
| |
Collapse
|
19
|
Yadavalli N, Ferguson SM. LRRK2 suppresses lysosome degradative activity in macrophages and microglia through MiT-TFE transcription factor inhibition. Proc Natl Acad Sci U S A 2023; 120:e2303789120. [PMID: 37487100 PMCID: PMC10400961 DOI: 10.1073/pnas.2303789120] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 06/12/2023] [Indexed: 07/26/2023] Open
Abstract
Cells maintain optimal levels of lysosome degradative activity to protect against pathogens, clear waste, and generate nutrients. Here, we show that LRRK2, a protein that is tightly linked to Parkinson's disease, negatively regulates lysosome degradative activity in macrophages and microglia via a transcriptional mechanism. Depletion of LRRK2 and inhibition of LRRK2 kinase activity enhanced lysosomal proteolytic activity and increased the expression of multiple lysosomal hydrolases. Conversely, the kinase hyperactive LRRK2 G2019S Parkinson's disease mutant suppressed lysosomal degradative activity and gene expression. We identified MiT-TFE transcription factors (TFE3, TFEB, and MITF) as mediators of LRRK2-dependent control of lysosomal gene expression. LRRK2 negatively regulated the abundance and nuclear localization of these transcription factors and their depletion prevented LRRK2-dependent changes in lysosome protein levels. These observations define a role for LRRK2 in controlling lysosome degradative activity and support a model wherein LRRK2 hyperactivity may increase Parkinson's disease risk by suppressing lysosome degradative activity.
Collapse
Affiliation(s)
- Narayana Yadavalli
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT06510
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT06510
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT06510
- Wu Tsai Institute, Yale University School of Medicine, New Haven, CT06510
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | - Shawn M. Ferguson
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT06510
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT06510
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT06510
- Wu Tsai Institute, Yale University School of Medicine, New Haven, CT06510
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
- Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT06510
| |
Collapse
|
20
|
Doxsey DD, Tettoni SD, Egri SB, Shen K. Redundant electrostatic interactions between GATOR1 and the Rag GTPase heterodimer drive efficient amino acid sensing in human cells. J Biol Chem 2023; 299:104880. [PMID: 37269949 PMCID: PMC10316081 DOI: 10.1016/j.jbc.2023.104880] [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: 04/10/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/05/2023] Open
Abstract
Cells need to coordinate nutrient availability with their growth and proliferation. In eukaryotic cells, this coordination is mediated by the mechanistic target of the rapamycin complex 1 (mTORC1) pathway. mTORC1 activation is regulated by two GTPase units, the Rag GTPase heterodimer and the Rheb GTPase. The RagA-RagC heterodimer controls the subcellular localization of mTORC1, and its nucleotide loading states are strictly controlled by upstream regulators including amino acid sensors. A critical negative regulator of the Rag GTPase heterodimer is GATOR1. In the absence of amino acids, GATOR1 stimulates GTP hydrolysis by the RagA subunit to turn off mTORC1 signaling. Despite the enzymatic specificity of GATOR1 to RagA, a recent cryo-EM structural model of the human GATOR1-Rag-Ragulator complex reveals an unexpected interface between Depdc5, a subunit of GATOR1, and RagC. Currently, there is no functional characterization of this interface, nor do we know its biological relevance. Here, combining structure-function analysis, enzymatic kinetic measurements, and cell-based signaling assays, we identified a critical electrostatic interaction between Depdc5 and RagC. This interaction is mediated by the positively charged Arg-1407 residue on Depdc5 and a patch of negatively charged residues on the lateral side of RagC. Abrogating this interaction impairs the GAP activity of GATOR1 and cellular response to amino acid withdrawal. Our results reveal how GATOR1 coordinates the nucleotide loading states of the Rag GTPase heterodimer, and thus precisely controls cellular behavior in the absence of amino acids.
Collapse
Affiliation(s)
- Dylan D Doxsey
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Steven D Tettoni
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Shawn B Egri
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Kuang Shen
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA; Department of Biochemistry & Molecular Pharmacology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA.
| |
Collapse
|
21
|
Ishii Y, Yamaji T, Sekizuka T, Homma Y, Mori S, Takeuchi T, Kukimoto I. Folliculin Prevents Lysosomal Degradation of Human Papillomavirus To Support Infectious Cell Entry. J Virol 2023; 97:e0005623. [PMID: 37167561 PMCID: PMC10231244 DOI: 10.1128/jvi.00056-23] [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: 01/12/2023] [Accepted: 04/20/2023] [Indexed: 05/13/2023] Open
Abstract
Human papillomavirus (HPV) infects epithelial basal cells in the mucosa and either proliferates with the differentiation of the basal cells or persists in them. Multiple host factors are required to support the HPV life cycle; however, the molecular mechanisms involved in cell entry are not yet fully understood. In this study, we performed a genome-wide clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR-associated protein 9 (Cas9) knockout (KO) screen in HeLa cells and identified folliculin (FLCN), a GTPase-activating protein for Rag GTPases, as an important host factor for HPV infection. The introduction of single guide RNAs for the FLCN gene into HeLa, HaCaT, and ectocervical Ect1 cells reduced infection by HPV18 pseudovirions (18PsVs) and 16PsVs. FLCN KO HeLa cells also exhibited strong resistance to infection with 18PsVs and 16PsVs; nevertheless, they remained highly susceptible to infections with vesicular stomatitis virus glycoprotein-pseudotyped lentivirus and adeno-associated virus. Immunofluorescence microscopy revealed that the numbers of virions binding to the cell surface were slightly increased in FLCN KO cells. However, virion internalization analysis showed that the internalized virions were rapidly degraded in FLCN KO cells. This degradation was blocked by treatment with the lysosome inhibitor bafilomycin A1. Furthermore, the virion degradation phenotype was also observed in Ras-related GTP-binding protein C (RagC) KO cells. These results suggest that FLCN prevents the lysosomal degradation of incoming HPV virions by enhancing lysosomal RagC activity. IMPORTANCE Cell entry by human papillomavirus (HPV) involves a cellular retrograde transport pathway from the endosome to the trans-Golgi network/Golgi apparatus. However, the mechanism by which this viral trafficking is safeguarded is poorly understood. This is the first study showing that the GTPase-activating protein folliculin (FLCN) protects incoming HPV virions from lysosomal degradation and supports infectious cell entry by activating the Rag GTPases, presumably through the suppression of excessive lysosomal biosynthesis. These findings provide new insights into the effects of small GTPase activity regulation on HPV cell entry and enhance our understanding of the HPV degradation pathway.
Collapse
Affiliation(s)
- Yoshiyuki Ishii
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Toshiyuki Yamaji
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yuta Homma
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Seiichiro Mori
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takamasa Takeuchi
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Iwao Kukimoto
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| |
Collapse
|
22
|
Ong AJS, Bladen CE, Tigani TA, Karamalakis AP, Evason KJ, Brown KK, Cox AG. The KEAP1-NRF2 pathway regulates TFEB/TFE3-dependent lysosomal biogenesis. Proc Natl Acad Sci U S A 2023; 120:e2217425120. [PMID: 37216554 PMCID: PMC10235939 DOI: 10.1073/pnas.2217425120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 04/17/2023] [Indexed: 05/24/2023] Open
Abstract
The maintenance of redox and metabolic homeostasis is integral to embryonic development. Nuclear factor erythroid 2-related factor 2 (NRF2) is a stress-induced transcription factor that plays a central role in the regulation of redox balance and cellular metabolism. Under homeostatic conditions, NRF2 is repressed by Kelch-like ECH-associated protein 1 (KEAP1). Here, we demonstrate that Keap1 deficiency induces Nrf2 activation and postdevelopmental lethality. Loss of viability is preceded by severe liver abnormalities characterized by an accumulation of lysosomes. Mechanistically, we demonstrate that loss of Keap1 promotes aberrant activation of transcription factor EB (TFEB)/transcription factor binding to IGHM Enhancer 3 (TFE3)-dependent lysosomal biogenesis. Importantly, we find that NRF2-dependent regulation of lysosomal biogenesis is cell autonomous and evolutionarily conserved. These studies identify a role for the KEAP1-NRF2 pathway in the regulation of lysosomal biogenesis and suggest that maintenance of lysosomal homeostasis is required during embryonic development.
Collapse
Affiliation(s)
- Athena Jessica S. Ong
- Peter MacCallum Cancer Centre, Melbourne, VIC3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC3010, Australia
| | - Cerys E. Bladen
- Peter MacCallum Cancer Centre, Melbourne, VIC3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC3010, Australia
| | - Tara A. Tigani
- Peter MacCallum Cancer Centre, Melbourne, VIC3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC3010, Australia
| | - Anthony P. Karamalakis
- Peter MacCallum Cancer Centre, Melbourne, VIC3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC3010, Australia
| | - Kimberley J. Evason
- Division of Anatomic Pathology, Department of Pathology, University of Utah, Salt Lake City, UT84112
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT84112, USA
| | - Kristin K. Brown
- Peter MacCallum Cancer Centre, Melbourne, VIC3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC3010, Australia
- Department of Biochemistry and Pharmacology, The University of Melbourne, Melbourne, VIC3010, Australia
| | - Andrew G. Cox
- Peter MacCallum Cancer Centre, Melbourne, VIC3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC3010, Australia
- Department of Biochemistry and Pharmacology, The University of Melbourne, Melbourne, VIC3010, Australia
| |
Collapse
|
23
|
Di Malta C, Zampelli A, Granieri L, Vilardo C, De Cegli R, Cinque L, Nusco E, Pece S, Tosoni D, Sanguedolce F, Sorrentino NC, Merino MJ, Nielsen D, Srinivasan R, Ball MW, Ricketts CJ, Vocke CD, Lang M, Karim B, Lanfrancone L, Schmidt LS, Linehan WM, Ballabio A. TFEB and TFE3 drive kidney cystogenesis and tumorigenesis. EMBO Mol Med 2023; 15:e16877. [PMID: 36987696 PMCID: PMC10165358 DOI: 10.15252/emmm.202216877] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/30/2023] Open
Abstract
Birt-Hogg-Dubé (BHD) syndrome is an inherited familial cancer syndrome characterized by the development of cutaneous lesions, pulmonary cysts, renal tumors and cysts and caused by loss-of-function pathogenic variants in the gene encoding the tumor-suppressor protein folliculin (FLCN). FLCN acts as a negative regulator of TFEB and TFE3 transcription factors, master controllers of lysosomal biogenesis and autophagy, by enabling their phosphorylation by the mechanistic Target Of Rapamycin Complex 1 (mTORC1). We have previously shown that deletion of Tfeb rescued the renal cystic phenotype of kidney-specific Flcn KO mice. Using Flcn/Tfeb/Tfe3 double and triple KO mice, we now show that both Tfeb and Tfe3 contribute, in a differential and cooperative manner, to kidney cystogenesis. Remarkably, the analysis of BHD patient-derived tumor samples revealed increased activation of TFEB/TFE3-mediated transcriptional program and silencing either of the two genes rescued tumorigenesis in human BHD renal tumor cell line-derived xenografts (CDXs). Our findings demonstrate in disease-relevant models that both TFEB and TFE3 are key drivers of renal tumorigenesis and suggest novel therapeutic strategies based on the inhibition of these transcription factors.
Collapse
Affiliation(s)
- Chiara Di Malta
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
- Medical Genetics Unit, Department of Medical and Translational ScienceFederico II UniversityNaplesItaly
| | - Angela Zampelli
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
| | - Letizia Granieri
- Department of Experimental OncologyEuropean Institute of Oncology IRCCS (IEO)MilanItaly
| | - Claudia Vilardo
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
| | | | - Laura Cinque
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
| | - Edoardo Nusco
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
| | - Salvatore Pece
- Department of Experimental OncologyEuropean Institute of Oncology IRCCS (IEO)MilanItaly
| | - Daniela Tosoni
- Department of Experimental OncologyEuropean Institute of Oncology IRCCS (IEO)MilanItaly
| | | | - Nicolina Cristina Sorrentino
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
- Department of Clinical Medicine and SurgeryFederico II UniversityNaplesItaly
| | - Maria J Merino
- Laboratory of Pathology, Center for Cancer Research, National Cancer InstituteNational Institutes of HealthBethesdaMDUSA
| | - Deborah Nielsen
- Urologic Oncology Branch, Center for Cancer ResearchNational Cancer Institute, National Institutes of HealthBethesdaMDUSA
| | - Ramaprasad Srinivasan
- Urologic Oncology Branch, Center for Cancer ResearchNational Cancer Institute, National Institutes of HealthBethesdaMDUSA
| | - Mark W Ball
- Urologic Oncology Branch, Center for Cancer ResearchNational Cancer Institute, National Institutes of HealthBethesdaMDUSA
| | - Christopher J Ricketts
- Urologic Oncology Branch, Center for Cancer ResearchNational Cancer Institute, National Institutes of HealthBethesdaMDUSA
| | - Cathy D Vocke
- Urologic Oncology Branch, Center for Cancer ResearchNational Cancer Institute, National Institutes of HealthBethesdaMDUSA
| | - Martin Lang
- Urologic Oncology Branch, Center for Cancer ResearchNational Cancer Institute, National Institutes of HealthBethesdaMDUSA
| | - Baktiar Karim
- Molecular Histopathology LaboratoryFrederick National Laboratory for Cancer ResearchFrederickMDUSA
| | - Luisa Lanfrancone
- Department of Experimental OncologyEuropean Institute of Oncology IRCCS (IEO)MilanItaly
| | - Laura S Schmidt
- Urologic Oncology Branch, Center for Cancer ResearchNational Cancer Institute, National Institutes of HealthBethesdaMDUSA
- Basic Science Program, Frederick National Laboratory for Cancer ResearchNational Cancer InstituteFrederickMDUSA
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer ResearchNational Cancer Institute, National Institutes of HealthBethesdaMDUSA
| | - Andrea Ballabio
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
- Medical Genetics Unit, Department of Medical and Translational ScienceFederico II UniversityNaplesItaly
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTXUSA
- Jan and Dan Duncan Neurological Research InstituteTexas Children's HospitalHoustonTXUSA
| |
Collapse
|
24
|
Malik N, Ferreira BI, Hollstein PE, Curtis SD, Trefts E, Novak SW, Yu J, Gilson R, Hellberg K, Fang L, Sheridan A, Hah N, Shadel GS, Manor U, Shaw RJ. Induction of lysosomal and mitochondrial biogenesis by AMPK phosphorylation of FNIP1. Science 2023; 380:eabj5559. [PMID: 37079666 PMCID: PMC10794112 DOI: 10.1126/science.abj5559] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 03/22/2023] [Indexed: 04/22/2023]
Abstract
Cells respond to mitochondrial poisons with rapid activation of the adenosine monophosphate-activated protein kinase (AMPK), causing acute metabolic changes through phosphorylation and prolonged adaptation of metabolism through transcriptional effects. Transcription factor EB (TFEB) is a major effector of AMPK that increases expression of lysosome genes in response to energetic stress, but how AMPK activates TFEB remains unresolved. We demonstrate that AMPK directly phosphorylates five conserved serine residues in folliculin-interacting protein 1 (FNIP1), suppressing the function of the folliculin (FLCN)-FNIP1 complex. FNIP1 phosphorylation is required for AMPK to induce nuclear translocation of TFEB and TFEB-dependent increases of peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC1α) and estrogen-related receptor alpha (ERRα) messenger RNAs. Thus, mitochondrial damage triggers AMPK-FNIP1-dependent nuclear translocation of TFEB, inducing sequential waves of lysosomal and mitochondrial biogenesis.
Collapse
Affiliation(s)
- Nazma Malik
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Bibiana I. Ferreira
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Pablo E. Hollstein
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Stephanie D. Curtis
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Elijah Trefts
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Sammy Weiser Novak
- Biophotonics Core, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Jingting Yu
- Bioinformatics Core, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Rebecca Gilson
- Biophotonics Core, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Kristina Hellberg
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Lingjing Fang
- Biophotonics Core, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Arlo Sheridan
- Biophotonics Core, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Nasun Hah
- Next Generation Sequencing Core, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Gerald S. Shadel
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Uri Manor
- Biophotonics Core, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Reuben J. Shaw
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| |
Collapse
|
25
|
Cui Z, Joiner AMN, Jansen RM, Hurley JH. Amino acid sensing and lysosomal signaling complexes. Curr Opin Struct Biol 2023; 79:102544. [PMID: 36804703 DOI: 10.1016/j.sbi.2023.102544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 01/05/2023] [Accepted: 01/11/2023] [Indexed: 02/18/2023]
Abstract
Amino acid pools in the cell are monitored by dedicated sensors, whose structures are now coming into view. The lysosomal Rag GTPases are central to this pathway, and the regulation of their GAP complexes, FLCN-FNIP and GATOR1, have been worked out in detail. For FLCN-FNIP, the entire chain of events from the arginine transporter SLC38A9 to substrate-specific mTORC1 activation has been visualized. The structure GATOR2 has been determined, hinting at an ordering of amino acid signaling across a larger size scale than anticipated. The centerpiece of lysosomal signaling, mTORC1, has been revealed to recognize its substrates by more nuanced and substrate-specific mechanisms than previous appreciated. Beyond the well-studied Rag GTPase and mTORC1 machinery, another lysosomal amino acid sensor/effector system, that of PQLC2 and the C9orf72-containing CSW complex, is coming into structural view. These developments hold promise for further insights into lysosomal physiology and lysosome-centric therapeutics.
Collapse
Affiliation(s)
- Zhicheng Cui
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
| | - Aaron M N Joiner
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
| | - Rachel M Jansen
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
| | - James H Hurley
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA; Helen Wills Neuroscience Institute, University of California, Berkeley, CA 94720, USA.
| |
Collapse
|
26
|
van de Beek I, Glykofridis IE, Oosterwijk JC, van den Akker PC, Diercks GFH, Bolling MC, Waisfisz Q, Mensenkamp AR, Balk JA, Zwart R, Postma AV, Meijers-Heijboer HEJ, van Moorselaar RJA, Wolthuis RMF, Houweling AC. PRDM10 directs FLCN expression in a novel disorder overlapping with Birt-Hogg-Dubé syndrome and familial lipomatosis. Hum Mol Genet 2023; 32:1223-1235. [PMID: 36440963 PMCID: PMC10026250 DOI: 10.1093/hmg/ddac288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 11/05/2022] [Accepted: 11/19/2022] [Indexed: 11/29/2022] Open
Abstract
Birt-Hogg-Dubé syndrome (BHD) is an autosomal dominant disorder characterized by fibrofolliculomas, pulmonary cysts, pneumothoraces and renal cell carcinomas. Here, we reveal a novel hereditary disorder in a family with skin and mucosal lesions, extensive lipomatosis and renal cell carcinomas. The proband was initially diagnosed with BHD based on the presence of fibrofolliculomas, but no pathogenic germline variant was detected in FLCN, the gene associated with BHD. By whole exome sequencing we identified a heterozygous missense variant (p.(Cys677Tyr)) in a zinc-finger encoding domain of the PRDM10 gene which co-segregated with the phenotype in the family. We show that PRDM10Cys677Tyr loses affinity for a regulatory binding motif in the FLCN promoter, abrogating cellular FLCN mRNA and protein levels. Overexpressing inducible PRDM10Cys677Tyr in renal epithelial cells altered the transcription of multiple genes, showing overlap but also differences with the effects of knocking out FLCN. We propose that PRDM10 controls an extensive gene program and acts as a critical regulator of FLCN gene transcription in human cells. The germline variant PRDM10Cys677Tyr curtails cellular folliculin expression and underlies a distinguishable syndrome characterized by extensive lipomatosis, fibrofolliculomas and renal cell carcinomas.
Collapse
Affiliation(s)
- Irma van de Beek
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Human Genetics, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Iris E Glykofridis
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Human Genetics and Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Jan C Oosterwijk
- University of Groningen, University Medical Center Groningen, Department of Genetics, Hanzeplein 1, Groningen, The Netherlands
| | - Peter C van den Akker
- University of Groningen, University Medical Center Groningen, Department of Genetics, Hanzeplein 1, Groningen, The Netherlands
| | - Gilles F H Diercks
- University of Groningen, University Medical Center Groningen, Department of Pathology, Hanzeplein 1, Groningen, The Netherlands
| | - Maria C Bolling
- University of Groningen, University Medical Center Groningen, Department of Dermatology, Hanzeplein 1, Groningen, The Netherlands
| | - Quinten Waisfisz
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Human Genetics, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Arjen R Mensenkamp
- Radboudumc, Department of Human Genetics, Geert Grooteplein Zuid 10, Nijmegen, The Netherlands
| | - Jesper A Balk
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Human Genetics and Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Rob Zwart
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Human Genetics, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Alex V Postma
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Human Genetics, De Boelelaan 1117, Amsterdam, The Netherlands
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Hanne E J Meijers-Heijboer
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Human Genetics and Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - R Jeroen A van Moorselaar
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Urology and Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Rob M F Wolthuis
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Human Genetics and Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Arjan C Houweling
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Human Genetics, De Boelelaan 1117, Amsterdam, The Netherlands
| |
Collapse
|
27
|
Jansen RM, Hurley JH. Longin domain GAP complexes in nutrient signalling, membrane traffic and neurodegeneration. FEBS Lett 2023; 597:750-761. [PMID: 36367440 PMCID: PMC10050129 DOI: 10.1002/1873-3468.14538] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 11/01/2022] [Accepted: 11/07/2022] [Indexed: 11/13/2022]
Abstract
Small GTPases act as molecular switches and control numerous cellular processes by their binding and hydrolysis of guanosine triphosphate (GTP). The activity of small GTPases is coordinated by guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs). Recent structural and functional studies have characterized a subset of GAPs whose catalytic units consist of longin domains. Longin domain containing GAPs regulate small GTPases that facilitate nutrient signalling, autophagy, vesicular trafficking and lysosome homeostasis. All known examples in this GAP family function as part of larger multiprotein complexes. The three characterized mammalian protein complexes in this class are FLCN:FNIP, GATOR1 and C9orf72:SMCR8. Each complex carries out a unique cellular function by regulating distinct small GTPases. In this article, we explore the roles of longin domain GAPs in nutrient sensing, membrane dynamic, vesicular trafficking and disease. Through a structural lens, we examine the mechanism of each longin domain GAP and highlight potential therapeutic applications.
Collapse
Affiliation(s)
- Rachel M. Jansen
- Department of Molecular and Cell Biology, University of California Berkeley; Berkeley CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
| | - James H. Hurley
- Department of Molecular and Cell Biology, University of California Berkeley; Berkeley CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| |
Collapse
|
28
|
Akter F, Bonini S, Ponnaiyan S, Kögler-Mohrbacher B, Bleibaum F, Damme M, Renard BY, Winter D. Multi-Cell Line Analysis of Lysosomal Proteomes Reveals Unique Features and Novel Lysosomal Proteins. Mol Cell Proteomics 2023; 22:100509. [PMID: 36791992 PMCID: PMC10025164 DOI: 10.1016/j.mcpro.2023.100509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/15/2023] Open
Abstract
Lysosomes, the main degradative organelles of mammalian cells, play a key role in the regulation of metabolism. It is becoming more and more apparent that they are highly active, diverse, and involved in a large variety of processes. The essential role of lysosomes is exemplified by the detrimental consequences of their malfunction, which can result in lysosomal storage disorders, neurodegenerative diseases, and cancer. Using lysosome enrichment and mass spectrometry, we investigated the lysosomal proteomes of HEK293, HeLa, HuH-7, SH-SY5Y, MEF, and NIH3T3 cells. We provide evidence on a large scale for cell type-specific differences of lysosomes, showing that levels of distinct lysosomal proteins are highly variable within one cell type, while expression of others is highly conserved across several cell lines. Using differentially stable isotope-labeled cells and bimodal distribution analysis, we furthermore identify a high confidence population of lysosomal proteins for each cell line. Multi-cell line correlation of these data reveals potential novel lysosomal proteins, and we confirm lysosomal localization for six candidates. All data are available via ProteomeXchange with identifier PXD020600.
Collapse
Affiliation(s)
- Fatema Akter
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Bonn, Germany; Department of Pharmacology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Sara Bonini
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Srigayatri Ponnaiyan
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Bonn, Germany
| | | | | | - Markus Damme
- Institute for Biochemistry, University of Kiel, Kiel, Germany
| | | | - Dominic Winter
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Bonn, Germany.
| |
Collapse
|
29
|
Caligaris M, Nicastro R, Hu Z, Tripodi F, Hummel JE, Pillet B, Deprez MA, Winderickx J, Rospert S, Coccetti P, Dengjel J, De Virgilio C. Snf1/AMPK fine-tunes TORC1 signaling in response to glucose starvation. eLife 2023; 12:84319. [PMID: 36749016 PMCID: PMC9937656 DOI: 10.7554/elife.84319] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 02/06/2023] [Indexed: 02/08/2023] Open
Abstract
The AMP-activated protein kinase (AMPK) and the target of rapamycin complex 1 (TORC1) are central kinase modules of two opposing signaling pathways that control eukaryotic cell growth and metabolism in response to the availability of energy and nutrients. Accordingly, energy depletion activates AMPK to inhibit growth, while nutrients and high energy levels activate TORC1 to promote growth. Both in mammals and lower eukaryotes such as yeast, the AMPK and TORC1 pathways are wired to each other at different levels, which ensures homeostatic control of growth and metabolism. In this context, a previous study (Hughes Hallett et al., 2015) reported that AMPK in yeast, that is Snf1, prevents the transient TORC1 reactivation during the early phase following acute glucose starvation, but the underlying mechanism has remained elusive. Using a combination of unbiased mass spectrometry (MS)-based phosphoproteomics, genetic, biochemical, and physiological experiments, we show here that Snf1 temporally maintains TORC1 inactive in glucose-starved cells primarily through the TORC1-regulatory protein Pib2. Our data, therefore, extend the function of Pib2 to a hub that integrates both glucose and, as reported earlier, glutamine signals to control TORC1. We further demonstrate that Snf1 phosphorylates the TORC1 effector kinase Sch9 within its N-terminal region and thereby antagonizes the phosphorylation of a C-terminal TORC1-target residue within Sch9 itself that is critical for its activity. The consequences of Snf1-mediated phosphorylation of Pib2 and Sch9 are physiologically additive and sufficient to explain the role of Snf1 in short-term inhibition of TORC1 in acutely glucose-starved cells.
Collapse
Affiliation(s)
- Marco Caligaris
- Department of Biology, University of FribourgFribourgSwitzerland
| | | | - Zehan Hu
- Department of Biology, University of FribourgFribourgSwitzerland
| | - Farida Tripodi
- Department of Biotechnology and Biosciences, University of Milano-BicoccaMilanoItaly
| | - Johannes Erwin Hummel
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of FreiburgFreiburgGermany
| | - Benjamin Pillet
- Department of Biology, University of FribourgFribourgSwitzerland
| | | | | | - Sabine Rospert
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of FreiburgFreiburgGermany,Signalling Research Centres BIOSS and CIBSS, University of FreiburgFreiburgGermany
| | - Paola Coccetti
- Department of Biotechnology and Biosciences, University of Milano-BicoccaMilanoItaly
| | - Jörn Dengjel
- Department of Biology, University of FribourgFribourgSwitzerland
| | | |
Collapse
|
30
|
Morleo M, Vieira HL, Pennekamp P, Palma A, Bento-Lopes L, Omran H, Lopes SS, Barral DC, Franco B. Crosstalk between cilia and autophagy: implication for human diseases. Autophagy 2023; 19:24-43. [PMID: 35613303 PMCID: PMC9809938 DOI: 10.1080/15548627.2022.2067383] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Macroautophagy/autophagy is a self-degradative process necessary for cells to maintain their energy balance during development and in response to nutrient deprivation. Autophagic processes are tightly regulated and have been found to be dysfunctional in several pathologies. Increasing experimental evidence points to the existence of an interplay between autophagy and cilia. Cilia are microtubule-based organelles protruding from the cell surface of mammalian cells that perform a variety of motile and sensory functions and, when dysfunctional, result in disorders known as ciliopathies. Indeed, selective autophagic degradation of ciliary proteins has been shown to control ciliogenesis and, conversely, cilia have been reported to control autophagy. Moreover, a growing number of players such as lysosomal and mitochondrial proteins are emerging as actors of the cilia-autophagy interplay. However, some of the published data on the cilia-autophagy axis are contradictory and indicate that we are just starting to understand the underlying molecular mechanisms. In this review, the current knowledge about this axis and challenges are discussed, as well as the implication for ciliopathies and autophagy-associated disorders.
Collapse
Affiliation(s)
- Manuela Morleo
- Telethon Institute of Genetics and Medicine (TIGEM), 80078, Pozzuoli, Italy,Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Helena L.A. Vieira
- CEDOC, NOVA Medical School, NMS, Universidade NOVA de Lisboa, Lisboa1169-056, Portugal,UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal,Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Petra Pennekamp
- Department of General Pediatrics, University Hospital Münster, University of Münster, Münster48149, Germany,Member of the European Reference Networks ERN-LUNG, Lisbon, Portugal
| | - Alessandro Palma
- Department of Onco-hematology, Gene and Cell Therapy, Bambino Gesù Children’s Hospital - IRCCS, Rome, Italy
| | - Liliana Bento-Lopes
- CEDOC, NOVA Medical School, NMS, Universidade NOVA de Lisboa, Lisboa1169-056, Portugal
| | - Heymut Omran
- Department of General Pediatrics, University Hospital Münster, University of Münster, Münster48149, Germany,Member of the European Reference Networks ERN-LUNG, Lisbon, Portugal
| | - Susana S. Lopes
- CEDOC, NOVA Medical School, NMS, Universidade NOVA de Lisboa, Lisboa1169-056, Portugal,Member of the European Reference Networks ERN-LUNG, Lisbon, Portugal
| | - Duarte C. Barral
- CEDOC, NOVA Medical School, NMS, Universidade NOVA de Lisboa, Lisboa1169-056, Portugal
| | - Brunella Franco
- Telethon Institute of Genetics and Medicine (TIGEM), 80078, Pozzuoli, Italy,Medical Genetics, Department of Translational Medical Science, University of Naples “Federico II”, Naples, Italy,Scuola Superiore Meridionale, School for Advanced Studies, Naples, Italy,CONTACT Brunella Franco CEDOC, NOVA Medical School, NMS, Universidade NOVA de Lisboa, Lisboa1169-056, Portugal
| |
Collapse
|
31
|
Intracellular galectin-3 is a lipopolysaccharide sensor that promotes glycolysis through mTORC1 activation. Nat Commun 2022; 13:7578. [PMID: 36481721 PMCID: PMC9732310 DOI: 10.1038/s41467-022-35334-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 11/29/2022] [Indexed: 12/13/2022] Open
Abstract
How the carbohydrate binding protein galectin-3 might act as a diabetogenic and tumorogenic factor remains to be investigated. Here we report that intracellular galectin-3 interacts with Rag GTPases and Ragulator on lysosomes. We show that galectin-3 senses lipopolysaccharide (LPS) to facilitate the interaction of Rag GTPases and Ragulator, leading to the activation of mTORC1. We find that the lipopolysaccharide/galectin-3-Rag GTPases/Ragulator-mTORC1 axis regulates a cohort of genes including GLUT1, and HK2, and PKM2 that are critically involved in glucose uptake and glycolysis. Indeed, galectin-3 deficiency severely compromises LPS-promoted glycolysis. Importantly, the expression of HK2 is significantly reduced in diabetes patients. In multiple types of cancer including hepatocellular carcinoma (HCC), galectin-3 is highly expressed, and its level of expression is positively correlated with that of HK2 and PKM2 and negatively correlated with the prognosis of HCC patients. Our study unravels that galectin-3 is a sensor of LPS, an important modulator of the mTORC1 signaling, and a critical regulator of glucose metabolism.
Collapse
|
32
|
Webster BR, Gopal N, Ball MW. Tumorigenesis Mechanisms Found in Hereditary Renal Cell Carcinoma: A Review. Genes (Basel) 2022; 13:2122. [PMID: 36421797 PMCID: PMC9690265 DOI: 10.3390/genes13112122] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/07/2022] [Accepted: 11/11/2022] [Indexed: 09/29/2023] Open
Abstract
Renal cell carcinoma is a heterogenous cancer composed of an increasing number of unique subtypes each with their own cellular and tumor behavior. The study of hereditary renal cell carcinoma, which composes just 5% of all types of tumor cases, has allowed for the elucidation of subtype-specific tumorigenesis mechanisms that can also be applied to their sporadic counterparts. This review will focus on the major forms of hereditary renal cell carcinoma and the genetic alterations contributing to their tumorigenesis, including von Hippel Lindau syndrome, Hereditary Papillary Renal Cell Carcinoma, Succinate Dehydrogenase-Deficient Renal Cell Carcinoma, Hereditary Leiomyomatosis and Renal Cell Carcinoma, BRCA Associated Protein 1 Tumor Predisposition Syndrome, Tuberous Sclerosis, Birt-Hogg-Dubé Syndrome and Translocation RCC. The mechanisms for tumorigenesis described in this review are beginning to be exploited via the utilization of novel targets to treat renal cell carcinoma in a subtype-specific fashion.
Collapse
Affiliation(s)
| | | | - Mark W. Ball
- Center for Cancer Research, Urologic Oncology Branch, National Cancer Institute/NIH, 10 Center Drive, CRC Room 2W-5940, Bethesda, MD 20892, USA
| |
Collapse
|
33
|
Asrani K, Woo J, Mendes AA, Schaffer E, Vidotto T, Villanueva CR, Feng K, Oliveira L, Murali S, Liu HB, Salles DC, Lam B, Argani P, Lotan TL. An mTORC1-mediated negative feedback loop constrains amino acid-induced FLCN-Rag activation in renal cells with TSC2 loss. Nat Commun 2022; 13:6808. [PMID: 36357396 PMCID: PMC9649702 DOI: 10.1038/s41467-022-34617-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 11/01/2022] [Indexed: 11/12/2022] Open
Abstract
The mechanistic target of rapamycin complex 1 (mTORC1) integrates inputs from growth factors and nutrients, but how mTORC1 autoregulates its activity remains unclear. The MiT/TFE transcription factors are phosphorylated and inactivated by mTORC1 following lysosomal recruitment by RagC/D GTPases in response to amino acid stimulation. We find that starvation-induced lysosomal localization of the RagC/D GAP complex, FLCN:FNIP2, is markedly impaired in a mTORC1-sensitive manner in renal cells with TSC2 loss, resulting in unexpected TFEB hypophosphorylation and activation upon feeding. TFEB phosphorylation in TSC2-null renal cells is partially restored by destabilization of the lysosomal folliculin complex (LFC) induced by FLCN mutants and is fully rescued by forced lysosomal localization of the FLCN:FNIP2 dimer. Our data indicate that a negative feedback loop constrains amino acid-induced, FLCN:FNIP2-mediated RagC activity in renal cells with constitutive mTORC1 signaling, and the resulting MiT/TFE hyperactivation may drive oncogenesis with loss of the TSC2 tumor suppressor.
Collapse
Affiliation(s)
- Kaushal Asrani
- grid.21107.350000 0001 2171 9311Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Juhyung Woo
- grid.21107.350000 0001 2171 9311Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Adrianna A. Mendes
- grid.21107.350000 0001 2171 9311Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Ethan Schaffer
- grid.21107.350000 0001 2171 9311Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Thiago Vidotto
- grid.21107.350000 0001 2171 9311Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Clarence Rachel Villanueva
- grid.21107.350000 0001 2171 9311Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Kewen Feng
- grid.21107.350000 0001 2171 9311Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Lia Oliveira
- grid.21107.350000 0001 2171 9311Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Sanjana Murali
- grid.21107.350000 0001 2171 9311Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Hans B. Liu
- grid.21107.350000 0001 2171 9311Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Daniela C. Salles
- grid.21107.350000 0001 2171 9311Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Brandon Lam
- grid.21107.350000 0001 2171 9311Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Pedram Argani
- grid.21107.350000 0001 2171 9311Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Tamara L. Lotan
- grid.21107.350000 0001 2171 9311Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD USA ,grid.21107.350000 0001 2171 9311Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD USA ,grid.21107.350000 0001 2171 9311Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| |
Collapse
|
34
|
Napolitano G, Di Malta C, Ballabio A. Non-canonical mTORC1 signaling at the lysosome. Trends Cell Biol 2022; 32:920-931. [PMID: 35654731 DOI: 10.1016/j.tcb.2022.04.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 01/21/2023]
Abstract
The mechanistic target of rapamycin complex 1 (mTORC1) signaling hub integrates multiple environmental cues to modulate cell growth and metabolism. Over the past decade considerable knowledge has been gained on the mechanisms modulating mTORC1 lysosomal recruitment and activation. However, whether and how mTORC1 is able to elicit selective responses to diverse signals has remained elusive until recently. We discuss emerging evidence for a 'non-canonical' mTORC1 signaling pathway that controls the function of microphthalmia/transcription factor E (MiT-TFE) transcription factors, key regulators of cell metabolism. This signaling pathway is mediated by a specific mechanism of substrate recruitment, and responds to stimuli that appear to converge on the lysosomal surface. We discuss the relevance of this pathway in physiological and disease conditions.
Collapse
Affiliation(s)
- Gennaro Napolitano
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078 Pozzuoli, Naples, Italy; Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Via Pansini 5, 80131 Naples, Italy.
| | - Chiara Di Malta
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078 Pozzuoli, Naples, Italy; Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Via Pansini 5, 80131 Naples, Italy.
| | - Andrea Ballabio
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078 Pozzuoli, Naples, Italy; Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Via Pansini 5, 80131 Naples, Italy; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA.
| |
Collapse
|
35
|
Chao X, Williams SN, Ding WX. Role of mechanistic target of rapamycin in autophagy and alcohol-associated liver disease. Am J Physiol Cell Physiol 2022; 323:C1100-C1111. [PMID: 36062877 PMCID: PMC9550572 DOI: 10.1152/ajpcell.00281.2022] [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: 06/30/2022] [Revised: 08/26/2022] [Accepted: 08/26/2022] [Indexed: 11/22/2022]
Abstract
Mechanistic target of rapamycin (mTOR) is a serine-threonine kinase and a cellular sensor for nutrient and energy status, which is critical in regulating cell metabolism and growth by governing the anabolic (protein and lipid synthesis) and catabolic process (autophagy). Alcohol-associated liver disease (ALD) is a major chronic liver disease worldwide that carries a huge financial burden. The spectrum of the pathogenesis of ALD includes steatosis, fibrosis, inflammation, ductular reaction, and eventual hepatocellular carcinoma, which is closely associated with metabolic changes that are regulated by mTOR. In this review, we summarized recent progress of alcohol consumption on the changes of mTORC1 and mTORC2 activity, the potential mechanisms and possible impact of the mTORC1 changes on autophagy in ALD. We also discussed the potential beneficial effects and limitations of targeting mTORC1 against ALD.
Collapse
Affiliation(s)
- Xiaojuan Chao
- Department of Pharmacology, Toxicology and Therapeutics, The University of Kansas Medical Center, Kansas City, Kansas
| | - Sha Neisha Williams
- Department of Pharmacology, Toxicology and Therapeutics, The University of Kansas Medical Center, Kansas City, Kansas
| | - Wen-Xing Ding
- Department of Pharmacology, Toxicology and Therapeutics, The University of Kansas Medical Center, Kansas City, Kansas
| |
Collapse
|
36
|
Jansen RM, Peruzzo R, Fromm SA, Yokom AL, Zoncu R, Hurley JH. Structural basis for FLCN RagC GAP activation in MiT-TFE substrate-selective mTORC1 regulation. SCIENCE ADVANCES 2022; 8:eadd2926. [PMID: 36103527 PMCID: PMC9473554 DOI: 10.1126/sciadv.add2926] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/26/2022] [Indexed: 05/04/2023]
Abstract
The mechanistic target of rapamycin complex 1 (mTORC1) regulates cell growth and catabolism in response to nutrients through phosphorylation of key substrates. The tumor suppressor folliculin (FLCN) is a RagC/D guanosine triphosphatase (GTPase)-activating protein (GAP) that regulates mTORC1 phosphorylation of MiT-TFE transcription factors, controlling lysosome biogenesis and autophagy. We determined the cryo-electron microscopy structure of the active FLCN complex (AFC) containing FLCN, FNIP2, the N-terminal tail of SLC38A9, the RagAGDP:RagCGDP.BeFx- GTPase dimer, and the Ragulator scaffold. Relative to the inactive lysosomal FLCN complex structure, FLCN reorients by 90°, breaks contact with RagA, and makes previously unseen contacts with RagC that position its Arg164 finger for catalysis. Disruption of the AFC-specific interfaces of FLCN and FNIP2 with RagC eliminated GAP activity and led to nuclear retention of TFE3, with no effect on mTORC1 substrates S6K or 4E-BP1. The structure provides a basis for regulation of an mTORC1 substrate-specific pathway and a roadmap to discover MiT-TFE family selective mTORC1 antagonists.
Collapse
Affiliation(s)
- Rachel M. Jansen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Roberta Peruzzo
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Simon A. Fromm
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Adam L. Yokom
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Roberto Zoncu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - James H. Hurley
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| |
Collapse
|
37
|
|
38
|
Abstract
The mechanistic target of rapamycin complex 1 (mTORC1) senses nutrient levels in the cell and based on the availability, regulates cellular growth and proliferation. Its activity is tightly modulated by two GTPase units, the Rag GTPases and the Rheb GTPase. The Rag GTPases are the central hub of amino acid sensing as they summarize the amino acid signals from upstream regulators and control the subcellular localization of mTORC1. Unique from canonical signaling GTPases, the Rag GTPases are obligatory heterodimers, and the two subunits coordinate their nucleotide loading states to regulate their functional states. Robust biochemical analysis is indispensable to understanding the molecular mechanism governing the GTPase cycle. This chapter discusses protocols for purifying and biochemically characterizing the Rag GTPase heterodimer. We described two purification protocols to recombinantly produce the Rag GTPase heterodimer in large quantities. We then described assays to quantitatively measure the nucleotide binding and hydrolysis by the Rag GTPases. These assays allow for a thorough investigation of this unique heterodimeric GTPase, and they could be applicable to investigations of other noncanonical GTPases.
Collapse
Affiliation(s)
- Dylan D Doxsey
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Kuang Shen
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, United States.
| |
Collapse
|
39
|
Glykofridis IE, Henneman AA, Balk JA, Goeij-de Haas R, Westland D, Piersma SR, Knol JC, Pham TV, Boekhout M, Zwartkruis FJT, Wolthuis RMF, Jimenez CR. Phosphoproteomic analysis of FLCN inactivation highlights differential kinase pathways and regulatory TFEB phosphoserines. Mol Cell Proteomics 2022; 21:100263. [PMID: 35863698 PMCID: PMC9421328 DOI: 10.1016/j.mcpro.2022.100263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 06/21/2022] [Accepted: 06/27/2022] [Indexed: 10/26/2022] Open
Abstract
In Birt-Hogg-Dubé (BHD) syndrome, germline mutations in the Folliculin (FLCN) gene lead to an increased risk of renal cancer. To address how FLCN affects cellular kinase signaling pathways, we analyzed comprehensive phosphoproteomic profiles of FLCNPOS and FLCNNEG human renal tubular epithelial cells (RPTEC/TERT1). In total, 15744 phosphorylated peptides were identified from 4329 phosphorylated proteins. INKA analysis revealed that FLCN loss alters the activity of numerous kinases, including tyrosine kinases EGFR, MET and the Ephrin receptor subfamily (EPHA2 and EPHB1), as well their downstream targets MAPK1/3. Validation experiments in the BHD renal tumor cell line UOK257 confirmed that FLCN loss contributes to enhanced MAPK1/3 and downstream RPS6K1/3 signaling. The clinically available MAPK inhibitor Ulixertinib showed enhanced toxicity in FLCNNEG cells. Interestingly, FLCN inactivation induced the phosphorylation of PIK3CD (Tyr524) without altering the phosphorylation of canonical Akt1/Akt2/mTOR/EIF4EBP1 phosphosites. Also, we identified that FLCN inactivation resulted in dephosphorylation of TFEB Ser109, Ser114 and Ser122, which may be caused by fact that FLCNNEG cells experience oxidative stress. Together, our study highlights differential phosphorylation of specific kinases and substrates in FLCNNEG renal cells. This provides insight into BHD-associated renal tumorigenesis and may point to several novel candidates for targeted therapies.
Collapse
Affiliation(s)
- Iris E Glykofridis
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Human Genetics, Cancer Center Amsterdam, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands
| | - Alex A Henneman
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands
| | - Jesper A Balk
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Human Genetics, Cancer Center Amsterdam, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands
| | - Richard Goeij-de Haas
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands
| | - Denise Westland
- University Medical Center Utrecht, Center for Molecular Medicine, Molecular Cancer Research, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
| | - Sander R Piersma
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands
| | - Jaco C Knol
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands
| | - Thang V Pham
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands
| | - Michiel Boekhout
- University Medical Center Utrecht, Center for Molecular Medicine, Molecular Cancer Research, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands; Oncode Institute, Amsterdam, The Netherlands
| | - Fried J T Zwartkruis
- University Medical Center Utrecht, Center for Molecular Medicine, Molecular Cancer Research, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
| | - Rob M F Wolthuis
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Human Genetics, Cancer Center Amsterdam, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands.
| | - Connie R Jimenez
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands.
| |
Collapse
|
40
|
Astanina E, Bussolino F, Doronzo G. Transcription factor EB controls both motogenic and mitogenic cell activities. FEBS Lett 2022; 596:1973-1980. [PMID: 35781277 DOI: 10.1002/1873-3468.14442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/09/2022] [Accepted: 06/26/2022] [Indexed: 11/10/2022]
Abstract
Transcription factor EB (TFEB) belongs to the microphthalmia family of bHLH-leucine zipper transcription factors and was first identified as an oncogene in a subset of renal cell carcinomas. In addition to exhibiting oncogenic activity, TFEB coordinates genetic programs connected with the cellular response to stress conditions, including roles in lysosome biogenesis, autophagy, modulation of metabolism. As is the case for other transcription factors, the activities of TFEB are not limited to a specific cellular condition such as the response to stress and recent findings indicate that TFEB has more widespread functions. Here, we review the emerging roles of TFEB in regulating cellular proliferation and motility. The well-established and emerging roles of TFEB suggest that this protein serves as a hub of signalling networks involved in many non-communicable diseases, such as cancer, ischaemic diseases and immune disorders, drug resistance mechanisms, and tissue generation.
Collapse
Affiliation(s)
- Elena Astanina
- Department of Oncology, University of Torino (IT).,Candiolo Cancer Institute-IRCCS-FPO, Candiolo (Torino) (IT)
| | - Federico Bussolino
- Department of Oncology, University of Torino (IT).,Candiolo Cancer Institute-IRCCS-FPO, Candiolo (Torino) (IT)
| | - Gabriella Doronzo
- Department of Oncology, University of Torino (IT).,Candiolo Cancer Institute-IRCCS-FPO, Candiolo (Torino) (IT)
| |
Collapse
|
41
|
Yue S, Li G, He S, Li T. The central role of mTORC1 in amino acid sensing. Cancer Res 2022; 82:2964-2974. [PMID: 35749594 DOI: 10.1158/0008-5472.can-21-4403] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/28/2022] [Accepted: 06/17/2022] [Indexed: 11/16/2022]
Abstract
The mechanistic target of rapamycin (mTOR) is a master regulator of cell growth that controls cell homeostasis in response to nutrients, growth factors, and other environmental cues. Recent studies have emphasized the importance of lysosomes as a hub for nutrient sensing, especially amino acid sensing by mTORC1. This review highlights recent advances in understanding the amino acid-mTORC1 signaling axis and the role of mTORC1 in cancer.
Collapse
|
42
|
Ornelas IM, Cini FA, Wießner I, Marcos E, de Araújo D, Goto-Silva L, Nascimento J, Silva SRB, Costa MN, Falchi M, Olivieri R, Palhano-Fontes F, Sequerra E, Martins-de-Souza D, Feilding A, Rennó-Costa C, Tófoli LF, Rehen SK, Ribeiro S. Nootropic effects of LSD: Behavioral, molecular and computational evidence. Exp Neurol 2022; 356:114148. [PMID: 35732217 DOI: 10.1016/j.expneurol.2022.114148] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 06/03/2022] [Accepted: 06/14/2022] [Indexed: 11/26/2022]
Abstract
The therapeutic use of classical psychedelic substances such as d-lysergic acid diethylamide (LSD) surged in recent years. Studies in rodents suggest that these effects are produced by increased neural plasticity, including stimulation of the mTOR pathway, a key regulator of metabolism, plasticity, and aging. Could psychedelic-induced neural plasticity be harnessed to enhance cognition? Here we show that LSD treatment enhanced performance in a novel object recognition task in rats, and in a visuo-spatial memory task in humans. A proteomic analysis of human brain organoids showed that LSD affected metabolic pathways associated with neural plasticity, including mTOR. To gain insight into the relation of neural plasticity, aging and LSD-induced cognitive gains, we emulated the experiments in rats and humans with a neural network model of a cortico-hippocampal circuit. Using the baseline strength of plasticity as a proxy for age and assuming an increase in plasticity strength related to LSD dose, the simulations provided a good fit for the experimental data. Altogether, the results suggest that LSD has nootropic effects.
Collapse
Affiliation(s)
- Isis M Ornelas
- D'Or Institute for Research and Education (IDOR), Rio de Janeiro, Brazil
| | - Felipe A Cini
- Brain Institute, Federal University of Rio Grande do Norte (UFRN), Natal, Brazil
| | - Isabel Wießner
- Brain Institute, Federal University of Rio Grande do Norte (UFRN), Natal, Brazil; Interdisciplinary Cooperation for Ayahuasca Research and Outreach (ICARO), School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | - Encarni Marcos
- Instituto de Neurociencias de Alicante, Consejo Superior de Investigaciones Científicas-Universidad Miguel Hernández de Elche, San Juan de Alicante, Spain
| | - Dráulio de Araújo
- Brain Institute, Federal University of Rio Grande do Norte (UFRN), Natal, Brazil
| | - Livia Goto-Silva
- D'Or Institute for Research and Education (IDOR), Rio de Janeiro, Brazil
| | - Juliana Nascimento
- D'Or Institute for Research and Education (IDOR), Rio de Janeiro, Brazil; Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Sergio R B Silva
- Brain Institute, Federal University of Rio Grande do Norte (UFRN), Natal, Brazil
| | - Marcelo N Costa
- D'Or Institute for Research and Education (IDOR), Rio de Janeiro, Brazil; Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Marcelo Falchi
- Interdisciplinary Cooperation for Ayahuasca Research and Outreach (ICARO), School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | - Rodolfo Olivieri
- Interdisciplinary Cooperation for Ayahuasca Research and Outreach (ICARO), School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | | | - Eduardo Sequerra
- Brain Institute, Federal University of Rio Grande do Norte (UFRN), Natal, Brazil
| | - Daniel Martins-de-Souza
- D'Or Institute for Research and Education (IDOR), Rio de Janeiro, Brazil; Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil; Instituto Nacional de Biomarcadores em Neuropsiquiatria (INBION), Conselho Nacional de Desenvolvimento Científico e Tecnológico, São Paulo, Brazil; Experimental Medicine Research Cluster (EMRC), University of Campinas, Campinas, Brazil
| | | | - César Rennó-Costa
- Digital Metropolis Institute, Federal University of Rio Grande do Norte (UFRN), Natal, Brazil.
| | - Luis Fernando Tófoli
- Interdisciplinary Cooperation for Ayahuasca Research and Outreach (ICARO), School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil.
| | - Stevens K Rehen
- D'Or Institute for Research and Education (IDOR), Rio de Janeiro, Brazil; Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| | - Sidarta Ribeiro
- Brain Institute, Federal University of Rio Grande do Norte (UFRN), Natal, Brazil.
| |
Collapse
|
43
|
mTOR substrate phosphorylation in growth control. Cell 2022; 185:1814-1836. [PMID: 35580586 DOI: 10.1016/j.cell.2022.04.013] [Citation(s) in RCA: 101] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/05/2022] [Accepted: 04/07/2022] [Indexed: 12/20/2022]
Abstract
The target of rapamycin (TOR), discovered 30 years ago, is a highly conserved serine/threonine protein kinase that plays a central role in regulating cell growth and metabolism. It is activated by nutrients, growth factors, and cellular energy. TOR forms two structurally and functionally distinct complexes, TORC1 and TORC2. TOR signaling activates cell growth, defined as an increase in biomass, by stimulating anabolic metabolism while inhibiting catabolic processes. With emphasis on mammalian TOR (mTOR), we comprehensively reviewed the literature and identified all reported direct substrates. In the context of recent structural information, we discuss how mTORC1 and mTORC2, despite having a common catalytic subunit, phosphorylate distinct substrates. We conclude that the two complexes recruit different substrates to phosphorylate a common, minimal motif.
Collapse
|
44
|
Yin Y, Xu D, Mao Y, Xiao L, Sun Z, Liu J, Zhou D, Xu Z, Liu L, Fu T, Ding C, Guo Q, Sun W, Zhou Z, Yang L, Jia Y, Chen X, Gan Z. FNIP1 regulates adipocyte browning and systemic glucose homeostasis in mice by shaping intracellular calcium dynamics. J Exp Med 2022; 219:213128. [PMID: 35412553 PMCID: PMC9008465 DOI: 10.1084/jem.20212491] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/14/2022] [Accepted: 03/08/2022] [Indexed: 12/02/2022] Open
Abstract
Metabolically beneficial beige adipocytes offer tremendous potential to combat metabolic diseases. The folliculin interacting protein 1 (FNIP1) is implicated in controlling cellular metabolism via AMPK and mTORC1. However, whether and how FNIP1 regulates adipocyte browning is unclear. Here, we demonstrate that FNIP1 plays a critical role in controlling adipocyte browning and systemic glucose homeostasis. Adipocyte-specific ablation of FNIP1 promotes a broad thermogenic remodeling of adipocytes, including increased UCP1 levels, high mitochondrial content, and augmented capacity for mitochondrial respiration. Mechanistically, FNIP1 binds to and promotes the activity of SERCA, a main Ca2+ pump responsible for cytosolic Ca2+ removal. Loss of FNIP1 resulted in enhanced intracellular Ca2+ signals and consequential activation of Ca2+-dependent thermogenic program in adipocytes. Furthermore, mice lacking adipocyte FNIP1 were protected against high-fat diet–induced insulin resistance and liver steatosis. Thus, these findings reveal a pivotal role of FNIP1 as a negative regulator of beige adipocyte thermogenesis and unravel an intriguing functional link between intracellular Ca2+ dynamics and adipocyte browning.
Collapse
Affiliation(s)
- Yujing Yin
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Department of Spine Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Dengqiu Xu
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Department of Spine Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Yan Mao
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Department of Spine Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Liwei Xiao
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Department of Spine Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Zongchao Sun
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Department of Spine Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Jing Liu
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Department of Spine Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Danxia Zhou
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Department of Spine Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Zhisheng Xu
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Department of Spine Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Lin Liu
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Department of Spine Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Tingting Fu
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Department of Spine Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Chenyun Ding
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Department of Spine Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Qiqi Guo
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Department of Spine Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Wanping Sun
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Department of Spine Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Zheng Zhou
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Department of Spine Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Likun Yang
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Department of Spine Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Yuhuan Jia
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Department of Spine Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Xinyi Chen
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Department of Spine Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Zhenji Gan
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Department of Spine Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing University Medical School, Nanjing University, Nanjing, China
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University Medical School, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, China
| |
Collapse
|
45
|
Jain V, Bose S, Arya AK, Arif T. Lysosomes in Stem Cell Quiescence: A Potential Therapeutic Target in Acute Myeloid Leukemia. Cancers (Basel) 2022; 14:cancers14071618. [PMID: 35406389 PMCID: PMC8996909 DOI: 10.3390/cancers14071618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/19/2022] [Accepted: 03/21/2022] [Indexed: 12/12/2022] Open
Abstract
Lysosomes are cellular organelles that regulate essential biological processes such as cellular homeostasis, development, and aging. They are primarily connected to the degradation/recycling of cellular macromolecules and participate in cellular trafficking, nutritional signaling, energy metabolism, and immune regulation. Therefore, lysosomes connect cellular metabolism and signaling pathways. Lysosome's involvement in the critical biological processes has rekindled clinical interest towards this organelle for treating various diseases, including cancer. Recent research advancements have demonstrated that lysosomes also regulate the maintenance and hemostasis of hematopoietic stem cells (HSCs), which play a critical role in the progression of acute myeloid leukemia (AML) and other types of cancer. Lysosomes regulate both HSCs' metabolic networks and identity transition. AML is a lethal type of blood cancer with a poor prognosis that is particularly associated with aging. Although the genetic landscape of AML has been extensively described, only a few targeted therapies have been produced, warranting the need for further research. This review summarizes the functions and importance of targeting lysosomes in AML, while highlighting the significance of lysosomes in HSCs maintenance.
Collapse
Affiliation(s)
- Vaibhav Jain
- Abramson Cancer Center, Department of Medicine, 421 Curie Blvd., Philadelphia, PA 19104, USA;
| | - Swaroop Bose
- Department of Dermatology, Mount Sinai Icahn School of Medicine, New York, NY 10029, USA;
| | - Awadhesh K. Arya
- Department of Anesthesiology, Shock, Trauma and Anesthesiology Research Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA;
| | - Tasleem Arif
- Department of Cell, Developmental, and Regenerative Biology, Mount Sinai Icahn School of Medicine, New York, NY 10029, USA
- Correspondence: ; Tel.: +212-241-4143; Fax: +212-860-9279
| |
Collapse
|
46
|
Folliculin promotes substrate-selective mTORC1 activity by activating RagC to recruit TFE3. PLoS Biol 2022; 20:e3001594. [PMID: 35358174 PMCID: PMC9004751 DOI: 10.1371/journal.pbio.3001594] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/12/2022] [Accepted: 03/07/2022] [Indexed: 12/30/2022] Open
Abstract
Mechanistic target of rapamycin complex I (mTORC1) is central to cellular metabolic regulation. mTORC1 phosphorylates a myriad of substrates, but how different substrate specificity is conferred on mTORC1 by different conditions remains poorly defined. Here, we show how loss of the mTORC1 regulator folliculin (FLCN) renders mTORC1 specifically incompetent to phosphorylate TFE3, a master regulator of lysosome biogenesis, without affecting phosphorylation of other canonical mTORC1 substrates, such as S6 kinase. FLCN is a GTPase-activating protein (GAP) for RagC, a component of the mTORC1 amino acid (AA) sensing pathway, and we show that active RagC is necessary and sufficient to recruit TFE3 onto the lysosomal surface, allowing subsequent phosphorylation of TFE3 by mTORC1. Active mutants of RagC, but not of RagA, rescue both phosphorylation and lysosomal recruitment of TFE3 in the absence of FLCN. These data thus advance the paradigm that mTORC1 substrate specificity is in part conferred by direct recruitment of substrates to the subcellular compartments where mTORC1 resides and identify potential targets for specific modulation of specific branches of the mTOR pathway. How does the mTORC1 complex, which influences myriad cellular processes, achieve specificity? This study shows that substrate specificity is in part conferred by modulating the recruitment of substrates, in this case the transcription factor TFE3, to mTORC1.
Collapse
|
47
|
Xie Z, Zhang W, Zhang Y. Loss of Slc38a4 imprinting is a major cause of mouse placenta hyperplasia in somatic cell nuclear transferred embryos at late gestation. Cell Rep 2022; 38:110407. [PMID: 35196486 PMCID: PMC8919768 DOI: 10.1016/j.celrep.2022.110407] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 11/02/2021] [Accepted: 01/26/2022] [Indexed: 12/12/2022] Open
Abstract
Placenta hyperplasia is commonly observed in cloned animals and is believed to impede the proper development of cloned embryos. However, the mechanism underlying this phenomenon is largely unknown. Here, we show that placenta hyperplasia of cloned mouse embryos occurs in both middle and late gestation. Interestingly, restoring paternal-specific expression of an amino acid transporter Slc38a4, which loses maternal H3K27me3-dependent imprinting and becomes biallelically expressed in cloned placentae, rescues the overgrowth of cloned placentae at late gestation. Molecular analyses reveal that loss of Slc38a4 imprinting leads to over-activation of the mechanistic target of rapamycin complex 1 (mTORC1) signaling pathway in cloned placentae, which is likely due to the increased amino acids transport by SLC38A4. Collectively, our study not only reveals loss of Slc38a4 imprinting is responsible for overgrowth of cloned placentae at late gestation but also suggests the underlying mechanism involves increased amino acid transport and over-activation of mTORC1.
Collapse
Affiliation(s)
- Zhenfei Xie
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA; The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
| | - Wenhao Zhang
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Yi Zhang
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, WAB-149G, 200 Longwood Avenue, Boston, MA 02115, USA.
| |
Collapse
|
48
|
Biondini M, Kiepas A, El-Houjeiri L, Annis MG, Hsu BE, Fortier AM, Morin G, Martina JA, Sirois I, Aguilar-Mahecha A, Gruosso T, McGuirk S, Rose AAN, Tokat UM, Johnson RM, Sahin O, Bareke E, St-Pierre J, Park M, Basik M, Majewski J, Puertollano R, Pause A, Huang S, Keler T, Siegel PM. HSP90 inhibitors induce GPNMB cell-surface expression by modulating lysosomal positioning and sensitize breast cancer cells to glembatumumab vedotin. Oncogene 2022; 41:1701-1717. [PMID: 35110681 DOI: 10.1038/s41388-022-02206-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 12/29/2021] [Accepted: 01/20/2022] [Indexed: 12/18/2022]
Abstract
Transmembrane glycoprotein NMB (GPNMB) is a prognostic marker of poor outcome in patients with triple-negative breast cancer (TNBC). Glembatumumab Vedotin, an antibody drug conjugate targeting GPNMB, exhibits variable efficacy against GPNMB-positive metastatic TNBC as a single agent. We show that GPNMB levels increase in response to standard-of-care and experimental therapies for multiple breast cancer subtypes. While these therapeutic stressors induce GPNMB expression through differential engagement of the MiTF family of transcription factors, not all are capable of increasing GPNMB cell-surface localization required for Glembatumumab Vedotin inhibition. Using a FACS-based genetic screen, we discovered that suppression of heat shock protein 90 (HSP90) concomitantly increases GPNMB expression and cell-surface localization. Mechanistically, HSP90 inhibition resulted in lysosomal dispersion towards the cell periphery and fusion with the plasma membrane, which delivers GPNMB to the cell surface. Finally, treatment with HSP90 inhibitors sensitizes breast cancers to Glembatumumab Vedotin in vivo, suggesting that combination of HSP90 inhibitors and Glembatumumab Vedotin may be a viable treatment strategy for patients with metastatic TNBC.
Collapse
Affiliation(s)
- Marco Biondini
- Goodman Cancer Research Institute, McGill University, Montreal, QC, Canada.,Department of Medicine, McGill University, Montreal, QC, Canada
| | - Alex Kiepas
- Goodman Cancer Research Institute, McGill University, Montreal, QC, Canada.,Department of Physiology, McGill University, Montreal, QC, Canada
| | - Leeanna El-Houjeiri
- Goodman Cancer Research Institute, McGill University, Montreal, QC, Canada.,Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Matthew G Annis
- Goodman Cancer Research Institute, McGill University, Montreal, QC, Canada.,Department of Medicine, McGill University, Montreal, QC, Canada
| | - Brian E Hsu
- Goodman Cancer Research Institute, McGill University, Montreal, QC, Canada.,Department of Medicine, McGill University, Montreal, QC, Canada
| | - Anne-Marie Fortier
- Goodman Cancer Research Institute, McGill University, Montreal, QC, Canada.,Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Geneviève Morin
- Goodman Cancer Research Institute, McGill University, Montreal, QC, Canada.,Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - José A Martina
- Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Isabelle Sirois
- Segal Cancer Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, Montreal, QC, Canada
| | - Adriana Aguilar-Mahecha
- Segal Cancer Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, Montreal, QC, Canada
| | - Tina Gruosso
- Goodman Cancer Research Institute, McGill University, Montreal, QC, Canada.,Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Shawn McGuirk
- Goodman Cancer Research Institute, McGill University, Montreal, QC, Canada.,Department of Physiology, McGill University, Montreal, QC, Canada
| | - April A N Rose
- Department of Oncology and Surgery, McGill University, Montreal, QC, Canada
| | - Unal M Tokat
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | | | - Ozgur Sahin
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC, USA
| | - Eric Bareke
- Genome Québec Innovation Center, McGill University, Montreal, QC, Canada.,Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Julie St-Pierre
- Department of Biochemistry, Microbiology and Immunology and Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
| | - Morag Park
- Goodman Cancer Research Institute, McGill University, Montreal, QC, Canada.,Department of Medicine, McGill University, Montreal, QC, Canada.,Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Mark Basik
- Segal Cancer Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, Montreal, QC, Canada.,Department of Oncology and Surgery, McGill University, Montreal, QC, Canada
| | - Jacek Majewski
- Genome Québec Innovation Center, McGill University, Montreal, QC, Canada.,Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Rosa Puertollano
- Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Arnim Pause
- Goodman Cancer Research Institute, McGill University, Montreal, QC, Canada.,Department of Medicine, McGill University, Montreal, QC, Canada
| | - Sidong Huang
- Goodman Cancer Research Institute, McGill University, Montreal, QC, Canada.,Department of Biochemistry, McGill University, Montreal, QC, Canada
| | | | - Peter M Siegel
- Goodman Cancer Research Institute, McGill University, Montreal, QC, Canada. .,Department of Medicine, McGill University, Montreal, QC, Canada. .,Department of Biochemistry, McGill University, Montreal, QC, Canada.
| |
Collapse
|
49
|
Hasegawa J, Tokuda E, Yao Y, Sasaki T, Inoki K, Weisman LS. PP2A-dependent TFEB activation is blocked by PIKfyve-induced mTORC1 activity. Mol Biol Cell 2022; 33:ar26. [PMID: 35020443 PMCID: PMC9250387 DOI: 10.1091/mbc.e21-06-0309] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Transcriptional factor EB (TFEB) is a master regulator of genes required for autophagy and lysosomal function. The nuclear localization of TFEB is blocked by the mechanistic target of rapamycin complex 1 (mTORC1)-dependent phosphorylation of TFEB at multiple sites including Ser-211. Here we show that inhibition of PIKfyve, which produces phosphatidylinositol 3,5-bisphosphate on endosomes and lysosomes, causes a loss of Ser-211 phosphorylation and concomitant nuclear localization of TFEB. We found that while mTORC1 activity toward S6K1, as well as other major mTORC1 substrates, is not impaired, PIKfyve inhibition specifically impedes the interaction of TFEB with mTORC1. This suggests that mTORC1 activity on TFEB is selectively inhibited due to loss of mTORC1 access to TFEB. In addition, we found that TFEB activation during inhibition of PIKfyve relies on the ability of protein phosphatase 2A (PP2A) but not calcineurin/PPP3 to dephosphorylate TFEB Ser-211. Thus when PIKfyve is inhibited, PP2A is dominant over mTORC1 for control of TFEB phosphorylation at Ser-S211. Together these findings suggest that mTORC1 and PP2A have opposing roles on TFEB via phosphorylation and dephosphorylation of Ser-211, respectively, and further that PIKfyve inhibits TFEB activity by facilitating mTORC1-dependent phosphorylation of TFEB.
Collapse
Affiliation(s)
- Junya Hasegawa
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109, USA.,Department of Biochemical Pathophysiology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Emi Tokuda
- Department of Biochemical Pathophysiology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Yao Yao
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109, USA
| | - Takehiko Sasaki
- Department of Biochemical Pathophysiology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Ken Inoki
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109, USA.,Department of Molecular and Integrative Physiology, University of Michigan Medical School, 1137 East Catherine Street, Ann Arbor, MI 48109, USA.,Department of Internal Medicine, University of Michigan Medical School, 1500 East Medical enter Drive, Ann Arbor, MI 48109, USA
| | - Lois S Weisman
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109, USA.,Department of Cell and Developmental Biology, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI 48109
| |
Collapse
|
50
|
Bouhamdani N, Comeau D, Turcotte S. A Compendium of Information on the Lysosome. Front Cell Dev Biol 2022; 9:798262. [PMID: 34977038 PMCID: PMC8714965 DOI: 10.3389/fcell.2021.798262] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/02/2021] [Indexed: 12/16/2022] Open
Abstract
For a long time, lysosomes were considered as mere waste bags for cellular constituents. Thankfully, studies carried out in the past 15 years were brimming with elegant and crucial breakthroughs in lysosome research, uncovering their complex roles as nutrient sensors and characterizing them as crucial multifaceted signaling organelles. This review presents the scientific knowledge on lysosome physiology and functions, starting with their discovery and reviewing up to date ground-breaking discoveries highlighting their heterogeneous functions as well as pending questions that remain to be answered. We also review the roles of lysosomes in anti-cancer drug resistance and how they undergo a series of molecular and functional changes during malignant transformation which lead to tumor aggression, angiogenesis, and metastases. Finally, we discuss the strategy of targeting lysosomes in cancer which could lead to the development of new and effective targeted therapies.
Collapse
Affiliation(s)
- Nadia Bouhamdani
- Department of Chemistry and Biochemistry, Université de Moncton, Moncton, NB, Canada.,Dr. Georges-L. Dumont University Hospital Centre, Clinical Research Sector, Vitalité Health Network, Moncton, NB, Canada.,Atlantic Cancer Research Institute, Moncton, NB, Canada
| | - Dominique Comeau
- Department of Chemistry and Biochemistry, Université de Moncton, Moncton, NB, Canada.,Atlantic Cancer Research Institute, Moncton, NB, Canada
| | - Sandra Turcotte
- Department of Chemistry and Biochemistry, Université de Moncton, Moncton, NB, Canada.,Atlantic Cancer Research Institute, Moncton, NB, Canada
| |
Collapse
|