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Rojas-Rivera D, Beltrán S, Muñoz-Carvajal F, Ahumada-Montalva P, Abarzúa L, Gomez L, Hernandez F, Bergmann CA, Labrador L, Calegaro-Nassif M, Bertrand MJM, Manque PA, Woehlbier U. The autophagy protein RUBCNL/PACER represses RIPK1 kinase-dependent apoptosis and necroptosis. Autophagy 2024:1-16. [PMID: 38873940 DOI: 10.1080/15548627.2024.2367923] [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: 11/16/2023] [Accepted: 06/10/2024] [Indexed: 06/15/2024] Open
Abstract
Mesenchymal stem cells (MSCs) are used in cell therapy; nonetheless, their application is limited by their poor survival after transplantation in a proinflammatory microenvironment. Macroautophagy/autophagy activation in MSCs constitutes a stress adaptation pathway, promoting cellular homeostasis. Our proteomics data indicate that RUBCNL/PACER (RUN and cysteine rich domain containing beclin 1 interacting protein like), a positive regulator of autophagy, is also involved in cell death. Hence, we screened MSC survival upon various cell death stimuli under loss or gain of function of RUBCNL. MSCs were protected from TNF (tumor necrosis factor)-induced regulated cell death when RUBCNL was expressed. TNF promotes inflammation by inducing RIPK1 kinase-dependent apoptosis or necroptosis. We determine that MSCs succumb to RIPK1 kinase-dependent apoptosis upon TNF sensing and necroptosis when caspases are inactivated. We show that RUBCNL is a negative regulator of both RIPK1-dependent apoptosis and necroptosis. Furthermore, RUBCNL mutants that lose the ability to regulate autophagy, retain their function in negatively regulating cell death. We also found that RUBCNL forms a complex with RIPK1, which disassembles in response to TNF. In line with this finding, RUBCNL expression limits assembly of RIPK1-TNFRSF1A/TNFR1 complex I, suggesting that complex formation between RUBCNL and RIPK1 represses TNF signaling. These results provide new insights into the crosstalk between the RIPK1-mediated cell death and autophagy machineries and suggest that RUBCNL, due to its functional duality in autophagy and apoptosis/necroptosis, could be targeted to improve the therapeutic efficacy of MSCs. Abbreviations: BAF: bafilomycin A1; CASP3: caspase 3; Caspases: cysteine-aspartic proteases; cCASP3: cleaved CASP3; CQ: chloroquine; CHX: cycloheximide; cPARP: cleaved poly (ADP-ribose) polymerase; DEPs: differential expressed proteins; ETO: etoposide; MEF: mouse embryonic fibroblast; MLKL: mixed lineage kinase domain-like; MSC: mesenchymal stem cell; MTORC1: mechanistic target of rapamycin kinase complex 1; Nec1s: necrostatin 1s; NFKB/NF-kB: nuclear factor of kappa light polypeptide gene enhancer in B cells; PLA: proximity ligation assay; RCD: regulated cell death; RIPK1: receptor (TNFRSF)-interacting serine-threonine kinase 1; RIPK3: receptor-interacting serine-threonine kinase 3; RUBCNL/PACER: RUN and cysteine rich domain containing beclin 1 interacting protein like; siCtrl: small interfering RNA nonsense; siRNA: small interfering RNA; TdT: terminal deoxynucleotidyl transferase; Tm: tunicamycin; TNF: tumor necrosis factor; TNFRSF1A/TNFR1: tumor necrosis factor receptor superfamily, member 1a.
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Affiliation(s)
- Diego Rojas-Rivera
- Cell Death & Biomedicine Laboratory, Centro de Biomedicina, Universidad Mayor, Santiago, Chile
- VIB Center for Inflammation Research, Universidad Mayor, Ghent, Belgium
| | - Sebastián Beltrán
- Center for Integrative Biology, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
- Programa de Doctorado en Genómica Integrativa, VRI, Facultad de Ciencia, Universidad Mayor, Santiago, Chile
- Escuela de Tecnología Médica, Facultad de Medicina y Ciencias de la Salud, Universidad Mayor, Santiago, Chile
| | | | - Pablo Ahumada-Montalva
- Cell Death & Biomedicine Laboratory, Centro de Biomedicina, Universidad Mayor, Santiago, Chile
- Programa de Doctorado en Neurobiología, VRI, Facultad de Ciencia, Universidad Mayor, Santiago, Chile
| | - Lorena Abarzúa
- Cell Death & Biomedicine Laboratory, Centro de Biomedicina, Universidad Mayor, Santiago, Chile
| | - Laura Gomez
- Center for Integrative Biology, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Fernanda Hernandez
- Center for Integrative Biology, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Cristian A Bergmann
- Center for Integrative Biology, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
- Programa de Doctorado en Genómica Integrativa, VRI, Facultad de Ciencia, Universidad Mayor, Santiago, Chile
| | - Luis Labrador
- Center for Integrative Biology, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
- Programa de Doctorado en Genómica Integrativa, VRI, Facultad de Ciencia, Universidad Mayor, Santiago, Chile
| | - Melissa Calegaro-Nassif
- Laboratorio de Autofagia y Neuroprotección, Centro de Biomedicina, Universidad Mayor, Santiago, Chile
| | - Mathieu J M Bertrand
- VIB Center for Inflammation Research, Universidad Mayor, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Patricio A Manque
- Center for Integrative Biology, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
- Centro de Oncologia de Precision (COP), Escuela de Medicina, Universidad Mayor, Santiago, Chile
| | - Ute Woehlbier
- Center for Integrative Biology, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
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Oyarce-Pezoa S, Rucatti GG, Muñoz-Carvajal F, Sanhueza N, Gomez W, Espinoza S, Leiva M, García N, Ponce DP, SanMartín CD, Rojas-Rivera D, Salvadores N, Behrens MI, Woehlbier U, Calegaro-Nassif M, Sanhueza M. The autophagy protein Def8 is altered in Alzheimer's disease and Aβ42-expressing Drosophila brains. Sci Rep 2023; 13:17137. [PMID: 37816871 PMCID: PMC10564863 DOI: 10.1038/s41598-023-44203-6] [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: 06/25/2023] [Accepted: 10/04/2023] [Indexed: 10/12/2023] Open
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disorder, characterized by protein accumulation in the brain as a main neuropathological hallmark. Among them, Aβ42 peptides tend to aggregate and create oligomers and plaques. Macroautophagy, a form of autophagy characterized by a double-membrane vesicle, plays a crucial role in maintaining neuronal homeostasis by degrading protein aggregates and dysfunctional organelles as a quality control process. Recently, DEF8, a relatively uncharacterized protein, has been proposed as a participant in vesicular traffic and autophagy pathways. We have reported increased DEF8 levels in lymphocytes from mild cognitive impairment (MCI) and early-stage AD patients and a neuronal profile in a murine transgenic AD model. Here, we analyzed DEF8 localization and levels in the postmortem frontal cortex of AD patients, finding increased levels compared to healthy controls. To evaluate the potential function of DEF8 in the nervous system, we performed an in silico assessment of its expression and network profiles, followed by an in vivo evaluation of a neuronal Def8 deficient model using a Drosophila melanogaster model of AD based on Aβ42 expression. Our findings show that DEF8 is an essential protein for maintaining cellular homeostasis in the nervous system, and it is upregulated under stress conditions generated by Aβ42 aggregation. This study suggests DEF8 as a novel actor in the physiopathology of AD, and its exploration may lead to new treatment avenues.
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Affiliation(s)
- Sebastián Oyarce-Pezoa
- Center for Resilience, Adaptation and Mitigation, Universidad Mayor, Temuco, Chile
- Laboratory of Autophagy and Neuroprotection, Vicerrectoría de Investigación, Universidad Mayor, Santiago, Chile
- PhD Program in Biomedicine, Universidad de los Andes, Santiago, Chile
- Center for Biomedical Research and Innovation (CiiB), Universidad de los Andes, Santiago, Chile
| | - Guilherme Gischkow Rucatti
- Center for Resilience, Adaptation and Mitigation, Universidad Mayor, Temuco, Chile
- Laboratory of Autophagy and Neuroprotection, Vicerrectoría de Investigación, Universidad Mayor, Santiago, Chile
- PhD Program in Neurobiology, Universidad Mayor, Santiago, Chile
| | - Francisco Muñoz-Carvajal
- Center for Resilience, Adaptation and Mitigation, Universidad Mayor, Temuco, Chile
- PhD Program in Neurobiology, Universidad Mayor, Santiago, Chile
| | - Nicole Sanhueza
- Center for Resilience, Adaptation and Mitigation, Universidad Mayor, Temuco, Chile
| | - Wileidy Gomez
- Laboratory of Autophagy and Neuroprotection, Vicerrectoría de Investigación, Universidad Mayor, Santiago, Chile
- PhD Program in Integrative Genomics, Universidad Mayor, Santiago, Chile
| | - Sandra Espinoza
- Laboratory of Autophagy and Neuroprotection, Vicerrectoría de Investigación, Universidad Mayor, Santiago, Chile
| | - Mario Leiva
- Center for Resilience, Adaptation and Mitigation, Universidad Mayor, Temuco, Chile
| | - Nicolás García
- Center for Resilience, Adaptation and Mitigation, Universidad Mayor, Temuco, Chile
| | - Daniela P Ponce
- Centro de Investigación Clínica Aplicada (CICA), Hospital Clínico Universidad de Chile, Santiago, Chile
| | - Carol D SanMartín
- Centro de Investigación Clínica Aplicada (CICA), Hospital Clínico Universidad de Chile, Santiago, Chile
- Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile
| | - Diego Rojas-Rivera
- Escuela de Biotecnología, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
- Escuela de Tecnología Médica, Facultad de Medicina y Ciencias de la Salud, Universidad Mayor, Santiago, Chile
| | - Natalia Salvadores
- Center for Resilience, Adaptation and Mitigation, Universidad Mayor, Temuco, Chile
- Escuela de Medicina, Facultad de Medicina y Ciencias de la Salud, Universidad Mayor, Temuco, Chile
| | - Maria I Behrens
- Centro de Investigación Clínica Aplicada (CICA), Hospital Clínico Universidad de Chile, Santiago, Chile
- Departamento de Neurociencia, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Departamento de Neurología y Psiquiatría, Clínica Alemana de Santiago, Santiago, Chile
- Departamento de Neurología y Neurocirugía, Hospital Clínico Universidad de Chile, Santiago, Chile
| | - Ute Woehlbier
- Center for Integrative Biology, Universidad Mayor, Santiago, Chile
- Escuela de Biotecnología, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Melissa Calegaro-Nassif
- Laboratory of Autophagy and Neuroprotection, Vicerrectoría de Investigación, Universidad Mayor, Santiago, Chile.
- Escuela de Biotecnología, Facultad de Ciencias, Universidad Mayor, Santiago, Chile.
- Escuela de Tecnología Médica, Facultad de Medicina y Ciencias de la Salud, Universidad Mayor, Santiago, Chile.
| | - Mario Sanhueza
- Center for Resilience, Adaptation and Mitigation, Universidad Mayor, Temuco, Chile.
- Escuela de Medicina, Facultad de Medicina y Ciencias de la Salud, Universidad Mayor, Temuco, Chile.
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Tanaka MT, Miki Y, Bettencourt C, Ozaki T, Tanji K, Mori F, Kakita A, Wakabayashi K. Involvement of autophagic protein DEF8 in Lewy bodies. Biochem Biophys Res Commun 2022; 623:170-175. [DOI: 10.1016/j.bbrc.2022.07.069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 07/18/2022] [Indexed: 11/28/2022]
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Neuronal Rubicon Represses Extracellular APP/Amyloid β Deposition in Alzheimer's Disease. Cells 2022; 11:cells11121860. [PMID: 35740989 PMCID: PMC9221152 DOI: 10.3390/cells11121860] [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: 05/01/2022] [Accepted: 05/25/2022] [Indexed: 02/04/2023] Open
Abstract
Alzheimer’s disease (AD) is the most prevalent age-associated neurodegenerative disease. A decrease in autophagy during aging contributes to brain disorders by accumulating potentially toxic substrates in neurons. Rubicon is a well-established inhibitor of autophagy in all cells. However, Rubicon participates in different pathways depending on cell type, and little information is currently available on neuronal Rubicon’s role in the AD context. Here, we investigated the cell-specific expression of Rubicon in postmortem brain samples from AD patients and 5xFAD mice and its impact on amyloid β burden in vivo and neuroblastoma cells. Further, we assessed Rubicon levels in human-induced pluripotent stem cells (hiPSCs), derived from early-to-moderate AD and in postmortem samples from severe AD patients. We found increased Rubicon levels in AD-hiPSCs and postmortem samples and a notable Rubicon localization in neurons. In AD transgenic mice lacking Rubicon, we observed intensified amyloid β burden in the hippocampus and decreased Pacer and p62 levels. In APP-expressing neuroblastoma cells, increased APP/amyloid β secretion in the medium was found when Rubicon was absent, which was not observed in cells depleted of Atg5, essential for autophagy, or Rab27a, required for exosome secretion. Our results propose an uncharacterized role of Rubicon on APP/amyloid β homeostasis, in which neuronal Rubicon is a repressor of APP/amyloid β secretion, defining a new way to target AD and other similar diseases therapeutically.
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Insulin-like growth factor 2 and autophagy gene expression alteration arise as potential biomarkers in Parkinson's disease. Sci Rep 2022; 12:2038. [PMID: 35132125 PMCID: PMC8821705 DOI: 10.1038/s41598-022-05941-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 01/20/2022] [Indexed: 11/10/2022] Open
Abstract
Insulin-like growth factor 2 (IGF2) and autophagy-related genes have been proposed as biomolecules of interest related to idiopathic Parkinson’s disease (PD). The objective of this study was to determine the IGF2 and IGF1 levels in plasma and peripheral blood mononuclear cells (PBMCs) from patients with moderately advanced PD and explore the potential correlation with autophagy-related genes in the same blood samples. IGF1 and IGF2 levels in patients' plasma were measured by ELISA, and the IGF2 expression levels were determined by real-time PCR and Western blot in PBMCs. The expression of autophagy-related genes was evaluated by real-time PCR. The results show a significant decrease in IGF2 plasma levels in PD patients compared with a healthy control group. We also report a dramatic decrease in IGF2 mRNA and protein levels in PBMCs from PD patients. In addition, we observed a downregulation of key components of the initial stages of the autophagy process. Although IGF2 levels were not directly correlated with disease severity, we found a correlation between its levels and autophagy gene profile expression in a sex-dependent pattern from the same samples. To further explore this correlation, we treated mice macrophages cell culture with α-synuclein and IGF2. While α-synuclein treatment decreased levels Atg5, IGF2 treatment reverted these effects, increasing Atg5 and Beclin1 levels. Our results suggest a relationship between IGF2 levels and the autophagy process in PD and their potential application as multi-biomarkers to determine PD patients' stages of the disease.
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He S, Deng Z, Li Z, Gao W, Zeng D, Shi Y, Zhao N, Xu F, Li T, Li H, Peng D. Signatures of 4 autophagy-related genes as diagnostic markers of MDD and their correlation with immune infiltration. J Affect Disord 2021; 295:11-20. [PMID: 34391068 DOI: 10.1016/j.jad.2021.08.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/31/2021] [Accepted: 08/03/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUND Major depressive disorder (MDD) is a debilitating mental illness and one of the primary causes of suicide. This study attempted to develop and validate a multigene joint signature for diagnosing MDD based on autophagy-related genes (ARGs) and to explore their biological role in MDD. METHODS We downloaded data from the Gene Expression Omnibus (GEO) database and retrieved ARGs from the Human Autophagy Database. The limma package in R software was used to identify differentially expressed genes (DEGs). We used CIBERSORT to analyze differences in the immune microenvironment between MDD patients and controls. Finally, we examined the correlation between diagnostic markers and infiltrating immune cells to better understand the molecular immune mechanism. RESULTS In this study, we identified 20 differentially expressed ARGs in MDD compared to controls. A signature of 4 autophagy-related genes (GPR18, PDK4, NRG1 and EPHB2) was obtained. ROC analysis showed that our model has good diagnostic performance (AUC=0.779, 95% CI=0.709-0.848). Bioinformatics analysis validated that GPR18 may represent a new candidate gene for MDD. Correlation analysis revealed that GPR18 was positively correlated with regulatory T cells (Treg), CD8+ T cells, naive B cells, and memory B cells and negatively correlated with M0 macrophages and neutrophils in MDD. LIMITATIONS This was a second mining of previously published data sets. Independent studies are warranted to validate and improve the clinical utility of the identified signature. CONCLUSIONS We identified a novel four-ARG gene signature that has good diagnostic performance and identified an association between ARG genes and the immune microenvironment in MDD.
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Affiliation(s)
- Shen He
- Division of Mood Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhifang Deng
- Department of Pharmacy, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science&Technology, Wuhan, Hubei, China
| | - Zhao Li
- Department of Anesthesiology, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Wenqi Gao
- Institute of Maternal and Child Health, Wuhan Children' s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University&Technology, Wuhan, Hubei, China
| | - Duan Zeng
- Department of Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yue Shi
- Department of Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Nan Zhao
- Shanghai Pudong New Area Mental Health Center, Tongji University School of Medicine, Shanghai, China
| | - Feikang Xu
- Department of Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tian Li
- School of Basic Medicine, Fourth Military Medical University, No. 169 Changle West Rd, Xi'an, China
| | - Huafang Li
- Department of Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Clinical Research Center for Mental Health, China.
| | - Daihui Peng
- Division of Mood Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Rao KSJ, Britton GB, Rocha Arrieta LL, Garcia-Cairasco N, Lazarowski A, Palacios A, Camins Espuny A, Maccioni RB. Translational Research and Drug Discovery for Neurodegeneration: Challenges for Latin America. J Alzheimers Dis 2021; 82:S1-S4. [PMID: 34092644 DOI: 10.3233/jad-210245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- K S Jagannatha Rao
- Centro de Neurociencia, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología, AIP (INDICASAT AIP), Panamá and Sistema Nacional de Investigación (SNI), SENACYT, Panamá
| | - Gabrielle B Britton
- Centro de Neurociencia, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología, AIP (INDICASAT AIP), Panamá and Sistema Nacional de Investigación (SNI), SENACYT, Panamá
| | - Luisa Lilia Rocha Arrieta
- Depto. Farmacobiología del Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México
| | - Norberto Garcia-Cairasco
- Full Professor of Physiology (Neurophysiology), Director of the Neurophysiology and Experimental Neuroethology Laboratory (LNNE), Physiology Department - Ribeirão Preto School of Medicine, University of São Paulo, Ribeirão Preto, SP, Brasil
| | - Alberto Lazarowski
- Instituto de Fidiopatologia y Bioquímica Clínica (INFIBIOC), Facultad de Farrmacia y Biouimican (FFyB), Universidad de Buenos Aires (UBA), Buenos Aires, Argentina
| | - Adrián Palacios
- Centro Interdisciplinario de Neurociencia de Valparaiso, Facultad de Ciencias, Universidad de Valparaiso, Valparaiso, Chile
| | - Antoni Camins Espuny
- Department of Pharmacology, Toxicology and Therapeutic Chemistry, Faculty of Pharmacy and Food Sciences, Barcelona, Spain
| | - Ricardo B Maccioni
- Full Professor, Departamento de Neurología y Neurocirugía, University of Chile, Santiago, Chile
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