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Xu W, Tang Y, Yang Y, Wang C, Liu C, Zhang J, Zhao L, Wang G. Depletion of CPNE7 sensitizes colorectal cancer to 5-fluorouracil by downregulating ATG9B expression. J Cell Mol Med 2024; 28:e18261. [PMID: 38526029 PMCID: PMC10962129 DOI: 10.1111/jcmm.18261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 02/10/2024] [Accepted: 02/20/2024] [Indexed: 03/26/2024] Open
Abstract
We aimed to explore the biological function of CPNE7 and determine the impact of CPNE7 on chemotherapy resistance in colorectal cancer (CRC) patients. According to the Gene Expression Profiling Interactive Analysis database and previously published data, CPNE7 was identified as a potential oncogene in CRC. RT-qPCR and Western blotting were performed to verify the expression of CPNE7. Chi-square test was used to evaluate the associations between CPNE7 and clinical features. Cell proliferation, colony formation, cell migration and invasion, cell cycle and apoptosis were assessed to determine the effects of CPNE7. Transcriptome sequencing was used to identify potential downstream regulatory genes, and gene set enrichment analysis was performed to investigate downstream pathways. The effect of CPNE7 on 5-fluorouracil chemosensitivity was verified by half maximal inhibitory concentration (IC50). Subcutaneous tumorigenesis assay was used to examine the role of CPNE7 in sensitivity of CRC to chemotherapy in vivo. Transmission electron microscopy was used to detect autophagosomes. CPNE7 was highly expressed in CRC tissues, and its expression was correlated with T stage and tumour site. Knockdown of CPNE7 inhibited the proliferation and colony formation of CRC cells and promoted apoptosis. Knockdown of CPNE7 suppressed the expression of ATG9B and enhanced the sensitivity of CRC cells to 5-fluorouracil in vitro and in vivo. Knockdown of CPNE7 reversed the induction of the autophagy pathway by rapamycin and reduced the number of autophagosomes. Depletion of CPNE7 attenuated the malignant proliferation of CRC cells and enhanced the chemosensitivity of CRC cells to 5-fluorouracil.
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Affiliation(s)
- Weile Xu
- The Department of General surgeryThe Second Hospital of Hebei Medical UniversityShijiazhuangHebeiChina
- The Department of General surgeryHebei Chest HospitalShijiazhuangHebeiChina
- The Second Department of SurgeryThe Fourth Hospital of Hebei Medical UniversityShijiazhuangHebeiChina
| | - Yujie Tang
- The Department of Gastrointestinal surgeryThe Third Hospital of Hebei Medical UniversityShijiazhuangHebeiChina
| | - Yang Yang
- The Department of Gastrointestinal surgeryThe Third Hospital of Hebei Medical UniversityShijiazhuangHebeiChina
| | - Changjing Wang
- The Department of Gastrointestinal surgeryThe Third Hospital of Hebei Medical UniversityShijiazhuangHebeiChina
| | - Chen Liu
- The Department of Gastrointestinal surgeryThe Third Hospital of Hebei Medical UniversityShijiazhuangHebeiChina
| | - Jianqing Zhang
- The Department of Gastrointestinal surgeryThe Third Hospital of Hebei Medical UniversityShijiazhuangHebeiChina
| | - Lianmei Zhao
- Scientific Research CenterThe Fourth Hospital of Hebei Medical UniversityShijiazhuangHebeiChina
| | - Guiying Wang
- The Department of General surgeryThe Second Hospital of Hebei Medical UniversityShijiazhuangHebeiChina
- The Second Department of SurgeryThe Fourth Hospital of Hebei Medical UniversityShijiazhuangHebeiChina
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2
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Schreurs RRCE, Koulis A, Booiman T, Boeser-Nunnink B, Cloherty APM, Rader AG, Patel KS, Kootstra NA, Ribeiro CMS. Autophagy-enhancing ATG16L1 polymorphism is associated with improved clinical outcome and T-cell immunity in chronic HIV-1 infection. Nat Commun 2024; 15:2465. [PMID: 38548722 PMCID: PMC10979031 DOI: 10.1038/s41467-024-46606-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 03/04/2024] [Indexed: 04/01/2024] Open
Abstract
Chronic HIV-1 infection is characterized by T-cell dysregulation that is partly restored by antiretroviral therapy. Autophagy is a critical regulator of T-cell function. Here, we demonstrate a protective role for autophagy in HIV-1 disease pathogenesis. Targeted analysis of genetic variation in core autophagy gene ATG16L1 reveals the previously unidentified rs6861 polymorphism, which correlates functionally with enhanced autophagy and clinically with improved survival of untreated HIV-1-infected individuals. T-cells carrying ATG16L1 rs6861(TT) genotype display improved antiviral immunity, evidenced by increased proliferation, revamped immune responsiveness, and suppressed exhaustion/immunosenescence features. In-depth flow-cytometric and transcriptional profiling reveal T-helper-cell-signatures unique to rs6861(TT) individuals with enriched regulation of pro-inflammatory networks and skewing towards immunoregulatory phenotype. Therapeutic enhancement of autophagy recapitulates the rs6861(TT)-associated T-cell traits in non-carriers. These data underscore the in vivo relevance of autophagy for longer-lasting T-cell-mediated HIV-1 control, with implications towards development of host-directed antivirals targeting autophagy to restore immune function in chronic HIV-1 infection.
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Affiliation(s)
- Renée R C E Schreurs
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam institute for Immunology & Infectious Diseases, Amsterdam, The Netherlands
| | - Athanasios Koulis
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam institute for Immunology & Infectious Diseases, Amsterdam, The Netherlands
| | - Thijs Booiman
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam institute for Immunology & Infectious Diseases, Amsterdam, The Netherlands
| | - Brigitte Boeser-Nunnink
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam institute for Immunology & Infectious Diseases, Amsterdam, The Netherlands
| | - Alexandra P M Cloherty
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam institute for Immunology & Infectious Diseases, Amsterdam, The Netherlands
| | - Anusca G Rader
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam institute for Immunology & Infectious Diseases, Amsterdam, The Netherlands
| | - Kharishma S Patel
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam institute for Immunology & Infectious Diseases, Amsterdam, The Netherlands
| | - Neeltje A Kootstra
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam institute for Immunology & Infectious Diseases, Amsterdam, The Netherlands
| | - Carla M S Ribeiro
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9, Amsterdam, The Netherlands.
- Amsterdam institute for Immunology & Infectious Diseases, Amsterdam, The Netherlands.
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3
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Zhang T, Ji T, Duan Z, Xue Y. Long non-coding RNA MLLT4 antisense RNA 1 induces autophagy to inhibit tumorigenesis of cervical cancer through modulating the myosin-9/ATG14 axis. Sci Rep 2024; 14:6379. [PMID: 38493244 PMCID: PMC10944523 DOI: 10.1038/s41598-024-55644-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 02/26/2024] [Indexed: 03/18/2024] Open
Abstract
The regulatory mechanism of long non-coding RNAs (lncRNAs) in autophagy is as yet not well established. In this research, we show that the long non-coding RNA MLLT4 antisense RNA 1 (lncRNA MLLT4-AS1) is induced by the MTORC inhibitor PP242 and rapamycin in cervical cells. Overexpression of MLLT4-AS1 promotes autophagy and inhibits tumorigenesis and the migration of cervical cancer cells, whereas knockdown of MLLT4-AS1 attenuates PP242-induced autophagy. Mass spectrometry, RNA fluorescence in situ hybridization (RNA-FISH), and immunoprecipitation assays were performed to identify the direct interactions between MLLT4-AS1 and other associated targets, such as myosin-9 and autophagy-related 14(ATG14). MLLT4-AS1 was upregulated by H3K27ac modification with PP242 treatment, and knockdown of MLLT4-AS1 reversed autophagy by modulating ATG14 expression. Mechanically, MLLT4-AS1 was associated with the myosin-9 protein, which further promoted the transcription activity of the ATG14 gene. In conclusion, we demonstrated that MLLT4-AS1 acts as a potential tumor suppressor in cervical cancer by inducing autophagy, and H3K27ac modification-induced upregulation of MLLT4-AS1 could cause autophagy by associating with myosin-9 and promoting ATG14 transcription.
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Affiliation(s)
- Tingting Zhang
- Department of Gynecology, The Second Affiliated Hospital of Medical College of Xi'an Jiaotong University, Xi'an, China
| | - Tiantian Ji
- Department of Gynecology, The Second Affiliated Hospital of Medical College of Xi'an Jiaotong University, Xi'an, China
| | - Zhao Duan
- Department of Gynecology, The Second Affiliated Hospital of Medical College of Xi'an Jiaotong University, Xi'an, China
| | - Yuanyuan Xue
- Department of Gynecology, The Second Affiliated Hospital of Medical College of Xi'an Jiaotong University, Xi'an, China.
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Safren N, Dao TP, Mohan HM, Huang C, Trotter B, Castañeda CA, Paulson H, Barmada S, Sharkey LM. Pathogenic mutations in UBQLN2 exhibit diverse aggregation propensity and neurotoxicity. Sci Rep 2024; 14:6049. [PMID: 38472280 PMCID: PMC10933299 DOI: 10.1038/s41598-024-55582-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
The ubiquitin-adaptor protein UBQLN2 promotes degradation of several aggregate-prone proteins implicated in neurodegenerative diseases. Missense UBQLN2 mutations also cause X-linked amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Previously we demonstrated that the liquid-like properties of UBQLN2 molecular assemblies are altered by a specific pathogenic mutation, P506T, and that the propensity of UBQLN2 to aggregate correlated with neurotoxicity. Here, we systematically assess the effects of multiple, spatially distinct ALS/FTD-linked missense mutations on UBQLN2 aggregation propensity, neurotoxicity, phase separation, and autophagic flux. In contrast to what we observed for the P506T mutation, no other tested pathogenic mutant exhibited a clear correlation between aggregation propensity and neurotoxicity. These results emphasize the unique nature of pathogenic UBQLN2 mutations and argue against a generalizable link between aggregation propensity and neurodegeneration in UBQLN2-linked ALS/FTD.
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Affiliation(s)
- Nathaniel Safren
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA.
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
| | - Thuy P Dao
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY, 13244, USA
| | - Harihar Milaganur Mohan
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Camellia Huang
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA
| | - Bryce Trotter
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA
| | - Carlos A Castañeda
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY, 13244, USA
| | - Henry Paulson
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, 48109-2200, USA
| | - Sami Barmada
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, 48109-2200, USA
| | - Lisa M Sharkey
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA.
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, 48109-2200, USA.
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5
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Wang Y, Ouyang S, Liu M, Si Q, Zhang X, Zhang X, Li J, Wang P, Ye H, Shi J, Song C, Wang K, Dai L. Humoral immune response to tumor-associated antigen Ubiquilin 1 (UBQLN1) and its tumor-promoting potential in lung cancer. BMC Cancer 2024; 24:283. [PMID: 38431566 PMCID: PMC10908023 DOI: 10.1186/s12885-024-12019-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 02/18/2024] [Indexed: 03/05/2024] Open
Abstract
BACKGROUND This study aims to investigate the expression of UBQLN1 in lung cancer (LC) tissue and the diagnostic capability of autoantibody to UBQLN1 (anti-UBQLN1) in the detection of LC and the discrimination of pulmonary nodules (PNs). METHODS Sera from 798 participants were used to discover and validate the level of autoantibodies via HuProt microarray and Enzyme-linked immunosorbent assay (ELISA). Logistic regression analysis was applied to establish model. Receiver operating characteristic curve (ROC) analysis was performed to evaluate the diagnostic potential. Immunohistochemistry was performed to detect UBQLN1 expression in 88 LC tissues and 88 para-tumor tissues. qRT-PCR and western blotting were performed to detect the expression of UBQLN1 at the mRNA and protein levels, respectively. Trans-well assay and cell counting kit-8 (CCK-8) was used to investigate the function of UBQLN1. RESULTS Anti-UBQLN1 was identified with the highest fold change by protein microarray. The level of anti-UBQLN1 in LC patients was obviously higher than that in NC or patients with benign lung disease of validation cohort 1 (P<0.05). The area under the curve (AUC) of anti-UBQLN1 was 0.610 (95%CI: 0.508-0.713) while reached at 0.822 (95%CI: 0.784-0.897) when combining anti-UBQLN1 with CEA, CYFRA21-1, CA125 and three CT indicators (vascular notch sign, lobulation sign and mediastinal lymph node enlargement) in the discrimination of PNs. UBQLN1 protein was overexpressed in lung adenocarcinoma (LUAD) tissues compared to para-tumor tissues. UBQLN1 knockdown remarkably inhibited the migration, invasion and proliferation of LUAD cell lines. CONCLUSIONS Anti-UBQLN1 might be a potential biomarker for the diagnosis of LC and the discrimination of PNs.
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Affiliation(s)
- Yulin Wang
- Henan Institute of Medical and Pharmaceutical Sciences & Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, Henan, 450052, China
- Henan Key Laboratory of Tumor Epidemiology, Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Songyun Ouyang
- Department of Respiratory and Sleep Medicine, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Man Liu
- Henan Institute of Medical and Pharmaceutical Sciences & Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, Henan, 450052, China
- Henan Key Laboratory of Tumor Epidemiology, Zhengzhou University, Zhengzhou, Henan, 450052, China
- Laboratory of Molecular Biology, Henan Luoyang Orthopedic Hospital (Henan Provincial Orthopedic Hospital), Zhengzhou, China
| | - Qiufang Si
- Henan Institute of Medical and Pharmaceutical Sciences & Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, Henan, 450052, China
- Henan Key Laboratory of Tumor Epidemiology, Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Xue Zhang
- Henan Institute of Medical and Pharmaceutical Sciences & Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, Henan, 450052, China
- Henan Key Laboratory of Tumor Epidemiology, Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Xiuzhi Zhang
- Henan Institute of Medical and Pharmaceutical Sciences & Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Jiaqi Li
- Henan Institute of Medical and Pharmaceutical Sciences & Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, Henan, 450052, China
- Henan Key Laboratory of Tumor Epidemiology, Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Peng Wang
- Henan Key Laboratory of Tumor Epidemiology, Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Hua Ye
- Henan Key Laboratory of Tumor Epidemiology, Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Jianxiang Shi
- Henan Institute of Medical and Pharmaceutical Sciences & Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, Henan, 450052, China
- Henan Key Laboratory of Tumor Epidemiology, Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Chunhua Song
- Henan Key Laboratory of Tumor Epidemiology, Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Kaijuan Wang
- Henan Key Laboratory of Tumor Epidemiology, Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Liping Dai
- Henan Institute of Medical and Pharmaceutical Sciences & Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, Henan, 450052, China.
- Henan Key Laboratory of Tumor Epidemiology, Zhengzhou University, Zhengzhou, Henan, 450052, China.
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Gross AS, Ghillebert R, Schuetter M, Reinartz E, Rowland A, Bishop BC, Stumpe M, Dengjel J, Graef M. A metabolite sensor subunit of the Atg1/ULK complex regulates selective autophagy. Nat Cell Biol 2024; 26:366-377. [PMID: 38316984 PMCID: PMC10940145 DOI: 10.1038/s41556-024-01348-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 01/03/2024] [Indexed: 02/07/2024]
Abstract
Cells convert complex metabolic information into stress-adapted autophagy responses. Canonically, multilayered protein kinase networks converge on the conserved Atg1/ULK kinase complex (AKC) to induce non-selective and selective forms of autophagy in response to metabolic changes. Here we show that, upon phosphate starvation, the metabolite sensor Pho81 interacts with the adaptor subunit Atg11 at the AKC via an Atg11/FIP200 interaction motif to modulate pexophagy by virtue of its conserved phospho-metabolite sensing SPX domain. Notably, core AKC components Atg13 and Atg17 are dispensable for phosphate starvation-induced autophagy revealing significant compositional and functional plasticity of the AKC. Our data indicate that, instead of functioning as a selective autophagy receptor, Pho81 compensates for partially inactive Atg13 by promoting Atg11 phosphorylation by Atg1 critical for pexophagy during phosphate starvation. Our work shows Atg11/FIP200 adaptor subunits bind not only selective autophagy receptors but also modulator subunits that convey metabolic information directly to the AKC for autophagy regulation.
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Affiliation(s)
- A S Gross
- Max Planck Research Group of Autophagy and Cellular Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
- Gregor Mendel Institute of Molecular Plant Biology, Vienna Biocenter, Vienna, Austria
| | - R Ghillebert
- Max Planck Research Group of Autophagy and Cellular Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - M Schuetter
- Max Planck Research Metabolomics Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - E Reinartz
- Max Planck Research Group of Autophagy and Cellular Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - A Rowland
- Max Planck Research Group of Autophagy and Cellular Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - B C Bishop
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - M Stumpe
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - J Dengjel
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - M Graef
- Max Planck Research Group of Autophagy and Cellular Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany.
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
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Infante T, Pepin ME, Ruocco A, Trama U, Mauro C, Napoli C. CDK5R1, GSE1, HSPG2 and WDFY3 as indirect epigenetic-sensitive genes in atrial fibrillation. Eur J Clin Invest 2024; 54:e14135. [PMID: 37991085 DOI: 10.1111/eci.14135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/14/2023] [Accepted: 11/14/2023] [Indexed: 11/23/2023]
Abstract
BACKGROUND Although mounting evidence supports that aberrant DNA methylation occurs in the hearts of patients with atrial fibrillation (AF), noninvasive epigenetic characterization of AF has not yet been defined. METHODS We investigated DNA methylome changes in peripheral blood CD4+ T cells isolated from 10 patients with AF relative to 11 healthy subjects (HS) who were enrolled in the DIANA clinical trial (NCT04371809) via reduced-representation bisulfite sequencing (RRBS). RESULTS An atrial-specific PPI network revealed 18 hub differentially methylated genes (DMGs), wherein ROC curve analysis revealed reasonable diagnostic performance of DNA methylation levels found within CDK5R1 (AUC = 0.76; p = 0.049), HSPG2 (AUC = 0.77; p = 0.038), WDFY3 (AUC = 0.78; p = 0.029), USP49 (AUC = 0.76; p = 0.049), GSE1 (AUC = 0.76; p = 0.049), AIFM1 (AUC = 0.76; p = 0.041), CDK5RAP2 (AUC = 0.81; p = 0.017), COL4A1 (AUC = 0.86; p < 0.001), SEPT8 (AUC = 0.90; p < 0.001), PFDN1 (AUC = 0.90; p < 0.01) and ACOT7 (AUC = 0.78; p = 0.032). Transcriptional profiling of the hub DMGs provided a significant overexpression of PSDM6 (p = 0.004), TFRC (p = 0.01), CDK5R1 (p < 0.001), HSPG2 (p = 0.01), WDFY3 (p < 0.001), USP49 (p = 0.004) and GSE1 (p = 0.021) in AF patients vs HS. CONCLUSIONS CDK5R1, GSE1, HSPG2 and WDFY3 resulted the best discriminatory genes both at methylation and gene expression level. Our results provide several candidate diagnostic biomarkers with the potential to advance precision medicine in AF.
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Affiliation(s)
- Teresa Infante
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Mark E Pepin
- Division of Internal Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Antonio Ruocco
- Cardiology Division, "A. Cardarelli" Hospital, Naples, Italy
| | - Ugo Trama
- General Direction of Health Care & Regional Health System Coordination, Drug & Device Politics, Campania Region, Naples, Italy
| | - Ciro Mauro
- Cardiology Division, "A. Cardarelli" Hospital, Naples, Italy
| | - Claudio Napoli
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Naples, Italy
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Tang X, Lin S, Luo H, Wang L, Zhong J, Xiong J, Lv H, Zhou F, Wan Z, Cao K. ATG9A as a potential diagnostic marker of intervertebral disc degeneration: Inferences from experiments and bioinformatics analysis incorporating sc-RNA-seq data. Gene 2024; 897:148084. [PMID: 38104954 DOI: 10.1016/j.gene.2023.148084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/02/2023] [Accepted: 12/13/2023] [Indexed: 12/19/2023]
Abstract
BACKGROUND Disfunctional autophagy plays a pivotal role in Intervertebral Disc Degeneration (IDD) progression. however, the connection between Autophagy-related gene 9A (ATG9A) and IDD has not been reported. METHODS Firstly, transcriptome datasets from the GEO and Autophagy-related genes (ARGs) from GeneCards were carried out using R. Following this, IDD-specific signature genes were identified through methods such as least absolute shrinkage and selection operator (LASSO), random forest (RF), and support vector machine (SVM) analyses. Validation of these findings proceeded through in vitro experiments, evaluation of independent datasets, and analysis of receiver operating characteristic (ROC) curves. Subsequent steps incorporated co-expression analysis, Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, Gene Set Enrichment Analysis (GSEA), and construction of competing endogenous RNA (ceRNA) network. The final section established the correlation between immune cell infiltration, ATG9A, and IDD utilizing the CIBERSORT algorithm and single-cell RNA (scRNA) sequencing data. RESULTS Research identified 87 differentially expressed genes, with only ATG9A noted as an IDD signature gene. Analysis of in vitro experiments and independent datasets uncovered a decrease in ATG9A expression within the degeneration group. The area under the curve (AUC) of ATG9A exceeded 0.8 following ROC analysis. Furthermore, immune cell infiltration and scRNA sequencing data analysis elucidated the substantial role of immune cells in IDD progression. A ceRNA network was constructed, centered around ATG9A, included 4 miRNAs and 22 lncRNAs. CONCLUSION ATG9A was identified as a diagnostic gene for IDD, indicating its viability as a effective target for therapy disease.
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Affiliation(s)
- Xiaokai Tang
- Orthopedic Hospital, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, China
| | - Sijian Lin
- The Department of Rehabilitation Medicine, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, China
| | - Hao Luo
- Orthopedic Hospital, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, China
| | - Lixia Wang
- Orthopedic Hospital, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, China
| | - Junlong Zhong
- Orthopedic Hospital, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, China
| | - Jiachao Xiong
- Orthopedic Hospital, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, China
| | - Hao Lv
- Orthopedic Hospital, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, China
| | - Faxin Zhou
- Orthopedic Hospital, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, China
| | - Zongmiao Wan
- Orthopedic Hospital, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, China
| | - Kai Cao
- Orthopedic Hospital, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, China.
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Rao S, Skulsuppaisarn M, Strong LM, Ren X, Lazarou M, Hurley JH, Hummer G. Three-step docking by WIPI2, ATG16L1, and ATG3 delivers LC3 to the phagophore. Sci Adv 2024; 10:eadj8027. [PMID: 38324698 PMCID: PMC10851258 DOI: 10.1126/sciadv.adj8027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 01/05/2024] [Indexed: 02/09/2024]
Abstract
The covalent attachment of ubiquitin-like LC3 proteins (microtubule-associated proteins 1A/1B light chain 3) prepares the autophagic membrane for cargo recruitment. We resolve key steps in LC3 lipidation by combining molecular dynamics simulations and experiments in vitro and in cellulo. We show how the E3-like ligaseautophagy-related 12 (ATG12)-ATG5-ATG16L1 in complex with the E2-like conjugase ATG3 docks LC3 onto the membrane in three steps by (i) the phosphatidylinositol 3-phosphate effector protein WD repeat domain phosphoinositide-interacting protein 2 (WIPI2), (ii) helix α2 of ATG16L1, and (iii) a membrane-interacting surface of ATG3. Phosphatidylethanolamine (PE) lipids concentrate in a region around the thioester bond between ATG3 and LC3, highlighting residues with a possible role in the catalytic transfer of LC3 to PE, including two conserved histidines. In a near-complete pathway from the initial membrane recruitment to the LC3 lipidation reaction, the three-step targeting of the ATG12-ATG5-ATG16L1 machinery establishes a high level of regulatory control.
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Affiliation(s)
- Shanlin Rao
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Marvin Skulsuppaisarn
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Lisa M. Strong
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- 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
| | - Xuefeng Ren
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- 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
| | - Michael Lazarou
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - James H. Hurley
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- 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
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Institute of Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
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10
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Wu Q, Ouyang Y. Association of ATG16L1 and ATG5 gene polymorphisms with susceptibility to hepatitis B virus infection and progression to HCC in central China. Microbiol Immunol 2024; 68:47-55. [PMID: 37991129 DOI: 10.1111/1348-0421.13104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 10/31/2023] [Accepted: 11/05/2023] [Indexed: 11/23/2023]
Abstract
Hepatitis B virus (HBV) infection is a severe public health problem worldwide. The relationship between polymorphisms of autophagy-related 16-like 1 gene (ATG16L1) and autophagy-related gene 5 (ATG5) with susceptibility to the stage of HBV infection has been reported in different populations. Nevertheless, this association is not seen in the population of central China. This study recruited 452 participants, including 246 HBV-infected patients (139 chronically infected HBV without hepatocellular carcinoma [HCC] and 107 HBV-related HCC patients) and 206 healthy controls. Genotyping of ATG16L1 rs2241880 and ATG5 rs688810 were performed using Sanger sequencing and polymerase chain reaction-restriction fragment length polymorphism, respectively. Our results indicated that the G allele of ATG16L1 rs2241880 was more frequent in healthy controls than in patients with chronicHBV infection. After adjusting for age and sex, an association between the ATG16L1 rs2241880 polymorphism and HBV infection was significant under the dominant and allele models (p = 0.009 and 0.003, respectively). However, no association between the ATG5 polymorphisms and HBV infection was observed. We also did not find a significant association between ATG16L1 and ATG5 polymorphisms and the progression of HBV-related HCC. Therefore, the genetic polymorphism of ATG16L1 rs2241880 may be associated with susceptibility to HBV infection in the population of central China.
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Affiliation(s)
- Qiaoyu Wu
- Department of Laboratory Medicine, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, China
| | - Yaoling Ouyang
- Department of Laboratory Medicine, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, China
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11
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Bhattacharya A, Torggler R, Reiter W, Romanov N, Licheva M, Ciftci A, Mari M, Kolb L, Kaiser D, Reggiori F, Ammerer G, Hollenstein DM, Kraft C. Decoding the function of Atg13 phosphorylation reveals a role of Atg11 in bulk autophagy initiation. EMBO Rep 2024; 25:813-831. [PMID: 38233718 PMCID: PMC10897315 DOI: 10.1038/s44319-023-00055-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 01/19/2024] Open
Abstract
Autophagy is initiated by the assembly of multiple autophagy-related proteins that form the phagophore assembly site where autophagosomes are formed. Atg13 is essential early in this process, and a hub of extensive phosphorylation. How these multiple phosphorylations contribute to autophagy initiation, however, is not well understood. Here we comprehensively analyze the role of phosphorylation events on Atg13 during nutrient-rich conditions and nitrogen starvation. We identify and functionally characterize 48 in vivo phosphorylation sites on Atg13. By generating reciprocal mutants, which mimic the dephosphorylated active and phosphorylated inactive state of Atg13, we observe that disrupting the dynamic regulation of Atg13 leads to insufficient or excessive autophagy, which are both detrimental to cell survival. We furthermore demonstrate an involvement of Atg11 in bulk autophagy even during nitrogen starvation, where it contributes together with Atg1 to the multivalency that drives phase separation of the phagophore assembly site. These findings reveal the importance of post-translational regulation on Atg13 early during autophagy initiation, which provides additional layers of regulation to control bulk autophagy activity and integrate cellular signals.
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Affiliation(s)
- Anuradha Bhattacharya
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104, Freiburg, Germany
| | - Raffaela Torggler
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Wolfgang Reiter
- Department for Biochemistry and Cell Biology, University of Vienna, Center for Molecular Biology, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 9, 1030, Vienna, Austria
- Mass Spectrometry Facility, Max Perutz Labs, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 7, Vienna, Austria
| | - Natalie Romanov
- Department for Biochemistry and Cell Biology, University of Vienna, Center for Molecular Biology, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 9, 1030, Vienna, Austria
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Mariya Licheva
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Akif Ciftci
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Muriel Mari
- Department of Biomedicine, Aarhus University, Ole Worms Allé 4, 8000, Aarhus C, Denmark
| | - Lena Kolb
- Department for Biochemistry and Cell Biology, University of Vienna, Center for Molecular Biology, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 9, 1030, Vienna, Austria
| | - Dominik Kaiser
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany
| | - Fulvio Reggiori
- Department of Biomedicine, Aarhus University, Ole Worms Allé 4, 8000, Aarhus C, Denmark
| | - Gustav Ammerer
- Department for Biochemistry and Cell Biology, University of Vienna, Center for Molecular Biology, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 9, 1030, Vienna, Austria
| | - David M Hollenstein
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany.
- Department for Biochemistry and Cell Biology, University of Vienna, Center for Molecular Biology, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 9, 1030, Vienna, Austria.
- Mass Spectrometry Facility, Max Perutz Labs, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 7, Vienna, Austria.
| | - Claudine Kraft
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany.
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany.
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12
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Simovic I, Hilmi I, Ng RT, Chew KS, Wong SY, Lee WS, Riordan S, Castaño-Rodríguez N. ATG16L1 rs2241880/T300A increases susceptibility to perianal Crohn's disease: An updated meta-analysis on inflammatory bowel disease risk and clinical outcomes. United European Gastroenterol J 2024; 12:103-121. [PMID: 37837511 PMCID: PMC10859713 DOI: 10.1002/ueg2.12477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 08/17/2023] [Indexed: 10/16/2023] Open
Abstract
BACKGROUND ATG16L1 plays a fundamental role in the degradative intracellular pathway known as autophagy, being a mediator of inflammation and microbial homeostasis. The variant rs2241880 can diminish these capabilities, potentially contributing to inflammatory bowel disease (IBD) pathogenesis. OBJECTIVES To perform an updated meta-analysis on the association between ATG16L1 rs2241880 and IBD susceptibility by exploring the impact of age, ethnicity, and geography. Moreover, to investigate the association between rs2241880 and clinical features. METHODS Literature searches up until September 2022 across 7 electronic public databases were performed for all case-control studies on ATG16L1 rs2241880 and IBD. Pooled odds ratios (ORP ) and 95% CI were calculated under the random effects model. RESULTS Our analyses included a total of 30,606 IBD patients, comprising 21,270 Crohn's disease (CD) and 9336 ulcerative colitis (UC) patients, and 33,329 controls. ATG16L1 rs2241880 was significantly associated with CD susceptibility, where the A allele was protective (ORP : 0.74, 95% CI: 0.72-0.77, p-value: <0.001), while the G allele was a risk factor (ORP : 1.23, 95% CI: 1.09-1.39, p-value: 0.001), depending on the minor allele frequencies observed in this multi-ancestry study sample. rs2241880 was predominantly relevant in Caucasians from North America and Europe, and in Latin American populations. Importantly, CD patients harbouring the G allele were significantly more predisposed to perianal disease (ORP : 1.21, 95% CI: 1.07-1.38, p-value: 0.003). CONCLUSIONS ATG16L1 rs2241880 (G allele) is a consistent risk factor for IBD in Caucasian cohorts and influences clinical outcomes. As its role in non-Caucasian populations remains ambiguous, further studies in under-reported populations are necessary.
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Affiliation(s)
- Isidora Simovic
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Ida Hilmi
- Department of Medicine, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Ruey Terng Ng
- Department of Paediatrics, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Kee Seang Chew
- Department of Paediatrics, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Shin Yee Wong
- Department of Paediatrics, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Way Seah Lee
- Department of Paediatrics, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Stephen Riordan
- Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Kuala Lumpur, Malaysia
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13
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Bali JS, Sambyal V, Mehrotra S, Gupta P, Guleria K, Uppal MS, Sudan M. Association of ATG10 rs1864183, ATG16L1 rs2241880 and miR-126 with esophageal cancer. Mol Biol Rep 2024; 51:231. [PMID: 38281293 DOI: 10.1007/s11033-023-09012-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/24/2023] [Indexed: 01/30/2024]
Abstract
BACKGROUND In India, esophageal cancer (EC) is among the major cause of cancer-related deaths in both sexes. In recent past, autophagy has emerged as one of the crucial process associated with cancer. In the development of EC, the role of autophagy and the precise molecular mechanism involved has yet to be fully understood. Recently, a small number of studies have proposed how variations in autophagy genes affect the growth and development of EC. Micro-RNA's are also known to play a critical role in the development of EC. Here, we examined the relationship between the risk of EC and two single-nucleotide polymorphisms (SNPs) in the key autophagy genes, ATG10 rs1864183 and ATG16L1 rs2241880. We also analyzed the association of miR-107 and miR-126 with EC as these miRNA's are associated with autophagy. METHODS AND RESULTS A total of 230 EC patients and 230 healthy controls from North-west Indian population were enrolled. ATG10 rs1864183 and ATG16L1 rs2241880 polymorphism were analyzed using TaqMan genotyping assay. Expression levels of miR-107 and miR-126 were analyzed through quantitative PCR using SYBR green chemistry. We found significant association of CT + CC genotype (OR 0.64, p = 0.022) in recessive model for ATG10 rs1864183 polymorphism with decreased EC risk. For ATG16L1 rs2241880 polymorphism significant association for AG genotype (OR 1.48, p = 0.05) and G allele (OR 1.43, p = 0.025) was observed for increased EC risk. Expression levels of miR-126 were also found to be significantly up regulated (p = 0.008). CONCLUSION Our results suggest that ATG10 rs1864183, ATG16L1 rs2241880 and miR-126 may be associated with esophageal carcinogenesis and warrant further investigation.
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Affiliation(s)
- Jagmohan Singh Bali
- Human Cytogenetics Laboratory, Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Vasudha Sambyal
- Human Cytogenetics Laboratory, Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, India.
| | - Sanjana Mehrotra
- Human Cytogenetics Laboratory, Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Priyanka Gupta
- Human Cytogenetics Laboratory, Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Kamlesh Guleria
- Human Cytogenetics Laboratory, Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Manjit Singh Uppal
- Department of Surgery, Sri Guru Ram Das Institute of Medical Sciences and Research, Vallah, Amritsar, Punjab, India
| | - Meena Sudan
- Department of Radiotherapy, Sri Guru Ram Das Institute of Medical Sciences and Research, Vallah, Amritsar, Punjab, India
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14
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Shima T, Kinjo T, Park S, Sonoda M. Perinatal clinical course of Vici syndrome associated with novel EPG5 variants: unique cardiac changes and difficulty with foetal diagnosis. BMJ Case Rep 2024; 17:e255847. [PMID: 38182173 PMCID: PMC10773411 DOI: 10.1136/bcr-2023-255847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2024] Open
Abstract
Vici syndrome is a genetic disorder involving autophagy dysfunction caused by biallelic pathogenic variants in ectopic P-granules 5 autophagy tethering factor (EPG5). We report the perinatal clinical course of a neonate with Vici syndrome with a unique cardiac presentation. Foetal ultrasonography (US) detected right ventricular hypertrophy, hypoplastic left ventricle and narrowing of the foramen ovale, which were alleviated after birth. Agenesis of the corpus callosum and cerebellar hypoplasia were missed antenatally. After delivery, the patient was clinically diagnosed with Vici syndrome and two novel pathogenic mutations were detected in EPG5 The T-cell receptor repertoire was selectively skewed in the Vβ2 family. Immunological prophylaxis and tube feeding were introduced. Early diagnosis helps parents accept their child's prognosis and decide on a care plan. However, US has limited potential to detect clinical phenotypes associated with Vici syndrome. Foetal MRI may detect the characteristic abnormalities and contribute to antenatal diagnosis.
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Affiliation(s)
- Takashi Shima
- Neonatology, Fukuoka Children's Hospital, Fukuoka, Japan
| | - Tadamune Kinjo
- Neonatology, Fukuoka Children's Hospital, Fukuoka, Japan
| | - Sungyeon Park
- Department of Hematology, Infection, and Immunology, Fukuoka Children's Hospital, Fukuoka, Japan
- Department of Pediatrics, Graduate School of Medical Science, Kyushu University Hospital, Fukuoka, Japan
| | - Motoshi Sonoda
- Neonatology, Fukuoka Children's Hospital, Fukuoka, Japan
- Department of Pediatrics, Graduate School of Medical Science, Kyushu University Hospital, Fukuoka, Japan
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15
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Tian Y, Okamoto K. The nascent polypeptide-associated complex subunit Egd1 is required for efficient selective mitochondrial degradation in budding yeast. Sci Rep 2024; 14:546. [PMID: 38177147 PMCID: PMC10767044 DOI: 10.1038/s41598-023-50245-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 12/17/2023] [Indexed: 01/06/2024] Open
Abstract
Selective degradation of dysfunctional or excess mitochondria is a fundamental process crucial for cell homeostasis in almost all eukaryotes. This process relies on autophagy, an intracellular self-eating system conserved from yeast to humans and is thus called mitophagy. Detailed mechanisms of mitophagy remain to be fully understood. Here we show that mitochondrial degradation in budding yeast, which requires the pro-mitophagic protein Atg32, is strongly reduced in cells lacking Egd1, a beta subunit of the nascent polypeptide-associated complex acting in cytosolic ribosome attachment and protein targeting to mitochondria. By contrast, loss of the sole alpha subunit Egd2 or the beta subunit paralogue Btt1 led to only a partial or slight reduction in mitophagy. We also found that phosphorylation of Atg32, a crucial step for priming mitophagy, is decreased in the absence of Egd1. Forced Atg32 hyperphosphorylation almost completely restored mitophagy in egd1-null cells. Together, we propose that Egd1 acts in Atg32 phosphorylation to facilitate mitophagy.
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Affiliation(s)
- Yuan Tian
- Laboratory of Mitochondrial Dynamics, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Koji Okamoto
- Laboratory of Mitochondrial Dynamics, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan.
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16
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Proikas-Cezanne T, Haas ML, Pastor-Maldonado CJ, Schüssele DS. Human WIPI β-propeller function in autophagy and neurodegeneration. FEBS Lett 2024; 598:127-139. [PMID: 38058212 DOI: 10.1002/1873-3468.14782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/10/2023] [Accepted: 11/10/2023] [Indexed: 12/08/2023]
Abstract
The four human WIPI β-propellers, WIPI1 through WIPI4, belong to the ancient PROPPIN family and fulfill scaffold functions in the control of autophagy. In this context, WIPI β-propellers function as PI3P effectors during autophagosome formation and loss of WIPI function negatively impacts autophagy and contributes to neurodegeneration. Of particular interest are mutations in WDR45, the human gene that encodes WIPI4. Sporadic WDR45 mutations are the cause of a rare human neurodegenerative disease called BPAN, hallmarked by high brain iron accumulation. Here, we discuss the current understanding of the functions of human WIPI β-propellers and address unanswered questions with a particular focus on the role of WIPI4 in autophagy and BPAN.
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Affiliation(s)
- Tassula Proikas-Cezanne
- Interfaculty Institute of Cell Biology, Department of Biology, Faculty of Science, Eberhard Karls University Tübingen, Germany
| | - Maximilian L Haas
- Interfaculty Institute of Cell Biology, Department of Biology, Faculty of Science, Eberhard Karls University Tübingen, Germany
| | - Carmen J Pastor-Maldonado
- Interfaculty Institute of Cell Biology, Department of Biology, Faculty of Science, Eberhard Karls University Tübingen, Germany
| | - David S Schüssele
- Interfaculty Institute of Cell Biology, Department of Biology, Faculty of Science, Eberhard Karls University Tübingen, Germany
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17
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Tooze SA, Zhang W, Lazzeri G, Gahlot D, Thukral L, Covino R, Nishimura T. Membrane association of the ATG8 conjugation machinery emerges as a key regulatory feature for autophagosome biogenesis. FEBS Lett 2024; 598:107-113. [PMID: 37259601 PMCID: PMC10952647 DOI: 10.1002/1873-3468.14676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 05/10/2023] [Accepted: 05/10/2023] [Indexed: 06/02/2023]
Abstract
Autophagy is a highly conserved intracellular pathway that is essential for survival in all eukaryotes. In healthy cells, autophagy is used to remove damaged intracellular components, which can be as simple as unfolded proteins or as complex as whole mitochondria. Once the damaged component is captured, the autophagosome engulfs it and closes, isolating the content from the cytoplasm. The autophagosome then fuses with the late endosome and/or lysosome to deliver its content to the lysosome for degradation. Formation of the autophagosome, sequestration or capture of content, and closure all require the ATG proteins, which constitute the essential core autophagy protein machinery. This brief 'nutshell' will highlight recent data revealing the importance of small membrane-associated domains in the ATG proteins. In particular, recent findings from two parallel studies reveal the unexpected key role of α-helical structures in the ATG8 conjugation machinery and ATG8s. These studies illustrate how unique membrane association modules can control the formation of autophagosomes.
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Affiliation(s)
- Sharon A. Tooze
- Molecular Cell Biology of Autophagy LaboratoryThe Francis Crick InstituteLondonUK
| | - Wenxin Zhang
- Molecular Cell Biology of Autophagy LaboratoryThe Francis Crick InstituteLondonUK
| | | | - Deepanshi Gahlot
- CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
- Academy of Scientific and Innovative Research (AcSIR)GhaziabadIndia
| | - Lipi Thukral
- CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
- Academy of Scientific and Innovative Research (AcSIR)GhaziabadIndia
| | | | - Taki Nishimura
- PRESTO, Japan Science and Technology AgencyTokyoJapan
- Department of Biochemistry and Molecular Biology, Graduate School of MedicineThe University of TokyoJapan
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18
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Wu M, Ying J, Lin X, Xu C, Zheng X, Zheng Y, Fang Z, Yan B, Zhang N, Mou Y, Tan F. Toxoplasma gondii autophagy-related protein ATG7 maintains apicoplast inheritance by stabilizing and lipidating ATG8. Biochim Biophys Acta Mol Basis Dis 2024; 1870:166891. [PMID: 37739091 DOI: 10.1016/j.bbadis.2023.166891] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/12/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023]
Abstract
ATG8/LC3-mediated autophagosome formation is a key rate-limiting step in the process of autophagy. The parasitic protist Toxoplasma gondii possesses a single ATG8 homolog (TgATG8), which can localize to either cytosolic autophagosome involved in delivery of autophagic material in bradyzoites, or the outermost membrane of apicoplast, a nonphotosynthetic plastid-like organelle, responsible for maintaining homeostasis in tachyzoites. However, mechanisms that regulate TgATG8 remain insufficiently understood. Here, a TgATG7 conditional knockdown line that we have generated is severely impaired in parasite's growth and exhibits significant defects in the organelle level, strikingly with a fragmentation of the mitochondrial network and a loss of the apicoplast. Specific TgATG7C1133S point mutant complemented line showed that these defects were associated with its E1-type enzyme activity. Both depletion of TgATG7 and mutation of its catalytic cysteine 1133 hindered TgATG8 lipidation and apicoplast localization. Unexpectedly, we also found that depletion of TgATG7 reduced the unlipidated TgATG8 protein level. Subsequently, we determined that TgATG7 was able to interact with TgATG8 directly via its C-terminal domain and multi-monoubiquitination stimulated proteasome-dependent degradation of TgATG8, while TgATG7 could inhibit the degradation through stabilization of TgATG8. Additionally, we identified a putative TgATG8 interacting fragment of TgATG7, 1281-1290aa. Depletion of the fragment impaired the parasite growth and apicoplast inheritance. To our knowledge, our study is the first to elucidate the role of TgATG7 and the ubiquitin-proteasome system in synergistically regulating the non-lipidated pool of TgATG8, suggesting a potential homeostatic mechanism responsible for balancing autophagic activity in T. gondii.
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Affiliation(s)
- Mimi Wu
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, Zhejiang, China; Department of Parasitology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jiaqi Ying
- School of the Second Clinical Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xuejing Lin
- Department of Parasitology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Chao Xu
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiaozi Zheng
- Teaching Center of Morphological Experiment, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yi Zheng
- Laser Confocal Microscope Lab, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zhouxi Fang
- Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Baolong Yan
- Department of Parasitology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Nu Zhang
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Yani Mou
- Department of Parasitology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Feng Tan
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, Zhejiang, China; Department of Parasitology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China.
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19
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Han D, Huang M, Chang Z, Sun W. KLF15 Transcriptionally Activates ATG14 to Promote Autophagy and Attenuate Damage of ox-LDL-Induced HAECs. Mol Biotechnol 2024; 66:112-122. [PMID: 37043109 DOI: 10.1007/s12033-023-00742-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/27/2023] [Indexed: 04/13/2023]
Abstract
Kruppel-like factor 15 (KLF15) is involved in many cardiovascular diseases and is abnormally expressed in atherosclerosis (AS), but the regulatory mechanism of KLF15 in AS has not been reported so far. RT-qPCR was used to detect the expression of KLF15 and ATG14 in AS patients. Subsequently, human aortic endothelial cells (HAECs) were induced by oxidized low densitylipoprotein (ox-LDL), and the expression of KLF15 in model cells was detected. KLF15 was overexpressed in cells by lipofection transfection, and then CCK8, flow cytometry, Western blot, ELISA, and related assay kits were used to detect cell viability, apoptosis, inflammatory response as well as oxidative stress, respectively. The targeted regulatory relationship between KLF15 and autophagy-related 14 (ATG14) was detected by ChIP and luciferase reporter assays. Following ATG14 silencing in KLF15-overexpressing cells, immunofluorescence and Western blot were used to detect the autophagy. Finally, after the addition of 3-Methyladenine (3-MA), an autophagy inhibitor, the aforementioned experiments were conducted again to further explore the mechanism. The expression of KLF15 and ATG14 were decreased in AS patients and ox-LDL-induced HAECs. Overexpression of KLF15 protected ox-LDL-induced HAECs from damage, which might be achieved through transcriptional regulation of ATG14. In addition, KLF15 could promote autophagy through transcriptional activation of ATG14. KLF15 transcriptionally activated ATG14 to promote autophagy and attenuate damage of ox-LDL-induced HAECs.
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Affiliation(s)
- Dong Han
- Department of Emergency, Affiliated Hospital of Jiangnan University, No. 1000 Hefeng Road, Wuxi, 214125, Jiangsu, China
| | - Ming Huang
- Department of Emergency, Affiliated Hospital of Jiangnan University, No. 1000 Hefeng Road, Wuxi, 214125, Jiangsu, China
| | - Zhen Chang
- Department of Emergency, Affiliated Hospital of Jiangnan University, No. 1000 Hefeng Road, Wuxi, 214125, Jiangsu, China
| | - Wei Sun
- Department of Emergency, Affiliated Hospital of Jiangnan University, No. 1000 Hefeng Road, Wuxi, 214125, Jiangsu, China.
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20
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Kraft C, Reggiori F. Phagophore closure, autophagosome maturation and autophagosome fusion during macroautophagy in the yeast Saccharomyces cerevisiae. FEBS Lett 2024; 598:73-83. [PMID: 37585559 DOI: 10.1002/1873-3468.14720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/07/2023] [Accepted: 08/07/2023] [Indexed: 08/18/2023]
Abstract
Macroautophagy, hereafter referred to as autophagy, is a complex process in which multiple membrane-remodeling events lead to the formation of a cisterna known as the phagophore, which then expands and closes into a double-membrane vesicle termed the autophagosome. During the past decade, enormous progress has been made in understanding the molecular function of the autophagy-related proteins and their role in generating these phagophores. In this Review, we discuss the current understanding of three membrane remodeling steps in autophagy that remain to be largely characterized; namely, the closure of phagophores, the maturation of the resulting autophagosomes into fusion-competent vesicles, and their fusion with vacuoles/lysosomes. Our review will mainly focus on the yeast Saccharomyces cerevisiae, which has been the leading model system for the study of molecular events in autophagy and has led to the discovery of the major mechanistic concepts, which have been found to be mostly conserved in higher eukaryotes.
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Affiliation(s)
- Claudine Kraft
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, Germany
| | - Fulvio Reggiori
- Department of Biomedicine, Aarhus University, Denmark
- Aarhus Institute of Advanced Studies (AIAS), Aarhus University, Denmark
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21
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Yue C, Lin B, Sun X, Xu X, Zhou C, Fan J. Autophagy-related risk signature based on CDNK2A to facilitate survival prediction of patients with endometrial cancer. J Gene Med 2024; 26:e3648. [PMID: 38282156 DOI: 10.1002/jgm.3648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 11/05/2023] [Accepted: 11/13/2023] [Indexed: 01/30/2024] Open
Abstract
BACKGROUND Autophagy plays an important role in immunity and inflammation. The present study aimed to explore the prognostic significance of autophagy-related genes (ARGs) in endometrial cancer (EC) using bioinformatics. METHODS The list of ARGs was obtained from the Human Autophagy Database. The differentially expressed ARGs (DEARGs) between the EC and normal endometrial tissue samples were screened from The Cancer Genome Atlas database. Cox regression analysis was performed on the DEARGs to screen the prognostic ARGs and construct risk signatures for overall survival (OS) and progression-free survival (PFS). The hub ARGs were identified from a protein-protein interaction network, and CDKN2A was obtained from the intersection of prognostic ARGs and hub ARGs. The association of CDKN2A expression with clinical characteristics and immune infiltration were analyzed. Finally, the role of CDKN2A in autophagy was confirmed in EC cell lines. RESULTS CDKN2A, PTK6 and DLC1 were used to establish risk signatures for predicting the survival of EC patients. Receiver operating characteristic curve analysis indicated that the risk signatures can accurately predict both OS and PFS. CDKN2A was the only hub prognostic ARG, and showed significant association with the age, survival status, grade, histological type, body mass index and FIGO (i.e. International Federation of Gynecology and Obstetrics) stage (p < 0.05). Furthermore, CDKN2A expression was also correlated with the infiltration of immune cells, indicating that CDKN2A might play a critical role in regulating the immune microenvironment and immune responses in EC. In addition, silencing of CDKN2A gene promoted autophagy in the HEC-1A cell line and upregulated the expression levels of autophagy-related proteins. CONCLUSIONS CDKN2A is a prognostic factor and therapeutic target in EC, and is likely associated with the tumor immune landscape and autophagy.
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Affiliation(s)
- Chaomin Yue
- Department of Obstetrics and Gynaecology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Baohua Lin
- Department of Obstetrics and Gynaecology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiang Sun
- Department of Obstetrics and Gynaecology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xindi Xu
- China Medical University, Shenyang, Liaoning, China
| | - Chufan Zhou
- Department of Obstetrics and Gynaecology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jiaying Fan
- Department of Obstetrics and Gynaecology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
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22
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Zhang N, Shen MY, Meng QL, Sun HP, Fan FY, Yi H, Yang YJ. FAT1 inhibits AML autophagy and proliferation via downregulating ATG4B expression. Biochim Biophys Acta Gen Subj 2024; 1868:130519. [PMID: 37952564 DOI: 10.1016/j.bbagen.2023.130519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/30/2023] [Accepted: 11/07/2023] [Indexed: 11/14/2023]
Abstract
BACKGROUND Emerging studies have shown that FAT atypical cadherin 1 (FAT1) and autophagy separately inhibits and promotes acute myeloid leukemia (AML) proliferation. However, it is unknown whether FAT1 were associated with autophagy in regulating AML proliferation. METHODS AML cell lines, 6-week-old male nude mice and AML patient samples were used in this study. qPCR/Western blot and cell viability/3H-TdR incorporation assays were separately used to detect mRNA/protein levels and cell activity/proliferation. Luciferase reporter assay was used to examine gene promoter activity. Co-IP analysis was used to detect the binding of proteins. RESULTS In this study, we for the first time demonstrated that FAT1 inhibited AML proliferation by decreasing AML autophagy level. Moreover, FAT1 weakened AML autophagy level via decreasing autophagy related 4B (ATG4B) expression. Mechanistically, we found that FAT1 reduced the phosphorylated and intranuclear SMAD family member 2/3 (smad2/3) protein levels, thus decreasing the activity of ATG4B gene promoter. Furthermore, we found that FAT1 competitively bound to TGF-βR II which decreased the binding of TGF-βR II to TGF-βR I and the subsequent phosphorylation of TGF-βR I, thus reducing the phosphorylation and intranuclear smad2/3. The experiments in nude mice showed that knockdown of FAT1 promoted AML autophagy and proliferation in vivo. CONCLUSIONS Collectively, these results revealed that FAT1 downregulates ATG4B expression via inhibiting TGFβ-smad2/3 signaling activity, thus decreasing the autophagy level and proliferation activity of AML cells. GENERAL SIGNIFICANCE Our study suggested that the "FAT1-TGFβ-smad2/3-ATG4B-autophagy" pathway may be a novel target for developing new targeted drugs to AML treatment.
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Affiliation(s)
- Nan Zhang
- Department of Hematology, People's Liberation Army The General Hospital of Western Theater Command, Chengdu 610083, China
| | - Meng-Yu Shen
- Department of Medical Laboratory Center, People's Liberation Army The General Hospital of Central Theater Command, Wuhan 430012, China
| | - Qing-Li Meng
- Department of Hematology, People's Liberation Army The General Hospital of Western Theater Command, Chengdu 610083, China
| | - Hao-Ping Sun
- Department of Hematology, People's Liberation Army The General Hospital of Western Theater Command, Chengdu 610083, China
| | - Fang-Yi Fan
- Department of Hematology, People's Liberation Army The General Hospital of Western Theater Command, Chengdu 610083, China
| | - Hai Yi
- Department of Hematology, People's Liberation Army The General Hospital of Western Theater Command, Chengdu 610083, China
| | - Yong-Jian Yang
- Department of Cardiology, People's Liberation Army The General Hospital of Western Theater Command, Chengdu 610083, China.
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23
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Nguyen A, Faesen AC. The role of the HORMA domain proteins ATG13 and ATG101 in initiating autophagosome biogenesis. FEBS Lett 2024; 598:114-126. [PMID: 37567770 DOI: 10.1002/1873-3468.14717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 08/13/2023]
Abstract
Autophagy is a process of regulated degradation. It eliminates damaged and unnecessary cellular components by engulfing them with a de novo-generated organelle: the double-membrane autophagosome. The past three decades have provided us with a detailed parts list of the autophagy initiation machinery, have developed important insights into how these processes function and have identified regulatory proteins. It is now clear that autophagosome biogenesis requires the timely assembly of a complex machinery. However, it is unclear how a putative stable machine is assembled and disassembled and how the different parts cooperate to perform its overall function. Although they have long been somewhat enigmatic in their precise role, HORMA domain proteins (first identified in Hop1p, Rev7p and MAD2 proteins) autophagy-related protein 13 (ATG13) and ATG101 of the ULK-kinase complex have emerged as important coordinators of the autophagy-initiating subcomplexes. Here, we will particularly focus on ATG13 and ATG101 and the role of their unusual metamorphosis in initiating autophagosome biogenesis. We will also explore how this metamorphosis could potentially be purposefully rate-limiting and speculate on how it could regulate the spontaneous self-assembly of the autophagy-initiating machinery.
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Affiliation(s)
- Anh Nguyen
- Laboratory of Biochemistry of Signal Dynamics, Max-Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Alex C Faesen
- Laboratory of Biochemistry of Signal Dynamics, Max-Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
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24
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Mallén-Ponce MJ, Pérez-Pérez ME. Redox-mediated activation of ATG3 promotes ATG8 lipidation and autophagy progression in Chlamydomonas reinhardtii. Plant Physiol 2023; 194:359-375. [PMID: 37772945 PMCID: PMC10756753 DOI: 10.1093/plphys/kiad520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/05/2023] [Accepted: 09/15/2023] [Indexed: 09/30/2023]
Abstract
Autophagy is one of the main degradative pathways used by eukaryotic organisms to eliminate useless or damaged intracellular material to maintain cellular homeostasis under stress conditions. Mounting evidence indicates a strong interplay between the generation of reactive oxygen species and the activation of autophagy. Although a tight redox regulation of autophagy has been shown in several organisms, including microalgae, the molecular mechanisms underlying this control remain poorly understood. In this study, we have performed an in-depth in vitro and in vivo redox characterization of ATG3, an E2-activating enzyme involved in ATG8 lipidation and autophagosome formation, from 2 evolutionary distant unicellular model organisms: the green microalga Chlamydomonas (Chlamydomonas reinhardtii) and the budding yeast Saccharomyces cerevisiae. Our results indicated that ATG3 activity from both organisms is subjected to redox regulation since these proteins require reducing equivalents to transfer ATG8 to the phospholipid phosphatidylethanolamine. We established the catalytic Cys of ATG3 as a redox target in algal and yeast proteins and showed that the oxidoreductase thioredoxin efficiently reduces ATG3. Moreover, in vivo studies revealed that the redox state of ATG3 from Chlamydomonas undergoes profound changes under autophagy-activating stress conditions, such as the absence of photoprotective carotenoids, the inhibition of fatty acid synthesis, or high light irradiance. Thus, our results indicate that the redox-mediated activation of ATG3 regulates ATG8 lipidation under oxidative stress conditions in this model microalga.
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Affiliation(s)
- Manuel J Mallén-Ponce
- Instituto de Bioquímica Vegetal y Fotosíntesis (IBVF), Consejo Superior de Investigaciones Científicas (CSIC)- Universidad de Sevilla, Sevilla 41092, Spain
| | - María Esther Pérez-Pérez
- Instituto de Bioquímica Vegetal y Fotosíntesis (IBVF), Consejo Superior de Investigaciones Científicas (CSIC)- Universidad de Sevilla, Sevilla 41092, Spain
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25
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Sun J, Shao Y, Wang S, Li X, Feng S, Wang W, Leroy P, Li C, Zheng H. An Arabidopsis Rab18 GTPase promotes autophagy by tethering ATG18a to the ER in response to nutrient starvation. Dev Cell 2023; 58:2947-2958.e5. [PMID: 38056450 DOI: 10.1016/j.devcel.2023.11.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 07/30/2023] [Accepted: 11/10/2023] [Indexed: 12/08/2023]
Abstract
The expansion of autophagosomes requires a controlled association with the endoplasmic reticulum (ER). However, the mechanisms governing this process are not well defined. In plants, ATG18a plays a key role in autophagosome formation in response to stress, yet the factors regulating the process are unknown. This study finds that ATG18a acts as a downstream effector of RABC1, a member of the poorly characterized Rab18/RabC GTPase subclass in plants. Active RABC1 interacts with ATG18a on the ER, particularly under nutrient starvation. In rabc1 mutants, autophagy is compromised, especially under nutrient deprivation, affecting the ER association and expansion of ATG18a-positive autophagosomes. Furthermore, both dominant-negative and constitutively active RABC1 forms inhibit autophagy. The dominant inactive RABC1 impedes the ER association of ATG18a, whereas the constitutively active RABC1 delays ATG18a detachment from the ER. Collectively, RABC1 regulates the ER association and the subsequent detachment of ATG18a-positive autophagosomes during nutrient starvation.
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Affiliation(s)
- Jiaqi Sun
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, Shandong, China; Department of Biology, McGill University, Montreal, QC H3B 1A1, Canada.
| | - Yang Shao
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, Shandong, China
| | - Songyang Wang
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, Shandong, China
| | - Xunzheng Li
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, Shandong, China
| | - Shuqing Feng
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, Shandong, China
| | - Weina Wang
- Department of Biology, McGill University, Montreal, QC H3B 1A1, Canada
| | - Pierre Leroy
- Department of Biology, McGill University, Montreal, QC H3B 1A1, Canada
| | - Chengyang Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Huanquan Zheng
- Department of Biology, McGill University, Montreal, QC H3B 1A1, Canada.
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26
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Gómez-Martín A, Fuentes JM, Jordán J, Galindo MF, Fernández-García JL. Comparative Genetic Analysis of the Promoters of the ATG16L1 and ATG5 Genes Associated with Sporadic Parkinson's Disease. Genes (Basel) 2023; 14:2171. [PMID: 38136993 PMCID: PMC10743014 DOI: 10.3390/genes14122171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/25/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
Sporadic Parkinson's disease, characterised by a decline in dopamine, usually manifests in people over 65 years of age. Although 10% of cases have a genetic (familial) basis, most PD is sporadic. Genome sequencing studies have associated several genetic variants with sporadic PD. Our aim was to analyse the promoter region of the ATG16L1 and ATG5 genes in sporadic PD patients and ethnically matched controls. Genotypes were obtained by using the Sanger method with primers designed by us. The number of haplotypes was estimated with DnaSP software, phylogeny was reconstructed in Network, and genetic divergence was explored with Fst. Seven and two haplotypes were obtained for ATG16L1 and ATG5, respectively. However, only ATG16L1 showed a significant contribution to PD and a significant excess of accumulated mutations that could influence sporadic PD disease. Of a total of seven haplotypes found, only four were unique to patients sharing the T allele (rs77820970). Recent studies using MAPT genes support the notion that the architecture of haplotypes is worthy of being considered genetically risky, as shown in our study, confirming that large-scale assessment in different populations could be relevant to understanding the role of population-specific heterogeneity. Finally, our data suggest that the architecture of certain haplotypes and ethnicity determine the risk of PD, linking haplotype variation and neurodegenerative processes.
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Affiliation(s)
- Ana Gómez-Martín
- Nursing Department, Faculty of Nursing and Occupational Therapy, University of Extremadura, Avda de la Universidad s/n, 10003 Cáceres, Spain
- Instituto de Investigación Biosanitaria de Extremadura (INUBE), 10003 Cáceres, Spain;
| | - José M. Fuentes
- Instituto de Investigación Biosanitaria de Extremadura (INUBE), 10003 Cáceres, Spain;
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Enfermería y Terapia Ocupa-cional, Universidad de Extremadura, 10003 Cáceres, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativa, Instituto de Salus Carlos III (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
| | - Joaquín Jordán
- Pharmacology, Medical Sciences Department, Albacete School of Medicine, University of Castilla-La Mancha, 02008 Albacete, Spain;
| | - María F. Galindo
- Pharmaceutical Technologic, Medical Sciences Department, Albacete School of Pharmacy, University of Castilla-La Mancha, 02008 Albacete, Spain;
| | - José Luis Fernández-García
- Animal Production and Food Science Department, Faculty of Veterinary Sciences, University of Extremadura, Avda. de la Universidad, s/n, 10003 Caceres, Spain
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27
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Feng X, Sun D, Li Y, Zhang J, Liu S, Zhang D, Zheng J, Xi Q, Liang H, Zhao W, Li Y, Xu M, He J, Liu T, Hasim A, Ma M, Xu P, Mi N. Local membrane source gathering by p62 body drives autophagosome formation. Nat Commun 2023; 14:7338. [PMID: 37957156 PMCID: PMC10643672 DOI: 10.1038/s41467-023-42829-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Autophagosomes are double-membrane vesicles generated intracellularly to encapsulate substrates for lysosomal degradation during autophagy. Phase separated p62 body plays pivotal roles during autophagosome formation, however, the underlying mechanisms are still not fully understood. Here we describe a spatial membrane gathering mode by which p62 body functions in autophagosome formation. Mass spectrometry-based proteomics reveals significant enrichment of vesicle trafficking components within p62 body. Combining cellular experiments and biochemical reconstitution assays, we confirm the gathering of ATG9 and ATG16L1-positive vesicles around p62 body, especially in Atg2ab DKO cells with blocked lipid transfer and vesicle fusion. Interestingly, p62 body also regulates ATG9 and ATG16L vesicle trafficking flux intracellularly. We further determine the lipid contents associated with p62 body via lipidomic profiling. Moreover, with in vitro kinase assay, we uncover the functions of p62 body as a platform to assemble ULK1 complex and invigorate PI3KC3-C1 kinase cascade for PI3P generation. Collectively, our study raises a membrane-based working model for multifaceted p62 body in controlling autophagosome biogenesis, and highlights the interplay between membraneless condensates and membrane vesicles in regulating cellular functions.
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Affiliation(s)
- Xuezhao Feng
- State Key Laboratory of Pathogenesis, Prevention and Treatment of Central Asian High Incidence Diseases, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
- Basic Medical College, Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
| | - Daxiao Sun
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany.
| | - Yanchang Li
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, 102206, Beijing, China
| | - Jinpei Zhang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of Central Asian High Incidence Diseases, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
- Basic Medical College, Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
| | - Shiyu Liu
- State Key Laboratory of Pathogenesis, Prevention and Treatment of Central Asian High Incidence Diseases, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
- Basic Medical College, Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
| | - Dachuan Zhang
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Jingxiang Zheng
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Qing Xi
- State Key Laboratory of Pathogenesis, Prevention and Treatment of Central Asian High Incidence Diseases, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
- Basic Medical College, Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
| | - Haisha Liang
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Wenkang Zhao
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Ying Li
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Mengbo Xu
- State Key Laboratory of Pathogenesis, Prevention and Treatment of Central Asian High Incidence Diseases, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
- Basic Medical College, Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
| | - Jiayu He
- State Key Laboratory of Pathogenesis, Prevention and Treatment of Central Asian High Incidence Diseases, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
- Basic Medical College, Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
| | - Tong Liu
- State Key Laboratory of Pathogenesis, Prevention and Treatment of Central Asian High Incidence Diseases, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
- Basic Medical College, Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
| | - Ayshamgul Hasim
- Basic Medical College, Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
- Department of Pathology, School of Basic Medicine, Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
| | - Meisheng Ma
- Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ping Xu
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, 102206, Beijing, China.
| | - Na Mi
- State Key Laboratory of Pathogenesis, Prevention and Treatment of Central Asian High Incidence Diseases, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, Xinjiang, China.
- Basic Medical College, Xinjiang Medical University, Urumqi, 830011, Xinjiang, China.
- Key Laboratory of High Incidence Disease Research in Xinjiang (Xinjiang Medical University), Ministry of Education, Urumqi, 830011, Xinjiang, China.
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Huang M, Zhang Y, Park J, Chowdhury K, Xu J, Lu A, Wang L, Zhang W, Ekser B, Yu L, Dong XC. ATG14 plays a critical role in hepatic lipid droplet homeostasis. Metabolism 2023; 148:155693. [PMID: 37741434 PMCID: PMC10591826 DOI: 10.1016/j.metabol.2023.155693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 09/17/2023] [Accepted: 09/20/2023] [Indexed: 09/25/2023]
Abstract
BACKGROUND & AIMS Autophagy-related 14 (ATG14) is a key regulator of autophagy. ATG14 is also localized to lipid droplet; however, the function of ATG14 on lipid droplet remains unclear. In this study, we aimed to elucidate the role of ATG14 in lipid droplet homeostasis. METHODS ATG14 loss-of-function and gain-of-function in lipid droplet metabolism were analyzed by fluorescence imaging in ATG14 knockdown or overexpression hepatocytes. Specific domains involved in the ATG14 targeting to lipid droplets were analyzed by deletion or site-specific mutagenesis. ATG14-interacting proteins were analyzed by co-immunoprecipitation. The effect of ATG14 on lipolysis was analyzed in human hepatocytes and mouse livers that were deficient in ATG14, comparative gene identification-58 (CGI-58), or both. RESULTS Our data show that ATG14 is enriched on lipid droplets in hepatocytes. Mutagenesis analysis reveals that the Barkor/ATG14 autophagosome targeting sequence (BATS) domain of ATG14 is responsible for the ATG14 localization to lipid droplets. Co-immunoprecipitation analysis illustrates that ATG14 interacts with adipose triglyceride lipase (ATGL) and CGI-58. Moreover, ATG14 also enhances the interaction between ATGL and CGI-58. In vitro lipolysis analysis demonstrates that ATG14 deficiency remarkably decreases triglyceride hydrolysis. CONCLUSIONS Our data suggest that ATG14 can directly enhance lipid droplet breakdown through interactions with ATGL and CGI-58.
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Affiliation(s)
- Menghao Huang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yang Zhang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jimin Park
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kushan Chowdhury
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jiazhi Xu
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Alex Lu
- Park Tudor School, Indianapolis, IN, USA
| | - Lu Wang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Wenjun Zhang
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Burcin Ekser
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Liqing Yu
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - X Charlie Dong
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA; Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN, USA..
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29
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Wenhao R, Yali C, Shaoming L, Jingjing Z, Ling G, Keqian Z. circAP1M2 activates ATG9A-associated autophagy by inhibiting miR-1249-3p to promote cisplatin resistance in oral squamous cell carcinoma. J Cell Physiol 2023; 238:2612-2624. [PMID: 37661341 DOI: 10.1002/jcp.31116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/14/2023] [Accepted: 08/18/2023] [Indexed: 09/05/2023]
Abstract
Cisplatin (CDDP) is the first-line chemotherapeutic agent for oral squamous cell carcinoma (OSCC). Susceptibility to drug resistance during treatment is a significant challenge in enhancing the therapeutic efficacy of OSCC. Autophagy is an essential element to guarantee the cancer cells' survival under chemo-stress conditions. We established a cisplatin-resistant OSCC cell line (CAL27/CDDP) and showed that circAP1M2 is a remarkably upregulated circular RNA in OSCC. Knockdown of circAP1M2 contributes to reversing cisplatin chemoresistance in vivo, while enhanced autophagic activity in cisplatin-resistant OSCC cells contributes to chemoresistance. Mechanistically, we showed that circAP1M2 induces autophagy-associated cisplatin resistance via the miR-1249-3p-ATG9A axis in OSCC cells. This study provides insights into the specific influence of a newly identified circular RNA circAP1M2 in OSCC regarding drug abuse and the treatment of a broad range of cancers that can benefit from cisplatin.
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Affiliation(s)
- Ren Wenhao
- Department of Oral and Maxillofacial Reconstruction, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
- Department of Oral and Maxillofacial Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Cheng Yali
- Department of Stomatology, Huaian Hospital of Huaian City, Huaian, Jiangsu, China
| | - Li Shaoming
- Department of Oral and Maxillofacial Reconstruction, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
- Department of Oral and Maxillofacial Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
- School of Stomatology of Qingdao University, Qingdao, Shandong, China
| | - Zheng Jingjing
- Department of Stomatology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Gao Ling
- Department of Oral and Maxillofacial Reconstruction, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
- Department of Oral and Maxillofacial Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
- Key Lab of Oral Clinical Medicine, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Zhi Keqian
- Department of Oral and Maxillofacial Reconstruction, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
- Department of Oral and Maxillofacial Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
- Key Lab of Oral Clinical Medicine, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
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30
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Tanaka Y, Ito SI, Honma Y, Hasegawa M, Kametani F, Suzuki G, Kozuma L, Takeya K, Eto M. Dysregulation of the progranulin-driven autophagy-lysosomal pathway mediates secretion of the nuclear protein TDP-43. J Biol Chem 2023; 299:105272. [PMID: 37739033 PMCID: PMC10641265 DOI: 10.1016/j.jbc.2023.105272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 09/04/2023] [Accepted: 09/12/2023] [Indexed: 09/24/2023] Open
Abstract
The cytoplasmic accumulation of the nuclear protein transactive response DNA-binding protein 43 kDa (TDP-43) has been linked to the progression of amyotrophic lateral sclerosis and frontotemporal lobar degeneration. TDP-43 secreted into the extracellular space has been suggested to contribute to the cell-to-cell spread of the cytoplasmic accumulation of TDP-43 throughout the brain; however, the underlying mechanisms remain unknown. We herein demonstrated that the secretion of TDP-43 was stimulated by the inhibition of the autophagy-lysosomal pathway driven by progranulin (PGRN), a causal protein of frontotemporal lobar degeneration. Among modulators of autophagy, only vacuolar-ATPase inhibitors, such as bafilomycin A1 (Baf), increased the levels of the full-length and cleaved forms of TDP-43 and the autophagosome marker LC3-II (microtubule-associated proteins 1A/1B light chain 3B) in extracellular vesicle fractions prepared from the culture media of HeLa, SH-SY5Y, or NSC-34 cells, whereas vacuolin-1, MG132, chloroquine, rapamycin, and serum starvation did not. The C-terminal fragment of TDP-43 was required for Baf-induced TDP-43 secretion. The Baf treatment induced the translocation of the aggregate-prone GFP-tagged C-terminal fragment of TDP-43 and mCherry-tagged LC3 to the plasma membrane. The Baf-induced secretion of TDP-43 was attenuated in autophagy-deficient ATG16L1 knockout HeLa cells. The knockdown of PGRN induced the secretion of cleaved TDP-43 in an autophagy-dependent manner in HeLa cells. The KO of PGRN in mouse embryonic fibroblasts increased the secretion of the cleaved forms of TDP-43 and LC3-II. The treatment inducing TDP-43 secretion increased the nuclear translocation of GFP-tagged transcription factor EB, a master regulator of the autophagy-lysosomal pathway in SH-SY5Y cells. These results suggest that the secretion of TDP-43 is promoted by dysregulation of the PGRN-driven autophagy-lysosomal pathway.
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Affiliation(s)
- Yoshinori Tanaka
- Biochemistry Unit, Faculty of Veterinary Medicine, Okayama University of Science, Imabari-shi, Ehime, Japan.
| | - Shun-Ichi Ito
- Biochemistry Unit, Faculty of Veterinary Medicine, Okayama University of Science, Imabari-shi, Ehime, Japan
| | - Yuki Honma
- Biochemistry Unit, Faculty of Veterinary Medicine, Okayama University of Science, Imabari-shi, Ehime, Japan
| | - Masato Hasegawa
- Department of Brain and Neurosciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Fuyuki Kametani
- Department of Brain and Neurosciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Genjiro Suzuki
- Department of Brain and Neurosciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Lina Kozuma
- Biochemistry Unit, Faculty of Veterinary Medicine, Okayama University of Science, Imabari-shi, Ehime, Japan
| | - Kosuke Takeya
- Biochemistry Unit, Faculty of Veterinary Medicine, Okayama University of Science, Imabari-shi, Ehime, Japan
| | - Masumi Eto
- Biochemistry Unit, Faculty of Veterinary Medicine, Okayama University of Science, Imabari-shi, Ehime, Japan
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31
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Vale-Costa S, Etibor TA, Brás D, Sousa AL, Ferreira M, Martins GG, Mello VH, Amorim MJ. ATG9A regulates the dissociation of recycling endosomes from microtubules to form liquid influenza A virus inclusions. PLoS Biol 2023; 21:e3002290. [PMID: 37983294 PMCID: PMC10695400 DOI: 10.1371/journal.pbio.3002290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 12/04/2023] [Accepted: 10/13/2023] [Indexed: 11/22/2023] Open
Abstract
It is now established that many viruses that threaten public health establish condensates via phase transitions to complete their lifecycles, and knowledge on such processes may offer new strategies for antiviral therapy. In the case of influenza A virus (IAV), liquid condensates known as viral inclusions, concentrate the 8 distinct viral ribonucleoproteins (vRNPs) that form IAV genome and are viewed as sites dedicated to the assembly of the 8-partite genomic complex. Despite not being delimited by host membranes, IAV liquid inclusions accumulate host membranes inside as a result of vRNP binding to the recycling endocytic marker Rab11a, a driver of the biogenesis of these structures. We lack molecular understanding on how Rab11a-recycling endosomes condensate specifically near the endoplasmic reticulum (ER) exit sites upon IAV infection. We show here that liquid viral inclusions interact with the ER to fuse, divide, and slide. We uncover that, contrary to previous indications, the reported reduction in recycling endocytic activity is a regulated process rather than a competition for cellular resources involving a novel role for the host factor ATG9A. In infection, ATG9A mediates the removal of Rab11a-recycling endosomes carrying vRNPs from microtubules. We observe that the recycling endocytic usage of microtubules is rescued when ATG9A is depleted, which prevents condensation of Rab11a endosomes near the ER. The failure to produce viral inclusions accumulates vRNPs in the cytosol and reduces genome assembly and the release of infectious virions. We propose that the ER supports the dynamics of liquid IAV inclusions, with ATG9A facilitating their formation. This work advances our understanding on how epidemic and pandemic influenza genomes are formed. It also reveals the plasticity of recycling endosomes to undergo condensation in response to infection, disclosing new roles for ATG9A beyond its classical involvement in autophagy.
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Affiliation(s)
- Sílvia Vale-Costa
- Cell Biology of Viral Infection Lab (CBV), Instituto Gulbenkian de Ciência (IGC)—Fundação Calouste Gulbenkian, Oeiras, Portugal
| | - Temitope Akhigbe Etibor
- Cell Biology of Viral Infection Lab (CBV), Instituto Gulbenkian de Ciência (IGC)—Fundação Calouste Gulbenkian, Oeiras, Portugal
| | - Daniela Brás
- Cell Biology of Viral Infection Lab (CBV), Instituto Gulbenkian de Ciência (IGC)—Fundação Calouste Gulbenkian, Oeiras, Portugal
| | - Ana Laura Sousa
- Electron Microscopy Facility (EMF), Instituto Gulbenkian de Ciência (IGC)—Fundação Calouste Gulbenkian, Oeiras, Portugal
| | - Mariana Ferreira
- Advanced Imaging Facility (AIF), Instituto Gulbenkian de Ciência (IGC)—Fundação Calouste Gulbenkian, Oeiras, Portugal
| | - Gabriel G. Martins
- Advanced Imaging Facility (AIF), Instituto Gulbenkian de Ciência (IGC)—Fundação Calouste Gulbenkian, Oeiras, Portugal
| | - Victor Hugo Mello
- Living Physics, Instituto Gulbenkian de Ciência (IGC)—Fundação Calouste Gulbenkian, Oeiras, Portugal
| | - Maria João Amorim
- Cell Biology of Viral Infection Lab (CBV), Instituto Gulbenkian de Ciência (IGC)—Fundação Calouste Gulbenkian, Oeiras, Portugal
- Cell Biology of Viral Infection Lab (CBV), Católica Biomedical Research Centre (CBR), Católica Medical School—Universidade Católica Portuguesa, Lisboa, Portugal
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32
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Bueno-Arribas M, Cruz-Cuevas C, Navas MA, Escalante R, Vincent O. Coiled-coil-mediated dimerization of Atg16 is required for binding to the PROPPIN Atg21. Open Biol 2023; 13:230192. [PMID: 37989223 PMCID: PMC10688262 DOI: 10.1098/rsob.230192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/13/2023] [Indexed: 11/23/2023] Open
Abstract
PROPPINs/WIPIs are β-propeller proteins that bind phosphoinositides and contribute to the recruitment of protein complexes involved in membrane remodelling processes such as autophagosome formation and endosomal trafficking. Yeast Atg21 and mammalian WIPI2 interact with Atg16/ATG16L1 to mediate recruitment of the lipidation machinery to the autophagosomal membrane. Here, we used the reverse double two-hybrid method (RD2H) to identify residues in Atg21 and Atg16 critical for protein-protein binding. Although our results are generally consistent with the crystal structure of the Atg21-Atg16 complex reported previously, they also reveal that dimerization of the Atg16 coiled-coil domain is required for Atg21 binding. Furthermore, most of the residues identified in Atg21 are conserved in WIPI2 and we showed that these residues also mediate ATG16L1 binding. Strikingly, these residues occupy the same position in the β-propeller structure as residues in PROPPINs/WIPIs Hsv2 and WIPI4 that mediate Atg2/ATG2A binding, supporting the idea that these proteins use different amino acids at the same position to interact with different autophagic proteins. Finally, our findings demonstrate the effectiveness of the RD2H system to identify critical residues for protein-protein interactions and the utility of this method to generate combinatory mutants with a complete loss of binding capacity.
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Affiliation(s)
- Miranda Bueno-Arribas
- Instituto de Investigaciones Biomédicas Sols-Morreale CSIC-UAM, Madrid, 28029, Spain
| | - Celia Cruz-Cuevas
- Instituto de Investigaciones Biomédicas Sols-Morreale CSIC-UAM, Madrid, 28029, Spain
| | - María-Angeles Navas
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad Complutense de Madrid, Madrid, Spain
| | - Ricardo Escalante
- Instituto de Investigaciones Biomédicas Sols-Morreale CSIC-UAM, Madrid, 28029, Spain
| | - Olivier Vincent
- Instituto de Investigaciones Biomédicas Sols-Morreale CSIC-UAM, Madrid, 28029, Spain
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33
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Popelka H, Lahiri V, Hawkins WD, da Veiga Leprevost F, Nesvizhskii AI, Klionsky DJ. The Intrinsically Disordered N Terminus in Atg12 from Yeast Is Necessary for the Functional Structure of the Protein. Int J Mol Sci 2023; 24:15036. [PMID: 37894717 PMCID: PMC10606595 DOI: 10.3390/ijms242015036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/29/2023] [Accepted: 10/02/2023] [Indexed: 10/29/2023] Open
Abstract
The Atg12 protein in yeast is an indispensable polypeptide in the highly conserved ubiquitin-like conjugation system operating in the macroautophagy/autophagy pathway. Atg12 is covalently conjugated to Atg5 through the action of Atg7 and Atg10; the Atg12-Atg5 conjugate binds Atg16 to form an E3 ligase that functions in a separate conjugation pathway involving Atg8. Atg12 is comprised of a ubiquitin-like (UBL) domain preceded at the N terminus by an intrinsically disordered protein region (IDPR), a domain that comprises a major portion of the protein but remains elusive in its conformation and function. Here, we show that the IDPR in unconjugated Atg12 is positioned in proximity to the UBL domain, a configuration that is important for the functional structure of the protein. A major deletion in the IDPR disrupts intactness of the UBL domain at the unconjugated C terminus, and a mutation in the predicted α0 helix in the IDPR prevents Atg12 from binding to Atg7 and Atg10, which ultimately affects the protein function in the ubiquitin-like conjugation cascade. These findings provide evidence that the IDPR is an indispensable part of the Atg12 protein from yeast.
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Affiliation(s)
- Hana Popelka
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; (V.L.); (W.D.H.); (D.J.K.)
| | - Vikramjit Lahiri
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; (V.L.); (W.D.H.); (D.J.K.)
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Wayne D. Hawkins
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; (V.L.); (W.D.H.); (D.J.K.)
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Felipe da Veiga Leprevost
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA; (F.d.V.L.); (A.I.N.)
| | - Alexey I. Nesvizhskii
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA; (F.d.V.L.); (A.I.N.)
| | - Daniel J. Klionsky
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; (V.L.); (W.D.H.); (D.J.K.)
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
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34
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Zhou X, Zhang Q, Zhao Y, Ding S, Yu GH. Integrated Multi-Omics Analyses Reveal That Autophagy-Mediated Cellular Metabolism Is Required for the Initiation of Pollen Germination. Int J Mol Sci 2023; 24:15014. [PMID: 37834462 PMCID: PMC10573924 DOI: 10.3390/ijms241915014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/25/2023] [Accepted: 09/30/2023] [Indexed: 10/15/2023] Open
Abstract
Autophagy is an evolutionarily conserved mechanism for degrading and recycling various cellular components, functioning in both normal development and stress conditions. This process is tightly regulated by a set of autophagy-related (ATG) proteins, including ATG2 in the ATG9 cycling system and ATG5 in the ATG12 conjugation system. Our recent research demonstrated that autophagy-mediated compartmental cytoplasmic deletion is essential for pollen germination. However, the precise mechanisms through which autophagy regulates pollen germination, ensuring its fertility, remain largely unknown. Here, we applied multi-omics analyses, including transcriptomic and metabolomic approaches, to investigate the downstream pathways of autophagy in the process of pollen germination. Although ATG2 and ATG5 play similar roles in regulating pollen germination, high-throughput transcriptomic analysis reveals that silencing ATG5 has a greater impact on the transcriptome than silencing ATG2. Cross-comparisons of transcriptome and proteome analysis reveal that gene expression at the mRNA level and protein level is differentially affected by autophagy. Furthermore, high-throughput metabolomics analysis demonstrates that pathways related to amino acid metabolism and aminoacyl-tRNA biosynthesis were affected by both ATG2 and ATG5 silencing. Collectively, our multi-omics analyses reveal the central role of autophagy in cellular metabolism, which is critical for initiating pollen germination and ensuring pollen fertility.
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Affiliation(s)
| | | | | | | | - Guang-Hui Yu
- College of Life Sciences, South-Central Minzu University, Wuhan 430074, China; (X.Z.)
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35
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Li Y, Li W, Huang L, Li H, He P, Xue C. Association of ATG4A single nucleotide polymorphism rs807185 on risk of microscopic polyangiitis in Chinese population. Int Immunopharmacol 2023; 123:110659. [PMID: 37494842 DOI: 10.1016/j.intimp.2023.110659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 05/08/2023] [Accepted: 07/14/2023] [Indexed: 07/28/2023]
Abstract
BACKGROUND Microscopic polyangiitis is a type of antineutrophil cytoplasmic antibody-associated vasculitis, characterized by a systemic, pauci-immune, necrotizing, small-vessel vasculitis without clinical or pathological evidence of necrotizing granulomatous inflammation. Many studies have linked autophagy-related gene polymorphisms to the development of immune diseases. However, the association between autophagy-related genes and microscopic polyangiitis remains unclear. OBJECTIVE We investigated the association between microscopic polyangiitis and the single nucleotide polymorphism rs807185 in autophagy-associated gene 4A (ATG4A) in the Chinese population. METHODS ATG4A single nucleotide polymorphism rs807185 frequency was identified using multiplex polymerase chain reaction and high-throughput sequencing in a cohort with microscopic polyangiitis (n = 181) and a healthy control group (n = 209). RESULTS We found that the control cohort had a higher prevalence of allele A of rs807185 compared to the microscopic polyangiitis cohort. The rs807185A allele was therefore linked to a lower risk of microscopic polyangiitis. CONCLUSION The single nucleotide polymorphism rs807185 allele A in ATG4A may have a protective effect against microscopic polyangiitis in the Chinese population, but the molecular mechanisms remain unclear.
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Affiliation(s)
- Yan Li
- Department of Nephrology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Wei Li
- Department of Nephrology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Li Huang
- Department of Nephrology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Huijia Li
- Department of Nephrology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Peipeng He
- Department of Nephrology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Chao Xue
- Department of Nephrology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China.
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36
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Sathiyaseelan P, Chittaranjan S, Kalloger SE, Chan J, Go NE, Jardon MA, Ho CJ, Hui T, Xu J, Chow C, Gao D, Johnson FD, Lockwood WW, Morin GB, Renouf DJ, Schaeffer DF, Gorski SM. Loss of ATG4B and ATG4A results in two-stage cell cycle defects in pancreatic ductal adenocarcinoma cells. J Cell Sci 2023; 136:jcs260644. [PMID: 37701987 PMCID: PMC10617609 DOI: 10.1242/jcs.260644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 07/17/2023] [Indexed: 09/14/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) exhibits elevated levels of autophagy, which promote tumor progression and treatment resistance. ATG4B is an autophagy-related cysteine protease under consideration as a potential therapeutic target, but it is largely unexplored in PDAC. Here, we investigated the clinical and functional relevance of ATG4B expression in PDAC. Using two PDAC patient cohorts, we found that low ATG4B mRNA or protein expression is associated with worse patient survival outcomes, poorly differentiated PDAC tumors and a lack of survival benefit from adjuvant chemotherapy. In PDAC cell lines, ATG4B knockout reduced proliferation, abolished processing of LC3B (also known as MAP1LC3B), and reduced GABARAP and GABARAPL1 levels, but increased ATG4A levels. ATG4B and ATG4A double knockout lines displayed a further reduction in proliferation, characterized by delays in G1-S phase transition and mitosis. Pro-LC3B accumulated aberrantly at the centrosome with a concomitant increase in centrosomal proteins PCM1 and CEP131, which was rescued by exogenous ATG4B. The two-stage cell cycle defects following ATG4B and ATG4A loss have important therapeutic implications for PDAC.
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Affiliation(s)
- Paalini Sathiyaseelan
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Suganthi Chittaranjan
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
| | - Steve E. Kalloger
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Pancreas Centre BC, Vancouver, BC, V5Z 1L8, Canada
| | - Jennifer Chan
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Nancy E. Go
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
| | - Mario A. Jardon
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
| | - Cally J. Ho
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Theodore Hui
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Jing Xu
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
| | - Christine Chow
- Genetic Pathology Evaluation Centre, Vancouver, BC, V6H 3Z6, Canada
| | - Dongxia Gao
- Genetic Pathology Evaluation Centre, Vancouver, BC, V6H 3Z6, Canada
| | - Fraser D. Johnson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
- Department of Integrative Oncology, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
| | - William W. Lockwood
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
- Department of Integrative Oncology, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
| | - Gregg B. Morin
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
| | - Daniel J. Renouf
- Pancreas Centre BC, Vancouver, BC, V5Z 1L8, Canada
- Division of Medical Oncology, BC Cancer, Vancouver, BC, V5Z 4E6, Canada
| | - David F. Schaeffer
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
- Pancreas Centre BC, Vancouver, BC, V5Z 1L8, Canada
- Division of Anatomical Pathology, Vancouver General Hospital, Vancouver, BC, V5Z 1M9, Canada
| | - Sharon M. Gorski
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
- Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
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Taraborrelli L, Şenbabaoğlu Y, Wang L, Lim J, Blake K, Kljavin N, Gierke S, Scherl A, Ziai J, McNamara E, Owyong M, Rao S, Calviello AK, Oreper D, Jhunjhunwala S, Argiles G, Bendell J, Kim TW, Ciardiello F, Wongchenko MJ, de Sauvage FJ, de Sousa E Melo F, Yan Y, West NR, Murthy A. Tumor-intrinsic expression of the autophagy gene Atg16l1 suppresses anti-tumor immunity in colorectal cancer. Nat Commun 2023; 14:5945. [PMID: 37741832 PMCID: PMC10517947 DOI: 10.1038/s41467-023-41618-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 09/12/2023] [Indexed: 09/25/2023] Open
Abstract
Microsatellite-stable colorectal cancer (MSS-CRC) is highly refractory to immunotherapy. Understanding tumor-intrinsic determinants of immunotherapy resistance is critical to improve MSS-CRC patient outcomes. Here, we demonstrate that high tumor expression of the core autophagy gene ATG16L1 is associated with poor clinical response to anti-PD-L1 therapy in KRAS-mutant tumors from IMblaze370 (NCT02788279), a large phase III clinical trial of atezolizumab (anti-PD-L1) in advanced metastatic MSS-CRC. Deletion of Atg16l1 in engineered murine colon cancer organoids inhibits tumor growth in primary (colon) and metastatic (liver and lung) niches in syngeneic female hosts, primarily due to increased sensitivity to IFN-γ-mediated immune pressure. ATG16L1 deficiency enhances programmed cell death of colon cancer organoids induced by IFN-γ and TNF, thus increasing their sensitivity to host immunity. In parallel, ATG16L1 deficiency reduces tumor stem-like populations in vivo independently of adaptive immune pressure. This work reveals autophagy as a clinically relevant mechanism of immune evasion and tumor fitness in MSS-CRC and provides a rationale for autophagy inhibition to boost immunotherapy responses in the clinic.
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Affiliation(s)
- Lucia Taraborrelli
- Department of Cancer Immunology, Genentech Inc., South San Francisco, USA
| | - Yasin Şenbabaoğlu
- Department of Oncology Bioinformatics, Genentech Inc., South San Francisco, USA
| | - Lifen Wang
- Department of Cancer Immunology, Genentech Inc., South San Francisco, USA
| | - Junghyun Lim
- Department of Cancer Immunology, Genentech Inc., South San Francisco, USA
| | - Kerrigan Blake
- Department of Cancer Immunology, Genentech Inc., South San Francisco, USA
| | - Noelyn Kljavin
- Department of Molecular Oncology, Genentech Inc., South San Francisco, USA
| | - Sarah Gierke
- Center for Advanced Light Microscopy, Genentech Inc., South San Francisco, USA
- Department of Pathology, Genentech Inc., South San Francisco, USA
| | - Alexis Scherl
- Department of Pathology, Genentech Inc., South San Francisco, USA
| | - James Ziai
- Department of Pathology, Genentech Inc., South San Francisco, USA
| | - Erin McNamara
- Department of In Vivo Pharmacology, Genentech Inc., South San Francisco, USA
| | - Mark Owyong
- Department of In Vivo Pharmacology, Genentech Inc., South San Francisco, USA
| | - Shilpa Rao
- Department of Oncology Bioinformatics, Genentech Inc., South San Francisco, USA
| | | | - Daniel Oreper
- Department of Oncology Bioinformatics, Genentech Inc., South San Francisco, USA
| | - Suchit Jhunjhunwala
- Department of Oncology Bioinformatics, Genentech Inc., South San Francisco, USA
| | - Guillem Argiles
- Vall d'Hebrón Institute of Oncology, Vall d'Hebrón University Hospital, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Johanna Bendell
- Sarah Cannon Research Institute/Tennessee Oncology, Nashville, TN, USA
| | - Tae Won Kim
- Department of Oncology, Medical Center, University of Ulsan, Seoul, Korea
| | - Fortunato Ciardiello
- Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Naples, Italy
| | | | | | | | - Yibing Yan
- Oncology Biomarker Development, Genentech, Inc., South San Francisco, CA, USA
| | - Nathaniel R West
- Department of Cancer Immunology, Genentech Inc., South San Francisco, USA.
| | - Aditya Murthy
- Department of Cancer Immunology, Genentech Inc., South San Francisco, USA.
- Gilead Sciences, Foster City, USA.
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38
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Liang J, Cai H, Hou C, Song F, Jiang Y, Wang Z, Qiu D, Zhu Y, Wang F, Yu D, Hou J. METTL14 inhibits malignant progression of oral squamous cell carcinoma by targeting the autophagy-related gene RB1CC1 in an m6A-IGF2BP2-dependent manner. Clin Sci (Lond) 2023; 137:1373-1389. [PMID: 37615536 PMCID: PMC10500204 DOI: 10.1042/cs20230219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 08/10/2023] [Accepted: 08/24/2023] [Indexed: 08/25/2023]
Abstract
N6-methyladenosine (m6A) plays crucial roles in tumorigenesis and autophagy. However, the underlying mechanisms mediated by m6A and autophagy in the malignant progression of oral squamous cell carcinoma (OSCC) remain unclear. In the present study, we revealed that down-regulated expression of METTL14 was correlated with advanced clinicopathological characteristics and poor prognosis in OSCC. METTL14 knockdown significantly inhibited autophagy and facilitated malignant progression in vitro, and promoted tumor growth and metastasis in vivo. A cell model of rapamycin-induced autophagy was established to identify RB1CC1 as a potential target gene involved in m6A-regulated autophagy in OSCC, through RNA sequencing and methylated RNA immunoprecipitation sequencing (meRIP-seq) analysis. Mechanistically, we confirmed that METTL14 posttranscriptionally enhanced RB1CC1 expression in an m6A-IGF2BP2-dependent manner, thereby affecting autophagy and progression in OSCC, through methylated RNA immunoprecipitation qRT-PCR (meRIP-qPCR), RNA stability assays, mutagenesis assays and dual-luciferase reporter. Collectively, our findings demonstrated that METTL14 serves as an OSCC suppressor by regulating the autophagy-related gene RB1CC1 through m6A modification, which may provide a new insight for the diagnosis and therapy of OSCC.
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Affiliation(s)
- Jianfeng Liang
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Hongshi Cai
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Chen Hou
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Fan Song
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Yaoqi Jiang
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Ziyi Wang
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Danqi Qiu
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Yue Zhu
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Fang Wang
- Department of Oral Surgery, Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200000, China
| | - Dongsheng Yu
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Jinsong Hou
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
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Ma Q, Xin J, Peng Q, Li N, Sun S, Hou H, Ma G, Wang N, Zhang L, Tam KY, Dussmann H, Prehn JHM, Wang H, Ying Z. UBQLN2 and HSP70 participate in Parkin-mediated mitophagy by facilitating outer mitochondrial membrane rupture. EMBO Rep 2023; 24:e55859. [PMID: 37501540 PMCID: PMC10481660 DOI: 10.15252/embr.202255859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 07/04/2023] [Accepted: 07/11/2023] [Indexed: 07/29/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are two aging-related neurodegenerative diseases that share common key features, including aggregation of pathogenic proteins, dysfunction of mitochondria, and impairment of autophagy. Mutations in ubiquilin 2 (UBQLN2), a shuttle protein in the ubiquitin-proteasome system (UPS), can cause ALS/FTD, but the mechanism underlying UBQLN2-mediated pathogenesis is still uncertain. Recent studies indicate that mitophagy, a selective form of autophagy which is crucial for mitochondrial quality control, is tightly associated with neurodegenerative diseases including Alzheimer's disease, Parkinson's disease, and ALS. In this study, we show that after Parkin-dependent ubiquitination of damaged mitochondria, UBQLN2 is recruited to poly-ubiquitinated mitochondria through the UBA domain. UBQLN2 cooperates with the chaperone HSP70 to promote UPS-driven degradation of outer mitochondrial membrane (OMM) proteins. The resulting rupture of the OMM triggers the autophagosomal recognition of the inner mitochondrial membrane receptor PHB2. UBQLN2 is required for Parkin-mediated mitophagy and neuronal survival upon mitochondrial damage, and the ALS/FTD pathogenic mutations in UBQLN2 impair mitophagy in primary cultured neurons. Taken together, our findings link dysfunctional mitophagy to UBQLN2-mediated neurodegeneration.
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Affiliation(s)
- Qilian Ma
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical SciencesSoochow UniversitySuzhouChina
- Department of Physiology & Medical Physics and FUTURE‐NEURO Research CentreRoyal College of Surgeons in IrelandDublinIreland
| | - Jiaqi Xin
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical SciencesSoochow UniversitySuzhouChina
| | - Qiang Peng
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical SciencesSoochow UniversitySuzhouChina
| | - Ningning Li
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical SciencesSoochow UniversitySuzhouChina
| | - Shan Sun
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical SciencesSoochow UniversitySuzhouChina
- Faculty of Health SciencesUniversity of MacauMacauChina
| | - Hongyu Hou
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical SciencesSoochow UniversitySuzhouChina
| | - Guoqiang Ma
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical SciencesSoochow UniversitySuzhouChina
| | - Nana Wang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical SciencesSoochow UniversitySuzhouChina
| | - Li Zhang
- Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear MedicineJiangsu Institute of Nuclear MedicineWuxiChina
| | - Kin Yip Tam
- Faculty of Health SciencesUniversity of MacauMacauChina
| | - Heiko Dussmann
- Department of Physiology & Medical Physics and FUTURE‐NEURO Research CentreRoyal College of Surgeons in IrelandDublinIreland
| | - Jochen HM Prehn
- Department of Physiology & Medical Physics and FUTURE‐NEURO Research CentreRoyal College of Surgeons in IrelandDublinIreland
| | - Hongfeng Wang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical SciencesSoochow UniversitySuzhouChina
| | - Zheng Ying
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical SciencesSoochow UniversitySuzhouChina
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Kaur N, de la Ballina LR, Haukaas HS, Torgersen ML, Radulovic M, Munson MJ, Sabirsh A, Stenmark H, Simonsen A, Carlsson SR, Lystad AH. TECPR1 is activated by damage-induced sphingomyelin exposure to mediate noncanonical autophagy. EMBO J 2023; 42:e113105. [PMID: 37409525 PMCID: PMC10476171 DOI: 10.15252/embj.2022113105] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 05/30/2023] [Accepted: 06/07/2023] [Indexed: 07/07/2023] Open
Abstract
Cells use noncanonical autophagy, also called conjugation of ATG8 to single membranes (CASM), to label damaged intracellular compartments with ubiquitin-like ATG8 family proteins in order to signal danger caused by pathogens or toxic compounds. CASM relies on E3 complexes to sense membrane damage, but so far, only the mechanism to activate ATG16L1-containing E3 complexes, associated with proton gradient loss, has been described. Here, we show that TECPR1-containing E3 complexes are key mediators of CASM in cells treated with a variety of pharmacological drugs, including clinically relevant nanoparticles, transfection reagents, antihistamines, lysosomotropic compounds, and detergents. Interestingly, TECPR1 retains E3 activity when ATG16L1 CASM activity is obstructed by the Salmonella Typhimurium pathogenicity factor SopF. Mechanistically, TECPR1 is recruited by damage-induced sphingomyelin (SM) exposure using two DysF domains, resulting in its activation and ATG8 lipidation. In vitro assays using purified human TECPR1-ATG5-ATG12 complex show direct activation of its E3 activity by SM, whereas SM has no effect on ATG16L1-ATG5-ATG12. We conclude that TECPR1 is a key activator of CASM downstream of SM exposure.
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Affiliation(s)
- Namrita Kaur
- Centre for Cancer Cell Reprogramming, Faculty of MedicineUniversity of OsloOsloNorway
- Department of Molecular Cell Biology, Institute for Cancer ResearchOslo University HospitalOsloNorway
| | - Laura Rodriguez de la Ballina
- Centre for Cancer Cell Reprogramming, Faculty of MedicineUniversity of OsloOsloNorway
- Department of Molecular Medicine, Institute of Basic Medical SciencesUniversity of OsloOsloNorway
| | - Håvard Styrkestad Haukaas
- Centre for Cancer Cell Reprogramming, Faculty of MedicineUniversity of OsloOsloNorway
- Department of Molecular Cell Biology, Institute for Cancer ResearchOslo University HospitalOsloNorway
| | - Maria Lyngaas Torgersen
- Centre for Cancer Cell Reprogramming, Faculty of MedicineUniversity of OsloOsloNorway
- Department of Molecular Cell Biology, Institute for Cancer ResearchOslo University HospitalOsloNorway
| | - Maja Radulovic
- Centre for Cancer Cell Reprogramming, Faculty of MedicineUniversity of OsloOsloNorway
- Department of Molecular Cell Biology, Institute for Cancer ResearchOslo University HospitalOsloNorway
| | - Michael J Munson
- Advanced Drug Delivery, Pharmaceutical SciencesBiopharmaceuticals R&D, AstraZenecaGothenburgSweden
| | - Alan Sabirsh
- Advanced Drug Delivery, Pharmaceutical SciencesBiopharmaceuticals R&D, AstraZenecaGothenburgSweden
| | - Harald Stenmark
- Centre for Cancer Cell Reprogramming, Faculty of MedicineUniversity of OsloOsloNorway
- Department of Molecular Cell Biology, Institute for Cancer ResearchOslo University HospitalOsloNorway
| | - Anne Simonsen
- Centre for Cancer Cell Reprogramming, Faculty of MedicineUniversity of OsloOsloNorway
- Department of Molecular Cell Biology, Institute for Cancer ResearchOslo University HospitalOsloNorway
- Department of Molecular Medicine, Institute of Basic Medical SciencesUniversity of OsloOsloNorway
| | - Sven R Carlsson
- Department of Medical Biochemistry and BiophysicsUniversity of UmeåUmeåSweden
| | - Alf Håkon Lystad
- Centre for Cancer Cell Reprogramming, Faculty of MedicineUniversity of OsloOsloNorway
- Department of Molecular Cell Biology, Institute for Cancer ResearchOslo University HospitalOsloNorway
- Department of Molecular Medicine, Institute of Basic Medical SciencesUniversity of OsloOsloNorway
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41
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Mareninova OA, Gretler SR, Lee GE, Pimienta M, Qin Y, Elperin JM, Ni J, Razga Z, Gukovskaya AS, Gukovsky I. Ethanol inhibits pancreatic acinar cell autophagy through upregulation of ATG4B, mediating pathological responses of alcoholic pancreatitis. Am J Physiol Gastrointest Liver Physiol 2023; 325:G265-G278. [PMID: 37431575 PMCID: PMC10511161 DOI: 10.1152/ajpgi.00053.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/23/2023] [Accepted: 07/01/2023] [Indexed: 07/12/2023]
Abstract
Excessive alcohol intake is a major risk factor for pancreatitis, sensitizing the exocrine pancreas to stressors by mechanisms that remain obscure. Impaired autophagy drives nonalcoholic pancreatitis, but the effects of ethanol (EtOH) and alcoholic pancreatitis on autophagy are poorly understood. Here, we find that ethanol reduces autophagosome formation in pancreatic acinar cells, both in a mouse model of alcoholic pancreatitis induced by a combination of EtOH diet and cerulein (a CCK ortholog) and in EtOH+CCK-treated acinar cells (ex vivo model). Ethanol treatments decreased pancreatic level of LC3-II, a key mediator of autophagosome formation. This was caused by ethanol-induced upregulation of ATG4B, a cysteine protease that, cell dependently, regulates the balance between cytosolic LC3-I and membrane-bound LC3-II. We show that ATG4B negatively regulates LC3-II in acinar cells subjected to EtOH treatments. Ethanol raised ATG4B level by inhibiting its degradation, enhanced ATG4B enzymatic activity, and strengthened its interaction with LC3-II. We also found an increase in ATG4B and impaired autophagy in a dissimilar, nonsecretagogue model of alcoholic pancreatitis induced by EtOH plus palmitoleic acid. Adenoviral ATG4B overexpression in acinar cells greatly reduced LC3-II and inhibited autophagy. Furthermore, it aggravated trypsinogen activation and necrosis, mimicking key responses of ex vivo alcoholic pancreatitis. Conversely, shRNA Atg4B knockdown enhanced autophagosome formation and alleviated ethanol-induced acinar cell damage. The results reveal a novel mechanism, whereby ethanol inhibits autophagosome formation and thus sensitizes pancreatitis, and a key role of ATG4B in ethanol's effects on autophagy. Enhancing pancreatic autophagy, particularly by downregulating ATG4B, could be beneficial in mitigating the severity of alcoholic pancreatitis.NEW & NOTEWORTHY Ethanol sensitizes mice and humans to pancreatitis, but the underlying mechanisms remain obscure. Autophagy is important for maintaining pancreatic acinar cell homeostasis, and its impairment drives pancreatitis. This study reveals a novel mechanism, whereby ethanol inhibits autophagosome formation through upregulating ATG4B, a key cysteine protease. ATG4B upregulation inhibits autophagy in acinar cells and aggravates pathological responses of experimental alcoholic pancreatitis. Enhancing pancreatic autophagy, particularly by down-regulating ATG4B, could be beneficial for treatment of alcoholic pancreatitis.
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Affiliation(s)
- Olga A Mareninova
- David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, United States
- Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, California, United States
- Southern California Research Center for Alcoholic Liver and Pancreatic Diseases and Cirrhosis, Los Angeles, California, United States
| | - Sophie R Gretler
- David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, United States
- Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, California, United States
- Southern California Research Center for Alcoholic Liver and Pancreatic Diseases and Cirrhosis, Los Angeles, California, United States
| | - Grace E Lee
- David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, United States
| | - Michael Pimienta
- David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, United States
| | - Yueqiu Qin
- David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, United States
- Division of Gastroenterology and Hepatology, Youjiang Medical University for Nationalities, Baise, China
| | - Jason M Elperin
- David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, United States
| | - Jinliang Ni
- David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, United States
- First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Zsolt Razga
- Institute of Pathology, University of Szeged, Szeged, Hungary
| | - Anna S Gukovskaya
- David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, United States
- Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, California, United States
- Southern California Research Center for Alcoholic Liver and Pancreatic Diseases and Cirrhosis, Los Angeles, California, United States
| | - Ilya Gukovsky
- David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, United States
- Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, California, United States
- Southern California Research Center for Alcoholic Liver and Pancreatic Diseases and Cirrhosis, Los Angeles, California, United States
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42
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Luo M, Law KC, He Y, Chung KK, Po MK, Feng L, Chung KP, Gao C, Zhuang X, Jiang L. Arabidopsis AUTOPHAGY-RELATED2 is essential for ATG18a and ATG9 trafficking during autophagosome closure. Plant Physiol 2023; 193:304-321. [PMID: 37195145 DOI: 10.1093/plphys/kiad287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 05/18/2023]
Abstract
As a fundamental metabolic pathway, autophagy plays important roles in plant growth and development, particularly under stress conditions. A set of autophagy-related (ATG) proteins is recruited for the formation of a double-membrane autophagosome. Among them, the essential roles of ATG2, ATG18, and ATG9 have been well established in plant autophagy via genetic analysis; however, the underlying molecular mechanism for ATG2 in plant autophagosome formation remains poorly understood. In this study, we focused on the specific role of ATG2 in the trafficking of ATG18a and ATG9 during autophagy in Arabidopsis (Arabidopsis thaliana). Under normal conditions, YFP-ATG18a proteins are partially localized on late endosomes and translocated to ATG8e-labeled autophagosomes upon autophagic induction. Real-time imaging analysis revealed sequential recruitment of ATG18a on the phagophore membrane, showing that ATG18a specifically decorated the closing edges and finally disassociated from the completed autophagosome. However, in the absence of ATG2, most of the YFP-ATG18a proteins are arrested on autophagosomal membranes. Ultrastructural and 3D tomography analysis showed that unclosed autophagosome structures are accumulated in the atg2 mutant, displaying direct connections with the endoplasmic reticulum membrane and vesicular structures. Dynamic analysis of ATG9 vesicles suggested that ATG2 depletion also affects the association between ATG9 vesicles and the autophagosomal membrane. Furthermore, using interaction and recruitment analysis, we mapped the interaction relationship between ATG2 and ATG18a, implying a possible role of ATG18a in recruiting ATG2 and ATG9 to the membrane. Our findings unveil a specific role of ATG2 in coordinating ATG18a and ATG9 trafficking to mediate autophagosome closure in Arabidopsis.
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Affiliation(s)
- Mengqian Luo
- Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kai Ching Law
- Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yilin He
- Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Ka Kit Chung
- Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Muk Kuen Po
- Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Lanlan Feng
- Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kin Pan Chung
- Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Caiji Gao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Xiaohong Zhuang
- Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Liwen Jiang
- Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
- CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China
- Institute of Plant Molecular Biology and Agricultural Biotechnology, The Chinese University of Hong Kong, Hong Kong, China
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43
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Wang N, Shibata Y, Paulo JA, Gygi SP, Rapoport TA. A conserved membrane curvature-generating protein is crucial for autophagosome formation in fission yeast. Nat Commun 2023; 14:4765. [PMID: 37553386 PMCID: PMC10409813 DOI: 10.1038/s41467-023-40530-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 07/26/2023] [Indexed: 08/10/2023] Open
Abstract
Organelles are shaped by curvature-generating proteins, which include the reticulons and REEPs that are involved in forming the endoplasmic reticulum (ER). A conserved REEP subfamily differs from the ER-shaping REEPs in abundance and membrane topology and has unidentified functions. Here, we show that Rop1, the single member of this family in the fission yeast Schizosacharomyces pombe, is crucial for the macroautophagy of organelles and cytosolic proteins. Rop1 is needed for the formation of phagophores, cup-like structures consisting of two closely apposed membrane sheets that encapsulate cargo. It is recruited at early stages to phagophores and is required for their maturation into autophagosomes. Rop1 function relies on its ability to generate high membrane curvature and on its colocalization with the autophagy component Atg2 that is thought to reside at the phagophore rim. We propose that Rop1 facilitates the formation and growth of the double-membrane structure of the autophagosome.
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Affiliation(s)
- Ning Wang
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Yoko Shibata
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Tom A Rapoport
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA.
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44
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Hitomi K, Kotani T, Noda NN, Kimura Y, Nakatogawa H. The Atg1 complex, Atg9, and Vac8 recruit PI3K complex I to the pre-autophagosomal structure. J Cell Biol 2023; 222:e202210017. [PMID: 37436710 PMCID: PMC10337603 DOI: 10.1083/jcb.202210017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 03/31/2023] [Accepted: 05/18/2023] [Indexed: 07/13/2023] Open
Abstract
In macroautophagy, cellular components are sequestered within autophagosomes and transported to lysosomes/vacuoles for degradation. Although phosphatidylinositol 3-kinase complex I (PI3KCI) plays a pivotal role in the regulation of autophagosome biogenesis, little is known about how this complex localizes to the pre-autophagosomal structure (PAS). In Saccharomyces cerevisiae, PI3KCI is composed of PI3K Vps34 and conserved subunits Vps15, Vps30, Atg14, and Atg38. In this study, we discover that PI3KCI interacts with the vacuolar membrane anchor Vac8, the PAS scaffold Atg1 complex, and the pre-autophagosomal vesicle component Atg9 via the Atg14 C-terminal region, the Atg38 C-terminal region, and the Vps30 BARA domain, respectively. While the Atg14-Vac8 interaction is constitutive, the Atg38-Atg1 complex interaction and the Vps30-Atg9 interaction are enhanced upon macroautophagy induction depending on Atg1 kinase activity. These interactions cooperate to target PI3KCI to the PAS. These findings provide a molecular basis for PAS targeting of PI3KCI during autophagosome biogenesis.
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Affiliation(s)
- Kanae Hitomi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Tetsuya Kotani
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Nobuo N. Noda
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Yayoi Kimura
- Advanced Medical Research Center, Yokohama City University, Yokohama, Japan
| | - Hitoshi Nakatogawa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
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45
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Shimizu T, Tamura N, Nishimura T, Saito C, Yamamoto H, Mizushima N. Comprehensive analysis of autophagic functions of WIPI family proteins and their implications for the pathogenesis of β-propeller associated neurodegeneration. Hum Mol Genet 2023; 32:2623-2637. [PMID: 37364041 PMCID: PMC10407718 DOI: 10.1093/hmg/ddad096] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/15/2023] [Accepted: 06/13/2023] [Indexed: 06/28/2023] Open
Abstract
β-propellers that bind polyphosphoinositides (PROPPINs) are an autophagy-related protein family conserved throughout eukaryotes. The PROPPIN family includes Atg18, Atg21 and Hsv2 in yeast and WD-repeat protein interacting with phosphoinositides (WIPI)1-4 in mammals. Mutations in the WIPI genes are associated with human neuronal diseases, including β-propeller associated neurodegeneration (BPAN) caused by mutations in WDR45 (encoding WIPI4). In contrast to yeast PROPPINs, the functions of mammalian WIPI1-WIPI4 have not been systematically investigated. Although the involvement of WIPI2 in autophagy has been clearly shown, the functions of WIPI1, WIPI3 and WIPI4 in autophagy remain poorly understood. In this study, we comprehensively analyzed the roles of WIPI proteins by using WIPI-knockout (single, double and quadruple knockout) HEK293T cells and recently developed HaloTag-based reporters, which enable us to monitor autophagic flux sensitively and quantitatively. We found that WIPI2 was nearly essential for autophagy. Autophagic flux was unaffected or only slightly reduced by single deletion of WIPI3 (encoded by WDR45B) or WIPI4 but was profoundly reduced by double deletion of WIPI3 and WIPI4. Furthermore, we revealed variable effects of BPAN-related missense mutations on the autophagic activity of WIPI4. BPAN is characterized by neurodevelopmental and neurodegenerative abnormalities, and we found a possible association between the magnitude of the defect of the autophagic activity of WIPI4 mutants and the severity of neurodevelopmental symptoms. However, some of the BPAN-related missense mutations, which produce neurodegenerative signs, showed almost normal autophagic activity, suggesting that non-autophagic functions of WIPI4 may be related to neurodegeneration in BPAN.
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Affiliation(s)
- Takahiro Shimizu
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Norito Tamura
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Taki Nishimura
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
- PRESTO, Japan Science and Technology Agency, Tokyo 102-0076, Japan
| | - Chieko Saito
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Hayashi Yamamoto
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
- Department of Molecular Oncology, Nippon Medical School, Institute for Advanced Medical Sciences, Tokyo 113-8602, Japan
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
- International Research Center for Neurointelligence (WPI-IRCN), UTIAS, The University of Tokyo, Tokyo 113-8655, Japan
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46
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Broadbent DG, Barnaba C, Perez GI, Schmidt JC. Quantitative analysis of autophagy reveals the role of ATG9 and ATG2 in autophagosome formation. J Cell Biol 2023; 222:e202210078. [PMID: 37115157 PMCID: PMC10148237 DOI: 10.1083/jcb.202210078] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 02/03/2023] [Accepted: 03/17/2023] [Indexed: 04/29/2023] Open
Abstract
Autophagy is a catabolic pathway required for the recycling of cytoplasmic materials. To define the mechanisms underlying autophagy it is critical to quantitatively characterize the dynamic behavior of autophagy factors in living cells. Using a panel of cell lines expressing HaloTagged autophagy factors from their endogenous loci, we analyzed the abundance, single-molecule dynamics, and autophagosome association kinetics of autophagy proteins involved in autophagosome biogenesis. We demonstrate that autophagosome formation is inefficient and ATG2-mediated tethering to donor membranes is a key commitment step in autophagosome formation. Furthermore, our observations support the model that phagophores are initiated by the accumulation of autophagy factors on mobile ATG9 vesicles, and that the ULK1 complex and PI3-kinase form a positive feedback loop required for autophagosome formation. Finally, we demonstrate that the duration of autophagosome biogenesis is ∼110 s. In total, our work provides quantitative insight into autophagosome biogenesis and establishes an experimental framework to analyze autophagy in human cells.
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Affiliation(s)
- David G. Broadbent
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
- College of Osteopathic Medicine, Michigan State University, East Lansing, MI, USA
- Department of Physiology, Michigan State University, East Lansing, MI, USA
| | - Carlo Barnaba
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
| | - Gloria I. Perez
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
| | - Jens C. Schmidt
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
- Department of Obstetrics and Gynecology, Michigan State University, East Lansing, MI, USA
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47
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Olivas TJ, Wu Y, Yu S, Luan L, Choi P, Guinn ED, Nag S, De Camilli PV, Gupta K, Melia TJ. ATG9 vesicles comprise the seed membrane of mammalian autophagosomes. J Cell Biol 2023; 222:e202208088. [PMID: 37115958 PMCID: PMC10148236 DOI: 10.1083/jcb.202208088] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 03/20/2023] [Accepted: 04/05/2023] [Indexed: 04/30/2023] Open
Abstract
As the autophagosome forms, its membrane surface area expands rapidly, while its volume is kept low. Protein-mediated transfer of lipids from another organelle to the autophagosome likely drives this expansion, but as these lipids are only introduced into the cytoplasmic-facing leaflet of the organelle, full membrane growth also requires lipid scramblase activity. ATG9 harbors scramblase activity and is essential to autophagosome formation; however, whether ATG9 is integrated into mammalian autophagosomes remains unclear. Here we show that in the absence of lipid transport, ATG9 vesicles are already competent to collect proteins found on mature autophagosomes, including LC3-II. Further, we use styrene-maleic acid lipid particles to reveal the nanoscale organization of protein on LC3-II membranes; ATG9 and LC3-II are each fully integrated into expanding autophagosomes. The ratios of these two proteins at different stages of maturation demonstrate that ATG9 proteins are not continuously integrated, but rather are present on the seed vesicles only and become diluted in the expanding autophagosome membrane.
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Affiliation(s)
- Taryn J. Olivas
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT, USA
| | - Yumei Wu
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT, USA
- Department of Neuroscience, School of Medicine, Yale University, New Haven, CT, USA
- Howard Hughes Medical Institute, School of Medicine, Yale University, New Haven, CT, USA
- Program in Cellular Neuroscience Neurodegeneration and Repair, School of Medicine, Yale University, New Haven, CT, USA
| | - Shenliang Yu
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT, USA
| | - Lin Luan
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT, USA
| | - Peter Choi
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT, USA
| | - Emily D. Guinn
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT, USA
| | - Shanta Nag
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT, USA
| | - Pietro V. De Camilli
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT, USA
- Department of Neuroscience, School of Medicine, Yale University, New Haven, CT, USA
- Howard Hughes Medical Institute, School of Medicine, Yale University, New Haven, CT, USA
- Program in Cellular Neuroscience Neurodegeneration and Repair, School of Medicine, Yale University, New Haven, CT, USA
| | - Kallol Gupta
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Thomas J. Melia
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT, USA
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48
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Dabrowski R, Tulli S, Graef M. Parallel phospholipid transfer by Vps13 and Atg2 determines autophagosome biogenesis dynamics. J Cell Biol 2023; 222:e202211039. [PMID: 37115156 PMCID: PMC10148235 DOI: 10.1083/jcb.202211039] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 03/30/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023] Open
Abstract
During autophagy, rapid membrane assembly expands small phagophores into large double-membrane autophagosomes. Theoretical modeling predicts that the majority of autophagosomal phospholipids are derived from highly efficient non-vesicular phospholipid transfer (PLT) across phagophore-ER contacts (PERCS). Currently, the phagophore-ER tether Atg2 is the only PLT protein known to drive phagophore expansion in vivo. Here, our quantitative live-cell imaging analysis reveals a poor correlation between the duration and size of forming autophagosomes and the number of Atg2 molecules at PERCS of starving yeast cells. Strikingly, we find that Atg2-mediated PLT is non-rate limiting for autophagosome biogenesis because membrane tether and the PLT protein Vps13 localizes to the rim and promotes the expansion of phagophores in parallel with Atg2. In the absence of Vps13, the number of Atg2 molecules at PERCS determines the duration and size of forming autophagosomes with an apparent in vivo transfer rate of ∼200 phospholipids per Atg2 molecule and second. We propose that conserved PLT proteins cooperate in channeling phospholipids across organelle contact sites for non-rate-limiting membrane assembly during autophagosome biogenesis.
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Affiliation(s)
- Rahel Dabrowski
- Max Planck Research Group of Autophagy and Cellular Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Susanna Tulli
- Max Planck Research Group of Autophagy and Cellular Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Martin Graef
- Max Planck Research Group of Autophagy and Cellular Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
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49
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Li X, Ma XL, Nan Y, Du YH, Yang Y, Lu DD, Zhang JF, Chen Y, Zhang L, Niu Y, Yuan L. 18β-glycyrrhetinic acid inhibits proliferation of gastric cancer cells through regulating the miR-345-5p/TGM2 signaling pathway. World J Gastroenterol 2023; 29:3622-3644. [PMID: 37398884 PMCID: PMC10311615 DOI: 10.3748/wjg.v29.i23.3622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/24/2023] [Accepted: 05/17/2023] [Indexed: 06/16/2023] Open
Abstract
BACKGROUND Gastric cancer (GC) is a common gastrointestinal malignancy worldwide. Based on cancer-related mortality, the current prevention and treatment strategies for GC still show poor clinical results. Therefore, it is important to find effective drug treatment targets.
AIM To explore the molecular mechanism of 18β-glycyrrhetinic acid (18β-GRA) regulating the miR-345-5p/TGM2 signaling pathway to inhibit the proliferation of GC cells.
METHODS CCK-8 assay was used to determine the effect of 18β-GRA on the survival rate of GES-1 cells and AGS and HGC-27 cells. Cell cycle and apoptosis were detected by flow cytometry, cell migration was detected by a wound healing assay, the effect of 18β-GRA on subcutaneous tumor growth in BALB/c nude mice was investigated, and the cell autophagy level was determined by MDC staining. TMT proteomic analysis was used to detect the differentially expressed autophagy-related proteins in GC cells after 18β-GRA intervention, and then the protein-protein interaction was predicted using STRING (https://string-db.org/). MicroRNAs (miRNAs) transcriptome analysis was used to detect the miRNA differential expression profile, and use miRBase (https://www.mirbase/) and TargetScan (https://www.targetscan.org/) to predict the miRNA and complementary binding sites. Quantitative real-time polymerase chain reaction was used to detect the expression level of miRNA in 18β-GRA treated cells, and western blot was used to detect the expression of autophagy related proteins. Finally, the effect of miR-345-5p on GC cells was verified by mir-345-5p overexpression.
RESULTS 18β-GRA could inhibit GC cells viability, promote cell apoptosis, block cell cycle, reduce cell wound healing ability, and inhibit the GC cells growth in vivo. MDC staining results showed that 18β-GRA could promote autophagy in GC cells. By TMT proteomic analysis and miRNAs transcriptome analysis, it was concluded that 18β-GRA could down-regulate TGM2 expression and up-regulate miR-345-5p expression in GC cells. Subsequently, we verified that TGM2 is the target of miR-345-5p, and that overexpression of miR-345-5p significantly inhibited the protein expression level of TGM2. Western blot showed that the expression of autophagy-related proteins of TGM2 and p62 was significantly reduced, and LC3II, ULK1 and AMPK expression was significantly increased in GC cells treated with 18β-GRA. Overexpression of miR-345-5p not only inhibited the expression of TGM2, but also inhibited the proliferation of GC cells by promoting cell apoptosis and arresting cell cycle.
CONCLUSION 18β-GRA inhibits the proliferation of GC cells and promotes autophagy by regulating the miR-345-5p/TGM2 signaling pathway.
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Affiliation(s)
- Xia Li
- College of Pharmacy, Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
| | - Xiao-Ling Ma
- Traditional Chinese Medicine College, Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
| | - Yi Nan
- Traditional Chinese Medicine College, Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
- Key Laboratory of Hui Ethnic Medicine Modernization of Ministry of Education, Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
| | - Yu-Hua Du
- College of Pharmacy, Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
| | - Yi Yang
- College of Basic Medicine, Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
| | - Dou-Dou Lu
- College of Clinical Medicine, Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
| | - Jun-Fei Zhang
- College of Clinical Medicine, Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
| | - Yan Chen
- Traditional Chinese Medicine College, Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
| | - Lei Zhang
- Key Laboratory of Hui Ethnic Medicine Modernization of Ministry of Education, Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
| | - Yang Niu
- Traditional Chinese Medicine College, Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
- Key Laboratory of Hui Ethnic Medicine Modernization of Ministry of Education, Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
| | - Ling Yuan
- College of Pharmacy, Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
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50
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Pazos I, Puig‐Tintó M, Betancur L, Cordero J, Jiménez‐Menéndez N, Abella M, Hernández AC, Duran AG, Adachi‐Fernández E, Belmonte‐Mateos C, Sabido‐Bozo S, Tosi S, Nezu A, Oliva B, Colombelli J, Graham TR, Yoshimori T, Muñiz M, Hamasaki M, Gallego O. The P4-ATPase Drs2 interacts with and stabilizes the multisubunit tethering complex TRAPPIII in yeast. EMBO Rep 2023; 24:e56134. [PMID: 36929574 PMCID: PMC10157312 DOI: 10.15252/embr.202256134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 02/10/2023] [Accepted: 02/17/2023] [Indexed: 03/17/2023] Open
Abstract
Multisubunit Tethering Complexes (MTCs) are a set of conserved protein complexes that tether vesicles at the acceptor membrane. Interactions with other components of the trafficking machinery regulate MTCs through mechanisms that are partially understood. Here, we systematically investigate the interactome that regulates MTCs. We report that P4-ATPases, a family of lipid flippases, interact with MTCs that participate in the anterograde and retrograde transport at the Golgi, such as TRAPPIII. We use the P4-ATPase Drs2 as a paradigm to investigate the mechanism and biological relevance of this interplay during transport of Atg9 vesicles. Binding of Trs85, the sole-specific subunit of TRAPPIII, to the N-terminal tail of Drs2 stabilizes TRAPPIII on membranes loaded with Atg9 and is required for Atg9 delivery during selective autophagy, a role that is independent of P4-ATPase canonical functions. This mechanism requires a conserved I(S/R)TTK motif that also mediates the interaction of the P4-ATPases Dnf1 and Dnf2 with MTCs, suggesting a broader role of P4-ATPases in MTC regulation.
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Affiliation(s)
- Irene Pazos
- Department of Medicine and Life Sciences (MELIS)Pompeu Fabra University (UPF)BarcelonaSpain
| | - Marta Puig‐Tintó
- Department of Medicine and Life Sciences (MELIS)Pompeu Fabra University (UPF)BarcelonaSpain
| | - Laura Betancur
- Department of Medicine and Life Sciences (MELIS)Pompeu Fabra University (UPF)BarcelonaSpain
| | - Jorge Cordero
- Department of Medicine and Life Sciences (MELIS)Pompeu Fabra University (UPF)BarcelonaSpain
| | | | - Marc Abella
- Department of Medicine and Life Sciences (MELIS)Pompeu Fabra University (UPF)BarcelonaSpain
| | - Altair C Hernández
- Department of Medicine and Life Sciences (MELIS)Pompeu Fabra University (UPF)BarcelonaSpain
| | - Ana G Duran
- Department of Medicine and Life Sciences (MELIS)Pompeu Fabra University (UPF)BarcelonaSpain
| | - Emi Adachi‐Fernández
- Department of Medicine and Life Sciences (MELIS)Pompeu Fabra University (UPF)BarcelonaSpain
| | - Carla Belmonte‐Mateos
- Department of Medicine and Life Sciences (MELIS)Pompeu Fabra University (UPF)BarcelonaSpain
| | - Susana Sabido‐Bozo
- Department of Cell BiologyUniversity of SevilleSevilleSpain
- Instituto de Biomedicina de Sevilla (IBiS)Hospital Universitario Virgen del Rocío/CSIC/Universidad de SevillaSevilleSpain
| | - Sébastien Tosi
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST)BarcelonaSpain
| | - Akiko Nezu
- Department of Genetics, Graduate School of MedicineOsaka UniversityOsakaJapan
- Department of Intracellular Membrane Dynamics, Graduate School of Frontier BiosciencesOsaka UniversityOsakaJapan
| | - Baldomero Oliva
- Department of Medicine and Life Sciences (MELIS)Pompeu Fabra University (UPF)BarcelonaSpain
- Structural Bioinformatics Lab (GRIB‐IMIM)BarcelonaSpain
| | - Julien Colombelli
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST)BarcelonaSpain
| | - Todd R Graham
- Department of Biological SciencesVanderbilt UniversityNashvilleTNUSA
| | - Tamotsu Yoshimori
- Department of Genetics, Graduate School of MedicineOsaka UniversityOsakaJapan
- Department of Intracellular Membrane Dynamics, Graduate School of Frontier BiosciencesOsaka UniversityOsakaJapan
| | - Manuel Muñiz
- Department of Cell BiologyUniversity of SevilleSevilleSpain
- Instituto de Biomedicina de Sevilla (IBiS)Hospital Universitario Virgen del Rocío/CSIC/Universidad de SevillaSevilleSpain
| | - Maho Hamasaki
- Department of Genetics, Graduate School of MedicineOsaka UniversityOsakaJapan
- Department of Intracellular Membrane Dynamics, Graduate School of Frontier BiosciencesOsaka UniversityOsakaJapan
| | - Oriol Gallego
- Department of Medicine and Life Sciences (MELIS)Pompeu Fabra University (UPF)BarcelonaSpain
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