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Wang H, Lakshmana MK, Fields GB. Identification of binding partners that facilitate membrane-type 5 matrix metalloproteinase (MT5-MMP) processing of amyloid precursor protein. J Cell Physiol 2024; 239:e31218. [PMID: 38345408 DOI: 10.1002/jcp.31218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 01/23/2024] [Accepted: 01/27/2024] [Indexed: 06/14/2024]
Abstract
One of the pathological hallmarks of Alzheimer's disease (AD) is the presence of extracellular deposits of amyloid beta (Aβ) peptide. In addition to Aβ as the core component of the amyloid plaque, the amyloid precursor protein (APP) processing fragment Aβ was also found accumulated around the plaque. The APPη pathway, mainly mediated by membrane-type 5 matrix metalloproteinase (MT5-MMP), represents an important factor in AD pathogenesis. The proamyloidogenic features of MT5-MMP could result from interactions with APP when trafficking between organelles, so determination of the location within the cell of APPη cleavage and interacting proteins of MT5-MMP affecting this process will be of priority in understanding the role of MT5-MMP in AD. In the present study, MT5-MMP was found to be located in the nucleus, cytosol, and cytosolic subcellular granules of CHO cells that stably expressed wild-type human APP751. MT5-MMP fusion proteins were constructed that could localize enzyme production in the Golgi apparatus, endosome, ER, mitochondria, or plasma membrane. The fusion proteins significantly increased sAPPη when directed to the endosome, Golgi apparatus, plasma membrane, or mitochondria. Since the C-terminal region of MT5-MMP is responsible for its intracellular location and trafficking, this domain was used as the bait in a yeast two-hybrid screen to identify MT5-MMP protein partners in a human brain cDNA library. Identified binding partners included N4BP2L1, TMX3, EIG121, bridging Integrator 1 (BIN1), RUFY4, HTRA1, and TMEM199. The binding of N4BP2L1, EIG121, BIN1, or TMX3 to MT5-MMP resulted in the most significant increase in sAPPη production. Thus, the action of MT5-MMP on APP occurs in multiple locations within the cell and is facilitated by site-specific binding partners.
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Affiliation(s)
- Hongjie Wang
- Department of Chemistry & Biochemistry, Institute for Human Health & Disease Intervention (I-HEALTH), Florida Atlantic University, Jupiter, Florida, USA
| | - Madepalli K Lakshmana
- Department of Immunology and Nano-Medicine, Florida International University, Miami, Florida, USA
| | - Gregg B Fields
- Department of Chemistry & Biochemistry, Institute for Human Health & Disease Intervention (I-HEALTH), Florida Atlantic University, Jupiter, Florida, USA
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Kim M, Park JH, Go M, Lee N, Seo J, Lee H, Kim D, Ha H, Kim T, Jeong MS, Kim S, Kim T, Kim HS, Kang D, Shim H, Lee SY. RUFY4 deletion prevents pathological bone loss by blocking endo-lysosomal trafficking of osteoclasts. Bone Res 2024; 12:29. [PMID: 38744829 PMCID: PMC11094054 DOI: 10.1038/s41413-024-00326-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 02/01/2024] [Accepted: 03/08/2024] [Indexed: 05/16/2024] Open
Abstract
Mature osteoclasts degrade bone matrix by exocytosis of active proteases from secretory lysosomes through a ruffled border. However, the molecular mechanisms underlying lysosomal trafficking and secretion in osteoclasts remain largely unknown. Here, we show with GeneChip analysis that RUN and FYVE domain-containing protein 4 (RUFY4) is strongly upregulated during osteoclastogenesis. Mice lacking Rufy4 exhibited a high trabecular bone mass phenotype with abnormalities in osteoclast function in vivo. Furthermore, deleting Rufy4 did not affect osteoclast differentiation, but inhibited bone-resorbing activity due to disruption in the acidic maturation of secondary lysosomes, their trafficking to the membrane, and their secretion of cathepsin K into the extracellular space. Mechanistically, RUFY4 promotes late endosome-lysosome fusion by acting as an adaptor protein between Rab7 on late endosomes and LAMP2 on primary lysosomes. Consequently, Rufy4-deficient mice were highly protected from lipopolysaccharide- and ovariectomy-induced bone loss. Thus, RUFY4 plays as a new regulator in osteoclast activity by mediating endo-lysosomal trafficking and have a potential to be specific target for therapies against bone-loss diseases such as osteoporosis.
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Affiliation(s)
- Minhee Kim
- Department of Life Science, Ewha Womans University, Seoul, 03760, South Korea
| | - Jin Hee Park
- Department of Life Science, Ewha Womans University, Seoul, 03760, South Korea
- The Research Center for Cellular Homeostasis, Ewha Womans University, Seoul, 03760, South Korea
| | - Miyeon Go
- Department of Life Science, Ewha Womans University, Seoul, 03760, South Korea
| | - Nawon Lee
- Department of Life Science, Ewha Womans University, Seoul, 03760, South Korea
| | - Jeongin Seo
- Department of Life Science, Ewha Womans University, Seoul, 03760, South Korea
| | - Hana Lee
- Department of Biomedical Engineering, Yonsei University, Wonju, 26493, South Korea
| | - Doyong Kim
- Department of Biomedical Engineering, Yonsei University, Wonju, 26493, South Korea
| | - Hyunil Ha
- KM Convergence Research Division, Korea Institute of Oriental Medicine, Daejeon, 34054, South Korea
| | - Taesoo Kim
- KM Convergence Research Division, Korea Institute of Oriental Medicine, Daejeon, 34054, South Korea
| | - Myeong Seon Jeong
- Chuncheon Center, Korea Basic Science Institute, Chuncheon, 24341, South Korea
| | - Suree Kim
- Fluorescence Core Imaging Center and Bioimaging Data Curation Center, Ewha Womans University, Seoul, 03760, South Korea
| | - Taesoo Kim
- Department of Life Science, Ewha Womans University, Seoul, 03760, South Korea
- The Research Center for Cellular Homeostasis, Ewha Womans University, Seoul, 03760, South Korea
- Multitasking Macrophage Research Center, Ewha Womans University, Seoul, 03760, South Korea
| | - Han Sung Kim
- Department of Biomedical Engineering, Yonsei University, Wonju, 26493, South Korea
| | - Dongmin Kang
- Department of Life Science, Ewha Womans University, Seoul, 03760, South Korea
- Fluorescence Core Imaging Center and Bioimaging Data Curation Center, Ewha Womans University, Seoul, 03760, South Korea
| | - Hyunbo Shim
- Department of Life Science, Ewha Womans University, Seoul, 03760, South Korea
| | - Soo Young Lee
- Department of Life Science, Ewha Womans University, Seoul, 03760, South Korea.
- The Research Center for Cellular Homeostasis, Ewha Womans University, Seoul, 03760, South Korea.
- Multitasking Macrophage Research Center, Ewha Womans University, Seoul, 03760, South Korea.
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Du H, Liu Z, Lu SY, Jiang L, Zhou L, Liu JF. Genomic evidence for human-mediated introgressive hybridization and selection in the developed breed. BMC Genomics 2024; 25:331. [PMID: 38565992 PMCID: PMC10986048 DOI: 10.1186/s12864-024-10259-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 03/26/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND The pig (Sus Scrofa) is one of the oldest domesticated livestock species that has undergone extensive improvement through modern breeding. European breeds have advantages in lean meat development and highly-productive body type, whereas Asian breeds possess extraordinary fat deposition and reproductive performance. Consequently, Eurasian breeds have been extensively used to develop modern commercial breeds for fast-growing and high prolificacy. However, limited by the sequencing technology, the genome architecture of some nascent developed breeds and the human-mediated impact on their genomes are still unknown. RESULTS Through whole-genome analysis of 178 individuals from an Asian locally developed pig breed, Beijing Black pig, and its two ancestors from two different continents, we found the pervasive inconsistent gene trees and species trees across the genome of Beijing Black pig, which suggests its introgressive hybrid origin. Interestingly, we discovered that this developed breed has more genetic relationships with European pigs and an unexpected introgression from Asian pigs to this breed, which indicated that human-mediated introgression could form the porcine genome architecture in a completely different type compared to native introgression. We identified 554 genomic regions occupied 63.30 Mb with signals of introgression from the Asian ancestry to Beijing Black pig, and the genes in these regions enriched in pathways associated with meat quality, fertility, and disease-resistant. Additionally, a proportion of 7.77% of genomic regions were recognized as regions that have been under selection. Moreover, combined with the results of a genome-wide association study for meat quality traits in the 1537 Beijing Black pig population, two important candidate genes related to meat quality traits were identified. DNAJC6 is related to intramuscular fat content and fat deposition, and RUFY4 is related to meat pH and tenderness. CONCLUSIONS Our research provides insight for analyzing the origins of nascent developed breeds and genome-wide selection remaining in the developed breeds mediated by humans during modern breeding.
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Affiliation(s)
- Heng Du
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University (West District), No.2 Yuanmingyuan West Road, 100193, Beijing, China
| | - Zhen Liu
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University (West District), No.2 Yuanmingyuan West Road, 100193, Beijing, China
| | - Shi-Yu Lu
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University (West District), No.2 Yuanmingyuan West Road, 100193, Beijing, China
| | - Li Jiang
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University (West District), No.2 Yuanmingyuan West Road, 100193, Beijing, China
| | - Lei Zhou
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University (West District), No.2 Yuanmingyuan West Road, 100193, Beijing, China.
| | - Jian-Feng Liu
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University (West District), No.2 Yuanmingyuan West Road, 100193, Beijing, China.
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Park JG, Jeon H, Hwang KY, Cha SS, Han RT, Cho H, Lee IG. Cargo specificity, regulation, and therapeutic potential of cytoplasmic dynein. Exp Mol Med 2024; 56:827-835. [PMID: 38556551 PMCID: PMC11059388 DOI: 10.1038/s12276-024-01200-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 01/05/2024] [Accepted: 01/10/2024] [Indexed: 04/02/2024] Open
Abstract
Intracellular retrograde transport in eukaryotic cells relies exclusively on the molecular motor cytoplasmic dynein 1. Unlike its counterpart, kinesin, dynein has a single isoform, which raises questions about its cargo specificity and regulatory mechanisms. The precision of dynein-mediated cargo transport is governed by a multitude of factors, including temperature, phosphorylation, the microtubule track, and interactions with a family of activating adaptor proteins. Activating adaptors are of particular importance because they not only activate the unidirectional motility of the motor but also connect a diverse array of cargoes with the dynein motor. Therefore, it is unsurprising that dysregulation of the dynein-activating adaptor transport machinery can lead to diseases such as spinal muscular atrophy, lower extremity, and dominant. Here, we discuss dynein motor motility within cells and in in vitro, and we present several methodologies employed to track the motion of the motor. We highlight several newly identified activating adaptors and their roles in regulating dynein. Finally, we explore the potential therapeutic applications of manipulating dynein transport to address diseases linked to dynein malfunction.
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Affiliation(s)
- Jin-Gyeong Park
- Biomedical Research Division, Korea Institute of Science and Technology, Seoul, 02792, South Korea
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, South Korea
| | - Hanul Jeon
- Biomedical Research Division, Korea Institute of Science and Technology, Seoul, 02792, South Korea
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul, 03760, South Korea
| | - Kwang Yeon Hwang
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, South Korea
| | - Sun-Shin Cha
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul, 03760, South Korea
| | - Rafael T Han
- Biomedical Research Division, Korea Institute of Science and Technology, Seoul, 02792, South Korea
- KHU-KIST Department of Converging Science and Technology, Kyunghee University, Seoul, 02447, South Korea
| | - Hyesung Cho
- Extreme Materials Research Center, Korea Institute of Science and Technology, Seoul, 02792, South Korea
| | - In-Gyun Lee
- Biomedical Research Division, Korea Institute of Science and Technology, Seoul, 02792, South Korea.
- Department of Biological Chemistry, University of Science and Technology, Daejeon, 34113, South Korea.
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Moreno-Campos R, Singleton EW, Uribe RA. A targeted CRISPR-Cas9 mediated F0 screen identifies genes involved in establishment of the enteric nervous system. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.28.573581. [PMID: 38234831 PMCID: PMC10793464 DOI: 10.1101/2023.12.28.573581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
The vertebrate enteric nervous system (ENS) is a crucial network of enteric neurons and glia resident within the entire gastrointestinal tract (GI). Overseeing essential GI functions such as gut motility and water balance, the ENS serves as a pivotal bidirectional link in the gut-brain axis. During early development, the ENS is primarily derived from enteric neural crest cells (ENCCs). Disruptions to ENCC development, as seen in conditions like Hirschsprung disease (HSCR), lead to absence of ENS in the GI, particularly in the colon. In this study, using zebrafish, we devised an in vivo F0 CRISPR-based screen employing a robust, rapid pipeline integrating single-cell RNA sequencing, CRISPR reverse genetics, and high-content imaging. Our findings unveil various genes, including those encoding for opioid receptors, as possible regulators of ENS establishment. In addition, we present evidence that suggests opioid receptor involvement in neurochemical coding of the larval ENS. In summary, our work presents a novel, efficient CRISPR screen targeting ENS development, facilitating the discovery of previously unknown genes, and increasing knowledge of nervous system construction.
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Affiliation(s)
- Rodrigo Moreno-Campos
- Biosciences Department, Rice University, Houston, Texas, 77005, U.S.A
- Laboratory of Neural Crest and Enteric Nervous System Development, Rice University, Houston, Texas, 77005, U.S.A
| | - Eileen W. Singleton
- Biosciences Department, Rice University, Houston, Texas, 77005, U.S.A
- Laboratory of Neural Crest and Enteric Nervous System Development, Rice University, Houston, Texas, 77005, U.S.A
| | - Rosa A. Uribe
- Biosciences Department, Rice University, Houston, Texas, 77005, U.S.A
- Laboratory of Neural Crest and Enteric Nervous System Development, Rice University, Houston, Texas, 77005, U.S.A
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6
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Maji S, Pirozzi M, Ruturaj, Pandey R, Ghosh T, Das S, Gupta A. Copper-independent lysosomal localisation of the Wilson disease protein ATP7B. Traffic 2023; 24:587-609. [PMID: 37846526 DOI: 10.1111/tra.12919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 09/10/2023] [Accepted: 09/23/2023] [Indexed: 10/18/2023]
Abstract
In hepatocytes, the Wilson disease protein ATP7B resides on the trans-Golgi network (TGN) and traffics to peripheral lysosomes to export excess intracellular copper through lysosomal exocytosis. We found that in basal copper or even upon copper chelation, a significant amount of ATP7B persists in the endolysosomal compartment of hepatocytes but not in non-hepatic cells. These ATP7B-harbouring lysosomes lie in close proximity of ~10 nm to the TGN. ATP7B constitutively distributes itself between the sub-domain of the TGN with a lower pH and the TGN-proximal lysosomal compartments. The presence of ATP7B on TGN-lysosome colocalising sites upon Golgi disruption suggested a possible exchange of ATP7B directly between the TGN and its proximal lysosomes. Manipulating lysosomal positioning significantly alters the localisation of ATP7B in the cell. Contrary to previous understanding, we found that upon copper chelation in a copper-replete hepatocyte, ATP7B is not retrieved back to TGN from peripheral lysosomes; rather, ATP7B recycles to these TGN-proximal lysosomes to initiate the next cycle of copper transport. We report a hitherto unknown copper-independent lysosomal localisation of ATP7B and the importance of TGN-proximal lysosomes but not TGN as the terminal acceptor organelle of ATP7B in its retrograde pathway.
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Affiliation(s)
- Saptarshi Maji
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India
| | | | - Ruturaj
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India
| | - Raviranjan Pandey
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India
| | - Tamal Ghosh
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India
| | - Santanu Das
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India
| | - Arnab Gupta
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India
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Chen X, Wang W, Yeh J, Wu Y, Oehler VG, Naresh KN, Liu YJ. Clinical Validation of FusionPlex RNA Sequencing and Its Utility in the Diagnosis and Classification of Hematologic Neoplasms. J Mol Diagn 2023; 25:932-944. [PMID: 37813298 DOI: 10.1016/j.jmoldx.2023.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 08/11/2023] [Accepted: 09/12/2023] [Indexed: 10/11/2023] Open
Abstract
Recurrent gene rearrangements result in gene fusions that encode chimeric proteins, driving the pathogenesis of many hematologic neoplasms. The fifth edition World Health Organization classification and International Consensus Classification 2022 include an expanding list of entities defined by such gene rearrangements. Therefore, sensitive and rapid methods are needed to identify a broad range of gene fusions for precise diagnosis and prognostication. In this study, we validated the FusionPlex Pan-Heme panel analysis using anchored multiplex PCR/targeted RNA next-generation sequencing for routine clinical testing. Furthermore, we assessed its utility in detecting gene fusions in myeloid and lymphoid neoplasms. The validation cohort of 61 cases demonstrated good concordance between the FusionPlex Pan-Heme panel and other methods, including chromosome analysis, fluorescence in situ hybridization, RT-PCR, and Sanger sequencing, with an analytic sensitivity and specificity of 95% and 100%, respectively. In an independent cohort of 28 patients indicated for FusionPlex testing, gene fusions were detected in 21 patients. The FusionPlex Pan-Heme panel analysis reliably detected fusion partners and patient-specific fusion sequences, allowing accurate classification of hematologic neoplasms and the discovery of new fusion partners, contributing to a better understanding of the pathogenesis of the diseases.
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Affiliation(s)
- Xueyan Chen
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington; Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Wenjing Wang
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Jeffrey Yeh
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Yu Wu
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Vivian G Oehler
- Department of Medicine, University of Washington, Seattle, Washington
| | - Kikkeri N Naresh
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington; Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Yajuan J Liu
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington.
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Hill SY, Hostyk J. A whole exome sequencing study to identify rare variants in multiplex families with alcohol use disorder. Front Psychiatry 2023; 14:1216493. [PMID: 37915799 PMCID: PMC10616827 DOI: 10.3389/fpsyt.2023.1216493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 09/22/2023] [Indexed: 11/03/2023] Open
Abstract
Background Alcohol use disorder (AUD) runs in families and is accompanied by genetic variation. Some families exhibit an extreme susceptibility in which multiple cases are found and often with an early onset of the disorder. Large scale genome-wide association studies have identified several genes with impressive statistical probabilities. Most of these genes are common variants. Our goal was to perform exome sequencing in families characterized by multiple cases (multiplex families) to determine if rare variants might be segregating with disease status. Methods A case-control approach was used to leverage the power of a large control sample of unrelated individuals (N = 8,983) with exome sequencing [Institute for Genomic Medicine (IGM)], for comparison with probands with AUD (N = 53) from families selected for AUD multiplex status. The probands were sequenced at IGM using similar protocols to those used for the archival controls. Specifically, the presence of a same-sex pair of adult siblings with AUD was the minimal criteria for inclusion. Using a gene-based collapsing analysis strategy, a search for qualifying variants within the sequence data was undertaken to identify ultra-rare non-synonymous variants. Results We searched 18,666 protein coding genes to identify an excess of rare deleterious genetic variation using whole exome sequence data in the 53 AUD individuals from a total of 282 family members. To complete a case/control analysis of unrelated individuals, probands were compared to unrelated controls. Case enrichment for 16 genes with significance at 10-4 and one at 10-5 are plausible candidates for follow-up studies. Six genes were ultra rare [minor allele frequency (MAF) of 0.0005]: CDSN, CHRNA9, IFT43, TLR6, SELENBP1, and GMPPB. Eight genes with MAF of 0.001: ZNF514, OXGR1, DIEXF, TMX4, MTBP, PON2, CRHBP, and ANKRD46 were identified along with three protein-truncating variants associated with loss-of-function: AGTRAP, ANKRD46, and PPA1. Using an ancestry filtered control group (N = 2,814), nine genes were found; three were also significant in the comparison to the larger control group including CHRNA9 previously implicated in alcohol and nicotine dependence. Conclusion This study implicates ultra-rare loss-of-function genes in AUD cases. Among the genes identified include those previously reported for nicotine and alcohol dependence (CHRNA9 and CRHBP).
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Affiliation(s)
- Shirley Y. Hill
- Department of Psychiatry, Psychology and Human Genetics, University of Pittsburgh, Pittsburgh, PA, United States
| | - Joseph Hostyk
- Institute for Genomic Medicine, Columbia University, New York, NY, United States
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9
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Char R, Liu Z, Jacqueline C, Davieau M, Delgado MG, Soufflet C, Fallet M, Chasson L, Chapuy R, Camosseto V, Strock E, Rua R, Almeida CR, Su B, Lennon-Duménil AM, Nal B, Roquilly A, Liang Y, Méresse S, Gatti E, Pierre P. RUFY3 regulates endolysosomes perinuclear positioning, antigen presentation and migration in activated phagocytes. Nat Commun 2023; 14:4290. [PMID: 37463962 PMCID: PMC10354229 DOI: 10.1038/s41467-023-40062-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 07/10/2023] [Indexed: 07/20/2023] Open
Abstract
Endo-lysosomes transport along microtubules and clustering in the perinuclear area are two necessary steps for microbes to activate specialized phagocyte functions. We report that RUN and FYVE domain-containing protein 3 (RUFY3) exists as two alternative isoforms distinguishable by the presence of a C-terminal FYVE domain and by their affinity for phosphatidylinositol 3-phosphate on endosomal membranes. The FYVE domain-bearing isoform (iRUFY3) is preferentially expressed in primary immune cells and up-regulated upon activation by microbes and Interferons. iRUFY3 is necessary for ARL8b + /LAMP1+ endo-lysosomes positioning in the pericentriolar organelles cloud of LPS-activated macrophages. We show that iRUFY3 controls macrophages migration, MHC II presentation and responses to Interferon-γ, while being important for intracellular Salmonella replication. Specific inactivation of rufy3 in phagocytes leads to aggravated pathologies in mouse upon LPS injection or bacterial pneumonia. This study highlights the role of iRUFY3 in controlling endo-lysosomal dynamics, which contributes to phagocyte activation and immune response regulation.
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Affiliation(s)
- Rémy Char
- Aix Marseille Université, CNRS, INSERM, CIML, 13288, Marseille, cedex 9, France
| | - Zhuangzhuang Liu
- School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, PR China
| | - Cédric Jacqueline
- Nantes Université, CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology, UMR1064, F-44000, Nantes, France
| | - Marion Davieau
- Nantes Université, CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology, UMR1064, F-44000, Nantes, France
| | - Maria-Graciela Delgado
- INSERM U932, Institut Curie, ANR-10-IDEX-0001-02 PSL* and ANR-11-LABX-0043, Paris, France
| | - Clara Soufflet
- Aix Marseille Université, CNRS, INSERM, CIML, 13288, Marseille, cedex 9, France
| | - Mathieu Fallet
- Aix Marseille Université, CNRS, INSERM, CIML, 13288, Marseille, cedex 9, France
| | - Lionel Chasson
- Aix Marseille Université, CNRS, INSERM, CIML, 13288, Marseille, cedex 9, France
| | - Raphael Chapuy
- Aix Marseille Université, CNRS, INSERM, CIML, 13288, Marseille, cedex 9, France
| | - Voahirana Camosseto
- Aix Marseille Université, CNRS, INSERM, CIML, 13288, Marseille, cedex 9, France
| | - Eva Strock
- Aix Marseille Université, CNRS, INSERM, CIML, 13288, Marseille, cedex 9, France
| | - Rejane Rua
- Aix Marseille Université, CNRS, INSERM, CIML, 13288, Marseille, cedex 9, France
| | - Catarina R Almeida
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Bing Su
- Shanghai Institute of Immunology, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, PR China
| | | | - Beatrice Nal
- Aix Marseille Université, CNRS, INSERM, CIML, 13288, Marseille, cedex 9, France
| | - Antoine Roquilly
- Nantes Université, CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology, UMR1064, F-44000, Nantes, France
| | - Yinming Liang
- School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, PR China
| | - Stéphane Méresse
- Aix Marseille Université, CNRS, INSERM, CIML, 13288, Marseille, cedex 9, France
| | - Evelina Gatti
- Aix Marseille Université, CNRS, INSERM, CIML, 13288, Marseille, cedex 9, France.
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810-193, Aveiro, Portugal.
| | - Philippe Pierre
- Aix Marseille Université, CNRS, INSERM, CIML, 13288, Marseille, cedex 9, France.
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810-193, Aveiro, Portugal.
- Shanghai Institute of Immunology, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, PR China.
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10
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Legaki E, Taka S, Papadopoulos NG. The complexity in DNA methylation analysis of allergic diseases. Curr Opin Allergy Clin Immunol 2023; 23:172-178. [PMID: 36752374 DOI: 10.1097/aci.0000000000000895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
PURPOSE OF REVIEW This review aims to report all the recent studies that are implicated in DNA methylation analysis in the field of allergy and to underline the complexity of the study methodologies and results. RECENT FINDINGS Although the growing number of DNA methylation studies have yet to point to a specific mechanism, herein we provide an overview of the majority of pathways considered to be implicated and highlight particular genes, like KNH2 , ATPAF2 and ZNF385A , for their potential as biomarkers. SUMMARY The epigenetic profile of respiratory allergic diseases, and particularly DNA methylation, has been investigated in various populations, so as to gain a better understanding of its role in pathogenesis. Through our analysis, multiple links are presented between differential DNA methylation loci and IgE sensitization, lung functionality and severity of the disease. Additionally, associations of this epigenetic change with maternal asthma, age, sex and environmental factors are described, thus uncovering specific gene families that, after further examination could be used as methylation biomarkers in cases of allergic disease.
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Affiliation(s)
- Evangelia Legaki
- Allergy and Clinical Immunology Unit, Second Pediatric Clinic, National and Kapodistrian University of Athens, Athens, Greece
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11
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Yan H, Zhu J, Ping Y, Yan M, Liao G, Yuan H, Zhou Y, Xiang F, Pang B, Xu J, Pang L. The Heterogeneous Cellular States of Glioblastoma Stem Cells Revealed by Single Cell Analysis. Stem Cells 2023; 41:111-125. [PMID: 36583266 DOI: 10.1093/stmcls/sxac088] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 12/12/2022] [Indexed: 12/31/2022]
Abstract
Glioblastoma stem cells (GSCs) contributed to the progression, treatment resistance, and relapse of glioblastoma (GBM). However, current researches on GSCs were performed usually outside the human tumor microenvironment, ignoring the importance of the cellular states of primary GSCs. In this study, we leveraged single-cell transcriptome sequencing data of 6 independent GBM cohorts from public databases, and combined lineage and stemness features to identify primary GSCs. We dissected the cell states of GSCs and correlated them with the clinical outcomes of patients. As a result, we constructed a cellular hierarchy where GSCs resided at the center. In addition, we identified and characterized 2 different and recurrent GSCs subpopulations: proliferative GSCs (pGSCs) and quiescent GSCs (qGSCs). The pGSCs showed high cell cycle activity, indicating rapid cell division, while qGSCs showed a quiescent state. Then we traced the processes of tumor development by pseudo-time analysis and tumor phylogeny, and found that GSCs accumulated throughout the whole tumor development period. During the process, pGSCs mainly contributed to the early stage and qGSCs were enriched in the later stage. Finally, we constructed an 8-gene prognostic signature reflecting pGSCs activity and found that patients whose tumors were enriched for the pGSC signature had poor clinical outcomes. Our study highlights the primary GSCs heterogeneity and its correlation to tumor development and clinical outcomes, providing the potential targets for GBM treatment.
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Affiliation(s)
- Haoteng Yan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.,Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, People's Republic of China.,Aging Translational Medicine Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, People's Republic of China
| | - Jiali Zhu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yanyan Ping
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Min Yan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Gaoming Liao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Huating Yuan
- Bioinformatics and BioMedical Bigdata Mining Laboratory, School of Big Health, Guizhou Medical University, Guiyang 550025, People's Republic of China
| | - Yao Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Fengyu Xiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Bo Pang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Jinyuan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Lin Pang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
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12
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Rawat S, Chatterjee D, Marwaha R, Charak G, Kumar G, Shaw S, Khatter D, Sharma S, de Heus C, Liv N, Klumperman J, Tuli A, Sharma M. RUFY1 binds Arl8b and mediates endosome-to-TGN CI-M6PR retrieval for cargo sorting to lysosomes. J Cell Biol 2023; 222:e202108001. [PMID: 36282215 PMCID: PMC9597352 DOI: 10.1083/jcb.202108001] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 08/26/2022] [Accepted: 09/29/2022] [Indexed: 11/22/2022] Open
Abstract
Arl8b, an Arf-like GTP-binding protein, regulates cargo trafficking and positioning of lysosomes. However, it is unknown whether Arl8b regulates lysosomal cargo sorting. Here, we report that Arl8b binds to the Rab4 and Rab14 interaction partner, RUN and FYVE domain-containing protein (RUFY) 1, a known regulator of cargo sorting from recycling endosomes. Arl8b determines RUFY1 endosomal localization through regulating its interaction with Rab14. RUFY1 depletion led to a delay in CI-M6PR retrieval from endosomes to the TGN, resulting in impaired delivery of newly synthesized hydrolases to lysosomes. We identified the dynein-dynactin complex as an RUFY1 interaction partner, and similar to a subset of activating dynein adaptors, the coiled-coil region of RUFY1 was required for interaction with dynein and the ability to mediate dynein-dependent organelle clustering. Our findings suggest that Arl8b and RUFY1 play a novel role on recycling endosomes, from where this machinery regulates endosomes to TGN retrieval of CI-M6PR and, consequently, lysosomal cargo sorting.
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Affiliation(s)
- Shalini Rawat
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali (IISERM), Punjab, India
| | - Dhruba Chatterjee
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali (IISERM), Punjab, India
| | - Rituraj Marwaha
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali (IISERM), Punjab, India
| | - Gitanjali Charak
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali (IISERM), Punjab, India
| | - Gaurav Kumar
- Division of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Shrestha Shaw
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali (IISERM), Punjab, India
| | - Divya Khatter
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali (IISERM), Punjab, India
| | - Sheetal Sharma
- Division of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Cecilia de Heus
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, Netherlands
| | - Nalan Liv
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, Netherlands
| | - Judith Klumperman
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, Netherlands
| | - Amit Tuli
- Division of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Mahak Sharma
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali (IISERM), Punjab, India
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13
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Kumar G, Chawla P, Dhiman N, Chadha S, Sharma S, Sethi K, Sharma M, Tuli A. RUFY3 links Arl8b and JIP4-Dynein complex to regulate lysosome size and positioning. Nat Commun 2022; 13:1540. [PMID: 35314681 PMCID: PMC8938454 DOI: 10.1038/s41467-022-29077-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 02/24/2022] [Indexed: 02/08/2023] Open
Abstract
The bidirectional movement of lysosomes on microtubule tracks regulates their whole-cell spatial arrangement. Arl8b, a small GTP-binding (G) protein, promotes lysosome anterograde trafficking mediated by kinesin-1. Herein, we report an Arl8b effector, RUFY3, which regulates the retrograde transport of lysosomes. We show that RUFY3 interacts with the JIP4-dynein-dynactin complex and facilitates Arl8b association with the retrograde motor complex. Accordingly, RUFY3 knockdown disrupts the positioning of Arl8b-positive endosomes and reduces Arl8b colocalization with Rab7-marked late endosomal compartments. Moreover, we find that RUFY3 regulates nutrient-dependent lysosome distribution, although autophagosome-lysosome fusion and autophagic cargo degradation are not impaired upon RUFY3 depletion. Interestingly, lysosome size is significantly reduced in RUFY3 depleted cells, which could be rescued by inhibition of the lysosome reformation regulatory factor PIKFYVE. These findings suggest a model in which the perinuclear cloud arrangement of lysosomes regulates both the positioning and size of these proteolytic compartments.
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Affiliation(s)
- Gaurav Kumar
- Divison of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Prateek Chawla
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Punjab, India
| | - Neha Dhiman
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Punjab, India
| | - Sanya Chadha
- Divison of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Sheetal Sharma
- Divison of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Kanupriya Sethi
- Divison of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Mahak Sharma
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Punjab, India
| | - Amit Tuli
- Divison of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India.
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14
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Keren-Kaplan T, Sarić A, Ghosh S, Williamson CD, Jia R, Li Y, Bonifacino JS. RUFY3 and RUFY4 are ARL8 effectors that promote coupling of endolysosomes to dynein-dynactin. Nat Commun 2022; 13:1506. [PMID: 35314674 PMCID: PMC8938451 DOI: 10.1038/s41467-022-28952-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 02/18/2022] [Indexed: 11/10/2022] Open
Abstract
The small GTPase ARL8 associates with endolysosomes, leading to the recruitment of several effectors that couple endolysosomes to kinesins for anterograde transport along microtubules, and to tethering factors for eventual fusion with other organelles. Herein we report the identification of the RUN- and FYVE-domain-containing proteins RUFY3 and RUFY4 as ARL8 effectors that promote coupling of endolysosomes to dynein-dynactin for retrograde transport along microtubules. Using various methodologies, we find that RUFY3 and RUFY4 interact with both GTP-bound ARL8 and dynein-dynactin. In addition, we show that RUFY3 and RUFY4 promote concentration of endolysosomes in the juxtanuclear area of non-neuronal cells, and drive redistribution of endolysosomes from the axon to the soma in hippocampal neurons. The function of RUFY3 in retrograde transport contributes to the juxtanuclear redistribution of endolysosomes upon cytosol alkalinization. These studies thus identify RUFY3 and RUFY4 as ARL8-dependent, dynein-dynactin adaptors or regulators, and highlight the role of ARL8 in the control of both anterograde and retrograde endolysosome transport.
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Affiliation(s)
- Tal Keren-Kaplan
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Amra Sarić
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Saikat Ghosh
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Chad D Williamson
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Rui Jia
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Yan Li
- Proteomics Core Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Juan S Bonifacino
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
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15
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Miao D, Shi J, Xiong Z, Xiao W, Meng X, Lv Q, Xie K, Yang H, Zhang X. As a prognostic biomarker of clear cell renal cell carcinoma RUFY4 predicts immunotherapy responsiveness in a PDL1-related manner. Cancer Cell Int 2022; 22:66. [PMID: 35135552 PMCID: PMC8822671 DOI: 10.1186/s12935-022-02480-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 01/21/2022] [Indexed: 12/28/2022] Open
Abstract
Background Clear cell renal cell carcinoma (ccRCC) is one of the most lethal malignancies in the urinary system and the existing immunotherapy has not achieved satisfactory outcomes. Therefore, this study aims at establishing a novel gene signature for immune infiltration and clinical outcome (overall survival and immunotherapy responsiveness) in ccRCC patients. Methods Based on RNA sequencing data and clinical information in The Cancer Genome Atlas (TCGA) database, we calculated proportions of immune cells in 611 samples using an online tool CIBERSORTx. Multivariate survival analysis was conducted to determine crucial survival-associated immune cells and immune-infiltration-related genes (IIRGs). Next, the clinical specimens and common renal cancer cell lines were applied to confirm IIRGs expression at protein and RNA levels. Finally, functional enrichment analyses and siRNA technology targeted to RUFY4 were implemented to verify its function of predicting immunotherapy response. Results Follicular helper T cells (TFHs) and Regulatory T cells (Tregs) were highly infiltrated in the tumor microenvironment (TME) and their relative proportions were independent prognostic factors for patients. Among IIRGs of TFHs and TREGs, RUFY4 was found to be highly activated in tumor microenvironment and its co-expression network was enriched in PDL1/PD1 checkpoint pathway in cancer. Additionally, knockdown of RUFY4 led to the decline of PDL1 and proliferation ability in ccRCC cell lines. Conclusion TFHs and Tregs were considered as prognostic biomarkers and RUFY4 was an immunotherapeutic predictor of ccRCC patients in a PDL1-Related manner. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-022-02480-7.
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Affiliation(s)
- Daojia Miao
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Jian Shi
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Zhiyong Xiong
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Wen Xiao
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Xiangui Meng
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Qingyang Lv
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Kairu Xie
- Department of Pathogenic Biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Hongmei Yang
- Department of Pathogenic Biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Xiaoping Zhang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China. .,Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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16
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Ohashi Y. Activation Mechanisms of the VPS34 Complexes. Cells 2021; 10:cells10113124. [PMID: 34831348 PMCID: PMC8624279 DOI: 10.3390/cells10113124] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/09/2021] [Accepted: 11/09/2021] [Indexed: 01/18/2023] Open
Abstract
Phosphatidylinositol-3-phosphate (PtdIns(3)P) is essential for cell survival, and its intracellular synthesis is spatially and temporally regulated. It has major roles in two distinctive cellular pathways, namely, the autophagy and endocytic pathways. PtdIns(3)P is synthesized from phosphatidylinositol (PtdIns) by PIK3C3C/VPS34 in mammals or Vps34 in yeast. Pathway-specific VPS34/Vps34 activity is the consequence of the enzyme being incorporated into two mutually exclusive complexes: complex I for autophagy, composed of VPS34/Vps34-Vps15/Vps15-Beclin 1/Vps30-ATG14L/Atg14 (mammals/yeast), and complex II for endocytic pathways, in which ATG14L/Atg14 is replaced with UVRAG/Vps38 (mammals/yeast). Because of its involvement in autophagy, defects in which are closely associated with human diseases such as cancer and neurodegenerative diseases, developing highly selective drugs that target specific VPS34/Vps34 complexes is an essential goal in the autophagy field. Recent studies on the activation mechanisms of VPS34/Vps34 complexes have revealed that a variety of factors, including conformational changes, lipid physicochemical parameters, upstream regulators, and downstream effectors, greatly influence the activity of these complexes. This review summarizes and highlights each of these influences as well as clarifying key questions remaining in the field and outlining future perspectives.
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Affiliation(s)
- Yohei Ohashi
- MRC Laboratory of Molecular Biology, Protein and Nucleic Acid Chemistry Division, Francis Crick Avenue, Cambridge CB2 0QH, UK
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Valečka J, Camosseto V, McEwan DG, Terawaki S, Liu Z, Strock E, Almeida CR, Su B, Dikic I, Liang Y, Gatti E, Pierre P. RUFY4 exists as two translationally regulated isoforms, that localize to the mitochondrion in activated macrophages. ROYAL SOCIETY OPEN SCIENCE 2021; 8:202333. [PMID: 34295519 PMCID: PMC8278043 DOI: 10.1098/rsos.202333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 06/22/2021] [Indexed: 05/11/2023]
Abstract
We report here that RUFY4, a newly characterized member of the 'RUN and FYVE domain-containing' family of proteins previously associated with autophagy enhancement, is highly expressed in alveolar macrophages (AM). We show that RUFY4 interacts with mitochondria upon stimulation by microbial-associated molecular patterns of AM and dendritic cells. RUFY4 interaction with mitochondria and other organelles is dependent on a previously uncharacterized OmpH domain located immediately upstream of its C-terminal FYVE domain. Further, we demonstrate that rufy4 messenger RNA can be translated from an alternative translation initiation codon, giving rise to a N-terminally truncated form of the molecule lacking most of its RUN domain and with enhanced potential for its interaction with mitochondria. Our observations point towards a role of RUFY4 in selective mitochondria clearance in activated phagocytes.
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Affiliation(s)
- Jan Valečka
- Aix Marseille Université, CNRS, INSERM, CIML, 13288 Marseille cedex 9, France
| | - Voahirana Camosseto
- Aix Marseille Université, CNRS, INSERM, CIML, 13288 Marseille cedex 9, France
| | - David G. McEwan
- Tumour Cell Death Laboratory, Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Seigo Terawaki
- Department of Pathobiochemistry, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Zhuangzhuang Liu
- School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, People's Republic of China
| | - Eva Strock
- Aix Marseille Université, CNRS, INSERM, CIML, 13288 Marseille cedex 9, France
| | - Catarina R. Almeida
- Institute for Research in Biomedicine (iBiMED) and Ilidio Pinho Foundation, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Bing Su
- Shanghai Institute of Immunology, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, People's Republic of China
| | - Ivan Dikic
- Institute of Biochemistry II, Goethe University School of Medicine, Theodor-Stern-Kai 7, 60590 Frankfurt (Main), Germany
| | - Yinming Liang
- School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, People's Republic of China
| | - Evelina Gatti
- Aix Marseille Université, CNRS, INSERM, CIML, 13288 Marseille cedex 9, France
- Institute for Research in Biomedicine (iBiMED) and Ilidio Pinho Foundation, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Philippe Pierre
- Aix Marseille Université, CNRS, INSERM, CIML, 13288 Marseille cedex 9, France
- Institute for Research in Biomedicine (iBiMED) and Ilidio Pinho Foundation, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal
- Shanghai Institute of Immunology, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, People's Republic of China
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