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Rajan AAN, Hutchins EJ. Post-transcriptional regulation as a conserved driver of neural crest and cancer-cell migration. Curr Opin Cell Biol 2024; 89:102400. [PMID: 39032482 DOI: 10.1016/j.ceb.2024.102400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 06/26/2024] [Accepted: 06/26/2024] [Indexed: 07/23/2024]
Abstract
Cells have evolved mechanisms to migrate for diverse biological functions. A process frequently deployed during metazoan cell migration is the epithelial-mesenchymal transition (EMT). During EMT, adherent epithelial cells undergo coordinated cellular transitions to mesenchymalize and reduce their intercellular attachments. This is achieved via tightly regulated changes in gene expression, which modulates cell-cell and cell-matrix adhesion to allow movement. The acquisition of motility and invasive properties following EMT allows some mesenchymal cells to migrate through complex environments to form tissues during embryogenesis; however, these processes may also be leveraged by cancer cells, which often co-opt these endogenous programs to metastasize. Post-transcriptional regulation is now emerging as a major conserved mechanism by which cells modulate EMT and migration, which we discuss here in the context of vertebrate development and cancer.
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Affiliation(s)
- Arvind Arul Nambi Rajan
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Erica J Hutchins
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA.
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2
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Satheeshan G, Si AK, Rutta J, Venkatesh T. Exosome theranostics: Comparative analysis of P body and exosome proteins and their mutations for clinical applications. Funct Integr Genomics 2024; 24:124. [PMID: 38995459 DOI: 10.1007/s10142-024-01404-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 07/02/2024] [Accepted: 07/04/2024] [Indexed: 07/13/2024]
Abstract
Exosomes are lipid-bilayered vesicles, originating from early endosomes that capture cellular proteins and genetic materials to form multi-vesicular bodies. These exosomes are secreted into extracellular fluids such as cerebrospinal fluid, blood, urine, and cell culture supernatants. They play a key role in intercellular communication by carrying active molecules like lipids, cytokines, growth factors, metabolites, proteins, and RNAs. Recently, the potential of exosomal delivery for therapeutic purposes has been explored due to their low immunogenicity, nano-scale size, and ability to cross cellular barriers. This review comprehensively examines the biogenesis of exosomes, their isolation techniques, and their diverse applications in theranostics. We delve into the mechanisms and methods for loading exosomes with mRNA, miRNA, proteins, and drugs, highlighting their transformative role in delivering therapeutic payloads. Additionally, the utility of exosomes in stem cell therapy is discussed, showcasing their potential in regenerative medicine. Insights into exosome cargo using pre- or post-loading techniques are critical for exosome theranostics. We review exosome databases such as ExoCarta, Expedia, and ExoBCD, which document exosome cargo. From these databases, we identified 25 proteins common to both exosomes and P-bodies, known for mutations in the COSMIC database. Exosome databases do not integrate with mutation analysis programs; hence, we performed mutation analysis using additional databases. Accounting for the mutation status of parental cells and exosomal cargo is crucial in exosome theranostics. This review provides a comprehensive report on exosome databases, proteins common to exosomes and P-bodies, and their mutation analysis, along with the latest studies on exosome-engineered theranostics.
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Affiliation(s)
- Greeshma Satheeshan
- Dept of Biochemistry and Molecular Biology, Central University of Kerala, Krishna building, Periye, Kasargod, 671316, Kerala, India
| | - Ayan Kumar Si
- Dept of Biochemistry and Molecular Biology, Central University of Kerala, Krishna building, Periye, Kasargod, 671316, Kerala, India
| | - Joel Rutta
- Dept of Biochemistry and Molecular Biology, Central University of Kerala, Krishna building, Periye, Kasargod, 671316, Kerala, India
| | - Thejaswini Venkatesh
- Dept of Biochemistry and Molecular Biology, Central University of Kerala, Krishna building, Periye, Kasargod, 671316, Kerala, India.
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3
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Zhang X, Yuan L, Zhang W, Zhang Y, Wu Q, Li C, Wu M, Huang Y. Liquid-liquid phase separation in diseases. MedComm (Beijing) 2024; 5:e640. [PMID: 39006762 PMCID: PMC11245632 DOI: 10.1002/mco2.640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 07/16/2024] Open
Abstract
Liquid-liquid phase separation (LLPS), an emerging biophysical phenomenon, can sequester molecules to implement physiological and pathological functions. LLPS implements the assembly of numerous membraneless chambers, including stress granules and P-bodies, containing RNA and protein. RNA-RNA and RNA-protein interactions play a critical role in LLPS. Scaffolding proteins, through multivalent interactions and external factors, support protein-RNA interaction networks to form condensates involved in a variety of diseases, particularly neurodegenerative diseases and cancer. Modulating LLPS phenomenon in multiple pathogenic proteins for the treatment of neurodegenerative diseases and cancer could present a promising direction, though recent advances in this area are limited. Here, we summarize in detail the complexity of LLPS in constructing signaling pathways and highlight the role of LLPS in neurodegenerative diseases and cancers. We also explore RNA modifications on LLPS to alter diseases progression because these modifications can influence LLPS of certain proteins or the formation of stress granules, and discuss the possibility of proper manipulation of LLPS process to restore cellular homeostasis or develop therapeutic drugs for the eradication of diseases. This review attempts to discuss potential therapeutic opportunities by elaborating on the connection between LLPS, RNA modification, and their roles in diseases.
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Affiliation(s)
- Xinyue Zhang
- College of Life and Health Sciences Northeastern University Shenyang China
| | - Lin Yuan
- Laboratory of Research in Parkinson's Disease and Related Disorders Health Sciences Institute China Medical University Shenyang China
| | - Wanlu Zhang
- College of Life and Health Sciences Northeastern University Shenyang China
| | - Yi Zhang
- College of Life and Health Sciences Northeastern University Shenyang China
| | - Qun Wu
- Department of Pediatrics Ruijin Hospital Affiliated to Shanghai Jiaotong University School of Medicine Shanghai China
| | - Chunting Li
- College of Life and Health Sciences Northeastern University Shenyang China
| | - Min Wu
- Wenzhou Institute University of Chinese Academy of Sciences Wenzhou Zhejiang China
- The Joint Research Center Affiliated Xiangshan Hospital of Wenzhou Medical University Ningbo China
| | - Yongye Huang
- College of Life and Health Sciences Northeastern University Shenyang China
- Key Laboratory of Bioresource Research and Development of Liaoning Province College of Life and Health Sciences Northeastern University Shenyang China
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Khan FA, Nsengimana B, Awan UA, Ji XY, Ji S, Dong J. Regulatory roles of N6-methyladenosine (m 6A) methylation in RNA processing and non-communicable diseases. Cancer Gene Ther 2024:10.1038/s41417-024-00789-1. [PMID: 38839892 DOI: 10.1038/s41417-024-00789-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/12/2024] [Accepted: 05/21/2024] [Indexed: 06/07/2024]
Abstract
Post-transcriptional RNA modification is an emerging epigenetic control mechanism in cells that is important in many different cellular and organismal processes. N6-methyladenosine (m6A) is one of the most prevalent, prolific, and ubiquitous internal transcriptional alterations in eukaryotic mRNAs, making it an important topic in the field of Epigenetics. m6A methylation acts as a dynamical regulatory process that regulates the activity of genes and participates in multiple physiological processes, by supporting multiple aspects of essential mRNA metabolic processes, including pre-mRNA splicing, nuclear export, translation, miRNA synthesis, and stability. Extensive research has linked aberrations in m6A modification and m6A-associated proteins to a wide range of human diseases. However, the impact of m6A on mRNA metabolism and its pathological connection between m6A and other non-communicable diseases, including cardiovascular disease, neurodegenerative disorders, liver diseases, and cancer remains in fragmentation. Here, we review the existing understanding of the overall role of mechanisms by which m6A exerts its activities and address new discoveries that highlight m6A's diverse involvement in gene expression regulation. We discuss m6A deposition on mRNA and its consequences on degradation, translation, and transcription, as well as m6A methylation of non-coding chromosomal-associated RNA species. This study could give new information about the molecular process, early detection, tailored treatment, and predictive evaluation of human non-communicable diseases like cancer. We also explore more about new data that suggests targeting m6A regulators in diseases may have therapeutic advantages.
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Affiliation(s)
- Faiz Ali Khan
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, China.
- Institute of Integrative Medicine, Fudan University, Shanghai, China.
- Department of Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), Lahore, Pakistan.
| | - Bernard Nsengimana
- Department of Hepatobiliary Surgery, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Usman Ayub Awan
- Division of Epidemiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xin-Ying Ji
- Center for Molecular Medicine, Faculty of Basic Medical Subjects, Shu-Qing Medical College of Zhengzhou, Zhengzhou, Henan, China.
| | - Shaoping Ji
- Center for Molecular Medicine, Faculty of Basic Medical Subjects, Shu-Qing Medical College of Zhengzhou, Zhengzhou, Henan, China.
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China.
| | - Jingcheng Dong
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, China.
- Institute of Integrative Medicine, Fudan University, Shanghai, China.
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Zhang C, Ni X, Tao C, Zhou Z, Wang F, Gu F, Cui X, Jiang S, Li Q, Lu H, Li D, Wu Z, Zhang R. Targeting PUF60 prevents tumor progression by retarding mRNA decay of oxidative phosphorylation in ovarian cancer. Cell Oncol (Dordr) 2024; 47:157-174. [PMID: 37632669 PMCID: PMC10899302 DOI: 10.1007/s13402-023-00859-w] [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] [Accepted: 08/04/2023] [Indexed: 08/28/2023] Open
Abstract
PURPOSE Ovarian cancer (OC) is the leading cause of death from gynecological malignancies, and its etiology and pathogenesis are currently unclear. Recent studies have found that PUF60 overexpressed in various cancers. However, the exact function of PUF60 in global RNA processing and its role in OC has been unclear. METHODS The expression of PUF60 and its relationship with clinical characteristics were analyzed by multiple database analysis and immunohistochemistry. Phenotypic effects of PUF60 on ovarian cancer cell proliferation and metastasis were examined by in vitro cell proliferation assay, migration assay, and in vivo xenograft models and lung metastasis models. RNA immunoprecipitation, seahorse analyses, RNA stability assay were used to study the effect of PUF60 on the stability of oxidative phosphorylation (OXPHOS)-related genes in OC. RESULTS We report PUF60 is highly expressed in OC with frequent amplification of up to 33.9% and its upregulation predicts a poor prognosis. PUF60 promotes the proliferation and migration of OC cells both in vitro and in vivo. Mechanistically, we demonstrated that silencing of PUF60 enhanced the stability of mRNA transcripts involved in OXPHOS and decreased the formation of processing bodies (P-bodies), ultimately elevating the OXPHOS level. CONCLUSION Our study unveils a novel function of PUF60 in OC energy metabolism. Thus, PUF60 may serve as a novel target for the treatment of patients with OC.
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Affiliation(s)
- Cancan Zhang
- Department of Obstetrics and Gynecology, Fengxian Hospital, The Third School of Clinical Medicine, Southern Medical University, 6600 Nanfeng Road, Shanghai, 201499, China
- Department of Obstetrics and Gynecology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China
| | - Xiaoge Ni
- Department of Obstetrics and Gynecology, Fengxian Hospital, The Third School of Clinical Medicine, Southern Medical University, 6600 Nanfeng Road, Shanghai, 201499, China
| | - Chunlin Tao
- Department of Obstetrics and Gynecology, Fengxian Hospital, The Third School of Clinical Medicine, Southern Medical University, 6600 Nanfeng Road, Shanghai, 201499, China
| | - Ziyang Zhou
- Department of Obstetrics and Gynecology, Fengxian Hospital, The Third School of Clinical Medicine, Southern Medical University, 6600 Nanfeng Road, Shanghai, 201499, China
| | - Fengmian Wang
- Department of Obstetrics and Gynecology, Fengxian Hospital, The Third School of Clinical Medicine, Southern Medical University, 6600 Nanfeng Road, Shanghai, 201499, China
| | - Fei Gu
- Department of Obstetrics and Gynecology, Fengxian Hospital, The Third School of Clinical Medicine, Southern Medical University, 6600 Nanfeng Road, Shanghai, 201499, China
| | - Xiaoxiao Cui
- Department of Obstetrics and Gynecology, Fengxian Hospital, The Third School of Clinical Medicine, Southern Medical University, 6600 Nanfeng Road, Shanghai, 201499, China
| | - Shuheng Jiang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 800 Dongchuan Road, Shanghai, 200240, China
| | - Qing Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 800 Dongchuan Road, Shanghai, 200240, China
| | - Huan Lu
- Department of Obstetrics and Gynecology, Fengxian Hospital, The Third School of Clinical Medicine, Southern Medical University, 6600 Nanfeng Road, Shanghai, 201499, China
| | - Dongxue Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 800 Dongchuan Road, Shanghai, 200240, China.
| | - Zhiyong Wu
- Gynecology Department, Shanghai Obstetrics and Gynecology Hospital of Fudan University, No. 419 Fangxie Road, Shanghai, 200011, China.
| | - Rong Zhang
- Department of Obstetrics and Gynecology, Fengxian Hospital, The Third School of Clinical Medicine, Southern Medical University, 6600 Nanfeng Road, Shanghai, 201499, China.
- Shanghai Geriatric Medical Center, Shanghai, China.
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Khan FA, Fang N, Zhang W, Ji S. The multifaceted role of Fragile X-Related Protein 1 (FXR1) in cellular processes: an updated review on cancer and clinical applications. Cell Death Dis 2024; 15:72. [PMID: 38238286 PMCID: PMC10796922 DOI: 10.1038/s41419-023-06413-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/22/2024]
Abstract
RNA-binding proteins (RBPs) modulate the expression level of several target RNAs (such as mRNAs) post-transcriptionally through interactions with unique binding sites in the 3'-untranslated region. There is mounting information that suggests RBP dysregulation plays a significant role in carcinogenesis. However, the function of FMR1 autosomal homolog 1(FXR1) in malignancies is just beginning to be unveiled. Due to the diversity of their RNA-binding domains and functional adaptability, FXR1 can regulate diverse transcript processing. Changes in FXR1 interaction with RNA networks have been linked to the emergence of cancer, although the theoretical framework defining these alterations in interaction is insufficient. Alteration in FXR1 expression or localization has been linked to the mRNAs of cancer suppressor genes, cancer-causing genes, and genes involved in genomic expression stability. In particular, FXR1-mediated gene regulation involves in several cellular phenomena related to cancer growth, metastasis, epithelial-mesenchymal transition, senescence, apoptosis, and angiogenesis. FXR1 dysregulation has been implicated in diverse cancer types, suggesting its diagnostic and therapeutic potential. However, the molecular mechanisms and biological effects of FXR1 regulation in cancer have yet to be understood. This review highlights the current knowledge of FXR1 expression and function in various cancer situations, emphasizing its functional variety and complexity. We further address the challenges and opportunities of targeting FXR1 for cancer diagnosis and treatment and propose future directions for FXR1 research in oncology. This work intends to provide an in-depth review of FXR1 as an emerging oncotarget with multiple roles and implications in cancer biology and therapy.
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Affiliation(s)
- Faiz Ali Khan
- Huaihe Hospital,Medical School, Henan University, Kaifeng, China
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Department of Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), Lahore, Pakistan
| | - Na Fang
- Huaihe Hospital,Medical School, Henan University, Kaifeng, China.
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China.
| | - Weijuan Zhang
- Huaihe Hospital,Medical School, Henan University, Kaifeng, China.
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China.
| | - Shaoping Ji
- Huaihe Hospital,Medical School, Henan University, Kaifeng, China.
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China.
- Zhengzhou Shuqing Medical College, Zhengzhou, China.
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Nsengimana B, Khan FA, Awan UA, Wang D, Fang N, Wei W, Zhang W, Ji S. Pseudogenes and Liquid Phase Separation in Epigenetic Expression. Front Oncol 2022; 12:912282. [PMID: 35875144 PMCID: PMC9305658 DOI: 10.3389/fonc.2022.912282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/13/2022] [Indexed: 11/24/2022] Open
Abstract
Pseudogenes have been considered as non-functional genes. However, peptides and long non-coding RNAs produced by pseudogenes are expressed in different tumors. Moreover, the dysregulation of pseudogenes is associated with cancer, and their expressions are higher in tumors compared to normal tissues. Recent studies show that pseudogenes can influence the liquid phase condensates formation. Liquid phase separation involves regulating different epigenetic stages, including transcription, chromatin organization, 3D DNA structure, splicing, and post-transcription modifications like m6A. Several membrane-less organelles, formed through the liquid phase separate, are also involved in the epigenetic regulation, and their defects are associated with cancer development. However, the association between pseudogenes and liquid phase separation remains unrevealed. The current study sought to investigate the relationship between pseudogenes and liquid phase separation in cancer development, as well as their therapeutic implications.
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Affiliation(s)
- Bernard Nsengimana
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Faiz Ali Khan
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- School of Life Sciences, Henan University, Kaifeng, China
- Department of Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), Lahore, Pakistan
| | - Usman Ayub Awan
- Department of Medical Laboratory Technology, The University of Haripur, Haripur, Pakistan
| | - Dandan Wang
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Na Fang
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Wenqiang Wei
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- *Correspondence: Wenqiang Wei, ; Weijuan Zhang, ; Shaoping Ji,
| | - Weijuan Zhang
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- *Correspondence: Wenqiang Wei, ; Weijuan Zhang, ; Shaoping Ji,
| | - Shaoping Ji
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- *Correspondence: Wenqiang Wei, ; Weijuan Zhang, ; Shaoping Ji,
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Liquid-liquid phase separation in tumor biology. Signal Transduct Target Ther 2022; 7:221. [PMID: 35803926 PMCID: PMC9270353 DOI: 10.1038/s41392-022-01076-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/16/2022] [Accepted: 06/21/2022] [Indexed: 12/12/2022] Open
Abstract
Liquid–liquid phase separation (LLPS) is a novel principle for explaining the precise spatial and temporal regulation in living cells. LLPS compartmentalizes proteins and nucleic acids into micron-scale, liquid-like, membraneless bodies with specific functions, which were recently termed biomolecular condensates. Biomolecular condensates are executors underlying the intracellular spatiotemporal coordination of various biological activities, including chromatin organization, genomic stability, DNA damage response and repair, transcription, and signal transduction. Dysregulation of these cellular processes is a key event in the initiation and/or evolution of cancer, and emerging evidence has linked the formation and regulation of LLPS to malignant transformations in tumor biology. In this review, we comprehensively summarize the detailed mechanisms of biomolecular condensate formation and biophysical function and review the recent major advances toward elucidating the multiple mechanisms involved in cancer cell pathology driven by aberrant LLPS. In addition, we discuss the therapeutic perspectives of LLPS in cancer research and the most recently developed drug candidates targeting LLPS modulation that can be used to combat tumorigenesis.
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