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Gomez‐Cardona E, Dehkordi MH, Van Baar K, Vitkauskaite A, Julien O, Fearnhead HO. An atlas of caspase cleavage events in differentiating muscle cells. Protein Sci 2024; 33:e5156. [PMID: 39180494 PMCID: PMC11344277 DOI: 10.1002/pro.5156] [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: 05/28/2024] [Revised: 08/02/2024] [Accepted: 08/11/2024] [Indexed: 08/26/2024]
Abstract
Executioner caspases, such as caspase-3, are known to induce apoptosis, but in other contexts, they can control very different fates, including cell differentiation and neuronal plasticity. While hundreds of caspase substrates are known to be specifically targeted during cell death, we know very little about how caspase activity brings about non-apoptotic fates. Here, we report the first proteome identification of cleavage events in C2C12 cells undergoing myogenic differentiation and its comparison to undifferentiated or dying C2C12 cells. These data have identified new caspase substrates, including caspase substrates specifically associated with differentiation, and show that caspases are regulating proteins involved in myogenesis in myotubes, several days after caspase-3 initiated differentiation. Cytoskeletal proteins emerged as a major group of non-apoptotic caspase substrates. We also identified proteins with well-established roles in muscle differentiation as substrates cleaved in differentiating cells.
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Affiliation(s)
- Erik Gomez‐Cardona
- Department of Biochemistry, Faculty of Medicine and DentistryUniversity of AlbertaAlbertaCanada
| | - Mahshid H. Dehkordi
- Pharmacology and Therapeutics, School of MedicineUniversity of GalwayGalwayIreland
| | - Kolden Van Baar
- Department of Biochemistry, Faculty of Medicine and DentistryUniversity of AlbertaAlbertaCanada
| | - Aiste Vitkauskaite
- Pharmacology and Therapeutics, School of MedicineUniversity of GalwayGalwayIreland
| | - Olivier Julien
- Department of Biochemistry, Faculty of Medicine and DentistryUniversity of AlbertaAlbertaCanada
| | - Howard O. Fearnhead
- Pharmacology and Therapeutics, School of MedicineUniversity of GalwayGalwayIreland
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2
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Liufu S, Lan Q, Liu X, Chen B, Xu X, Ai N, Li X, Yu Z, Ma H. Transcriptome Analysis Reveals the Age-Related Developmental Dynamics Pattern of the Longissimus Dorsi Muscle in Ningxiang Pigs. Genes (Basel) 2023; 14:genes14051050. [PMID: 37239410 DOI: 10.3390/genes14051050] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 05/02/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
The growth and development of the Longissimus Dorsi muscle are complex, playing an important role in the determination of pork quality. The study of the Longissimus Dorsi muscle at the mRNA level is particularly crucial for finding molecular approaches to improving meat quality in pig breeding. The current study utilized transcriptome technology to explore the regulatory mechanisms of muscle growth and intramuscular fat (IMF) deposition in the Longissimus Dorsi muscle at three core developmental stages (natal stage on day 1, growing stage on day 60, and finishing stage on day 210) in Ningxiang pigs. Our results revealed 441 differentially expressed genes (DEGs) in common for day 1 vs. day 60 and day 60 vs. day 210, and GO (Gene Ontology) analysis showed that candidate genes RIPOR2, MEGF10, KLHL40, PLEC, TBX3, FBP2, and HOMER1 may be closely related to muscle growth and development, while KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis showed that DEGs (UBC, SLC27A5, RXRG, PRKCQ, PRKAG2, PPARGC1A, PLIN5, PLIN4, IRS2, and CPT1B) involved the PPAR (Peroxisome Proliferator-Activated Receptor) signaling pathway and adipocytokine signaling pathway, which might play a pivotal role in the regulation of IMF deposition. PPI (Protein-Protein Interaction Networks) analysis found that the STAT1 gene was the top hub gene. Taken together, our results provide evidence for the molecular mechanisms of growth and development and IMF deposition in Longissimus Dorsi muscle to optimize carcass mass.
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Affiliation(s)
- Sui Liufu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Qun Lan
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Xiaolin Liu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Bohe Chen
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Xueli Xu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Nini Ai
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Xintong Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Zonggang Yu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Haiming Ma
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
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Olmedo-Nieva L, Muñoz-Bello JO, Martínez-Ramírez I, Martínez-Gutiérrez AD, Ortiz-Pedraza Y, González-Espinosa C, Madrid-Marina V, Torres-Poveda K, Bahena-Roman M, Lizano M. RIPOR2 Expression Decreased by HPV-16 E6 and E7 Oncoproteins: An Opportunity in the Search for Prognostic Biomarkers in Cervical Cancer. Cells 2022; 11:3942. [PMID: 36497200 PMCID: PMC9740487 DOI: 10.3390/cells11233942] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/26/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022] Open
Abstract
High-risk human papillomavirus (HPV) infection is the main risk factor for cervical cancer (CC) development, where the continuous expression of E6 and E7 oncoproteins maintain the malignant phenotype. In Mexico, around 70% of CC cases are diagnosed in advanced stages, impacting the survival of patients. The aim of this work was to identify biomarkers affected by HPV-16 E6 and E7 oncoproteins that impact the prognosis of CC patients. Expression profiles dependent on E6 and E7 oncoproteins, as well as their relationship with biological processes and cellular signaling pathways, were analyzed in CC cells. A comparison among expression profiles of E6- and E7-expressing cells and that from a CC cohort obtained from The Cancer Genome Atlas (TCGA) demonstrated that the expression of 13 genes impacts the overall survival (OS). A multivariate analysis revealed that the downregulated expression of RIPOR2 was strongly associated with a worse OS. RIPOR2, including its transcriptional variants, were overwhelmingly depleted in E6- and E7-expressing cells. Finally, in a Mexican cohort, it was found that in premalignant cervical lesions, RIPOR2 expression decreases as the lesions progress; meanwhile, decreased RIPOR2 expression was also associated with a worse OS in CC patients.
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Affiliation(s)
- Leslie Olmedo-Nieva
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología, Avenida San Fernando 22, Sección XVI, Tlalpan, Mexico City 14080, Mexico
| | - J. Omar Muñoz-Bello
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología, Avenida San Fernando 22, Sección XVI, Tlalpan, Mexico City 14080, Mexico
| | - Imelda Martínez-Ramírez
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología, Avenida San Fernando 22, Sección XVI, Tlalpan, Mexico City 14080, Mexico
| | | | - Yunuen Ortiz-Pedraza
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología, Avenida San Fernando 22, Sección XVI, Tlalpan, Mexico City 14080, Mexico
| | - Claudia González-Espinosa
- Departamento de Farmacobiología, Centro de Investigación y de Estudios Avanzados, Unidad Sede Sur, Calzada de los Tenorios 235, Granjas Coapa, Tlalpan, Mexico City 14330, Mexico
| | - Vicente Madrid-Marina
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos 62100, Mexico
| | - Kirvis Torres-Poveda
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos 62100, Mexico
| | - Margarita Bahena-Roman
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos 62100, Mexico
| | - Marcela Lizano
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología, Avenida San Fernando 22, Sección XVI, Tlalpan, Mexico City 14080, Mexico
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Circuito Exterior S/N, Ciudad Universitaria, Mexico City 04510, Mexico
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Xu F, Zou C, Gao Y, Shen J, Liu T, He Q, Li S, Xu S. Comprehensive analyses identify RIPOR2 as a genomic instability-associated immune prognostic biomarker in cervical cancer. Front Immunol 2022; 13:930488. [PMID: 36091054 PMCID: PMC9458976 DOI: 10.3389/fimmu.2022.930488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 08/05/2022] [Indexed: 12/14/2022] Open
Abstract
Cervical cancer (CC) is a malignancy that tends to have a poor prognosis when detected at an advanced stage; however, there are few studies on the early detection of CC at the genetic level. The tumor microenvironment (TME) and genomic instability (GI) greatly affect the survival of tumor patients via effects on carcinogenesis, tumor growth, and resistance. It is necessary to identify biomarkers simultaneously correlated with components of the TME and with GI, as these could predict the survival of patients and the efficacy of immunotherapy. In this study, we extracted somatic mutational data and transcriptome information of CC cases from The Cancer Genome Atlas, and the GSE44001 dataset from the Gene Expression Omnibus database was downloaded for external verification. Stromal components differed most between genomic unstable and genomic stable groups. Differentially expressed genes were screened out on the basis of GI and StromalScore, using somatic mutation information and ESTIMATE methods. We obtained the intersection of GI- and StromalScore-related genes and used them to establish a four-gene signature comprising RIPOR2, CCL22, PAMR1, and FBN1 for prognostic prediction. We described immunogenomic characteristics using this risk model, with methods including CIBERSORT, gene set enrichment analysis (GSEA), and single-sample GSEA. We further explored the protective factor RIPOR2, which has a close relationship with ImmuneScore. A series of in vitro experiments, including immunohistochemistry, immunofluorescence, quantitative reverse transcription PCR, transwell assay, CCK8 assay, EdU assay, cell cycle detection, colony formation assay, and Western blotting were performed to validate RIPOR2 as an anti-tumor signature. Combined with integrative bioinformatic analyses, these experiments showed a strong relationship between RIPOR2 with tumor mutation burden, expression of genes related to DNA damage response (especially PARP1), TME-related scores, activation of immune checkpoint activation, and efficacy of immunotherapy. To summarize, RIPOR2 was successfully identified through comprehensive analyses of the TME and GI as a potential biomarker for forecasting the prognosis and immunotherapy response, which could guide clinical strategies for the treatment of CC patients.
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Affiliation(s)
- Fangfang Xu
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Chang Zou
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yueqing Gao
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jiacheng Shen
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Tingwei Liu
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Qizhi He
- Department of Pathology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
- *Correspondence: Shaohua Xu, ; Shuangdi Li, ; Qizhi He,
| | - Shuangdi Li
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
- *Correspondence: Shaohua Xu, ; Shuangdi Li, ; Qizhi He,
| | - Shaohua Xu
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
- *Correspondence: Shaohua Xu, ; Shuangdi Li, ; Qizhi He,
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Chen YC, Hsiao CC, Wu CC, Chao TY, Leung SY, Chang YP, Tseng CC, Lee CP, Hsu PY, Wang TY, Wang PW, Chen TW, Lin MC. Next generation sequencing reveals miR-431-3p/miR-1303 as immune-regulating microRNAs for active tuberculosis. J Infect 2022; 85:519-533. [DOI: 10.1016/j.jinf.2022.08.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/22/2022] [Accepted: 08/27/2022] [Indexed: 11/29/2022]
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A Genome-Wide Search for Candidate Genes of Meat Production in Jalgin Merino Considering Known Productivity Genes. Genes (Basel) 2022; 13:genes13081337. [PMID: 35893074 PMCID: PMC9331477 DOI: 10.3390/genes13081337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/23/2022] [Accepted: 07/24/2022] [Indexed: 11/17/2022] Open
Abstract
In a group of Jalgin merino rams with no significant influence on the dispersion of the phenotypes of known productivity genes (MSTN, MEF2B, FABP4, etc.), a genome-wide search for associations of individual polymorphisms with intravital indicators of meat productivity was performed. Using the Ovine Infinium HD BeadChip 600K, 606,000 genome loci were evaluated. Twenty-three substitutions were found to be significantly associated with external measurements of the body and ultrasonic parameters. This made it possible to describe 14 candidate genes, the structural features of which can cause changes in animal phenotypes. No closely spaced genes were found for two substitutions. The identified polymorphisms were found in the exons, introns, and adjacent regions of the following genes and transcripts: CDCA2, ENSOARG00000014477, C4BPA, RIPOR2, ENSOARG00000007198, ENSOARG00000026965 (LincRNA), ENSOARG00000026436 (LincRNA), ENSOARG00000026782 (LincRNA), TENM3, RTL8A, MOSPD1, RTL8С, RIMS2, and P4HA3. The detected genes affect the metabolic pathways of cell differentiation and proliferation and are associated with the regulation of the immune system. This confirms their possible participation in the formation of the phenotypes of productivity parameters in animals and indicates the need for further study of the structure of candidate genes in order to identify their internal polymorphisms.
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Zheng B, Song K, Sun L, Gao Y, Qu Y, Ren C, Yan P, Chen W, Guo W, Zhou C, Yue B. Siglec-15-induced autophagy promotes invasion and metastasis of human osteosarcoma cells by activating the epithelial-mesenchymal transition and Beclin-1/ATG14 pathway. Cell Biosci 2022; 12:109. [PMID: 35842729 PMCID: PMC9287887 DOI: 10.1186/s13578-022-00846-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 07/06/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Pulmonary metastasis is the main cause of poor prognosis in osteosarcoma. Sialic acid-bound immunoglobulin lectin 15 (Siglec-15) has been demonstrated to be obviously correlated with pulmonary metastasis in osteosarcoma patients. However, the effect of Siglec-15 on autophagy in osteosarcoma remains unclear, while the role and mechanism of Siglec-15-related autophagy in lung metastasis also remain unknown. METHODS The expression levels of Siglec-15 and Beclin-1 were detected in osteosarcoma tissues using immunohistochemistry (IHC). The effect of Siglec-15 on metastasis was investigated using Transwell, wound healing and animal experiments with osteosarcoma cells. Corresponding proteins were confirmed using Western blotting when Siglec-15 or Beclin-1 was silenced or overexpressed. Changes in autophagy and the cytoskeleton were detected using immunofluorescence and transmission electron microscopy. RESULTS Siglec-15 and Beclin-1 expression was evaluated both in lung metastases and in patients who presented with pulmonary metastasis of osteosarcoma. Immunoprecipitation experiments revealed that Siglec-15 interacts directly with Beclin-1, an important autophagic protein. Moreover, loss of Siglec-15 distinctly inhibited autophagy and reduced Beclin-1/ATG14 expression. The decreased invasion and migration caused by Siglec-15 silencing could be reversed by Beclin-1 overexpression. Additionally, autophagy can promote the epithelial-mesenchymal transition (EMT) and affect cytoskeletal rearrangement, which was confirmed by overexpression or silencing of Beclin-1. CONCLUSIONS These findings confirmed the role of Siglec-15 in the regulation of autophagy and elaborated the relationship and mechanisms between autophagy and the metastasis of osteosarcoma cells.
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Affiliation(s)
- Bingxin Zheng
- Department of Orthopedic Oncology, The Affiliated Hospital of Qingdao University, No. 59 Haier Road, Qingdao, 266000, People's Republic of China
| | - Keliang Song
- Department of Orthopedic Oncology, The Affiliated Hospital of Qingdao University, No. 59 Haier Road, Qingdao, 266000, People's Republic of China
| | - Lingling Sun
- Department of Pathology, The Affiliated Hospital of Qingdao University, Qingdao, People's Republic of China
| | - Yang Gao
- Medical Department, The Affiliated Hospital of Qingdao University, Qingdao, People's Republic of China
| | - Yan Qu
- Industrial Investment Department, Haier, Qingdao, People's Republic of China
| | - Chongmin Ren
- Department of Orthopedic Oncology, The Affiliated Hospital of Qingdao University, No. 59 Haier Road, Qingdao, 266000, People's Republic of China
| | - Peng Yan
- Department of Orthopedic Oncology, The Affiliated Hospital of Qingdao University, No. 59 Haier Road, Qingdao, 266000, People's Republic of China
| | - Wenfang Chen
- Department of Physiology, Medical College of Qingdao University, Qingdao, People's Republic of China
| | - Wei Guo
- Musculoskeletal Tumor Center, Peking University People's Hospital, Beijing, People's Republic of China
| | - Chuanli Zhou
- Department of Spinal Surgery, The Affiliated Hospital of Qingdao University, No. 59 Haier Road, Qingdao, 266000, People's Republic of China.
| | - Bin Yue
- Department of Orthopedic Oncology, The Affiliated Hospital of Qingdao University, No. 59 Haier Road, Qingdao, 266000, People's Republic of China.
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