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Sun J, Durmaz AD, Babu A, Macabenta F, Stathopoulos A. Two sequential gene expression programs bridged by cell division support long-distance collective cell migration. Development 2024; 151:dev202262. [PMID: 38646822 PMCID: PMC11165717 DOI: 10.1242/dev.202262] [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: 08/14/2023] [Accepted: 04/08/2024] [Indexed: 04/23/2024]
Abstract
The precise assembly of tissues and organs relies on spatiotemporal regulation of gene expression to coordinate the collective behavior of cells. In Drosophila embryos, the midgut musculature is formed through collective migration of caudal visceral mesoderm (CVM) cells, but how gene expression changes as cells migrate is not well understood. Here, we have focused on ten genes expressed in the CVM and the cis-regulatory sequences controlling their expression. Although some genes are continuously expressed, others are expressed only early or late during migration. Late expression relates to cell cycle progression, as driving string/Cdc25 causes earlier division of CVM cells and accelerates the transition to late gene expression. In particular, we found that the cell cycle effector transcription factor E2F1 is a required input for the late gene CG5080. Furthermore, whereas late genes are broadly expressed in all CVM cells, early gene transcripts are polarized to the anterior or posterior ends of the migrating collective. We show this polarization requires transcription factors Snail, Zfh1 and Dorsocross. Collectively, these results identify two sequential gene expression programs bridged by cell division that support long-distance directional migration of CVM cells.
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Affiliation(s)
- Jingjing Sun
- California Institute of Technology, Division of Biology and Biological Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Ayse Damla Durmaz
- California Institute of Technology, Division of Biology and Biological Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
- Faculty of Biology, Ludwig-Maximilians Universität München, München, 82152 DE, Germany
| | - Aswini Babu
- California Institute of Technology, Division of Biology and Biological Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Frank Macabenta
- California Institute of Technology, Division of Biology and Biological Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
- California State University, Monterey Bay, Seaside, CA 93955, USA
| | - Angelike Stathopoulos
- California Institute of Technology, Division of Biology and Biological Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
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Jiang X, Gao YL, Li JY, Tong YY, Meng ZY, Yang SG, Zhu CT. An anoikis-related lncRNA signature is a useful tool for predicting the prognosis of patients with lung adenocarcinoma. Heliyon 2023; 9:e22200. [PMID: 38053861 PMCID: PMC10694177 DOI: 10.1016/j.heliyon.2023.e22200] [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: 05/25/2023] [Revised: 08/15/2023] [Accepted: 11/06/2023] [Indexed: 12/07/2023] Open
Abstract
Background Anoikis-related long non-coding RNAs (ARLs) play a critical role in tumor metastasis and progression, suggesting that they may serve as risk markers for cancer. This study aimed to investigate the prognostic value of ARLs in patients with lung adenocarcinoma (LUAD). Methods Clinical data, RNA sequencing (RNA-seq) data, and mutation data from the LUAD project were obtained from The Cancer Genome Atlas (TCGA) database. The Molecular Signatures Database (MSigDB) and the GeneCard database were used to collect an anoikis-related gene (ARG) set. Pearson correlation analysis was performed to identify ARLs. LASSO and Cox regression were then used to establish a prognostic risk signature for ARLs. The median risk score served as the basis for categorizing patients into high and low-risk groups. Kaplan-Meier analysis was utilized to compare the prognosis between these two groups. The study also examined the associations between risk scores and prognosis, clinicopathological characteristics, immune status, tumor mutation burden (TMB), and chemotherapeutic agents. LncRNA expression was assessed using quantitative real-time PCR (qRT-PCR). Results A total of 480 RNA expression profiles, 501 ARGs, and 2698 ARLs were obtained from the database. A prognostic ARL signature for LUAD was established, consisting of 9 lncRNAs. Patients in the low-risk group exhibited significantly better prognosis compared to those in the high-risk group (P < 0.001). The 9 lncRNAs from the ARL signature were identified as independent prognostic factors (P < 0.001). The signature demonstrated high accuracy in predicting LUAD prognosis, with area under the curve values exceeding 0.7. The risk scores for ARLs showed strong negative correlations with stroma score (P = 5.9E-07, R = -0.23), immune score (P = 9.7E-09, R = -0.26), and microenvironment score (P = 8E-11, R = -0.29). Additionally, the low-risk group exhibited significantly higher TMB compared to the high-risk group (P = 4.6E-05). High-risk status was significantly associated with lower half-maximal inhibitory concentrations for most chemotherapeutic drugs. Conclusion This newly constructed signature based on nine ARLs is a useful instrument for the risk stratification of LUAD patients. The signature has potential clinical significance for predicting the prognosis of LUAD patients and guiding personalized immunotherapy.
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Affiliation(s)
- Xin Jiang
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
- Department of Transfusion Medicine, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China
| | - Yu-lu Gao
- Department of Laboratory Medicine, Kunshan Affiliated Hospital of Nanjing University of Chinese Medicine, Kunshan, 215300, China
| | - Jia-yan Li
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
- Department of Transfusion Medicine, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China
| | - Ying-ying Tong
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Zhao-yang Meng
- Department of Pharmacy, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China
| | - Shi-gui Yang
- Department of Public Health, Zhejiang University School of Medicine, Hangzhou, 310000, China
| | - Chang-tai Zhu
- Department of Transfusion Medicine, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China
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Frasch M, Ismat A, Reim I, Raufer J. The RNF220 domain nuclear factor Teyrha-Meyrha (Tey) regulates the migration and differentiation of specific visceral and somatic muscles in Drosophila. Development 2023; 150:dev201457. [PMID: 37642089 PMCID: PMC10508689 DOI: 10.1242/dev.201457] [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: 12/13/2022] [Accepted: 08/21/2023] [Indexed: 08/31/2023]
Abstract
Development of the visceral musculature of the Drosophila midgut encompasses a closely coordinated sequence of migration events of cells from the trunk and caudal visceral mesoderm that underlies the formation of the stereotypic orthogonal pattern of circular and longitudinal midgut muscles. Our study focuses on the last step of migration and morphogenesis of longitudinal visceral muscle precursors and shows that these multinucleated precursors utilize dynamic filopodial extensions to migrate in dorsal and ventral directions over the forming midgut tube. The establishment of maximal dorsoventral distances from one another, and anteroposterior alignments, lead to the equidistant coverage of the midgut with longitudinal muscle fibers. We identify Teyrha-Meyhra (Tey), a tissue-specific nuclear factor related to the RNF220 domain protein family, as a crucial regulator of this process of muscle migration and morphogenesis that is further required for proper differentiation of longitudinal visceral muscles. In addition, Tey is expressed in a single somatic muscle founder cell in each hemisegment, regulates the migration of this founder cell, and is required for proper pathfinding of its developing myotube to specific myotendinous attachment sites.
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Affiliation(s)
- Manfred Frasch
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Department of Biology, Division of Developmental Biology, Staudtstrasse 5, 91058 Erlangen, Germany
| | - Afshan Ismat
- Department of Biology, University of St. Thomas, Saint Paul, MN 55105, USA
| | - Ingolf Reim
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Department of Biology, Division of Developmental Biology, Staudtstrasse 5, 91058 Erlangen, Germany
| | - Jasmin Raufer
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Department of Biology, Division of Developmental Biology, Staudtstrasse 5, 91058 Erlangen, Germany
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Zhao X, Wang Z, Tang Z, Hu J, Zhou Y, Ge J, Dong J, Xu S. An anoikis-related gene signature for prediction of the prognosis in prostate cancer. Front Oncol 2023; 13:1169425. [PMID: 37664042 PMCID: PMC10469923 DOI: 10.3389/fonc.2023.1169425] [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: 02/19/2023] [Accepted: 06/21/2023] [Indexed: 09/05/2023] Open
Abstract
Purpose This study presents a novel approach to predict postoperative biochemical recurrence (BCR) in prostate cancer (PCa) patients which involves constructing a signature based on anoikis-related genes (ARGs). Methods In this study, we utilised data from TCGA-PARD and GEO databases to identify specific ARGs in prostate cancer. We established a signature of these ARGs using Cox regression analysis and evaluated their clinical predictive efficacy and immune-related status through various methods such as Kaplan-Meier survival analysis, subject work characteristics analysis, and CIBERSORT method. Our findings suggest that these ARGs may have potential as biomarkers for prostate cancer prognosis and treatment. To investigate the biological pathways of genes associated with anoikis, we utilised GSVA, GO, and KEGG. The expression of ARGs was confirmed by the HPA database. Furthermore, we conducted PPI analysis to identify the core network of ARGs in PCa. Results Based on analysis of the TCGA database, a set of eight ARGs were identified as prognostic signature genes for prostate cancer. The reliability and validity of this signature were well verified in both the TCGA and GEO codifications. Using this signature, patients were classified into two groups based on their risk for developing BCR. There was a significant difference in BCR-free time between the high and low risk groups (P < 0.05).This signature serves as a dependable and unbiased prognostic factor for predicting biochemical recurrence (BCR) in prostate cancer (PCa) patients. It outperforms clinicopathological characteristics in terms of accuracy and reliability. PLK1 may play a potential regulatory role as a core gene in the development of prostate cancer. Conclusion This signature suggests the potential role of ARGs in the development and progression of PCa and can effectively predict the risk of BCR in PCa patients after surgery. It also provides a basis for further research into the mechanism of ARGs in PCa and for the clinical management of patients with PCa.
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Affiliation(s)
- Xiaodong Zhao
- Jinling School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Urology, Eastern Theater General Hospital of Medical School Of Nan Jing University, Nanjing, Jiangsu, China
| | - Zuheng Wang
- Jinling School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Urology, Eastern Theater General Hospital of Medical School Of Nan Jing University, Nanjing, Jiangsu, China
| | - Zilu Tang
- Jinling School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Urology, Eastern Theater General Hospital of Medical School Of Nan Jing University, Nanjing, Jiangsu, China
| | - Jun Hu
- Jinling School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Urology, Eastern Theater General Hospital of Medical School Of Nan Jing University, Nanjing, Jiangsu, China
| | - Yulin Zhou
- Department of Urology, Eastern Theater General Hospital of Medical School Of Nan Jing University, Nanjing, Jiangsu, China
| | - Jingping Ge
- Department of Urology, Eastern Theater General Hospital of Medical School Of Nan Jing University, Nanjing, Jiangsu, China
| | - Jie Dong
- Department of Urology, Eastern Theater General Hospital of Medical School Of Nan Jing University, Nanjing, Jiangsu, China
| | - Song Xu
- Jinling School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Urology, Eastern Theater General Hospital of Medical School Of Nan Jing University, Nanjing, Jiangsu, China
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Chen J, Sun M, Chen C, Kang M, Qian B, Sun J, Ma X, Zhou J, Huang L, Jiang B, Fang Y. Construction of a novel anoikis-related prognostic model and analysis of its correlation with infiltration of immune cells in neuroblastoma. Front Immunol 2023; 14:1135617. [PMID: 37081871 PMCID: PMC10111050 DOI: 10.3389/fimmu.2023.1135617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 03/23/2023] [Indexed: 04/22/2023] Open
Abstract
Background Anoikis resistance (AR) plays an important role in the process of metastasis, which is an important factor affecting the risk stage of neuroblastoma (NB). This study aims to construct an anoikis-related prognostic model and analyze the characteristics of hub genes, important pathways and tumor microenvironment of anoikis-related subtypes of NB, so as to provide help for the clinical diagnosis, treatment and research of NB. Methods We combined transcriptome data of GSE49710 and E-MTAB-8248, screened anoikis-related genes (Args) closely related to the prognosis of NB by univariate cox regression analysis, and divided the samples into anoikis-related subtypes by consistent cluster analysis. WGCNA was used to screen hub genes, GSVA and GSEA were used to analyze the differentially enriched pathways between anoikis-related subtypes. We analyzed the infiltration levels of immune cells between different groups by SsGSEA and CIBERSORT. Lasso and multivariate regression analyses were used to construct a prognostic model. Finally, we analyzed drug sensitivity through the GDSC database. Results 721 cases and 283 Args were included in this study. All samples were grouped into two subtypes with different prognoses. The analyses of WGCNA, GSVA and GSEA suggested the existence of differentially expressed hub genes and important pathways in the two subtypes. We further constructed an anoikis-related prognostic model, in which 15 Args participated. This model had more advantages in evaluating the prognoses of NB than other commonly used clinical indicators. The infiltration levels of 9 immune cells were significantly different between different risk groups, and 13 Args involved in the model construction were correlated with the infiltration levels of immune cells. There was a relationship between the infiltration levels of 6 immune cells and riskscores. Finally, we screened 15 drugs with more obvious effects on NB in high-risk group. Conclusion There are two anoikis-related subtypes with different prognoses in the population of NB. The anoikis-related prognostic model constructed in this study can accurately predict the prognoses of children with NB, and has a good guiding significance for clinical diagnosis, treatment and research of NB.
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Affiliation(s)
- Ji Chen
- Department of General Surgery, Children’s Hospital of Nanjing Medical University, Nanjing, China
| | - Mengjiao Sun
- Department of Hematology and Oncology, Children’s Hospital of Nanjing Medical University, Nanjing, China
| | - Chuqin Chen
- Department of Hematology and Oncology, Children’s Hospital of Nanjing Medical University, Nanjing, China
| | - Meiyun Kang
- Department of Hematology and Oncology, Children’s Hospital of Nanjing Medical University, Nanjing, China
| | - Bo Qian
- Department of Cardiothoracic Surgery, Children’s Hospital of Nanjing Medical University, Nanjing, China
| | - Jing Sun
- Department of Hematology and Oncology, Children’s Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaopeng Ma
- Department of Hematology and Oncology, Children’s Hospital of Nanjing Medical University, Nanjing, China
| | - Jianfeng Zhou
- Department of General Surgery, Children’s Hospital of Nanjing Medical University, Nanjing, China
| | - Lei Huang
- Department of General Surgery, Children’s Hospital of Nanjing Medical University, Nanjing, China
- *Correspondence: Lei Huang, ; Bin Jiang, ; Yongjun Fang,
| | - Bin Jiang
- Department of General Surgery, Children’s Hospital of Nanjing Medical University, Nanjing, China
- *Correspondence: Lei Huang, ; Bin Jiang, ; Yongjun Fang,
| | - Yongjun Fang
- Department of Hematology and Oncology, Children’s Hospital of Nanjing Medical University, Nanjing, China
- *Correspondence: Lei Huang, ; Bin Jiang, ; Yongjun Fang,
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