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Zhang T, Li C, Deng J, Jia Y, Qu L, Ning Z. Chicken Hypothalamic and Ovarian DNA Methylome Alteration in Response to Forced Molting. Animals (Basel) 2023; 13:ani13061012. [PMID: 36978553 PMCID: PMC10044502 DOI: 10.3390/ani13061012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/12/2023] [Accepted: 03/03/2023] [Indexed: 03/18/2023] Open
Abstract
Epigenetic modifications play an important role in regulating animal adaptation to external stress. To explore how DNA methylation regulates the expression levels of related genes during forced molting (FM) of laying hens, the hypothalamus and ovary tissues were analyzed at five periods using Whole-Genome Bisulfite Sequencing. The results show that methylation levels fluctuated differently in the exon, intron, 5′UTR, 3′UTR, promoter, and intergenic regions of the genome during FM. In addition, 16 differentially methylated genes (DMGs) regulating cell aging, immunity, and development were identified in the two reversible processes of starvation and redevelopment during FM. Comparing DMGs with differentially expressed genes (DEGs) obtained in the same periods, five hypermethylated DMGs (DSTYK, NKTR, SMOC1, SCAMP3, and ATOH8) that inhibited the expression of DEGs were found. Therefore, DMGs epigenetically modify the DEGs during the FM process of chickens, leading to the rapid closure and restart of their reproductive function and a re-increase in the egg-laying rate. Therefore, this study further confirmed that epigenetic modifications could regulate gene expression during FM and provides theoretical support for the subsequent optimization of FM technology.
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Affiliation(s)
- Tongyu Zhang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Chengfeng Li
- Hubei Shendan Healthy Food Co., Ltd., Xiaogan 432600, China
| | - Jianwen Deng
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yaxiong Jia
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100091, China
| | - Lujiang Qu
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- State Key Laboratory of Animal Nutrition, Beijing 100193, China
| | - Zhonghua Ning
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- State Key Laboratory of Animal Nutrition, Beijing 100193, China
- Correspondence:
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Guo G, Gong K, Beckley N, Zhang Y, Yang X, Chkheidze R, Hatanpaa KJ, Garzon-Muvdi T, Koduru P, Nayab A, Jenks J, Sathe AA, Liu Y, Xing C, Wu SY, Chiang CM, Mukherjee B, Burma S, Wohlfeld B, Patel T, Mickey B, Abdullah K, Youssef M, Pan E, Gerber DE, Tian S, Sarkaria JN, McBrayer SK, Zhao D, Habib AA. EGFR ligand shifts the role of EGFR from oncogene to tumour suppressor in EGFR-amplified glioblastoma by suppressing invasion through BIN3 upregulation. Nat Cell Biol 2022; 24:1291-1305. [PMID: 35915159 PMCID: PMC9389625 DOI: 10.1038/s41556-022-00962-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 06/14/2022] [Indexed: 02/03/2023]
Abstract
The epidermal growth factor receptor (EGFR) is a prime oncogene that is frequently amplified in glioblastomas. Here we demonstrate a new tumour-suppressive function of EGFR in EGFR-amplified glioblastomas regulated by EGFR ligands. Constitutive EGFR signalling promotes invasion via activation of a TAB1-TAK1-NF-κB-EMP1 pathway, resulting in large tumours and decreased survival in orthotopic models. Ligand-activated EGFR promotes proliferation and surprisingly suppresses invasion by upregulating BIN3, which inhibits a DOCK7-regulated Rho GTPase pathway, resulting in small hyperproliferating non-invasive tumours and improved survival. Data from The Cancer Genome Atlas reveal that in EGFR-amplified glioblastomas, a low level of EGFR ligands confers a worse prognosis, whereas a high level of EGFR ligands confers an improved prognosis. Thus, increased EGFR ligand levels shift the role of EGFR from oncogene to tumour suppressor in EGFR-amplified glioblastomas by suppressing invasion. The tumour-suppressive function of EGFR can be activated therapeutically using tofacitinib, which suppresses invasion by increasing EGFR ligand levels and upregulating BIN3.
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Affiliation(s)
- Gao Guo
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ke Gong
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Hubei Province Key Laboratory of Allergy and Immunology and Department of Immunology, School of Basic Medical Sciences, Taikang Medical School, Wuhan University, Wuhan, China
| | - Nicole Beckley
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yue Zhang
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiaoyao Yang
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Rati Chkheidze
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kimmo J Hatanpaa
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Tomas Garzon-Muvdi
- Department of Neurosurgery, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Prasad Koduru
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Arifa Nayab
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jennifer Jenks
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Adwait Amod Sathe
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yan Liu
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chao Xing
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Shwu-Yuan Wu
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Pharamacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Cheng-Ming Chiang
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Pharamacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Bipasha Mukherjee
- Department of Neurosurgery, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Sandeep Burma
- Department of Neurosurgery, University of Texas Health San Antonio, San Antonio, TX, USA
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Bryan Wohlfeld
- Department of Neurosurgery, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Toral Patel
- Department of Neurosurgery, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Bruce Mickey
- Department of Neurosurgery, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kalil Abdullah
- Department of Neurosurgery, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Michael Youssef
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Edward Pan
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - David E Gerber
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Division of Hematology-Oncology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Shulan Tian
- Department of Quantitative Heath Sciences, Mayo Clinic, Rochester, MN, USA
| | - Jann N Sarkaria
- Department of Radiation Oncology, Mayo Clinic, Rochester, MN, USA
| | - Samuel K McBrayer
- Department of Pediatrics and Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Dawen Zhao
- Departments of Biomedical Engineering and Cancer Biology, Wake Forest School of Medicine, Winston Salem, NC, USA
| | - Amyn A Habib
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- VA North Texas Health Care System, Dallas, TX, USA.
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Liu S, Hu C, Luo Y, Yao K. Genome-wide DNA methylation profiles may reveal new possible epigenetic pathogenesis of sporadic congenital cataract. Epigenomics 2020; 12:771-788. [PMID: 32516005 DOI: 10.2217/epi-2019-0254] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Aim: To investigate the possible epigenetic pathogenesis of sporadic congenital cataract. Materials & methods: We conducted whole genome bisulfite sequencing on peripheral blood from sporadic binocular or monocular congenital cataract patients and cataract-free participants. Results: We found massive differentially methylated regions within the whole genomes between any two groups. Meanwhile, we identified five genes (ACTN4, ACTG1, TUBA1A, TUBA1C, TUBB4B) for the binocular and control groups and TUBA1A for the monocular and control groups as the core differentially methylated region-related genes. The proteins encoded by these core genes are involved in building cytoskeleton and intercellular junctions. Conclusion: Changes in the methylation levels of core genes may disturb the function of cytoskeleton and intercellular junctions, eventually leading to sporadic congenital cataract.
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Affiliation(s)
- Siyu Liu
- Eye Center of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310031, PR China.,Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, Zhejiang Province 310031, PR China
| | - Chenyang Hu
- Eye Center of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310031, PR China.,Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, Zhejiang Province 310031, PR China
| | - Yueqiu Luo
- Eye Center of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310031, PR China.,Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, Zhejiang Province 310031, PR China
| | - Ke Yao
- Eye Center of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310031, PR China.,Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, Zhejiang Province 310031, PR China
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Chen Y, Fan D, Zhang X, Han S, Wei X, Wang Y, Song L. MicroRNA-184 is a key molecule responsible for the transforming growth factor-β 2 -induced epithelial-mesenchymal transition in human lens epithelial-B3 cells. Clin Exp Ophthalmol 2020; 48:821-829. [PMID: 32356563 DOI: 10.1111/ceo.13774] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 04/09/2020] [Accepted: 04/16/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND TGF-β2-induced epithelial-mesenchymal transition (EMT) is an important mechanism for posterior capsule opacity (PCO) in lens epithelial cells (LECs). This study aimed to investigate if MicroRNA-184 (miR-184) plays a role in the TGF-β2-induced EMT in LECs. METHODS Human LECs (HLE-B3 cells) were used in this study. Quantitative real-time polymerase chain reaction (PCR) (qRT-PCR) was performed to analyse miR-184 expressions in HLE-B3 treated with TGF-β2 at different concentrations (0-15 ng/mL) and different time (10 ng/mL, 0-48 hours). After transfection of miR-184 mimics or miR-184 inhibitor, cells were treated with 10 ng/mL TGF-β2 for 24 hours, and the expression levels of miR-184, E-cadherin, vimentin, zinc finger E-box binding homeobox 2 (ZEB2), α-Smooth muscle actin (α-SMA), Collagen 1 and bin3 were determined by qRT-PCR and Western blot, respectively. RESULTS TGF-β2 treatment significantly downregulated E-cadherin and upregulated vimentin generally in a dose-dependent and time-dependent manner. TGF-β2 treatment significantly elevated the level of miR-184 in both dose- and time-dependent manners. In addition, transfection of miR-184 inhibitor RNA significantly attenuated TGF-β2-induced downregulation of E-cadherin as well as upregulation of vimentin, ZEB2, α-SMA and Collagen 1, whereas transfection of miR-184 mimic further enhanced the effects of TGF-β2 on the expressions of these markers. Furthermore, TGF-β2 treatment significantly downregulated bin3, and transfection of miR-184 mimic and miR-184 inhibitor significantly enhanced and attenuated the inhibition effect of TGF-β2 on bin3, respectively. CONCLUSIONS miR-184 plays a key role in the TGF-β2-induced EMT in LECs, and bin3 may be a downstream protein.
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Affiliation(s)
- Yang Chen
- Department of Ophthalmology, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, China
| | - Dongsheng Fan
- Department of Ophthalmology, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, China
| | - Xinli Zhang
- Department of Ophthalmology, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, China
| | - Shaoping Han
- Department of Ophthalmology, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, China
| | - Xiaoyue Wei
- Department of Ophthalmology, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, China
| | - Yongshu Wang
- Department of Ophthalmology, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, China
| | - Lili Song
- Department of Ophthalmology, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, China
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Chen X, Xiao Y, Guo W, Zhou M, Huang S, Mo M, Li Z, Li G, Liu H, Peng G, Wu Z, Wu Y, Yang C, Pei Z, Chen C, Xu P. Relationship between variants of 17 newly loci and Parkinson's disease in a Chinese population. Neurobiol Aging 2019; 73:230.e1-230.e4. [DOI: 10.1016/j.neurobiolaging.2018.08.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 07/26/2018] [Accepted: 08/15/2018] [Indexed: 10/28/2022]
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Cui J, Liu Y, Zhang H, Wang Y, Liu G, Zhang W, Zhang C. Low BIN3 Expression is an Independent Predictor of Unfavorable Survival in Patients With Primary Colorectal Cancer. Technol Cancer Res Treat 2017. [PMCID: PMC5762098 DOI: 10.1177/1533034617747774] [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] [Indexed: 11/24/2022] Open
Abstract
This study aimed to explore the mechanisms of bridging integrator-3 dysregulation, its prognostic value, and related signaling pathways in colorectal cancer . Bioinformatic analysis was performed based on the data from The Cancer Genome Atlas–colorectal cancer and Human Protein Atlas. Colorectal cancer cell lines, LoVo and HT29 cells, were used as in vitro cell model to assess the effect of demethylation on bridging integrator-3 expression. Results showed that bridging integrator-3 was downregulated in colorectal cancer tissues compared to normal colon and rectum tissues. Heatmap of bridging integrator-3 messenger RNA expression, exon expression, and DNA methylation indicated a negative correlation between bridging integrator-3 expression and methylation of some CpG sites within the coding sequence. Demethylation treatment significantly increased bridging integrator-3 expression in LoVo and HT29 cells. Low bridging integrator-3 messenger RNA and exon expression were associated with significantly worse overall survival (P = .015 and .013, respectively). Multivariate analysis confirmed that low bridging integrator-3 messenger RNA expression was an independent prognostic factor of unfavorable overall survival (Hazard Ratio (HR) = 1.596, 95% confidence interval: 1.024-2.486; P = .039). High bridging integrator-3 DNA methylation was also associated with significantly worse overall survival (P = .013). Kyoto Encyclopedia of Genes and Genomes analysis indicated that the genes correlated with bridging integrator-3 (absolute Pearson r ≥ 0.3, n = 121) were enriched in sphingolipid signaling pathway, natural killer cell-mediated cytotoxicity, p53 signaling pathway, and apoptosis. Based on these findings, we infer that DNA hypermethylation might be an important mechanism of suppressed bridging integrator-3 expression in colorectal cancer . Its low expression is an independent predictor of unfavorable survival in patients with primary colorectal cancer . Bridging integrator-3 might act as a tumor suppressor via modulating natural killer cell-mediated cytotoxicity, p53 signaling pathway, and apoptosis.
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Affiliation(s)
- Jifang Cui
- Department of Gastroenterology, Tianjin Union Medical Center, Tianjin, China
| | - Yandi Liu
- Department of Gastroenterology, Tianjin Union Medical Center, Tianjin, China
| | - Heng Zhang
- Medical Oncology, Tianjin Union Medical Center, Tianjin, China
| | - Yijia Wang
- Department of Pathology, Tianjin Union Medical Center, Tianjin, China
| | - Guang Liu
- Department of Pathology, Tianjin Union Medical Center, Tianjin, China
| | - Weihua Zhang
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin, China
| | - Chunze Zhang
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin, China
- Chunze Zhang, MD, No. 190, Jieyuan Road, Tianjin 300121, China.
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Hamada N, Fujimichi Y. Role of carcinogenesis related mechanisms in cataractogenesis and its implications for ionizing radiation cataractogenesis. Cancer Lett 2015; 368:262-74. [DOI: 10.1016/j.canlet.2015.02.017] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 02/09/2015] [Accepted: 02/10/2015] [Indexed: 12/20/2022]
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8
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Leguen I, Le Cam A, Montfort J, Peron S, Fautrel A. Transcriptomic Analysis of Trout Gill Ionocytes in Fresh Water and Sea Water Using Laser Capture Microdissection Combined with Microarray Analysis. PLoS One 2015; 10:e0139938. [PMID: 26439495 PMCID: PMC4595143 DOI: 10.1371/journal.pone.0139938] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 09/18/2015] [Indexed: 12/22/2022] Open
Abstract
Fish gills represent a complex organ composed of several cell types that perform multiple physiological functions. Among these cells, ionocytes are implicated in the maintenance of ion homeostasis. However, because the ionocyte represents only a small percent of whole gill tissue, its specific transcriptome can be overlooked among the numerous cell types included in the gill. The objective of this study is to better understand ionocyte functions by comparing the RNA expression of this cell type in freshwater and seawater acclimated rainbow trout. To realize this objective, ionocytes were captured from gill cryosections using laser capture microdissection after immunohistochemistry. Then, transcriptome analyses were performed on an Agilent trout oligonucleotide microarray. Gene expression analysis identified 108 unique annotated genes differentially expressed between freshwater and seawater ionocytes, with a fold change higher than 3. Most of these genes were up-regulated in freshwater cells. Interestingly, several genes implicated in ion transport, extracellular matrix and structural cellular proteins appeared up-regulated in freshwater ionocytes. Among them, several ion transporters, such as CIC2, SLC26A6, and NBC, were validated by qPCR and/or in situ hybridization. The latter technique allowed us to localize the transcripts of these ion transporters in only ionocytes and more particularly in the freshwater cells. Genes involved in metabolism and also several genes implicated in transcriptional regulation, cell signaling and the cell cycle were also enhanced in freshwater ionocytes. In conclusion, laser capture microdissection combined with microarray analysis allowed for the determination of the transcriptional signature of scarce cells in fish gills, such as ionocytes, and aided characterization of the transcriptome of these cells in freshwater and seawater acclimated trout.
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Affiliation(s)
- Isabelle Leguen
- INRA, UR1037 Fish Physiology and Genomics, Rennes, France
- * E-mail:
| | - Aurélie Le Cam
- INRA, UR1037 Fish Physiology and Genomics, Rennes, France
| | | | - Sandrine Peron
- INRA, UR1037 Fish Physiology and Genomics, Rennes, France
| | - Alain Fautrel
- INSERM UMR991, Rennes, France
- Université de Rennes 1 Plateforme H2P2, Biosit, Rennes, France
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Simionescu-Bankston A, Pichavant C, Canner JP, Apponi LH, Wang Y, Steeds C, Olthoff JT, Belanto JJ, Ervasti JM, Pavlath GK. Creatine kinase B is necessary to limit myoblast fusion during myogenesis. Am J Physiol Cell Physiol 2015; 308:C919-31. [PMID: 25810257 DOI: 10.1152/ajpcell.00029.2015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 03/19/2015] [Indexed: 11/22/2022]
Abstract
Myoblast fusion is critical for proper muscle growth and regeneration. During myoblast fusion, the localization of some molecules is spatially restricted; however, the exact reason for such localization is unknown. Creatine kinase B (CKB), which replenishes local ATP pools, localizes near the ends of cultured primary mouse myotubes. To gain insights into the function of CKB, we performed a yeast two-hybrid screen to identify CKB-interacting proteins. We identified molecules with a broad diversity of roles, including actin polymerization, intracellular protein trafficking, and alternative splicing, as well as sarcomeric components. In-depth studies of α-skeletal actin and α-cardiac actin, two predominant muscle actin isoforms, demonstrated their biochemical interaction and partial colocalization with CKB near the ends of myotubes in vitro. In contrast to other cell types, specific knockdown of CKB did not grossly affect actin polymerization in myotubes, suggesting other muscle-specific roles for CKB. Interestingly, knockdown of CKB resulted in significantly increased myoblast fusion and myotube size in vitro, whereas knockdown of creatine kinase M had no effect on these myogenic parameters. Our results suggest that localized CKB plays a key role in myotube formation by limiting myoblast fusion during myogenesis.
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Affiliation(s)
- Adriana Simionescu-Bankston
- Graduate Program in Biochemistry, Cell and Developmental Biology, Emory University School of Medicine, Atlanta, Georgia; Department of Pharmacology, Emory University School of Medicine, Atlanta, Georgia; and
| | - Christophe Pichavant
- Department of Pharmacology, Emory University School of Medicine, Atlanta, Georgia; and
| | - James P Canner
- Department of Pharmacology, Emory University School of Medicine, Atlanta, Georgia; and
| | - Luciano H Apponi
- Department of Pharmacology, Emory University School of Medicine, Atlanta, Georgia; and
| | - Yanru Wang
- Department of Pharmacology, Emory University School of Medicine, Atlanta, Georgia; and
| | - Craig Steeds
- Department of Pharmacology, Emory University School of Medicine, Atlanta, Georgia; and
| | - John T Olthoff
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota
| | - Joseph J Belanto
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota
| | - James M Ervasti
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota
| | - Grace K Pavlath
- Department of Pharmacology, Emory University School of Medicine, Atlanta, Georgia; and
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Suetsugu S, Kurisu S, Takenawa T. Dynamic shaping of cellular membranes by phospholipids and membrane-deforming proteins. Physiol Rev 2014; 94:1219-48. [PMID: 25287863 DOI: 10.1152/physrev.00040.2013] [Citation(s) in RCA: 150] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
All cellular compartments are separated from the external environment by a membrane, which consists of a lipid bilayer. Subcellular structures, including clathrin-coated pits, caveolae, filopodia, lamellipodia, podosomes, and other intracellular membrane systems, are molded into their specific submicron-scale shapes through various mechanisms. Cells construct their micro-structures on plasma membrane and execute vital functions for life, such as cell migration, cell division, endocytosis, exocytosis, and cytoskeletal regulation. The plasma membrane, rich in anionic phospholipids, utilizes the electrostatic nature of the lipids, specifically the phosphoinositides, to form interactions with cytosolic proteins. These cytosolic proteins have three modes of interaction: 1) electrostatic interaction through unstructured polycationic regions, 2) through structured phosphoinositide-specific binding domains, and 3) through structured domains that bind the membrane without specificity for particular phospholipid. Among the structured domains, there are several that have membrane-deforming activity, which is essential for the formation of concave or convex membrane curvature. These domains include the amphipathic helix, which deforms the membrane by hemi-insertion of the helix with both hydrophobic and electrostatic interactions, and/or the BAR domain superfamily, known to use their positively charged, curved structural surface to deform membranes. Below the membrane, actin filaments support the micro-structures through interactions with several BAR proteins as well as other scaffold proteins, resulting in outward and inward membrane micro-structure formation. Here, we describe the characteristics of phospholipids, and the mechanisms utilized by phosphoinositides to regulate cellular events. We then summarize the precise mechanisms underlying the construction of membrane micro-structures and their involvements in physiological and pathological processes.
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Affiliation(s)
- Shiro Suetsugu
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan; Biosignal Research Center, Kobe University, Kobe, Hyogo, Japan; and Graduate School of Medicine, Kobe University, Kobe, Hyogo, Japan
| | - Shusaku Kurisu
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan; Biosignal Research Center, Kobe University, Kobe, Hyogo, Japan; and Graduate School of Medicine, Kobe University, Kobe, Hyogo, Japan
| | - Tadaomi Takenawa
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan; Biosignal Research Center, Kobe University, Kobe, Hyogo, Japan; and Graduate School of Medicine, Kobe University, Kobe, Hyogo, Japan
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11
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Manthey AL, Terrell AM, Lachke SA, Polson SW, Duncan MK. Development of novel filtering criteria to analyze RNA-sequencing data obtained from the murine ocular lens during embryogenesis. GENOMICS DATA 2014; 2:369-374. [PMID: 25478318 PMCID: PMC4248573 DOI: 10.1016/j.gdata.2014.10.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Next-generation sequencing of the transcriptome (RNA-Seq) is a powerful method that allows for the quantitative determination of absolute gene expression, and can be used to investigate how these levels change in response to an experimental manipulation or disease condition. The sensitivity of this method allows one to analyze transcript levels of all expressed genes, including low abundance transcripts that encode important regulatory molecules, providing valuable insights into the global effects of experimental manipulations. However, this increased sensitivity can also make it challenging to ascertain which expression changes are biologically significant. Here, we describe a novel set of filtering criteria - based on biological insights and computational approaches - that were applied to prioritize genes for further study from an extensive number of differentially expressed transcripts in lenses lacking Smad interacting protein 1 (Sip1) obtained via RNA-Seq by Manthey and colleagues in Mechanisms of Development (Manthey et al., 2014). Notably, this workflow allowed an original list of over 7,100 statistically significant differentially expressed genes (DEGs) to be winnowed down to 190 DEGs that likely play a biologically significant role in Sip1 function during lens development. Focusing on genes whose expression was upregulated or downregulated in a manner opposite to what normally occurs during lens development, we identified 78 genes that appear to be strongly dependent on Sip1 function. From these data (GEO accession number GSE49949), it appears that Sip1 regulates multiple genes in the lens that are generally distinct from those regulated by Sip1 in other cellular contexts, including genes whose expression is prominent in the early head ectoderm, from which the lens differentiates. Further, the analysis criteria outlined here represent a filtering scheme that can be used to prioritize genes in future RNA-Seq investigations performed at this stage of ocular lens development.
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Affiliation(s)
- Abby L. Manthey
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Anne M. Terrell
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Salil A. Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Shawn W. Polson
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
| | - Melinda K. Duncan
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
- Corresponding author at: Melinda K. Duncan, Professor, Department of Biological Sciences, University of Delaware, Newark DE 19716.
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Bykhovskaya Y, Seldin MF, Liu Y, Ransom M, Li X, Rabinowitz YS. Independent origin of c.57 C > T mutation in MIR184 associated with inherited corneal and lens abnormalities. Ophthalmic Genet 2014; 36:95-7. [PMID: 25373792 DOI: 10.3109/13816810.2014.977491] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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13
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Simionescu-Bankston A, Leoni G, Wang Y, Pham PP, Ramalingam A, DuHadaway JB, Faundez V, Nusrat A, Prendergast GC, Pavlath GK. The N-BAR domain protein, Bin3, regulates Rac1- and Cdc42-dependent processes in myogenesis. Dev Biol 2013; 382:160-71. [PMID: 23872330 DOI: 10.1016/j.ydbio.2013.07.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 07/01/2013] [Accepted: 07/05/2013] [Indexed: 11/28/2022]
Abstract
Actin dynamics are necessary at multiple steps in the formation of multinucleated muscle cells. BAR domain proteins can regulate actin dynamics in several cell types, but have been little studied in skeletal muscle. Here, we identify novel functions for the N-BAR domain protein, Bridging integrator 3 (Bin3), during myogenesis in mice. Bin3 plays an important role in regulating myofiber size in vitro and in vivo. During early myogenesis, Bin3 promotes migration of differentiated muscle cells, where it colocalizes with F-actin in lamellipodia. In addition, Bin3 forms a complex with Rac1 and Cdc42, Rho GTPases involved in actin polymerization, which are known to be essential for myotube formation. Importantly, a Bin3-dependent pathway is a major regulator of Rac1 and Cdc42 activity in differentiated muscle cells. Overall, these data classify N-BAR domain proteins as novel regulators of actin-dependent processes in myogenesis, and further implicate BAR domain proteins in muscle growth and repair.
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Affiliation(s)
- Adriana Simionescu-Bankston
- Graduate Program in Biochemistry, Cell and Developmental Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA
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14
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Hoffmann A, Huang Y, Suetsugu-Maki R, Ringelberg CS, Tomlinson CR, Del Rio-Tsonis K, Tsonis PA. Implication of the miR-184 and miR-204 competitive RNA network in control of mouse secondary cataract. Mol Med 2012; 18:528-38. [PMID: 22270329 DOI: 10.2119/molmed.2011.00463] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Accepted: 01/17/2012] [Indexed: 11/06/2022] Open
Abstract
The high recurrence rate of secondary cataract (SC) is caused by the intrinsic differentiation activity of residual lens epithelial cells after extra-capsular lens removal. The objective of this study was to identify changes in the microRNA (miRNA) expression profile during mouse SC formation and to selectively manipulate miRNA expression for potential therapeutic intervention. To model SC, mouse cataract surgery was performed and temporal changes in the miRNA expression pattern were determined by microarray analysis. To study the potential SC counterregulative effect of miRNAs, a lens capsular bag in vitro model was used. Within the first 3 wks after cataract surgery, microarray analysis demonstrated SC-associated expression pattern changes of 55 miRNAs. Of the identified miRNAs, miR-184 and miR-204 were chosen for further investigations. Manipulation of miRNA expression by the miR-184 inhibitor (anti-miR-184) and the precursor miRNA for miR-204 (pre-miR-204) attenuated SC-associated expansion and migration of lens epithelial cells and signs of epithelial to mesenchymal transition such as α-smooth muscle actin expression. In addition, pre-miR-204 attenuated SC-associated expression of the transcription factor Meis homeobox 2 (MEIS2). Examination of miRNA target binding sites for miR-184 and miR-204 revealed an extensive range of predicted target mRNA sequences that were also a target to a complex network of other SC-associated miRNAs with possible opposing functions. The identification of the SC-specific miRNA expression pattern together with the observed in vitro attenuation of SC by anti-miR-184 and pre-miR-204 suggest that miR-184 and miR-204 play a significant role in the control of SC formation in mice that is most likely regulated by a complex competitive RNA network.
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Affiliation(s)
- Andrea Hoffmann
- Department of Biology and Center for Tissue Regeneration and Engineering, University of Dayton, Dayton, Ohio 45469-2320, USA
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15
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A cluster of cooperating tumor-suppressor gene candidates in chromosomal deletions. Proc Natl Acad Sci U S A 2012; 109:8212-7. [PMID: 22566646 DOI: 10.1073/pnas.1206062109] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The large chromosomal deletions frequently observed in cancer genomes are often thought to arise as a "two-hit" mechanism in the process of tumor-suppressor gene (TSG) inactivation. Using a murine model system of hepatocellular carcinoma (HCC) and in vivo RNAi, we test an alternative hypothesis, that such deletions can arise from selective pressure to attenuate the activity of multiple genes. By targeting the mouse orthologs of genes frequently deleted on human 8p22 and adjacent regions, which are lost in approximately half of several other major epithelial cancers, we provide evidence suggesting that multiple genes on chromosome 8p can cooperatively inhibit tumorigenesis in mice, and that their cosuppression can synergistically promote tumor growth. In addition, in human HCC patients, the combined down-regulation of functionally validated 8p TSGs is associated with poor survival, in contrast to the down-regulation of any individual gene. Our data imply that large cancer-associated deletions can produce phenotypes distinct from those arising through loss of a single TSG, and as such should be considered and studied as distinct mutational events.
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Tian L, Huang K, DuHadaway JB, Prendergast GC, Stambolian D. Genomic Profiling of miRNAs in Two Human Lens Cell Lines. Curr Eye Res 2010; 35:812-8. [DOI: 10.3109/02713683.2010.489182] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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17
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Ramalingam A, Wang X, Gabello M, Valenzano MC, Soler AP, Ko A, Morin PJ, Mullin JM. Dietary methionine restriction improves colon tight junction barrier function and alters claudin expression pattern. Am J Physiol Cell Physiol 2010; 299:C1028-35. [PMID: 20739626 DOI: 10.1152/ajpcell.00482.2009] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The beneficial effects of caloric restriction in increasing longevity and forestalling age-related diseases are well known. Dietary restriction of methionine also renders similar benefits. We recently showed in a renal epithelial cell culture system that reduction of culture medium methionine by 80% resulted in altered tight junctional (TJ) claudin composition and also improved epithelial barrier function (51). In the current study, we examined the effect of dietary restriction of methionine on TJ barrier function in rat gastrointestinal tissue to see whether this phenomenon also holds true in a tissue model and for a different epithelial cell type. After 28 days on methionine-restricted (MR) diet, rats showed small but significant reductions in the plasma and (intracellular) colonocyte levels of methionine. Colon mucosal sheets from rats on the MR diet showed increased transepithelial electrical resistance with concomitant decrease in paracellular diffusion of (14)C-D-mannitol, suggesting improved barrier function relative to rats on control diet. This improved barrier function could not be explained by changes in colon crypt length or frequency. Neither was the colonocyte mitotic index nor the apoptotic frequency altered significantly. However, TJ composition/structure was being altered by the MR diet. RT-PCR and Western blot analysis showed an increase in the abundance of claudin-3 and an apparent change in the posttranslational modification of occludin, data reinforcing a paracellular barrier alteration. Overall, our data suggest that reduction in dietary intake of methionine results in improved epithelial barrier function by inducing altered TJ protein composition.
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Reid JF, Gariboldi M, Sokolova V, Capobianco P, Lampis A, Perrone F, Signoroni S, Costa A, Leo E, Pilotti S, Pierotti MA. Integrative approach for prioritizing cancer genes in sporadic colon cancer. Genes Chromosomes Cancer 2010; 48:953-62. [PMID: 19672874 DOI: 10.1002/gcc.20697] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The current multistep carcinogenesis models of colon cancer do not fully capture the genetic heterogeneity of the disease, which is additionally complicated by the presence of passenger and driver genetic alterations. The aim of this study was to select in the context of this significant heterogeneity additional genes functionally related to colon cancer development. High-throughput copy number and gene expression data of 36 microsatellite stable sporadic colon cancers resected from patients of a single institution characterized for mutations in APC, KRAS, TP53 and loss of 18q were analyzed. Genes whose expression correlated with the underlying copy number pattern were selected, and their association with the above listed mutations and overall survival was evaluated. Gain of 20q was strongly associated with TP53 mutation, and overall survival with alterations on 7p, 8p, 13q, 18q, and 20q. An association with 18q loss and gain of 8q24 was also observed. New candidate genes with a potential role in colon cancer are PLCG1 on 20q, DBC1 on 8q21, and NDGR1 on 8p24. In addition, an unexpected pattern of loss and mutability was found in the region upstream of the KRAS gene. By integrating copy number alterations with gene expression and mutations in colon cancer associated genes, we have developed a strategy that identifies previously known molecular features and additional players in the molecular landscape of colon cancer.
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Affiliation(s)
- James F Reid
- Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori Milano, Italy
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Martínez-Climent JA, Fontan L, Fresquet V, Robles E, Ortiz M, Rubio A. Integrative oncogenomic analysis of microarray data in hematologic malignancies. Methods Mol Biol 2010; 576:231-277. [PMID: 19882266 DOI: 10.1007/978-1-59745-545-9_13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
During the last decade, gene expression microarrays and array-based comparative genomic hybridization (array-CGH) have unraveled the complexity of human tumor genomes more precisely and comprehensively than ever before. More recently, the simultaneous assessment of global changes in messenger RNA (mRNA) expression and in DNA copy number through "integrative oncogenomic" analyses has allowed researchers the access to results uncovered through the analysis of one-dimensional data sets, thus accelerating cancer gene discovery. In this chapter, we discuss the major contributions of DNA microarrays to the study of hematological malignancies, focusing on the integrative oncogenomic approaches that correlate genomic and transcriptomic data. We also present the basic aspects of these methodologies and their present and future application in clinical oncology.
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Affiliation(s)
- Jose A Martínez-Climent
- Division of Oncology, Center for Applied Medical Research, University of Navarra, Pamplona, Spain
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20
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Pyrzynska B, Pilecka I, Miaczynska M. Endocytic proteins in the regulation of nuclear signaling, transcription and tumorigenesis. Mol Oncol 2009; 3:321-38. [PMID: 19577966 DOI: 10.1016/j.molonc.2009.06.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2009] [Revised: 06/01/2009] [Accepted: 06/02/2009] [Indexed: 01/14/2023] Open
Abstract
Accumulating evidence argues that many proteins governing membrane sorting during endocytosis participate also in nuclear signaling and transcriptional regulation, mostly by modulating the activity of various nuclear factors. Some adaptors and accessory proteins acting in clathrin-mediated internalization, as well as endosomal sorting proteins can undergo nuclear translocation and affect gene expression directly, while for others the effects may be more indirect. Although it is often unclear to what extent the endocytic and nuclear functions are interrelated, several of such proteins are implicated in the regulation of cell proliferation and tumorigenesis, arguing that their dual-function nature may be of physiological importance.
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Affiliation(s)
- Beata Pyrzynska
- International Institute of Molecular and Cell Biology, Laboratory of Cell Biology, 02-109 Warsaw, Poland
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Tabarés-Seisdedos R, Rubenstein JLR. Chromosome 8p as a potential hub for developmental neuropsychiatric disorders: implications for schizophrenia, autism and cancer. Mol Psychiatry 2009; 14:563-89. [PMID: 19204725 DOI: 10.1038/mp.2009.2] [Citation(s) in RCA: 174] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Defects in genetic and developmental processes are thought to contribute susceptibility to autism and schizophrenia. Presumably, owing to etiological complexity identifying susceptibility genes and abnormalities in the development has been difficult. However, the importance of genes within chromosomal 8p region for neuropsychiatric disorders and cancer is well established. There are 484 annotated genes located on 8p; many are most likely oncogenes and tumor-suppressor genes. Molecular genetics and developmental studies have identified 21 genes in this region (ADRA1A, ARHGEF10, CHRNA2, CHRNA6, CHRNB3, DKK4, DPYSL2, EGR3, FGF17, FGF20, FGFR1, FZD3, LDL, NAT2, NEF3, NRG1, PCM1, PLAT, PPP3CC, SFRP1 and VMAT1/SLC18A1) that are most likely to contribute to neuropsychiatric disorders (schizophrenia, autism, bipolar disorder and depression), neurodegenerative disorders (Parkinson's and Alzheimer's disease) and cancer. Furthermore, at least seven nonprotein-coding RNAs (microRNAs) are located at 8p. Structural variants on 8p, such as copy number variants, microdeletions or microduplications, might also contribute to autism, schizophrenia and other human diseases including cancer. In this review, we consider the current state of evidence from cytogenetic, linkage, association, gene expression and endophenotyping studies for the role of these 8p genes in neuropsychiatric disease. We also describe how a mutation in an 8p gene (Fgf17) results in a mouse with deficits in specific components of social behavior and a reduction in its dorsomedial prefrontal cortex. We finish by discussing the biological connections of 8p with respect to neuropsychiatric disorders and cancer, despite the shortcomings of this evidence.
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Affiliation(s)
- R Tabarés-Seisdedos
- Teaching Unit of Psychiatry and Psychological Medicine, Department of Medicine, CIBER-SAM, University of Valencia, Valencia, Spain.
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Prendergast GC, Muller AJ, Ramalingam A, Chang MY. BAR the door: cancer suppression by amphiphysin-like genes. Biochim Biophys Acta Rev Cancer 2008; 1795:25-36. [PMID: 18930786 DOI: 10.1016/j.bbcan.2008.09.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2008] [Revised: 08/26/2008] [Accepted: 09/03/2008] [Indexed: 11/17/2022]
Abstract
The evolutionarily conserved amphiphysin-like genes Bin1 and Bin3 function in membrane and actin dynamics, cell polarity, and stress signaling. Recent genetic studies in mice discriminate non-essential roles in endocytic processes commonly ascribed to amphiphysins from essential roles in cancer suppression. Bin1 acts in default pathways of apoptosis and senescence that are triggered by the Myc and Raf oncogenes in primary cells, and Bin1 gene products display a 'moonlighting function' in the nucleus where a variety of other 'endocytic' proteins are also found. Together, genetic investigations in yeast, flies, and mice suggest that amphiphysin-like adapter proteins may suppress cancer by helping integrate cell polarity signals generated by actin and vesicle dynamics with central regulators of cell cycle arrest, apoptosis, and immune surveillance.
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