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Sabharwal V, Boyanapalli SPP, Shee A, Nonet ML, Nandi A, Chaudhuri D, Koushika SP. F-box protein FBXB-65 regulates anterograde transport of the kinesin-3 motor UNC-104 through a PTM near its cargo-binding PH domain. J Cell Sci 2024; 137:jcs261553. [PMID: 38477340 PMCID: PMC11058344 DOI: 10.1242/jcs.261553] [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: 08/15/2023] [Accepted: 03/06/2024] [Indexed: 03/14/2024] Open
Abstract
Axonal transport in neurons is essential for cargo movement between the cell body and synapses. Caenorhabditis elegans UNC-104 and its homolog KIF1A are kinesin-3 motors that anterogradely transport precursors of synaptic vesicles (pre-SVs) and are degraded at synapses. However, in C. elegans, touch neuron-specific knockdown of the E1 ubiquitin-activating enzyme, uba-1, leads to UNC-104 accumulation at neuronal ends and synapses. Here, we performed an RNAi screen and identified that depletion of fbxb-65, which encodes an F-box protein, leads to UNC-104 accumulation at neuronal distal ends, and alters UNC-104 net anterograde movement and levels of UNC-104 on cargo without changing synaptic UNC-104 levels. Split fluorescence reconstitution showed that UNC-104 and FBXB-65 interact throughout the neuron. Our theoretical model suggests that UNC-104 might exhibit cooperative cargo binding that is regulated by FBXB-65. FBXB-65 regulates an unidentified post-translational modification (PTM) of UNC-104 in a region beside the cargo-binding PH domain. Both fbxb-65 and UNC-104, independently of FBXB-65, regulate axonal pre-SV distribution, transport of pre-SVs at branch points and organismal lifespan. FBXB-65 regulates a PTM of UNC-104 and the number of motors on the cargo surface, which can fine-tune cargo transport to the synapse.
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Affiliation(s)
- Vidur Sabharwal
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | | | - Amir Shee
- Institute of Physics, Sachivalaya Marg, Bhubaneswar 751005, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
- Northwestern Institute on Complex Systems and ESAM, Northwestern University, Evanston, IL 60208, USA
| | - Michael L Nonet
- Department of Neuroscience, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Amitabha Nandi
- Department of Physics, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Debasish Chaudhuri
- Institute of Physics, Sachivalaya Marg, Bhubaneswar 751005, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
| | - Sandhya P Koushika
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
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Nagel S, Scherr M, MacLeod RAF, Pommerenke C, Koeppel M, Meyer C, Kaufmann M, Dallmann I, Drexler HG. NKL homeobox gene activities in normal and malignant myeloid cells. PLoS One 2019; 14:e0226212. [PMID: 31825998 PMCID: PMC6905564 DOI: 10.1371/journal.pone.0226212] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/21/2019] [Indexed: 12/30/2022] Open
Abstract
Recently, we have documented a hematopoietic NKL-code mapping physiological expression patterns of NKL homeobox genes in early hematopoiesis and in lymphopoiesis, which spotlights genes deregulated in lymphoid malignancies. Here, we enlarge this map to include normal NKL homeobox gene expressions in myelopoiesis by analyzing public expression profiling data and primary samples from developing and mature myeloid cells. We thus uncovered differential activities of six NKL homeobox genes, namely DLX2, HHEX, HLX, HMX1, NKX3-1 and VENTX. We further examined public expression profiling data of 251 acute myeloid leukemia (AML) and 183 myelodysplastic syndrome (MDS) patients, thereby identifying 24 deregulated genes. These results revealed frequent deregulation of NKL homeobox genes in myeloid malignancies. For detailed analysis we focused on NKL homeobox gene NANOG, which acts as a stem cell factor and is correspondingly expressed alone in hematopoietic progenitor cells. We detected aberrant expression of NANOG in a small subset of AML patients and in AML cell line NOMO-1, which served as a model. Karyotyping and genomic profiling discounted rearrangements of the NANOG locus at 12p13. But gene expression analyses of AML patients and AML cell lines after knockdown and overexpression of NANOG revealed regulators and target genes. Accordingly, NKL homeobox genes HHEX, DLX5 and DLX6, stem cell factors STAT3 and TET2, and the NOTCH-pathway were located upstream of NANOG while NKL homeobox genes HLX and VENTX, transcription factors KLF4 and MYB, and anti-apoptosis-factor MIR17HG represented target genes. In conclusion, we have extended the NKL-code to the myeloid lineage and thus identified several NKL homeobox genes deregulated in AML and MDS. These data indicate a common oncogenic role of NKL homeobox genes in both lymphoid and myeloid malignancies. For misexpressed NANOG we identified an aberrant regulatory network, which contributes to the understanding of the oncogenic activity of NKL homeobox genes.
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Affiliation(s)
- Stefan Nagel
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- * E-mail:
| | - Michaela Scherr
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Roderick A. F. MacLeod
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Claudia Pommerenke
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Max Koeppel
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Corinna Meyer
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Maren Kaufmann
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Iris Dallmann
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Hans G. Drexler
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Abdi K, Lai CH, Paez-Gonzalez P, Lay M, Pyun J, Kuo CT. Uncovering inherent cellular plasticity of multiciliated ependyma leading to ventricular wall transformation and hydrocephalus. Nat Commun 2018; 9:1655. [PMID: 29695808 PMCID: PMC5916891 DOI: 10.1038/s41467-018-03812-w] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Accepted: 03/14/2018] [Indexed: 12/26/2022] Open
Abstract
Specialized, differentiated cells often perform unique tasks that require them to maintain a stable phenotype. Multiciliated ependymal cells (ECs) are unique glial cells lining the brain ventricles, important for cerebral spinal fluid circulation. While functional ECs are needed to prevent hydrocephalus, they have also been reported to generate new neurons: whether ECs represent a stable cellular population remains unclear. Via a chemical screen we found that mature ECs are inherently plastic, with their multiciliated state needing constant maintenance by the Foxj1 transcription factor, which paradoxically is rapidly turned over by the ubiquitin-proteasome system leading to cellular de-differentiation. Mechanistic analyses revealed a novel NF-κB-independent IKK2 activity stabilizing Foxj1 in mature ECs, and we found that known IKK2 inhibitors including viruses and growth factors robustly induced Foxj1 degradation, EC de-differentiation, and hydrocephalus. Although mature ECs upon de-differentiation can divide and regenerate multiciliated ECs, we did not detect evidence supporting EC’s neurogenic potential. Multiciliated ependymal cells (ECs) in the mammalian brain are glial cells facilitating cerebral spinal fluid movement. This study describes an inherent cellular plasticity of ECs as maintained by Foxj1 and IKK2 signaling, and shows resulting hydrocephalus when EC de-differentiation is triggered.
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Affiliation(s)
- Khadar Abdi
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Chun-Hsiang Lai
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, 27710, USA
| | | | - Mark Lay
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Joon Pyun
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Chay T Kuo
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, 27710, USA. .,Department of Neurobiology, Duke University School of Medicine, Durham, NC, 27710, USA. .,Preston Robert Tisch Brain Tumor Center, Duke University School of Medicine, Durham, NC, 27710, USA. .,Brumley Neonatal/Perinatal Research Institute, Duke University School of Medicine, Durham, NC, 27710, USA. .,Institute for Brain Sciences, Duke University School of Medicine, Durham, NC, 27710, USA.
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Nagel S, Pommerenke C, Meyer C, Kaufmann M, MacLeod RAF, Drexler HG. Identification of a tumor suppressor network in T-cell leukemia. Leuk Lymphoma 2017; 58:2196–2207. [PMID: 28142295 DOI: 10.1080/10428194.2017.1283029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
To identify novel cancer-related genes targeted by copy number alterations, we performed genomic profiling of T-cell acute lymphoblastic leukemia (T-ALL) cell lines. In 3/8, we identified a shared deletion at chromosomal position 2p16.3-p21. Within the minimally deleted region, we recognized several candidate tumor suppressor (TS) genes, including FBXO11 and FOXN2. An additional deletion at chromosome 14q23.2-q32.11 included FOXN3, highlighting this class of FOX genes as potential TS. Quantitative expression analyses of FBXO11, FOXN2, and FOXN3 confirmed reduced transcript levels in the identified cell lines. Moreover, reduced expression of these genes was also observed in about 7% of T-ALL patients, showing their clinical relevance in this malignancy. Bioinformatic analyses revealed concurrent reduction of FOXN2 and/or FOXN3 together with homeobox gene ZHX1. Consistently, experiments demonstrated that both FOXN2 and FOXN3 directly activated transcription of ZHX1. Taken together, we identified novel TS genes forming a regulatory network in T-cell development and leukemogenesis.
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Affiliation(s)
- Stefan Nagel
- a Department of Human and Animal Cell Lines , Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures , Braunschweig , Germany
| | - Claudia Pommerenke
- a Department of Human and Animal Cell Lines , Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures , Braunschweig , Germany
| | - Corinna Meyer
- a Department of Human and Animal Cell Lines , Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures , Braunschweig , Germany
| | - Maren Kaufmann
- a Department of Human and Animal Cell Lines , Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures , Braunschweig , Germany
| | - Roderick A F MacLeod
- a Department of Human and Animal Cell Lines , Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures , Braunschweig , Germany
| | - Hans G Drexler
- a Department of Human and Animal Cell Lines , Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures , Braunschweig , Germany
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Sang Y, Yan F, Ren X. The role and mechanism of CRL4 E3 ubiquitin ligase in cancer and its potential therapy implications. Oncotarget 2016; 6:42590-602. [PMID: 26460955 PMCID: PMC4767455 DOI: 10.18632/oncotarget.6052] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 09/23/2015] [Indexed: 12/21/2022] Open
Abstract
CRLs (Cullin-RING E3 ubiquitin ligases) are the largest E3 ligase family in eukaryotes, which ubiquitinate a wide range of substrates involved in cell cycle regulation, signal transduction, transcriptional regulation, DNA damage response, genomic integrity, tumor suppression and embryonic development. CRL4 E3 ubiquitin ligase, as one member of CRLs family, consists of a RING finger domain protein, cullin4 (CUL4) scaffold protein and DDB1–CUL4 associated substrate receptors. The CUL4 subfamily includes two members, CUL4A and CUL4B, which share extensively sequence identity and functional redundancy. Aberrant expression of CUL4 has been found in a majority of tumors. Given the significance of CUL4 in cancer, understanding its detailed aspects of pathogenesis of human malignancy would have significant value for the treatment of cancer. Here, the work provides an overview to address the role of CRL4 E3 ubiquitin ligase in cancer development and progression, and discuss the possible mechanisms of CRL4 ligase involving in many cellular processes associated with tumor. Finally, we discuss its potential value in cancer therapy.
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Affiliation(s)
- Youzhou Sang
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,National Clinical Research Center of Cancer, Tianjin, China.,Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
| | - Fan Yan
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,National Clinical Research Center of Cancer, Tianjin, China.,Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
| | - Xiubao Ren
- Department of Biotherapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,National Clinical Research Center of Cancer, Tianjin, China.,Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
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Randle SJ, Laman H. F-box protein interactions with the hallmark pathways in cancer. Semin Cancer Biol 2015; 36:3-17. [PMID: 26416465 DOI: 10.1016/j.semcancer.2015.09.013] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 09/18/2015] [Accepted: 09/23/2015] [Indexed: 12/24/2022]
Abstract
F-box proteins (FBP) are the substrate specifying subunit of Skp1-Cul1-FBP (SCF)-type E3 ubiquitin ligases and are responsible for directing the ubiquitination of numerous proteins essential for cellular function. Due to their ability to regulate the expression and activity of oncogenes and tumour suppressor genes, FBPs themselves play important roles in cancer development and progression. In this review, we provide a comprehensive overview of FBPs and their targets in relation to their interaction with the hallmarks of cancer cell biology, including the regulation of proliferation, epigenetics, migration and invasion, metabolism, angiogenesis, cell death and DNA damage responses. Each cancer hallmark is revealed to have multiple FBPs which converge on common signalling hubs or response pathways. We also highlight the complex regulatory interplay between SCF-type ligases and other ubiquitin ligases. We suggest six highly interconnected FBPs affecting multiple cancer hallmarks, which may prove sensible candidates for therapeutic intervention.
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Affiliation(s)
- Suzanne J Randle
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, United Kingdom
| | - Heike Laman
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, United Kingdom.
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Abstract
F-box proteins, which are the substrate-recognition subunits of SKP1-cullin 1-F-box protein (SCF) E3 ligase complexes, have pivotal roles in multiple cellular processes through ubiquitylation and subsequent degradation of target proteins. Dysregulation of F-box protein-mediated proteolysis leads to human malignancies. Notably, inhibitors that target F-box proteins have shown promising therapeutic potential, urging us to review the current understanding of how F-box proteins contribute to tumorigenesis. As the physiological functions for many of the 69 putative F-box proteins remain elusive, additional genetic and mechanistic studies will help to define the role of each F-box protein in tumorigenesis, thereby paving the road for the rational design of F-box protein-targeted anticancer therapies.
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Affiliation(s)
- Zhiwei Wang
- 1] Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA. [2] The Cyrus Tang Hematology Center, Jiangsu Institute of Hematology, the First Affiliated Hospital, Soochow University, Suzhou 215123, P. R. China. [3]
| | - Pengda Liu
- 1] Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA. [2]
| | - Hiroyuki Inuzuka
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
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Kasper LH, Fukuyama T, Lerach S, Chang Y, Xu W, Wu S, Boyd KL, Brindle PK. Genetic interaction between mutations in c-Myb and the KIX domains of CBP and p300 affects multiple blood cell lineages and influences both gene activation and repression. PLoS One 2013; 8:e82684. [PMID: 24340053 PMCID: PMC3858336 DOI: 10.1371/journal.pone.0082684] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 10/28/2013] [Indexed: 02/06/2023] Open
Abstract
Adult blood cell production or definitive hematopoiesis requires the transcription factor c-Myb. The closely related KAT3 histone acetyltransferases CBP (CREBBP) and p300 (EP300) bind c-Myb through their KIX domains and mice homozygous for a p300 KIX domain mutation exhibit multiple blood defects. Perplexingly, mice homozygous for the same KIX domain mutation in CBP have normal blood. Here we test the hypothesis that the CBP KIX domain contributes subordinately to hematopoiesis via a genetic interaction with c-Myb. We assessed hematopoiesis in mice bearing compound mutations of c-Myb and/or the KIX domains of CBP and p300, and measured the effect of KIX domain mutations on c-Myb-dependent gene expression. We found that in the context of a p300 KIX mutation, the CBP KIX domain mutation affects platelets, B cells, T cells, and red cells. Gene interaction (epistasis) analysis provides mechanistic evidence that blood defects in KIX mutant mice are consistent with reduced c-Myb and KIX interaction. Lastly, we demonstrated that the CBP and p300 KIX domains contribute to both c-Myb-dependent gene activation and repression. Together these results suggest that the KIX domains of CBP, and especially p300, are principal mediators of c-Myb-dependent gene activation and repression that is required for definitive hematopoiesis.
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Affiliation(s)
- Lawryn H. Kasper
- Department of Biochemistry, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Tomofusa Fukuyama
- Department of Biochemistry, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Stephanie Lerach
- Department of Biochemistry, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Yunchao Chang
- Department of Biochemistry, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Wu Xu
- Department of Biochemistry, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Song Wu
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Kelli L. Boyd
- Veterinary Pathology Core, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Paul K. Brindle
- Department of Biochemistry, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
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CRL4A-FBXW5-mediated degradation of DLC1 Rho GTPase-activating protein tumor suppressor promotes non-small cell lung cancer cell growth. Proc Natl Acad Sci U S A 2013; 110:16868-73. [PMID: 24082123 DOI: 10.1073/pnas.1306358110] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
DLC1 encodes a RhoA GTPase-activating protein and tumor suppressor lost in cancer by genomic deletion or epigenetic silencing and loss of DLC1 gene transcription. We unexpectedly identified non-small cell lung cancer (NSCLC) cell lines and tumor tissue that expressed DLC1 mRNA yet lacked DLC1 protein expression. We determined that DLC1 was ubiquitinated and degraded by cullin 4A-RING ubiquitin ligase (CRL4A) complex interaction with DDB1 and the FBXW5 substrate receptor. siRNA-mediated suppression of cullin 4A, DDB1, or FBXW5 expression restored DLC1 protein expression in NSCLC cell lines. FBXW5 suppression-induced DLC1 reexpression was associated with a reduction in the levels of activated RhoA-GTP and in RhoA effector signaling. Finally, FBXW5 suppression caused a DLC1-dependent decrease in NSCLC anchorage-dependent and -independent proliferation. In summary, we identify a posttranslational mechanism for loss of DLC1 and a linkage between CRL4A-FBXW5-associated oncogenesis and regulation of RhoA signaling.
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