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Ando W, Sogabe M, Ishikawa S, Uematsu T, Furuya H, Yokomori H, Kohgo Y, Otori K, Nakano T, Endo S, Tsubochi H, Okazaki I. Matrix metalloproteinase‑1 and microRNA‑486‑5p in urinary exosomes can be used to detect early lung cancer: A preliminary report. Oncol Lett 2024; 27:127. [PMID: 38333640 PMCID: PMC10851336 DOI: 10.3892/ol.2024.14261] [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: 03/01/2023] [Accepted: 12/21/2023] [Indexed: 02/10/2024] Open
Abstract
The present study describes a novel molecular-genetic method suitable for lung cancer (LC) screening in the work-place and at community health centers. Using urinary-isolated exosomes from 35 patients with LC and 40 healthy volunteers, the expression ratio of MMP-1/CD63, and the relative expression levels of both microRNA (miRNA)-21 and miRNA-486-5p were measured. MMP-1/CD63 expression ratio was significantly higher in patients with LC than in the healthy controls {1.342 [95% confidence interval (CI): 0.890-1.974] vs. 0.600 (0.490-0.900); P<0.0001}. The relative expression of miRNA-486-5p in male healthy controls was significantly different from that in female healthy controls, whereas there was no significant difference in miRNA-21. Receiver operating characteristic curve (ROC) analysis of MMP-1/CD63 showed 92.5% sensitivity and 54.3% specificity, whereas miRNA-486-5p showed 85% sensitivity and 70.8% specificity for men, and 70.0% sensitivity and 72.7% specificity for women. The logistic regression model used to evaluate the association of LC with the combination of MMP-1/CD63 and miRNA-486-5p revealed that the area under the ROC curve was 0.954 (95% CI: 0.908-1.000), and the model had 89% sensitivity and 88% specificity after adjusting for age, sex and smoking status. These data suggested that the combined analysis of MMP-1/CD63 and miRNA-486-5p in urinary exosomes may be used to detect patients with early-stage LC in the work-place and at community health centers, although confirmational studies are warranted.
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Affiliation(s)
- Wataru Ando
- Department of Clinical Pharmacy, Center for Clinical Pharmacy and Sciences, Kitasato University School of Pharmacy, Tokyo 108-8641, Japan
| | - Masaya Sogabe
- Department of General Thoracic Surgery, Jichi Medical University Saitama Medical Center, Saitama 330-0834, Japan
- Center for Respiratory Diseases, International University of Health and Welfare Hospital, Nasu-Shiobara, Tochigi 329-2763, Japan
- Department of Chest Surgery, International University of Health and Welfare Hospital, Nasu-Shiobara, Tochigi 329-2763, Japan
| | - Shigemi Ishikawa
- Center for Respiratory Diseases, International University of Health and Welfare Hospital, Nasu-Shiobara, Tochigi 329-2763, Japan
- Department of Chest Surgery, International University of Health and Welfare Hospital, Nasu-Shiobara, Tochigi 329-2763, Japan
| | - Takayuki Uematsu
- Biomedical Laboratory, Division of Biomedical Research, Kitasato University Medical Center, Kitamoto, Saitama 364-8501, Japan
| | - Hiroyuki Furuya
- Basic Clinical Science and Public Health, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan
| | - Hiroaki Yokomori
- Department of Internal Medicine, Kitasato University Medical Center, Kitamoto, Saitama 364-8501, Japan
| | - Yutaka Kohgo
- Department of Internal Medicine, International University of Health and Welfare Hospital, Nasu-Shiobara, Tochigi 329-2763, Japan
- Department of Preventive Medicine, International University of Health and Welfare Hospital, Nasu-Shiobara, Tochigi 329-2763, Japan
| | - Katsuya Otori
- Research and Education Center for Clinical Pharmacy, Division of Clinical Pharmacy, Laboratory of Pharmacy Practice and Science 1, Kitasato University School of Pharmacy, Sagamihara, Kanagawa 252-0375, Japan
| | - Tomoyuki Nakano
- Center for Respiratory Diseases, International University of Health and Welfare Hospital, Nasu-Shiobara, Tochigi 329-2763, Japan
- Department of Chest Surgery, International University of Health and Welfare Hospital, Nasu-Shiobara, Tochigi 329-2763, Japan
| | - Shunsuke Endo
- Department of General Thoracic Surgery, Jichi Medical University Saitama Medical Center, Saitama 330-0834, Japan
| | - Hiroyoshi Tsubochi
- Department of General Thoracic Surgery, Jichi Medical University, Shimotsuke, Tochigi 329-0498, Japan
| | - Isao Okazaki
- Department of Health and Welfare, Higashi Nippon International University, Iwaki, Fukushima 970-8023, Japan
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Cowell LM, King M, West H, Broadsmith M, Genever P, Pownall ME, Isaacs HV. Regulation of gene expression downstream of a novel Fgf/Erk pathway during Xenopus development. PLoS One 2023; 18:e0286040. [PMID: 37856433 PMCID: PMC10586617 DOI: 10.1371/journal.pone.0286040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 05/08/2023] [Indexed: 10/21/2023] Open
Abstract
Activation of Map kinase/Erk signalling downstream of fibroblast growth factor (Fgf) tyrosine kinase receptors regulates gene expression required for mesoderm induction and patterning of the anteroposterior axis during Xenopus development. We have proposed that a subset of Fgf target genes are activated in the embyo in response to inhibition of a transcriptional repressor. Here we investigate the hypothesis that Cic (Capicua), which was originally identified as a transcriptional repressor negatively regulated by receptor tyrosine kinase/Erk signalling in Drosophila, is involved in regulating Fgf target gene expression in Xenopus. We characterise Xenopus Cic and show that it is widely expressed in the embryo. Fgf overexpression or ectodermal wounding, both of which potently activate Erk, reduce Cic protein levels in embryonic cells. In keeping with our hypothesis, we show that Cic knockdown and Fgf overexpression have overlapping effects on embryo development and gene expression. Transcriptomic analysis identifies a cohort of genes that are up-regulated by Fgf overexpression and Cic knockdown. We investigate two of these genes as putative targets of the proposed Fgf/Erk/Cic axis: fos and rasl11b, which encode a leucine zipper transcription factor and a ras family GTPase, respectively. We identify Cic consensus binding sites in a highly conserved region of intron 1 in the fos gene and Cic sites in the upstream regions of several other Fgf/Cic co-regulated genes, including rasl11b. We show that expression of fos and rasl11b is blocked in the early mesoderm when Fgf and Erk signalling is inhibited. In addition, we show that fos and rasl11b expression is associated with the Fgf independent activation of Erk at the site of ectodermal wounding. Our data support a role for a Fgf/Erk/Cic axis in regulating a subset of Fgf target genes during gastrulation and is suggestive that Erk signalling is involved in regulating Cic target genes at the site of ectodermal wounding.
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Affiliation(s)
- Laura M. Cowell
- Department of Biology, University of York, Heslington, York, United Kingdom
| | - Michael King
- Department of Biology, University of York, Heslington, York, United Kingdom
| | - Helena West
- Department of Biology, University of York, Heslington, York, United Kingdom
| | - Matthew Broadsmith
- Department of Biology, University of York, Heslington, York, United Kingdom
| | - Paul Genever
- Department of Biology, University of York, Heslington, York, United Kingdom
| | | | - Harry V. Isaacs
- Department of Biology, University of York, Heslington, York, United Kingdom
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3
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Thomas NJ, Luck C, Shlimon N, Ponce RK, Kosibaty Z, Okimoto RA. Mapping chromatin state and transcriptional response in CIC-DUX4 undifferentiated round cell sarcoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.11.561932. [PMID: 37873100 PMCID: PMC10592754 DOI: 10.1101/2023.10.11.561932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
CIC-DUX4 is a rare and understudied transcription factor fusion oncoprotein. CIC-DUX4 co-opts native gene targets to drive a lethal form of human sarcoma. The molecular underpinnings that lead to oncogenic reprograming and CIC-DUX4 sarcomagenesis remain largely undefined. Through an integrative ChIP and RNA-Seq analysis using patient-derived CIC-DUX4 cells, we define CIC-DUX4 mediated chromatin states and function. We show that CIC-DUX4 primarily localizes to proximal and distal cis-regulatory elements where it associates with active histone marks. Our findings nominate key signaling pathways and molecular targets that enable CIC-DUX4 to mediate tumor cell survival. Collectively, our data demonstrate how the CIC-DUX4 fusion oncoprotein impacts chromatin state and transcriptional responses to drive an oncogenic program in undifferentiated sarcoma. Significance CIC-DUX4 sarcoma is a rare and lethal sarcoma that affects children, adolescent young adults, and adults. CIC-DUX4 sarcoma is associated with rapid metastatic dissemination and relative insensitivity to chemotherapy. There are no current standard-of-care therapies for CIC-DUX4 sarcoma leading to universally poor outcomes for patients. Through a deep mechanistic understanding of how the CIC-DUX4 fusion oncoprotein reprograms chromatin state and function, we aim to improve outcomes for CIC-DUX4 patients.
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Brennan KJ, Weilert M, Krueger S, Pampari A, Liu HY, Yang AWH, Morrison JA, Hughes TR, Rushlow CA, Kundaje A, Zeitlinger J. Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation. Dev Cell 2023; 58:1898-1916.e9. [PMID: 37557175 PMCID: PMC10592203 DOI: 10.1016/j.devcel.2023.07.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 05/09/2023] [Accepted: 07/13/2023] [Indexed: 08/11/2023]
Abstract
Chromatin accessibility is integral to the process by which transcription factors (TFs) read out cis-regulatory DNA sequences, but it is difficult to differentiate between TFs that drive accessibility and those that do not. Deep learning models that learn complex sequence rules provide an unprecedented opportunity to dissect this problem. Using zygotic genome activation in Drosophila as a model, we analyzed high-resolution TF binding and chromatin accessibility data with interpretable deep learning and performed genetic validation experiments. We identify a hierarchical relationship between the pioneer TF Zelda and the TFs involved in axis patterning. Zelda consistently pioneers chromatin accessibility proportional to motif affinity, whereas patterning TFs augment chromatin accessibility in sequence contexts where they mediate enhancer activation. We conclude that chromatin accessibility occurs in two tiers: one through pioneering, which makes enhancers accessible but not necessarily active, and the second when the correct combination of TFs leads to enhancer activation.
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Affiliation(s)
- Kaelan J Brennan
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Melanie Weilert
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Sabrina Krueger
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Anusri Pampari
- Department of Computer Science, Stanford University, Palo Alto, CA 94305, USA
| | - Hsiao-Yun Liu
- Department of Biology, New York University, New York, NY 10003, USA
| | - Ally W H Yang
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Jason A Morrison
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Timothy R Hughes
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | | | - Anshul Kundaje
- Department of Computer Science, Stanford University, Palo Alto, CA 94305, USA; Department of Genetics, Stanford University, Palo Alto, CA 94305, USA
| | - Julia Zeitlinger
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Pathology & Laboratory Medicine, The University of Kansas Medical Center, Kansas City, KS 66160, USA.
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5
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Takemon Y, LeBlanc VG, Song J, Chan SY, Lee SD, Trinh DL, Ahmad ST, Brothers WR, Corbett RD, Gagliardi A, Moradian A, Cairncross JG, Yip S, Aparicio SAJR, Chan JA, Hughes CS, Morin GB, Gorski SM, Chittaranjan S, Marra MA. Multi-Omic Analysis of CIC's Functional Networks Reveals Novel Interaction Partners and a Potential Role in Mitotic Fidelity. Cancers (Basel) 2023; 15:2805. [PMID: 37345142 DOI: 10.3390/cancers15102805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 06/23/2023] Open
Abstract
CIC encodes a transcriptional repressor and MAPK signalling effector that is inactivated by loss-of-function mutations in several cancer types, consistent with a role as a tumour suppressor. Here, we used bioinformatic, genomic, and proteomic approaches to investigate CIC's interaction networks. We observed both previously identified and novel candidate interactions between CIC and SWI/SNF complex members, as well as novel interactions between CIC and cell cycle regulators and RNA processing factors. We found that CIC loss is associated with an increased frequency of mitotic defects in human cell lines and an in vivo mouse model and with dysregulated expression of mitotic regulators. We also observed aberrant splicing in CIC-deficient cell lines, predominantly at 3' and 5' untranslated regions of genes, including genes involved in MAPK signalling, DNA repair, and cell cycle regulation. Our study thus characterises the complexity of CIC's functional network and describes the effect of its loss on cell cycle regulation, mitotic integrity, and transcriptional splicing, thereby expanding our understanding of CIC's potential roles in cancer. In addition, our work exemplifies how multi-omic, network-based analyses can be used to uncover novel insights into the interconnected functions of pleiotropic genes/proteins across cellular contexts.
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Affiliation(s)
- Yuka Takemon
- Genome Science and Technology Graduate Program, University of British Columbia, Vancouver, BC V5Z 4S6, Canada
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Véronique G LeBlanc
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Jungeun Song
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Susanna Y Chan
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Stephen Dongsoo Lee
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Diane L Trinh
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Shiekh Tanveer Ahmad
- Department of Pathology & Laboratory Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB T2N 4Z6, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - William R Brothers
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Richard D Corbett
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Alessia Gagliardi
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Annie Moradian
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - J Gregory Cairncross
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB T2N 4Z6, Canada
- Department of Clinical Neurosciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Stephen Yip
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 1Z7, Canada
| | - Samuel A J R Aparicio
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 1Z7, Canada
| | - Jennifer A Chan
- Department of Pathology & Laboratory Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB T2N 4Z6, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Christopher S Hughes
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Gregg B Morin
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Sharon M Gorski
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Suganthi Chittaranjan
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
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6
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Franke K, Bal G, Li Z, Zuberbier T, Babina M. Clorfl86/RHEX Is a Negative Regulator of SCF/KIT Signaling in Human Skin Mast Cells. Cells 2023; 12:cells12091306. [PMID: 37174705 PMCID: PMC10177086 DOI: 10.3390/cells12091306] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/20/2023] [Accepted: 04/30/2023] [Indexed: 05/15/2023] Open
Abstract
Mast cells (MCs) are key effector cells in allergic and inflammatory diseases, and the SCF/KIT axis regulates most aspects of the cells' biology. Using terminally differentiated skin MCs, we recently reported on proteome-wide phosphorylation changes initiated by KIT dimerization. C1orf186/RHEX was revealed as one of the proteins to become heavily phosphorylated. Its function in MCs is undefined and only some information is available for erythroblasts. Using public databases and our own data, we now report that RHEX exhibits highly restricted expression with a clear dominance in MCs. While expression is most pronounced in mature MCs, RHEX is also abundant in immature/transformed MC cell lines (HMC-1, LAD2), suggesting early expression with further increase during differentiation. Using RHEX-selective RNA interference, we reveal that RHEX unexpectedly acts as a negative regulator of SCF-supported skin MC survival. This finding is substantiated by RHEX's interference with KIT signal transduction, whereby ERK1/2 and p38 both were more strongly activated when RHEX was attenuated. Comparing RHEX and capicua (a recently identified repressor) revealed that each protein preferentially suppresses other signaling modules elicited by KIT. Induction of immediate-early genes strictly requires ERK1/2 in SCF-triggered MCs; we now demonstrate that RHEX diminution translates to this downstream event, and thereby enhances NR4A2, JUNB, and EGR1 induction. Collectively, our study reveals RHEX as a repressor of KIT signaling and function in MCs. As an abundant and selective lineage marker, RHEX may have various roles in the lineage, and the provided framework will enable future work on its involvement in other crucial processes.
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Affiliation(s)
- Kristin Franke
- Institute of Allergology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Hindenburgdamm 30, 12203 Berlin, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology and Allergology IA, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Gürkan Bal
- Institute of Allergology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Hindenburgdamm 30, 12203 Berlin, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology and Allergology IA, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Zhuoran Li
- Institute of Allergology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Hindenburgdamm 30, 12203 Berlin, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology and Allergology IA, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Torsten Zuberbier
- Institute of Allergology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Hindenburgdamm 30, 12203 Berlin, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology and Allergology IA, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Magda Babina
- Institute of Allergology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Hindenburgdamm 30, 12203 Berlin, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology and Allergology IA, Hindenburgdamm 30, 12203 Berlin, Germany
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7
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Sievers P, Sill M, Schrimpf D, Abdullaev Z, Donson AM, Lake JA, Friedel D, Scheie D, Tynninen O, Rauramaa T, Vepsäläinen KL, Samuel D, Chapman R, Grundy RG, Pajtler KW, Tauziède-Espariat A, Métais A, Varlet P, Snuderl M, Jacques TS, Aldape K, Reuss DE, Korshunov A, Wick W, Pfister SM, von Deimling A, Sahm F, Jones DTW. Pediatric-type high-grade neuroepithelial tumors with CIC gene fusion share a common DNA methylation signature. NPJ Precis Oncol 2023; 7:30. [PMID: 36964296 PMCID: PMC10039012 DOI: 10.1038/s41698-023-00372-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 03/10/2023] [Indexed: 03/26/2023] Open
Abstract
Pediatric neoplasms in the central nervous system (CNS) show extensive clinical and molecular heterogeneity and are fundamentally different from those occurring in adults. Molecular genetic testing contributes to accurate diagnosis and enables an optimal clinical management of affected children. Here, we investigated a rare, molecularly distinct type of pediatric high-grade neuroepithelial tumor (n = 18), that was identified through unsupervised visualization of genome-wide DNA methylation array data, together with copy number profiling, targeted next-generation DNA sequencing, and RNA transcriptome sequencing. DNA and/or RNA sequencing revealed recurrent fusions involving the capicua transcriptional repressor (CIC) gene in 10/10 tumor samples analyzed, with the most common fusion being CIC::LEUTX (n = 9). In addition, a CIC::NUTM1 fusion was detected in one of the tumors. Apart from the detected fusion events, no additional oncogenic alteration was identified in these tumors. The histopathological review demonstrated a morphologically heterogeneous group of high-grade neuroepithelial tumors with positive immunostaining for markers of glial differentiation in combination with weak and focal expression of synaptophysin, CD56 and CD99. All tumors were located in the supratentorial compartment, occurred during childhood (median age 8.5 years) and typically showed early relapses. In summary, we expand the spectrum of pediatric-type tumors of the CNS by reporting a previously uncharacterized group of rare high-grade neuroepithelial tumors that share a common DNA methylation signature and recurrent gene fusions involving the transcriptional repressor CIC. Downstream functional consequences of the fusion protein CIC::LEUTX and potential therapeutic implications need to be further investigated.
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Affiliation(s)
- Philipp Sievers
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Martin Sill
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Schrimpf
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Zied Abdullaev
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Andrew M Donson
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jessica A Lake
- Center for Cancer and Blood Disorders, Children's Hospital Colorado, Aurora, CO, USA
| | - Dennis Friedel
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Scheie
- Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Olli Tynninen
- Department of Pathology, HUSLAB, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Tuomas Rauramaa
- Department of Pathology, Kuopio University Hospital, University of Kuopio, Kuopio, Finland
- Unit of Pathology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | - Kaisa L Vepsäläinen
- Department of Pediatrics, Kuopio University Hospital, University of Kuopio, Kuopio, Finland
| | - David Samuel
- Department of Hematology/Oncology, Valley Children's Hospital, Madera, CA, USA
| | - Rebecca Chapman
- Children's Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
| | - Richard G Grundy
- Children's Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
| | - Kristian W Pajtler
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany
| | - Arnault Tauziède-Espariat
- Department of Neuropathology, GHU Paris-Psychiatry and Neuroscience, Sainte-Anne Hospital, Paris, France
- Institut de Psychiatrie et Neurosciences de Paris (IPNP), UMR S1266, INSERM, IMA-BRAIN, Paris, France
| | - Alice Métais
- Department of Neuropathology, GHU Paris-Psychiatry and Neuroscience, Sainte-Anne Hospital, Paris, France
- Institut de Psychiatrie et Neurosciences de Paris (IPNP), UMR S1266, INSERM, IMA-BRAIN, Paris, France
| | - Pascale Varlet
- Department of Neuropathology, GHU Paris-Psychiatry and Neuroscience, Sainte-Anne Hospital, Paris, France
- Institut de Psychiatrie et Neurosciences de Paris (IPNP), UMR S1266, INSERM, IMA-BRAIN, Paris, France
| | - Matija Snuderl
- Department of Pathology, NYU Langone Medical Center, New York, NY, USA
| | - Thomas S Jacques
- Developmental Biology and Cancer Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
- Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - David E Reuss
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andrey Korshunov
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Wolfgang Wick
- Clinical Cooperation Unit Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felix Sahm
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
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8
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Park JW, Kilic O, Deo M, Jimenez-Cowell K, Demirdizen E, Kim H, Turcan Ş. CIC reduces xCT/SLC7A11 expression and glutamate release in glioma. Acta Neuropathol Commun 2023; 11:13. [PMID: 36647117 PMCID: PMC9843885 DOI: 10.1186/s40478-023-01507-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 01/04/2023] [Indexed: 01/18/2023] Open
Abstract
Capicua (CIC) is an important downstream molecule of RTK/RAS/MAPK pathway. The regulatory mechanism of CIC underlying tumorigenesis in oligodendroglioma, where CIC is frequently mutated, has yet to be fully elucidated. Using patient-derived glioma lines, RNA-sequencing and bioinformatic analysis of publicly available databases, we investigated how CIC loss- or gain-of-function regulates its downstream targets, cell proliferation and glutamate release. Our results indicate an increased frequency of CIC truncating mutations in oligodendroglioma during progression. In vitro, CIC modulation had a modest effect on cell proliferation in glioma lines, and no significant changes in the expression of ETV1, ETV4 and ETV5. Transcriptional repression of known CIC targets was observed in gliomas expressing non-phosphorylatable CIC variant on Ser173 which was unable to interact with 14-3-3. These data outline a mechanism by which the repressor function of CIC is inhibited by 14-3-3 in gliomas. Using transcriptional profiling, we found that genes related to glutamate release were upregulated because of CIC depletion. In addition, loss of CIC leads to increased extracellular glutamate. Consistent with this, CIC restoration in an oligodendroglioma line reduced the levels of extracellular glutamate, neuronal toxicity and xCT/SLC7A11 expression. Our findings may provide a molecular basis for the prevention of glioma-associated seizures.
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Affiliation(s)
- Jong-Whi Park
- grid.5253.10000 0001 0328 4908Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, INF 460, 69120 Heidelberg, Germany ,grid.256155.00000 0004 0647 2973Department of Life Sciences, Gachon University, Incheon, 21999 South Korea
| | - Omer Kilic
- grid.5253.10000 0001 0328 4908Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, INF 460, 69120 Heidelberg, Germany
| | - Minh Deo
- grid.5253.10000 0001 0328 4908Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, INF 460, 69120 Heidelberg, Germany
| | - Kevin Jimenez-Cowell
- grid.5253.10000 0001 0328 4908Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, INF 460, 69120 Heidelberg, Germany
| | - Engin Demirdizen
- grid.5253.10000 0001 0328 4908Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, INF 460, 69120 Heidelberg, Germany
| | - Hyunggee Kim
- grid.222754.40000 0001 0840 2678Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841 South Korea
| | - Şevin Turcan
- grid.5253.10000 0001 0328 4908Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, INF 460, 69120 Heidelberg, Germany
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9
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Park J, Park GY, Lee J, Park J, Kim S, Kim E, Park SY, Yoon JH, Lee Y. ERK phosphorylation disrupts the intramolecular interaction of capicua to promote cytoplasmic translocation of capicua and tumor growth. Front Mol Biosci 2022; 9:1030725. [PMID: 36619173 PMCID: PMC9814488 DOI: 10.3389/fmolb.2022.1030725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
Activation of receptor tyrosine kinase signaling inactivates capicua (CIC), a transcriptional repressor that functions as a tumor suppressor, via degradation and/or cytoplasmic translocation. Although CIC is known to be inactivated by phosphorylation, the mechanisms underlying the cytoplasmic translocation of CIC remain poorly understood. Therefore, we aimed to evaluate the roles of extracellular signal-regulated kinase (ERK), p90RSK, and c-SRC in the epidermal growth factor receptor (EGFR) activation-induced cytoplasmic translocation of CIC and further investigated the molecular basis for this process. We found that nuclear ERK induced the cytoplasmic translocation of CIC-S. We identified 12 serine and threonine (S/T) residues within CIC, including S173 and S301 residues that are phosphorylated by p90RSK, which contribute to the cytoplasmic translocation of CIC-S when phosphorylated. The amino-terminal (CIC-S-N) and carboxyl-terminal (CIC-S-C) regions of CIC-S were found to interact with each other to promote their nuclear localization. EGF treatment disrupted the interaction between CIC-S-N and CIC-S-C and induced their cytoplasmic translocation. Alanine substitution for the 12 S/T residues blocked the cytoplasmic translocation of CIC-S and consequently enhanced the tumor suppressor activity of CIC-S. Our study demonstrates that ERK-mediated disruption of intramolecular interaction of CIC is critical for the cytoplasmic translocation of CIC, and suggests that the nuclear retention of CIC may represent a strategy for cancer therapy.
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Affiliation(s)
- Jongmin Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, South Korea
| | - Guk-Yeol Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, South Korea
| | - Jongeun Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, South Korea
| | - Joonyoung Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, South Korea
| | - Soeun Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, South Korea
| | - Eunjeong Kim
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, South Korea
| | - Seung-Yeol Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, South Korea
| | - Jong Hyuk Yoon
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu, South Korea
| | - Yoontae Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, South Korea,Institute of Convergence Science, Yonsei University, Seoul, South Korea,*Correspondence: Yoontae Lee,
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10
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Han X, Cao X, Aguiar-Pulido V, Yang W, Karki M, Ramirez PAP, Cabrera RM, Lin YL, Wlodarczyk BJ, Shaw GM, Ross ME, Zhang C, Finnell RH, Lei Y. CIC missense variants contribute to susceptibility for spina bifida. Hum Mutat 2022; 43:2021-2032. [PMID: 36054333 PMCID: PMC9772115 DOI: 10.1002/humu.24460] [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: 11/12/2021] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 01/29/2023]
Abstract
Neural tube defects (NTDs) are congenital malformations resulting from abnormal embryonic development of the brain, spine, or spinal column. The genetic etiology of human NTDs remains poorly understood despite intensive investigation. CIC, homolog of the Capicua transcription repressor, has been reported to interact with ataxin-1 (ATXN1) and participate in the pathogenesis of spinocerebellar ataxia type 1. Our previous study demonstrated that CIC loss of function (LoF) variants contributed to the cerebral folate deficiency syndrome by downregulating folate receptor 1 (FOLR1) expression. Given the importance of folate transport in neural tube formation, we hypothesized that CIC variants could contribute to increased risk for NTDs by depressing embryonic folate concentrations. In this study, we examined CIC variants from whole-genome sequencing (WGS) data of 140 isolated spina bifida cases and identified eight missense variants of CIC gene. We tested the pathogenicity of the observed variants through multiple in vitro experiments. We determined that CIC variants decreased the FOLR1 protein level and planar cell polarity (PCP) pathway signaling in a human cell line (HeLa). In a murine cell line (NIH3T3), CIC loss of function variants downregulated PCP signaling. Taken together, this study provides evidence supporting CIC as a risk gene for human NTD.
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Affiliation(s)
- Xiao Han
- Department of Reproductive Medicine Center, Henan
Provincial People’s Hospital, People’s Hospital of Zhengzhou
University, Zhengzhou, Henan Province, People’s Republic of China
- Center for Precision Environmental Health, Department of
Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77031,
USA
| | - Xuanye Cao
- Center for Precision Environmental Health, Department of
Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77031,
USA
| | - Vanessa Aguiar-Pulido
- Center for Neurogenetics, Brain and Mind Research
Institute, Weill Cornell Medicine, New York, NY, USA
- Department of Computer Science, University of Miami, Coral
Gables, FL 33146, USA
| | - Wei Yang
- Department of Pediatrics, Stanford University School of
Medicine, Stanford, CA, USA
| | - Menuka Karki
- Center for Precision Environmental Health, Department of
Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77031,
USA
| | - Paula Andrea Pimienta Ramirez
- Center for Precision Environmental Health, Department of
Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77031,
USA
| | - Robert M. Cabrera
- Center for Precision Environmental Health, Department of
Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77031,
USA
| | - Ying Linda Lin
- Center for Precision Environmental Health, Department of
Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77031,
USA
| | - Bogdan J. Wlodarczyk
- Center for Precision Environmental Health, Department of
Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77031,
USA
| | - Gary M. Shaw
- Department of Pediatrics, Stanford University School of
Medicine, Stanford, CA, USA
| | - M. Elizabeth Ross
- Center for Neurogenetics, Brain and Mind Research
Institute, Weill Cornell Medicine, New York, NY, USA
| | - Cuilian Zhang
- Department of Reproductive Medicine Center, Henan
Provincial People’s Hospital, People’s Hospital of Zhengzhou
University, Zhengzhou, Henan Province, People’s Republic of China
| | - Richard H. Finnell
- Center for Precision Environmental Health, Department of
Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77031,
USA
- Departments of Molecular and Human Genetics and Medicine,
Baylor College of Medicine, Houston, TX 77031, USA
| | - Yunping Lei
- Center for Precision Environmental Health, Department of
Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77031,
USA
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11
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Gupta N, Song H, Wu W, Ponce RK, Lin YK, Kim JW, Small EJ, Feng FY, Huang FW, Okimoto RA. The CIC-ERF co-deletion underlies fusion-independent activation of ETS family member, ETV1, to drive prostate cancer progression. eLife 2022; 11:e77072. [PMID: 36383412 PMCID: PMC9668335 DOI: 10.7554/elife.77072] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 10/16/2022] [Indexed: 11/13/2022] Open
Abstract
Human prostate cancer can result from chromosomal rearrangements that lead to aberrant ETS gene expression. The mechanisms that lead to fusion-independent ETS factor upregulation and prostate oncogenesis remain relatively unknown. Here, we show that two neighboring transcription factors, Capicua (CIC) and ETS2 repressor factor (ERF), which are co-deleted in human prostate tumors can drive prostate oncogenesis. Concurrent CIC and ERF loss commonly occur through focal genomic deletions at chromosome 19q13.2. Mechanistically, CIC and ERF co-bind the proximal regulatory element and mutually repress the ETS transcription factor, ETV1. Targeting ETV1 in CIC and ERF-deficient prostate cancer limits tumor growth. Thus, we have uncovered a fusion-independent mode of ETS transcriptional activation defined by concurrent loss of CIC and ERF.
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Affiliation(s)
- Nehal Gupta
- Department of Medicine, University of CaliforniaSan FranciscoUnited States
| | - Hanbing Song
- Department of Medicine, University of CaliforniaSan FranciscoUnited States
| | - Wei Wu
- Department of Medicine, University of CaliforniaSan FranciscoUnited States
| | - Rovingaile K Ponce
- Department of Medicine, University of CaliforniaSan FranciscoUnited States
| | - Yone K Lin
- Department of Medicine, University of CaliforniaSan FranciscoUnited States
| | - Ji Won Kim
- Department of Medicine, University of CaliforniaSan FranciscoUnited States
| | - Eric J Small
- Department of Medicine, University of CaliforniaSan FranciscoUnited States
- Helen Diller Family Comprehensive Cancer Center, University of CaliforniaSan FranciscoUnited States
| | - Felix Y Feng
- Department of Medicine, University of CaliforniaSan FranciscoUnited States
- Helen Diller Family Comprehensive Cancer Center, University of CaliforniaSan FranciscoUnited States
- Department of Radiation Oncology, University of CaliforniaSan FranciscoUnited States
| | - Franklin W Huang
- Department of Medicine, University of CaliforniaSan FranciscoUnited States
- Helen Diller Family Comprehensive Cancer Center, University of CaliforniaSan FranciscoUnited States
| | - Ross A Okimoto
- Department of Medicine, University of CaliforniaSan FranciscoUnited States
- Helen Diller Family Comprehensive Cancer Center, University of CaliforniaSan FranciscoUnited States
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12
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Franke K, Kirchner M, Mertins P, Zuberbier T, Babina M. The SCF/KIT axis in human mast cells: Capicua acts as potent KIT repressor and ERK predominates PI3K. Allergy 2022; 77:3337-3349. [PMID: 35652819 DOI: 10.1111/all.15396] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 04/28/2022] [Accepted: 05/11/2022] [Indexed: 01/28/2023]
Abstract
BACKGROUND The SCF/KIT axis regulates nearly all aspects of mast cell (MC) biology. A comprehensive view of SCF-triggered phosphorylation dynamics is lacking. The relationship between signaling modules and SCF-supported functions likewise remains ill-defined. METHODS Mast cells were isolated from human skin; upon stimulation by SCF, global phosphoproteomic changes were analyzed by LC-MS/MS and selectively validated by immunoblotting. MC survival was inspected by YoPro; BrdU incorporation served to monitor proliferation. Gene expression was quantified by RT-qPCR and cytokines by ELISA. Pharmacological inhibitors were supplemented by ERK1 and/or ERK2 knockdown. CIC translocation and degradation were studied in nuclear and cytoplasmic fractions. CIC's impact on KIT signaling and function was assessed following RNA interference. RESULTS ≈5400 out of ≈10,500 phosphosites experienced regulation by SCF. The MEK/ERK cascade was strongly induced surpassing STAT5 > PI3K/Akt > p38 > JNK. Comparison between MEK/ERK's and PI3K's support of basic programs (apoptosis, proliferation) revealed equipotency between modules. In functional outputs (gene expression, cytokines), ERK was the most influential kinase. OSM and LIF production was identified in skin MCs. Strikingly, SCF triggered massive phosphorylation of a protein not associated with KIT previously: CIC. Phosphorylation was followed by CIC's cytoplasmic appearance and degradation, the latter sensitive to protease but not preoteasome inhibition. Both shuttling and degradation were ERK-dependent. Conversely, CIC-siRNA facilitated KIT signaling, functional outputs, and survival. CONCLUSION The SCF/KIT axis shows notable strength in MCs, and MEK/ERK as most prominent module. An inhibitory circuit exists between KIT and CIC. CIC stabilization in MCs may turn out as a therapeutic option to interfere with allergic and MC-driven diseases.
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Affiliation(s)
- Kristin Franke
- Institute of Allergology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.,Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology and Allergology IA, Berlin, Germany
| | - Marieluise Kirchner
- Core Unit Proteomics, Berlin Institute of Health at Charité- Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany
| | - Philipp Mertins
- Core Unit Proteomics, Berlin Institute of Health at Charité- Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany
| | - Torsten Zuberbier
- Institute of Allergology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.,Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology and Allergology IA, Berlin, Germany
| | - Magda Babina
- Institute of Allergology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.,Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology and Allergology IA, Berlin, Germany
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13
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Capicua suppresses YAP1 to limit tumorigenesis and maintain drug sensitivity in human cancer. Cell Rep 2022; 41:111443. [DOI: 10.1016/j.celrep.2022.111443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 07/28/2022] [Accepted: 09/09/2022] [Indexed: 11/23/2022] Open
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14
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Noncanonical function of Capicua as a growth termination signal in Drosophila oogenesis. Proc Natl Acad Sci U S A 2022; 119:e2123467119. [PMID: 35881788 PMCID: PMC9351367 DOI: 10.1073/pnas.2123467119] [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] [Indexed: 01/28/2023] Open
Abstract
Capicua (Cic) proteins are conserved HMG-box transcriptional repressors that control receptor tyrosine kinase (RTK) signaling responses and are implicated in human neurological syndromes and cancer. While Cic is known to exist as short (Cic-S) and long (Cic-L) isoforms with identical HMG-box and associated core regions but distinct N termini, most previous studies have focused on Cic-S, leaving the function of Cic-L unexplored. Here we show that Cic-L acts in two capacities during Drosophila oogenesis: 1) as a canonical sensor of RTK signaling in somatic follicle cells, and 2) as a regulator of postmitotic growth in germline nurse cells. In these latter cells, Cic-L behaves as a temporal signal that terminates endoreplicative growth before they dump their contents into the oocyte. We show that Cic-L is necessary and sufficient for nurse cell endoreplication arrest and induces both stabilization of CycE and down-regulation of Myc. Surprisingly, this function depends mainly on the Cic-L-specific N-terminal module, which is capable of acting independently of the Cic HMG-box-containing core. Mirroring these observations, basal metazoans possess truncated Cic-like proteins composed only of Cic-L N-terminal sequences, suggesting that this module plays unique, ancient roles unrelated to the canonical function of Cic.
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15
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Keenan SE, Avdeeva M, Yang L, Alber DS, Wieschaus EF, Shvartsman SY. Dynamics of Drosophila endoderm specification. Proc Natl Acad Sci U S A 2022; 119:e2112892119. [PMID: 35412853 PMCID: PMC9169638 DOI: 10.1073/pnas.2112892119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 02/06/2022] [Indexed: 11/18/2022] Open
Abstract
During early Drosophila embryogenesis, a network of gene regulatory interactions orchestrates terminal patterning, playing a critical role in the subsequent formation of the gut. We utilized CRISPR gene editing at endogenous loci to create live reporters of transcription and light-sheet microscopy to monitor the individual components of the posterior gut patterning network across 90 min prior to gastrulation. We developed a computational approach for fusing imaging datasets of the individual components into a common multivariable trajectory. Data fusion revealed low intrinsic dimensionality of posterior patterning and cell fate specification in wild-type embryos. The simple structure that we uncovered allowed us to construct a model of interactions within the posterior patterning regulatory network and make testable predictions about its dynamics at the protein level. The presented data fusion strategy is a step toward establishing a unified framework that would explore how stochastic spatiotemporal signals give rise to highly reproducible morphogenetic outcomes.
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Affiliation(s)
- Shannon E. Keenan
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08540
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540
| | - Maria Avdeeva
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010
| | - Liu Yang
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540
| | - Daniel S. Alber
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08540
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540
| | - Eric F. Wieschaus
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540
| | - Stanislav Y. Shvartsman
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540
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16
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Ponce RKM, Thomas NJ, Bui NQ, Kondo T, Okimoto RA. WEE1 kinase is a therapeutic vulnerability in CIC-DUX4 undifferentiated sarcoma. JCI Insight 2022; 7:152293. [PMID: 35315355 PMCID: PMC8986087 DOI: 10.1172/jci.insight.152293] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 02/09/2022] [Indexed: 01/08/2023] Open
Abstract
CIC-DUX4 rearrangements define an aggressive and chemotherapy-insensitive subset of undifferentiated sarcomas. The CIC-DUX4 fusion drives oncogenesis through direct transcriptional upregulation of cell cycle and DNA replication genes. Notably, CIC-DUX4–mediated CCNE1 upregulation compromises the G1/S transition to confer a dependence on the G2/M cell cycle checkpoint. Through an integrative transcriptional and kinase activity screen using patient-derived specimens, we now show that CIC-DUX4 sarcomas depend on the G2/M checkpoint regulator WEE1 as part of an adaptive survival mechanism. Specifically, CIC-DUX4 sarcomas depended on WEE1 activity to limit DNA damage and unscheduled mitotic entry. Consequently, genetic or pharmacologic WEE1 inhibition in vitro and in vivo led to rapid DNA damage–associated apoptotic induction of patient-derived CIC-DUX4 sarcomas. Thus, we identified WEE1 as a vulnerability targetable by therapeutic intervention in CIC-DUX4 sarcomas.
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Affiliation(s)
| | | | - Nam Q Bui
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Tadashi Kondo
- Division of Rare Cancer Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Ross A Okimoto
- Department of Medicine, UCSF, San Francisco, California, USA.,Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
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17
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ERK signaling dissolves ERF repression condensates in living embryos. Proc Natl Acad Sci U S A 2022; 119:2119187119. [PMID: 35217620 PMCID: PMC8892517 DOI: 10.1073/pnas.2119187119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2022] [Indexed: 12/23/2022] Open
Abstract
Phase separation underlies the organization of the nucleus, including the biogenesis of nucleoli and the packaging of heterochromatin. Here we explore the regulation of transcription factor condensates involved in gene repression by ERK signaling in gastrulating embryos of a simple proto-vertebrate (Ciona). ERK signaling induces nuclear export of the transcriptional repressor Ets-2 repressive factor (ERF), which has been linked to various human developmental disorders. Using high-resolution imaging, we show that ERF is localized within discrete nuclear condensates that dissolve upon ERK activation. Interestingly, we observe dynamic pulses of assembly and dissociation during interphase, providing visualization of a nuclear phase separation process regulated by cell signaling. We discuss the implications of these observations for producing sharp on/off switches in gene activity and suppressing noise in cell-cell signaling events.
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18
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Kogure Y, Kameda T, Koya J, Yoshimitsu M, Nosaka K, Yasunaga JI, Imaizumi Y, Watanabe M, Saito Y, Ito Y, McClure MB, Tabata M, Shingaki S, Yoshifuji K, Chiba K, Okada A, Kakiuchi N, Nannya Y, Kamiunten A, Tahira Y, Akizuki K, Sekine M, Shide K, Hidaka T, Kubuki Y, Kitanaka A, Hidaka M, Nakano N, Utsunomiya A, Sica RA, Acuna-Villaorduna A, Janakiram M, Shah U, Ramos JC, Shibata T, Takeuchi K, Takaori-Kondo A, Miyazaki Y, Matsuoka M, Ishitsuka K, Shiraishi Y, Miyano S, Ogawa S, Ye BH, Shimoda K, Kataoka K. Whole-genome landscape of adult T-cell leukemia/lymphoma. Blood 2022; 139:967-982. [PMID: 34695199 PMCID: PMC8854674 DOI: 10.1182/blood.2021013568] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 10/11/2021] [Indexed: 11/20/2022] Open
Abstract
Adult T-cell leukemia/lymphoma (ATL) is an aggressive neoplasm immunophenotypically resembling regulatory T cells, associated with human T-cell leukemia virus type-1. Here, we performed whole-genome sequencing (WGS) of 150 ATL cases to reveal the overarching landscape of genetic alterations in ATL. We discovered frequent (33%) loss-of-function alterations preferentially targeting the CIC long isoform, which were overlooked by previous exome-centric studies of various cancer types. Long but not short isoform-specific inactivation of Cic selectively increased CD4+CD25+Foxp3+ T cells in vivo. We also found recurrent (13%) 3'-truncations of REL, which induce transcriptional upregulation and generate gain-of-function proteins. More importantly, REL truncations are also common in diffuse large B-cell lymphoma, especially in germinal center B-cell-like subtype (12%). In the non-coding genome, we identified recurrent mutations in regulatory elements, particularly splice sites, of several driver genes. In addition, we characterized the different mutational processes operative in clustered hypermutation sites within and outside immunoglobulin/T-cell receptor genes and identified the mutational enrichment at the binding sites of host and viral transcription factors, suggesting their activities in ATL. By combining the analyses for coding and noncoding mutations, structural variations, and copy number alterations, we discovered 56 recurrently altered driver genes, including 11 novel ones. Finally, ATL cases were classified into 2 molecular groups with distinct clinical and genetic characteristics based on the driver alteration profile. Our findings not only help to improve diagnostic and therapeutic strategies in ATL, but also provide insights into T-cell biology and have implications for genome-wide cancer driver discovery.
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Affiliation(s)
- Yasunori Kogure
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Takuro Kameda
- Division of Hematology, Diabetes, and Endocrinology, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Junji Koya
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Makoto Yoshimitsu
- Department of Hematology and Rheumatology, Kagoshima University Hospital, Kagoshima, Japan
| | - Kisato Nosaka
- Department of Hematology, Rheumatology, and Infectious Disease, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Jun-Ichirou Yasunaga
- Department of Hematology, Rheumatology, and Infectious Disease, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Yoshitaka Imaizumi
- Department of Hematology, Atomic Bomb Disease and Hibakusha Medicine Unit, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Mizuki Watanabe
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yuki Saito
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
- Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan
| | - Yuta Ito
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
- Division of Clinical Oncology and Hematology, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo, Japan
| | - Marni B McClure
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Mariko Tabata
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Sumito Shingaki
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Kota Yoshifuji
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
- Department of Hematology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kenichi Chiba
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Ai Okada
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Nobuyuki Kakiuchi
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yasuhito Nannya
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ayako Kamiunten
- Division of Hematology, Diabetes, and Endocrinology, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Yuki Tahira
- Division of Hematology, Diabetes, and Endocrinology, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Keiichi Akizuki
- Division of Hematology, Diabetes, and Endocrinology, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Masaaki Sekine
- Division of Hematology, Diabetes, and Endocrinology, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Kotaro Shide
- Division of Hematology, Diabetes, and Endocrinology, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Tomonori Hidaka
- Division of Hematology, Diabetes, and Endocrinology, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Yoko Kubuki
- Division of Hematology, Diabetes, and Endocrinology, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Akira Kitanaka
- Department of Laboratory Medicine, Kawasaki Medical School, Kurashiki, Japan
| | - Michihiro Hidaka
- Department of Hematology, National Hospital Organization Kumamoto Medical Center, Kumamoto, Japan
| | - Nobuaki Nakano
- Department of Hematology, Imamura General Hospital, Kagoshima, Japan
| | - Atae Utsunomiya
- Department of Hematology, Imamura General Hospital, Kagoshima, Japan
| | - R Alejandro Sica
- Department of Oncology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY
| | - Ana Acuna-Villaorduna
- Department of Oncology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY
| | - Murali Janakiram
- Department of Oncology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY
| | - Urvi Shah
- Department of Oncology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY
| | - Juan Carlos Ramos
- Division of Hematology/Oncology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
- Laboratory of Molecular Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kengo Takeuchi
- Division of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
- Department of Pathology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
- Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yasushi Miyazaki
- Department of Hematology, Atomic Bomb Disease and Hibakusha Medicine Unit, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Masao Matsuoka
- Department of Hematology, Rheumatology, and Infectious Disease, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Kenji Ishitsuka
- Department of Hematology and Rheumatology, Kagoshima University Hospital, Kagoshima, Japan
| | - Yuichi Shiraishi
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Satoru Miyano
- M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - B Hilda Ye
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY; and
| | - Kazuya Shimoda
- Division of Hematology, Diabetes, and Endocrinology, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Keisuke Kataoka
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
- Division of Hematology, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
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19
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CIC rearranged sarcomas: A Single Institution Experience of the Potential Pitfalls in Interpreting CIC FISH Results. Pathol Res Pract 2022; 231:153773. [DOI: 10.1016/j.prp.2022.153773] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 01/14/2022] [Accepted: 01/15/2022] [Indexed: 11/19/2022]
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20
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Kim S, Park GY, Park JS, Park J, Hong H, Lee Y. Regulation of positive and negative selection and TCR signaling during thymic T cell development by capicua. eLife 2021; 10:71769. [PMID: 34895467 PMCID: PMC8700290 DOI: 10.7554/elife.71769] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 12/10/2021] [Indexed: 12/27/2022] Open
Abstract
Central tolerance is achieved through positive and negative selection of thymocytes mediated by T cell receptor (TCR) signaling strength. Thus, dysregulation of the thymic selection process often leads to autoimmunity. Here, we show that Capicua (CIC), a transcriptional repressor that suppresses autoimmunity, controls the thymic selection process. Loss of CIC prior to T-cell lineage commitment impairs both positive and negative selection of thymocytes. CIC deficiency attenuated TCR signaling in CD4+CD8+ double-positive (DP) cells, as evidenced by a decrease in CD5 and phospho-ERK levels and calcium flux. We identified Spry4, Dusp4, Dusp6, and Spred1 as CIC target genes that could inhibit TCR signaling in DP cells. Furthermore, impaired positive selection and TCR signaling were partially rescued in Cic and Spry4 double mutant mice. Our findings indicate that CIC is a transcription factor required for thymic T cell development and suggests that CIC acts at multiple stages of T cell development and differentiation to prevent autoimmunity.
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Affiliation(s)
- Soeun Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Guk-Yeol Park
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Jong Seok Park
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Jiho Park
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Hyebeen Hong
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Yoontae Lee
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea.,Institute of Convergence Science, Yonsei University, Seoul, Republic of Korea
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21
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López-Varea A, Vega-Cuesta P, Ruiz-Gómez A, Ostalé CM, Molnar C, Hevia CF, Martín M, Organista MF, de Celis J, Culí J, Esteban N, de Celis JF. Genome-wide phenotypic RNAi screen in the Drosophila wing: phenotypic description of functional classes. G3 (BETHESDA, MD.) 2021; 11:6380434. [PMID: 34599810 PMCID: PMC8664486 DOI: 10.1093/g3journal/jkab349] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 09/23/2021] [Indexed: 01/01/2023]
Abstract
The Drosophila genome contains approximately 14,000 protein-coding genes encoding all the necessary information to sustain cellular physiology, tissue organization, organism development, and behavior. In this manuscript, we describe in some detail the phenotypes in the adult fly wing generated after knockdown of approximately 80% of Drosophila genes. We combined this phenotypic description with a comprehensive molecular classification of the Drosophila proteins into classes that summarize the main expected or known biochemical/functional aspect of each protein. This information, combined with mRNA expression levels and in situ expression patterns, provides a simplified atlas of the Drosophila genome, from housekeeping proteins to the components of the signaling pathways directing wing development, that might help to further understand the contribution of each gene group to wing formation.
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Affiliation(s)
- Ana López-Varea
- Centro de Biología Molecular "Severo Ochoa," CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Patricia Vega-Cuesta
- Centro de Biología Molecular "Severo Ochoa," CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Ana Ruiz-Gómez
- Centro de Biología Molecular "Severo Ochoa," CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Cristina M Ostalé
- Centro de Biología Molecular "Severo Ochoa," CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Cristina Molnar
- Centro de Biología Molecular "Severo Ochoa," CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain.,IRB Barcelona, Barcelona 08028, Spain
| | - Covadonga F Hevia
- Centro de Biología Molecular "Severo Ochoa," CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Mercedes Martín
- Centro de Biología Molecular "Severo Ochoa," CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Maria F Organista
- Centro de Biología Molecular "Severo Ochoa," CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Jesus de Celis
- Centro de Biología Molecular "Severo Ochoa," CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Joaquín Culí
- Centro de Biología Molecular "Severo Ochoa," CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Nuria Esteban
- Centro de Biología Molecular "Severo Ochoa," CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Jose F de Celis
- Centro de Biología Molecular "Severo Ochoa," CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
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22
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Lee SD, Song J, LeBlanc VG, Marra MA. Integrative multi-omic analysis reveals neurodevelopmental gene dysregulation in CIC-knockout and IDH1 mutant cells. J Pathol 2021; 256:297-309. [PMID: 34767259 PMCID: PMC9305137 DOI: 10.1002/path.5835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 10/22/2021] [Accepted: 11/09/2021] [Indexed: 11/18/2022]
Abstract
Capicua (CIC)'s transcriptional repressor function is implicated in neurodevelopment and in oligodendroglioma (ODG) aetiology. However, CIC's role in these contexts remains obscure, primarily from our currently limited knowledge regarding its biological functions. Moreover, CIC mutations in ODG invariably co‐occur with a neomorphic IDH1/2 mutation, yet the functional relationship between these two genetic events is unknown. Here, we analysed models derived from an E6/E7/hTERT‐immortalized (i.e. p53‐ and RB‐deficient) normal human astrocyte cell line. To examine the consequences of CIC loss, we compared transcriptomic and epigenomic profiles between CIC wild‐type and knockout cell lines, with and without mutant IDH1 expression. Our analyses revealed dysregulation of neurodevelopmental genes in association with CIC loss. CIC ChIP‐seq was also performed to expand upon the currently limited ensemble of known CIC target genes. Among the newly identified direct CIC target genes were EPHA2 and ID1, whose functions are linked to neurodevelopment and the tumourigenicity of in vivo glioma tumour models. NFIA, a known mediator of gliogenesis, was discovered to be uniquely overexpressed in CIC‐knockout cells expressing mutant IDH1‐R132H protein. These results identify neurodevelopment and specific genes within this context as candidate targets through which CIC alterations may contribute to the progression of IDH‐mutant gliomas. © 2021 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Stephen D Lee
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Jungeun Song
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | | | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
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23
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Cabral de Carvalho Corrêa D, Tesser-Gamba F, Dias Oliveira I, Saba da Silva N, Capellano AM, de Seixas Alves MT, Benevides Silva FA, Dastoli PA, Cavalheiro S, Caminada de Toledo SR. Molecular profiling of pediatric and adolescent ependymomas: identification of genetic variants using a next-generation sequencing panel. J Neurooncol 2021; 155:13-23. [PMID: 34570300 DOI: 10.1007/s11060-021-03848-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 09/15/2021] [Indexed: 10/20/2022]
Abstract
PURPOSE Ependymoma (EPN) accounts for approximately 10% of all primary central nervous system (CNS) tumors in children and in most cases, chemotherapy is ineffective and treatment remains challenging. We investigated molecular alterations, with a potential prognostic marker and therapeutic target in EPNs of childhood and adolescence, using a next-generation sequencing (NGS) panel specific for pediatric neoplasms. METHODS We selected 61 samples with initial diagnosis of EPN from patients treated at Pediatric Oncology Institute-GRAACC/UNIFESP. All samples were divided according to the anatomical compartment of the CNS - 42 posterior fossa (PF), 14 supratentorial (ST), and five spinal (SP). NGS was performed to identify somatic genetic variants in tumor samples using the Oncomine Childhood Cancer Research Assay® (OCCRA®) panel, from Thermo Fisher Scientific®. RESULTS Genetic variants were identified in 24 of 61 (39.3%) tumors and over 90% of all variants were pathogenic or likely pathogenic. The most commonly variants detected were in CIC, ASXL1, and JAK2 genes and have not been reported in EPN yet. MN1-BEND2 fusion, alteration recently described in a new CNS tumor type, was identified in one ST sample that was reclassified as astroblastoma. Additionally, YAP1-MAMLD1 fusion, a rare event associated with good outcome in ST-EPN, was observed in two patients diagnosed under 2 years old. CONCLUSIONS Molecular profiling by the OCCRA® panel showed novel alterations in pediatric and adolescent EPNs, which highlights the clinical importance in identifying genetic variants for patients' prognosis and therapeutic orientation.
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Affiliation(s)
- Débora Cabral de Carvalho Corrêa
- Department of Pediatrics, Pediatric Oncology Institute-GRAACC, Federal University of Sao Paulo, Sao Paulo, SP, Brazil.,Division of Genetics, Department of Morphology and Genetics, Federal University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Francine Tesser-Gamba
- Department of Pediatrics, Pediatric Oncology Institute-GRAACC, Federal University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Indhira Dias Oliveira
- Department of Pediatrics, Pediatric Oncology Institute-GRAACC, Federal University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Nasjla Saba da Silva
- Department of Pediatrics, Pediatric Oncology Institute-GRAACC, Federal University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Andrea Maria Capellano
- Department of Pediatrics, Pediatric Oncology Institute-GRAACC, Federal University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Maria Teresa de Seixas Alves
- Department of Pediatrics, Pediatric Oncology Institute-GRAACC, Federal University of Sao Paulo, Sao Paulo, SP, Brazil.,Department of Pathology, Federal University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Frederico Adolfo Benevides Silva
- Department of Pediatrics, Pediatric Oncology Institute-GRAACC, Federal University of Sao Paulo, Sao Paulo, SP, Brazil.,Department of Imaging Diagnosis, Federal University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Patrícia Alessandra Dastoli
- Department of Pediatrics, Pediatric Oncology Institute-GRAACC, Federal University of Sao Paulo, Sao Paulo, SP, Brazil.,Department of Neurology and Neurosurgery, Federal University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Sergio Cavalheiro
- Department of Pediatrics, Pediatric Oncology Institute-GRAACC, Federal University of Sao Paulo, Sao Paulo, SP, Brazil.,Department of Neurology and Neurosurgery, Federal University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Silvia Regina Caminada de Toledo
- Department of Pediatrics, Pediatric Oncology Institute-GRAACC, Federal University of Sao Paulo, Sao Paulo, SP, Brazil. .,Division of Genetics, Department of Morphology and Genetics, Federal University of Sao Paulo, Sao Paulo, SP, Brazil. .,Pediatric Oncology Institute-Grupo de Apoio ao Adolescente e à Criança com Câncer/Federal University of Sao Paulo (IOP-GRAACC/UNIFESP), 743 Botucatu Street, 8th Floor - Genetics Laboratory, Vila Clementino, Sao Paulo, SP, 04023-062, Brazil.
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24
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Patel AL, Zhang L, Keenan SE, Rushlow CA, Fradin C, Shvartsman SY. Capicua is a fast-acting transcriptional brake. Curr Biol 2021; 31:3639-3647.e5. [PMID: 34166605 DOI: 10.1016/j.cub.2021.05.061] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/18/2021] [Accepted: 05/27/2021] [Indexed: 10/21/2022]
Abstract
Even though transcriptional repressors are studied with ever-increasing molecular resolution, the temporal aspects of gene repression remain poorly understood. Here, we address the dynamics of transcriptional repression by Capicua (Cic), which is essential for normal development and is commonly mutated in human cancers and neurodegenerative diseases.1,2 We report the speed limit for Cic-dependent gene repression based on live imaging and optogenetic perturbations in the early Drosophila embryo, where Cic was originally discovered.3 Our measurements of Cic concentration and intranuclear mobility, along with real-time monitoring of the activity of Cic target genes, reveal remarkably fast transcriptional repression within minutes of removing an optogenetic de-repressive signal. In parallel, quantitative analyses of transcriptional bursting of Cic target genes support a repression mechanism providing a fast-acting brake on burst generation. This work sets quantitative constraints on potential mechanisms for gene regulation by Cic.
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Affiliation(s)
- Aleena L Patel
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08540, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA
| | - Lili Zhang
- Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Shannon E Keenan
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08540, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA
| | | | - Cécile Fradin
- Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4K1, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada.
| | - Stanislav Y Shvartsman
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA; Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA.
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25
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Ong SLM, Szuhai K, Bovée JVMG. Gene fusions in vascular tumors and their underlying molecular mechanisms. Expert Rev Mol Diagn 2021; 21:897-909. [PMID: 34225547 DOI: 10.1080/14737159.2021.1950533] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
INTRODUCTION The group of vascular tumors contains many different entities, and is considered difficult by pathologists, as they often have overlapping histological characteristics. Chromosomal translocations have been identified in ~20% of mesenchymal tumors and are considered the drivers of tumor formation. Many translocations have been discovered over the past decade through next-generation sequencing. This technological advancement has also revealed several recurrent gene fusions in vascular tumors. AREAS COVERED This review will discuss the various vascular tumors for which recurrent gene fusions have been identified. The gene fusions and the presumed molecular mechanisms underlying tumorigenesis are shown, and potential implications for targeted therapies discussed. The identification of these gene fusions in vascular tumors has improved diagnostic accuracy, especially since several of these fusions can be easily detected using surrogate immunohistochemical markers. EXPERT OPINION The identification of gene fusions in a subset of vascular tumors over the past decade has improved diagnostic accuracy, and has provided the pathologists with novel diagnostic tools to accurately diagnose these often difficult tumors. Moreover, the increased understanding of the underlying molecular mechanisms can guide the development of targeted therapeutic strategies.
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Affiliation(s)
- Sheena L M Ong
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Karoly Szuhai
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Judith V M G Bovée
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
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26
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Chopra R, Bushart DD, Cooper JP, Yellajoshyula D, Morrison LM, Huang H, Handler HP, Man LJ, Dansithong W, Scoles DR, Pulst SM, Orr HT, Shakkottai VG. Altered Capicua expression drives regional Purkinje neuron vulnerability through ion channel gene dysregulation in spinocerebellar ataxia type 1. Hum Mol Genet 2020; 29:3249-3265. [PMID: 32964235 PMCID: PMC7689299 DOI: 10.1093/hmg/ddaa212] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/19/2020] [Accepted: 09/17/2020] [Indexed: 12/22/2022] Open
Abstract
Selective neuronal vulnerability in neurodegenerative disease is poorly understood. Using the ATXN1[82Q] model of spinocerebellar ataxia type 1 (SCA1), we explored the hypothesis that regional differences in Purkinje neuron degeneration could provide novel insights into selective vulnerability. ATXN1[82Q] Purkinje neurons from the anterior cerebellum were found to degenerate earlier than those from the nodular zone, and this early degeneration was associated with selective dysregulation of ion channel transcripts and altered Purkinje neuron spiking. Efforts to understand the basis for selective dysregulation of channel transcripts revealed modestly increased expression of the ATXN1 co-repressor Capicua (Cic) in anterior cerebellar Purkinje neurons. Importantly, disrupting the association between ATXN1 and Cic rescued the levels of these ion channel transcripts, and lentiviral overexpression of Cic in the nodular zone accelerated both aberrant Purkinje neuron spiking and neurodegeneration. These findings reinforce the central role for Cic in SCA1 cerebellar pathophysiology and suggest that only modest reductions in Cic are needed to have profound therapeutic impact in SCA1.
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Affiliation(s)
- Ravi Chopra
- Medical Scientist Training Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Neurology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Neurology, Washington University in St. Louis, Saint Louis, MO 63110, USA
| | - David D Bushart
- Department of Neurology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
- Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - John P Cooper
- Department of Neurology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | | | - Logan M Morrison
- Department of Neurology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Haoran Huang
- Department of Neurology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Hillary P Handler
- Department of Laboratory Medicine and Pathology, Institute for Translational Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA
| | - Luke J Man
- Department of Neurology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Warunee Dansithong
- Department of Neurology, University of Utah, Salt Lake City, UT 84132, USA
| | - Daniel R Scoles
- Department of Neurology, University of Utah, Salt Lake City, UT 84132, USA
| | - Stefan M Pulst
- Department of Neurology, University of Utah, Salt Lake City, UT 84132, USA
| | - Harry T Orr
- Department of Laboratory Medicine and Pathology, Institute for Translational Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA
| | - Vikram G Shakkottai
- Department of Neurology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
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27
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Guo T, Ma S. Recent Advances in the Discovery of Multitargeted Tyrosine Kinase Inhibitors as Anticancer Agents. ChemMedChem 2020; 16:600-620. [PMID: 33179854 DOI: 10.1002/cmdc.202000658] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/28/2020] [Indexed: 12/18/2022]
Abstract
The treatment of cancer has been one of the most significant challenges for the medical field. Further research on the signal transduction pathway of tumor cells is driving the rapid development of antitumor agents targeting tyrosine kinases. However, most of the currently approved tyrosine kinase inhibitors based on the "single target/single drug" design are becoming less and less effective in the treatment of complex, heterogeneous, and multigenic cancers; this also results in resistance to chemotherapy. In contrast, multitargeted tyrosine kinase inhibitors (MT-TKIs) can effectively block multiple pathways of intracellular signal transduction. Therefore, they have therapeutic advantages over single-targeted inhibitors and have become a hotspot in antitumor drug research in recent years. This minireview summarizes recent advances in the discovery of MT-TKIs based on their chemical structures. In particular, we describe the kinase inhibitory and antitumor activity of promising compounds, as well as their structure - activity relationships (SARs).
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Affiliation(s)
- Ting Guo
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, West Wenhua Road 44, Jinan, 250012, P. R. China
| | - Shutao Ma
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, West Wenhua Road 44, Jinan, 250012, P. R. China
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28
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Yoshiya S, Itoh S, Yoshizumi T, Yugawa K, Kurihara T, Toshima T, Harada N, Hashisako M, Yonemasu H, Fukuzawa K, Oda Y, Mori M. Impact of Capicua on Pancreatic Cancer Progression. Ann Surg Oncol 2020; 28:3198-3207. [PMID: 33216264 DOI: 10.1245/s10434-020-09339-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/17/2020] [Indexed: 12/27/2022]
Abstract
BACKGROUND The transcription factor capicua (CIC) regulates mammalian development and homeostasis. Growing evidence shows that CIC suppresses various human cancers by directly repressing the downstream cancer-related target genes. This study investigated the clinical and biologic significance of CIC expression in pancreatic cancer (PC). METHODS The study reviewed 132 patients with PC who underwent curative resection. The patients were divided into two groups according to CIC immunoreactivity score by immunohistochemistry, and the associations between CIC expression, clinicopathologic characteristics, and postoperative prognosis were investigated. Moreover, the influence of CIC expression on the malignant potential of PC cells was assessed with cell proliferation, motility assays, and use of quantitative real time-polymerase chain reaction and Western blot on the downstream target genes of CIC in knockdown experiments. RESULTS The low-CIC expression group showed a higher proportion of lymphatic invasion (72.9% vs. 53.1%; p = 0.024), intrapancreatic neural invasion (94.1% vs. 81.3%; p = 0.021), and extrapancreatic plexus invasion (30.9% vs. 7.8%; p = 0.0006) than the high-CIC expression group as well as significantly worse overall survival (p = 0.0002) and recurrence-free survival (p = 0.0041) rates. Low CIC expression was an independent risk factor for poor prognosis (p = 0.038). Pancreatic cancer cells with knockdown CIC significantly enhanced cell motilities and cell cycle progression, promoted expression levels of ETV4 and MMP-9, and induced EMT. CONCLUSIONS The study elucidated the association of low CIC expression with a poor prognosis for patients with PC and suggested that the CIC-ETV4-MMP-9 axis might control PC progression.
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Affiliation(s)
- Shohei Yoshiya
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.,Department of Surgery, Oita Red Cross Hospital, Oita, Japan
| | - Shinji Itoh
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.
| | - Tomoharu Yoshizumi
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kyohei Yugawa
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.,Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takeshi Kurihara
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.,Department of Surgery, Oita Red Cross Hospital, Oita, Japan
| | - Takeo Toshima
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Noboru Harada
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Mikiko Hashisako
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.,Department of Anatomic Pathology, Oita Red Cross Hospital, Oita, Japan
| | | | - Kengo Fukuzawa
- Department of Surgery, Oita Red Cross Hospital, Oita, Japan
| | - Yoshinao Oda
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masaki Mori
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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Wong D, Sogerer L, Lee SS, Wong V, Lum A, Levine AB, Marra MA, Yip S. TRIM25 promotes Capicua degradation independently of ERK in the absence of ATXN1L. BMC Biol 2020; 18:154. [PMID: 33115448 PMCID: PMC7594423 DOI: 10.1186/s12915-020-00895-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 10/09/2020] [Indexed: 12/14/2022] Open
Abstract
Background Aberrations in Capicua (CIC) have recently been implicated as a negative prognostic factor in a multitude of cancer types through the derepression of targets downstream of the mitogen-activated protein kinase (MAPK) signaling cascade, such as oncogenic E26 transformation-specific (ETS) transcription factors. The Ataxin-family protein ATXN1L has previously been reported to interact with CIC in both developmental and disease contexts to facilitate the repression of CIC target genes and promote the post-translational stability of CIC. However, little is known about the mechanisms at the base of ATXN1L-mediated CIC post-translational stability. Results Functional in vitro studies utilizing ATXN1LKO human cell lines revealed that loss of ATXN1L leads to the accumulation of polyubiquitinated CIC protein, promoting its degradation through the proteasome. Although transcriptomic signatures of ATXN1LKO cell lines indicated upregulation of the mitogen-activated protein kinase pathway, ERK activity was found to contribute to CIC function but not stability. Degradation of CIC protein following loss of ATXN1L was instead observed to be mediated by the E3 ubiquitin ligase TRIM25 which was further validated using glioma-derived cell lines and the TCGA breast carcinoma and liver hepatocellular carcinoma cohorts. Conclusions The post-translational regulation of CIC through ATXN1L and TRIM25 independent of ERK activity suggests that the regulation of CIC stability and function is more intricate than previously appreciated and involves several independent pathways. As CIC status has become a prognostic factor in several cancer types, further knowledge into the mechanisms which govern CIC stability and function may prove useful for future therapeutic approaches.
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Affiliation(s)
- Derek Wong
- Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.,Molecular Oncology, BC Cancer Agency, Vancouver, Canada
| | - Lisa Sogerer
- Department of Electrical and Computer Engineering, Technical University of Munich, Munich, Germany
| | - Samantha S Lee
- Department of Biological and Chemical Engineering, University of British Columbia, Vancouver, Canada
| | - Victor Wong
- Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Amy Lum
- Molecular Oncology, BC Cancer Agency, Vancouver, Canada
| | - Adrian B Levine
- Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Stephen Yip
- Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada. .,Molecular Oncology, BC Cancer Agency, Vancouver, Canada. .,Vancouver General Hospital, Vancouver, Canada.
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HLA-DPA1 gene is a potential predictor with prognostic values in multiple myeloma. BMC Cancer 2020; 20:915. [PMID: 32972413 PMCID: PMC7513295 DOI: 10.1186/s12885-020-07393-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 09/09/2020] [Indexed: 02/08/2023] Open
Abstract
Background Multiple myeloma (MM) is an incurable hematological tumor, which is closely related to hypoxic bone marrow microenvironment. However, the underlying mechanisms are still far from fully understood. We took integrated bioinformatics analysis with expression profile GSE110113 downloaded from National Center for Biotechnology Information-Gene Expression Omnibus (NCBI-GEO) database, and screened out major histocompatibility complex, class II, DP alpha 1 (HLA-DPA1) as a hub gene related to hypoxia in MM. Methods Differentially expressed genes (DEGs) were filtrated with R package “limma”. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were performed using “clusterProfiler” package in R. Then, protein-protein interaction (PPI) network was established. Hub genes were screened out according to Maximal Clique Centrality (MCC). PrognoScan evaluated all the significant hub genes for survival analysis. ScanGEO was used for visualization of gene expression in different clinical studies. P and Cox p value < 0.05 was considered to be statistical significance. Results HLA-DPA1 was finally picked out as a hub gene in MM related to hypoxia. MM patients with down-regulated expression of HLA-DPA1 has statistically significantly shorter disease specific survival (DSS) (COX p = 0.005411). Based on the clinical data of GSE47552 dataset, HLA-DPA1 expression showed significantly lower in MM patients than that in healthy donors (HDs) (p = 0.017). Conclusion We identified HLA-DPA1 as a hub gene in MM related to hypoxia. HLA-DPA1 down-regulated expression was associated with MM patients’ poor outcome. Further functional and mechanistic studies are need to investigate HLA-DPA1 as potential therapeutic target.
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31
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Capicua in Human Cancer. Trends Cancer 2020; 7:77-86. [PMID: 32978089 DOI: 10.1016/j.trecan.2020.08.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 12/11/2022]
Abstract
Capicua (CIC) is a highly conserved transcriptional repressor that is differentially regulated through mitogen-activated protein kinase (MAPK) signaling or genetic alteration across human cancer. CIC contributes to tumor progression and metastasis through direct transcriptional control of effector target genes. Recent findings indicate that CIC dysregulation is mechanistically linked and restricted to specific cancer subtypes, yet convergence on key downstream transcriptional nodes are critical for CIC-regulated oncogenesis across these cancers. In this review, we focus on how differential regulation of CIC through functional and genetic mechanisms contributes to subtype-specific cancer phenotypes and we propose new therapeutic strategies to effectively target CIC-altered cancers.
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32
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Williams EA, Sharaf R, Decker B, Werth AJ, Toma H, Montesion M, Sokol ES, Pavlick DC, Shah N, Williams KJ, Venstrom JM, Alexander BM, Ross JS, Albacker LA, Lin DI, Ramkissoon SH, Elvin JA. CDKN2C-Null Leiomyosarcoma: A Novel, Genomically Distinct Class of TP53/ RB1-Wild-Type Tumor With Frequent CIC Genomic Alterations and 1p/19q-Codeletion. JCO Precis Oncol 2020; 4:PO.20.00040. [PMID: 33015533 PMCID: PMC7529542 DOI: 10.1200/po.20.00040] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2020] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Leiomyosarcoma (LMS) harbors frequent mutations in TP53 and RB1 but few actionable genomic alterations. Here, we searched for recurrent actionable genomic alterations in LMS that occur in the absence of common untreatable oncogenic drivers. METHODS Tissues from 276,645 unique advanced cancers, including 2,570 uterine and soft tissue LMS, were sequenced by hybrid-capture-based next-generation DNA and RNA sequencing/comprehensive genomic profiling of up to 406 genes. We characterized clinicopathologic features of relevant patient cases. RESULTS Overall, 77 LMS exhibited homozygous copy loss of CDKN2C at chromosome 1p32.3 (3.0% of LMS). Genomic alterations (GAs) in TP53, RB1, and ATRX were rare compared with the remainder of the LMS cohort (11.7% v 73.4%, 0% v 54.5%, 2.6% v 24.5%, respectively; all P < .0001). CDKN2C-null LMS patient cases were significantly enriched for GAs in CIC (40.3% v 1.4%) at 19q13.2, CDKN2A (46.8% v 7.0%), and RAD51B (16.9% v 1.7%; all P < .0001). Chromosome arm-level aneuploidy analysis of available LMS patient cases (n = 1,284) found that 81% (58 of 72) of CDKN2C-null LMS exhibited 1p/19q-codeletion, a significant enrichment compared with 5.1% in the remainder of the LMS cohort (P < .0001). In total, 99% of CDKN2C-null LMS were in women; the median age was 61 years at surgery (range, 36-81 years). Fifty-five patient cases were uterine primary, four were nonuterine, and the remaining 18 were of uncertain primary site. Sixty percent of cases showed at least focal epithelioid variant histology. Most patients had advanced-stage disease, with 62% of confirmed uterine primary LMS at International Federation of Gynecology and Obstetrics stage IVB. We further validated our findings in two publicly available datasets: The Cancer Genome Atlas and the Project GENIE initiative. CONCLUSION CDKN2C-null LMS defines a genomically distinct tumor that may have prognostic and/or therapeutic clinical implications, including possible use of specific cyclin-dependent kinase inhibitors.
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Affiliation(s)
| | | | - Brennan Decker
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Adrienne J. Werth
- Christiana Hospital, Department of Obstetrics and Gynecology, Newark, DE
| | - Helen Toma
- Christiana Hospital, Department of Obstetrics and Gynecology, Newark, DE
| | | | | | | | | | - Kevin Jon Williams
- Department of Physiology, Department of Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA
| | | | | | - Jeffrey S. Ross
- Foundation Medicine, Cambridge, MA
- Department of Pathology, State University of New York Upstate Medical University, Syracuse, NY
| | | | | | - Shakti H. Ramkissoon
- Foundation Medicine, Cambridge, MA
- Wake Forest Comprehensive Cancer Center and Department of Pathology, Wake Forest School of Medicine, Winston-Salem, NC
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Cao X, Wolf A, Kim SE, Cabrera RM, Wlodarczyk BJ, Zhu H, Parker M, Lin Y, Steele JW, Han X, Ramaekers VT, Steinfeld R, Finnell RH, Lei Y. CIC de novo loss of function variants contribute to cerebral folate deficiency by downregulating FOLR1 expression. J Med Genet 2020; 58:484-494. [PMID: 32820034 PMCID: PMC7895856 DOI: 10.1136/jmedgenet-2020-106987] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 05/27/2020] [Accepted: 06/05/2020] [Indexed: 01/09/2023]
Abstract
Background Cerebral folate deficiency (CFD) syndrome is characterised by a low concentration of 5-methyltetrahydrofolate in cerebrospinal fluid, while folate levels in plasma and red blood cells are in the low normal range. Mutations in several folate pathway genes, including FOLR1 (folate receptor alpha, FRα), DHFR (dihydrofolate reductase) and PCFT (proton coupled folate transporter) have been previously identified in patients with CFD. Methods In an effort to identify causal mutations for CFD, we performed whole exome sequencing analysis on eight CFD trios and identified eight de novo mutations in seven trios. Results Notably, we found a de novo stop gain mutation in the capicua (CIC) gene. Using 48 sporadic CFD samples as a validation cohort, we identified three additional rare variants in CIC that are putatively deleterious mutations. Functional analysis indicates that CIC binds to an octameric sequence in the promoter regions of folate transport genes: FOLR1, PCFT and reduced folate carrier (Slc19A1; RFC1). The CIC nonsense variant (p.R353X) downregulated FOLR1 expression in HeLa cells as well as in the induced pluripotent stem cell (iPSCs) derived from the original CFD proband. Folate binding assay demonstrated that the p.R353X variant decreased cellular binding of folic acid in cells. Conclusion This study indicates that CIC loss of function variants can contribute to the genetic aetiology of CFD through regulating FOLR1 expression. Our study described the first mutations in a non-folate pathway gene that can contribute to the aetiology of CFD.
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Affiliation(s)
- Xuanye Cao
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Annika Wolf
- Department of Pediatric Neurology, University Medical Center Göttingen, Gottingen, Niedersachsen, Germany
| | - Sung-Eun Kim
- Department of Pediatrics, University of Texas at Austin, Austin, Texas, USA
| | - Robert M Cabrera
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Bogdan J Wlodarczyk
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Huiping Zhu
- Department of Nutritional Sciences, University of Texas at Austin Dell Medical School, Austin, Texas, USA
| | - Margaret Parker
- Department of Pediatrics, University of Texas at Austin, Austin, Texas, USA
| | - Ying Lin
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - John W Steele
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA.,Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Xiao Han
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Vincent Th Ramaekers
- Department of Pediatric Neurology, University Hospital Center Liège, Liège, Belgium
| | - Robert Steinfeld
- Department of Pediatric Neurology, University Medical Center Göttingen, Gottingen, Niedersachsen, Germany .,University Children's Hospital Zurich, Zurich, Switzerland
| | - Richard H Finnell
- Department of Pediatrics, University of Texas at Austin, Austin, Texas, USA .,Center for Precision Environmental Health, Departments of Molecular and Cellular Biology and Medicine, Houston, Texas, USA.,Departments of Molecular and Human Genetics and Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Yunping Lei
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
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Hamaratoglu F, Atkins M. Rounding up the Usual Suspects: Assessing Yorkie, AP-1, and Stat Coactivation in Tumorigenesis. Int J Mol Sci 2020; 21:E4580. [PMID: 32605129 PMCID: PMC7370090 DOI: 10.3390/ijms21134580] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/16/2020] [Accepted: 06/18/2020] [Indexed: 12/18/2022] Open
Abstract
Can hyperactivation of a few key signaling effectors be the underlying reason for the majority of epithelial cancers despite different driver mutations? Here, to address this question, we use the Drosophila model, which allows analysis of gene expression from tumors with known initiating mutations. Furthermore, its simplified signaling pathways have numerous well characterized targets we can use as pathway readouts. In Drosophila tumor models, changes in the activities of three pathways, Jun N-terminal Kinase (JNK), Janus Kinase / Signal Transducer and Activator of Transcription (JAK/STAT), and Hippo, mediated by AP-1 factors, Stat92E, and Yorkie, are reported frequently. We hypothesized this may indicate that these three pathways are commonly deregulated in tumors. To assess this, we mined the available transcriptomic data and evaluated the activity levels of eight pathways in various tumor models. Indeed, at least two out of our three suspects contribute to tumor development in all Drosophila cancer models assessed, despite different initiating mutations or tissues of origin. Surprisingly, we found that Notch signaling is also globally activated in all models examined. We propose that these four pathways, JNK, JAK/STAT, Hippo, and Notch, are paid special attention and assayed for systematically in existing and newly developed models.
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Affiliation(s)
| | - Mardelle Atkins
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX 77341, USA
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35
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Primary spinal intramedullary Ewing-like sarcoma harboring CIC-DUX4 translocation: a similar cytological appearance as its soft tissue counterpart but no lobulation in association with desmoplastic stroma. Brain Tumor Pathol 2020; 37:111-117. [PMID: 32449046 DOI: 10.1007/s10014-020-00366-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 05/14/2020] [Indexed: 01/16/2023]
Abstract
The CIC-DUX4 translocation is the most common genetic alteration of small round cell sarcomas without EWSR1 rearrangement. These "Ewing-like sarcomas" usually occur in peripheral soft tissues, and rare primary central nervous system (CNS) tumors have been described. We report a rare case of primary spinal intramedullary Ewing-like sarcoma harboring CIC-DUX4 translocation. A 23-year-old man presented with weakness in the extremities. Magnetic resonance imaging revealed a large intramedullary tumor spanning C3-C5 with heterogeneous enhancement following gadolinium administration. Histologically, most of the tumor displayed dense myeloid proliferation composed of medium- to slightly small-sized primitive cells. Postoperatively, he received local adjuvant radiation therapy without tumor progression for 10 months. Target RNA sequencing analysis revealed the CIC-DUX4 fusion gene. Methylation array analysis resulted in a diagnosis of "methylation class CNS Ewing sarcoma family tumor with CIC alteration". Although this tumor lacked characteristic histological features such as lobular structures in association with desmoplastic stroma, relatively uniform nuclei with prominent nucleoli and eosinophilic cytoplasm, which are often found in CIC-rearranged sarcomas of soft tissue, were identified. Recently, many CNS and soft tissue tumors require genetic analysis for precise diagnosis. To consider certain molecular testing, careful histological examination is essential.
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Lee Y. Regulation and function of capicua in mammals. Exp Mol Med 2020; 52:531-537. [PMID: 32238859 PMCID: PMC7210929 DOI: 10.1038/s12276-020-0411-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/27/2020] [Accepted: 03/03/2020] [Indexed: 12/20/2022] Open
Abstract
Capicua (CIC) is an evolutionarily conserved transcription factor. CIC contains a high-mobility group (HMG) box that recognizes specific DNA sequences to regulate the expression of various target genes. CIC was originally identified in Drosophila melanogaster as a transcriptional repressor that suppresses the receptor tyrosine kinase signaling pathway. This molecule controls normal organ growth and tissue patterning as well as embryogenesis in Drosophila. Recent studies have also demonstrated its extensive functions in mammals. For example, CIC regulates several developmental and physiological processes, including lung development, abdominal wall closure during embryogenesis, brain development and function, neural stem cell homeostasis, T cell differentiation, and enterohepatic circulation of bile acids. CIC is also associated with the progression of various types of cancer and neurodegeneration in spinocerebellar ataxia type-1, systemic autoimmunity, and liver injury. In this review, I provide a broad overview of our current understanding of the regulation and functions of CIC in mammals and discuss future research directions.
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Affiliation(s)
- Yoontae Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Republic of Korea.
- Yonsei University, Seoul, Republic of Korea.
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Inactivation of Transcriptional Repressor Capicua Confers Sorafenib Resistance in Human Hepatocellular Carcinoma. Cell Mol Gastroenterol Hepatol 2020; 10:269-285. [PMID: 32169577 PMCID: PMC7305345 DOI: 10.1016/j.jcmgh.2020.02.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 02/17/2020] [Accepted: 02/25/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Sorafenib is a multireceptor tyrosine kinase inhibitor that can prolong overall survival in patients with advanced hepatocellular carcinoma (HCC). Although most HCC patients who receive sorafenib ultimately show disease progression, it still is unclear whether and how HCC cells acquire chemoresistance during sorafenib treatment in human beings. METHODS We analyzed surgically resected HCC tissues from a patient who received sorafenib for prevention of HCC recurrence after surgery (Adjuvant Sorafenib for Hepatocellular Carcinoma after Resection or Ablation trial) and established patient-derived HCC cells. Whole-exome sequence analysis was performed to detect mutations in sorafenib-resistant clones. We examined 30 advanced HCC cases immunohistochemically and 140 HCC cases enrolled in the Adjuvant Sorafenib for Hepatocellular Carcinoma after Resection or Ablation trial using microarray analysis to evaluate the association of Capicua Transcriptional Repressor (CIC) status with sorafenib treatment response. RESULTS We found a CIC mutation in recurrent HCC specimens after sorafenib. CIC encodes Capicua, a general sensor of receptor tyrosine kinase signaling. HCC cells established from the recurrent tumor specimen showed chemoresistance to sorafenib in vitro and in vivo. Established sorafenib-resistant Huh1 and Huh7 cell lines showed reduced expression of Capicua without mutations. Immunohistochemical analysis showed that HCC patients with low Capicua expression showed poor overall survival. Microarray analysis showed that the CIC gene signature could predict the preventive effect of adjuvant sorafenib treatment on HCC recurrence. Intriguingly, although CIC knockdown induced sorafenib resistance in HCC cell lines, regorafenib suppressed growth of sorafenib-resistant, Capicua-inactivated HCC cells and inhibited extracellular signal-regulated kinase phosphorylation. CONCLUSIONS Evaluation of Capicua status may be pivotal to predict response to sorafenib, and regorafenib treatment could be effective to treat HCC with functional Capicua impairment.
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Keenan SE, Blythe SA, Marmion RA, Djabrayan NJV, Wieschaus EF, Shvartsman SY. Rapid Dynamics of Signal-Dependent Transcriptional Repression by Capicua. Dev Cell 2020; 52:794-801.e4. [PMID: 32142631 DOI: 10.1016/j.devcel.2020.02.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 12/04/2019] [Accepted: 01/31/2020] [Indexed: 12/21/2022]
Abstract
Optogenetic perturbations, live imaging, and time-resolved ChIP-seq assays in Drosophila embryos were used to dissect the ERK-dependent control of the HMG-box repressor Capicua (Cic), which plays critical roles in development and is deregulated in human spinocerebellar ataxia and cancers. We established that Cic target genes are activated before significant downregulation of nuclear localization of Cic and demonstrated that their activation is preceded by fast dissociation of Cic from the regulatory DNA. We discovered that both Cic-DNA binding and repression are rapidly reinstated in the absence of ERK activation, revealing that inductive signaling must be sufficiently sustained to ensure robust transcriptional response. Our work provides a quantitative framework for the mechanistic analysis of dynamics and control of transcriptional repression in development.
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Affiliation(s)
- Shannon E Keenan
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08540, USA; The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA
| | - Shelby A Blythe
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Robert A Marmion
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA
| | - Nareg J-V Djabrayan
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA
| | - Eric F Wieschaus
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
| | - Stanislav Y Shvartsman
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08540, USA; The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010, USA.
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Wong D, Yip S. Making heads or tails - the emergence of capicua (CIC) as an important multifunctional tumour suppressor. J Pathol 2020; 250:532-540. [PMID: 32073140 DOI: 10.1002/path.5400] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 01/31/2020] [Accepted: 02/12/2020] [Indexed: 12/24/2022]
Abstract
Capicua, encoded by the gene CIC, is an evolutionarily conserved high-mobility group-box transcription factor downstream of the receptor tyrosine kinase and mitogen-activated protein kinase pathways. It was initially discovered and studied in Drosophila. Recurrent mutations in CIC were first identified in oligodendroglioma, a subtype of low-grade glioma. Subsequent studies have identified CIC aberrations in multiple types of cancer and have established CIC as a potent tumour suppressor involved in regulating pathways related to cell growth and proliferation, invasion and treatment resistance. The most well-known and studied targets of mammalian CIC are the oncogenic E-Twenty Six transcription factors ETV1/4/5, which have been found to be elevated in cancers with CIC aberrations. Here, we review the role of CIC in normal mammalian development, oncogenesis and tumour progression, and the functional interactors that mediate them. © 2020 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Derek Wong
- Molecular Oncology, British Columbia Cancer Research Center, Vancouver, British Columbia, Canada.,Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Stephen Yip
- Molecular Oncology, British Columbia Cancer Research Center, Vancouver, British Columbia, Canada.,Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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Yoe J, Kim D, Kim S, Lee Y. Capicua restricts cancer stem cell-like properties in breast cancer cells. Oncogene 2020; 39:3489-3506. [PMID: 32108163 DOI: 10.1038/s41388-020-1230-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 02/14/2020] [Accepted: 02/17/2020] [Indexed: 12/27/2022]
Abstract
Cancer stem cells (CSCs) play a central role in cancer initiation, progression, therapeutic resistance, and recurrence in patients. Here we present Capicua (CIC), a developmental transcriptional repressor, as a suppressor of CSC properties in breast cancer cells. CIC deficiency critically enhances CSC self-renewal and multiple CSC subpopulations of breast cancer cells without altering their growth rate or invasiveness. Loss of CIC relieves repression of ETV4 and ETV5 expression, consequently promoting self-renewal capability, EpCAM+/CD44+/CD24low/- expression, and ALDH activity. In xenograft models, CIC deficiency significantly increases CSC frequency and drives tumor initiation through derepression of ETV4. Consistent with the experimental data, the CD44high/CD24low CSC-like feature is inversely correlated with CIC levels in breast cancer patients. We also identify SOX2 as a downstream target gene of CIC that partly promotes CSC properties. Taken together, our study demonstrates that CIC suppresses breast cancer formation via restricting cancer stemness and proposes CIC as a potential regulator of stem cell maintenance.
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Affiliation(s)
- Jeehyun Yoe
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Donghyo Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Sanguk Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, 37673, Republic of Korea.,Division of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Yoontae Lee
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, 37673, Republic of Korea. .,Division of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, 37673, Republic of Korea.
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Abstract
Terminal regions of the early Drosophila embryo are patterned by the highly conserved ERK cascade, giving rise to the nonsegmented terminal structures of the future larva. In less than an hour, this signaling event establishes several gene expression boundaries and sets in motion a sequence of elaborate morphogenetic events. Genetic studies of terminal patterning discovered signaling components and transcription factors that are involved in numerous developmental contexts and deregulated in human diseases. This review summarizes current understanding of signaling and morphogenesis during terminal patterning and discusses several open questions that can now be rigorously investigated using live imaging, omics, and optogenetic approaches. The anatomical simplicity of the terminal patterning system and its amenability to a broad range of increasingly sophisticated genetic perturbations will continue to make it a premier quantitative model for studying multiple aspects of tissue patterning by dynamically controlled cell signaling pathways.
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Bunda S, Heir P, Li ASC, Mamatjan Y, Zadeh G, Aldape K. c-Src Phosphorylates and Inhibits the Function of the CIC Tumor Suppressor Protein. Mol Cancer Res 2020; 18:774-786. [PMID: 32029440 DOI: 10.1158/1541-7786.mcr-18-1370] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 08/28/2019] [Accepted: 02/03/2020] [Indexed: 11/16/2022]
Abstract
Capicua (CIC) is a transcriptional repressor that counteracts activation of genes in response to receptor tyrosine kinase (RTK)/Ras/ERK signaling. Following activation of RTK, ERK enters the nucleus and serine-phosphorylates CIC, releasing it from its targets to permit gene expression. We recently showed that ERK triggers ubiquitin-mediated degradation of CIC in glioblastoma (GBM). In this study, we examined whether another important downstream effector of RTK/EGFR, the non-RTK c-Src, affects CIC repressor function in GBM. We found that c-Src binds and tyrosine-phosphorylates CIC on residue 1455 to promote nuclear export of CIC. On the other hand, CIC-mutant allele (CIC-Y1455F), that escapes c-Src-mediated tyrosine phosphorylation, remains localized to the nucleus and retains strong repressor function against CIC targets, the oncogenic transcription factors ETV1 and ETV5. Furthermore, we show that the orally available Src family kinase inhibitor, dasatinib, which prevents EGF-mediated tyrosine phosphorylation of CIC and attenuates elevated ETV1 and ETV5 levels, reduces viability of GBM cells and glioma stem cells (GSC), but not of their control cells with undetectable c-Src activity. In fact, GBM cells and GSC expressing the tyrosine-defective CIC mutant (Y1455F) lose sensitivity to dasatinib, further endorsing the effect of dasatinib on Src-mediated tyrosine phosphorylation of CIC. These findings elucidate important mechanisms of CIC regulation and provide the rationale to target c-Src alongside ERK pathway inhibitors as a way to fully restore CIC tumor suppressor function in neoplasms such as GBM. IMPLICATIONS: c-Src tyrosine-phosphorylates CIC exports to cytoplasm and inactivates its repressor function in GBM.
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Affiliation(s)
- Severa Bunda
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Pardeep Heir
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Annie Si Cong Li
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Yasin Mamatjan
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Gelareh Zadeh
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, Toronto, Ontario, Canada. .,Division of Neurosurgery, Toronto Western Hospital, Toronto, Ontario, Canada.,Institute of Medical Science, Toronto, Ontario, Canada
| | - Kenneth Aldape
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, Toronto, Ontario, Canada. .,Laboratory of Pathology, NCI, Bethesda, Maryland
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Lee JS, Kim E, Lee J, Kim D, Kim H, Kim CJ, Kim S, Jeong D, Lee Y. Capicua suppresses colorectal cancer progression via repression of ETV4 expression. Cancer Cell Int 2020; 20:42. [PMID: 32042269 PMCID: PMC7003492 DOI: 10.1186/s12935-020-1111-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 01/17/2020] [Indexed: 02/08/2023] Open
Abstract
Background Although major driver gene mutations have been identified, the complex molecular heterogeneity of colorectal cancer (CRC) remains unclear. Capicua (CIC) functions as a tumor suppressor in various types of cancers; however, its role in CRC progression has not been examined. Methods Databases for gene expression profile in CRC patient samples were used to evaluate the association of the levels of CIC and Polyoma enhancer activator 3 (PEA3) group genes (ETS translocation variant 1 (ETV1), ETV4, and ETV5), the best-characterized CIC targets in terms of CIC functions, with clinicopathological features of CRC. CIC and ETV4 protein levels were also examined in CRC patient tissue samples. Gain- and loss-of function experiments in cell lines and mouse xenograft models were performed to investigate regulatory functions of CIC and ETV4 in CRC cell growth and invasion. qRT-PCR and western blot analyses were performed to verify the CIC regulation of ETV4 expression in CRC cells. Rescue experiments were conducted using siRNA against ETV4 and CIC-deficient CRC cell lines. Results CIC expression was decreased in the tissue samples of CRC patients. Cell invasion, migration, and proliferation were enhanced in CIC-deficient CRC cells and suppressed in CIC-overexpressing cells. Among PEA3 group genes, ETV4 levels were most dramatically upregulated and inversely correlated with the CIC levels in CRC patient samples. Furthermore, derepression of ETV4 was more prominent in CIC-deficient CRC cells, when compared with that observed for ETV1 and ETV5. The enhanced cell proliferative and invasive capabilities in CIC-deficient CRC cells were completely recovered by knockdown of ETV4. Conclusion Collectively, the CIC-ETV4 axis is not only a key module that controls CRC progression but also a novel therapeutic and/or diagnostic target for CRC.
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Affiliation(s)
- Jeon-Soo Lee
- 1Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk Republic of Korea
| | - Eunjeong Kim
- 1Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk Republic of Korea
| | - Jongeun Lee
- 1Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk Republic of Korea
| | - Donghyo Kim
- 1Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk Republic of Korea
| | - Hyeongjoo Kim
- 3Soonchunhyang Medical Science Research Institute, Soonchunhyang University, Cheonan, Chungnam Republic of Korea
| | - Chang-Jin Kim
- 4Department of Pathology, College of Medicine, Soonchunhyang University, Room 601, 31 Soonchunhyang 6gil, Dongnam-gu, Cheonan, Chungnam 31151 Republic of Korea
| | - Sanguk Kim
- 1Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk Republic of Korea.,2Division of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology, Pohang, Gyeongbuk Republic of Korea
| | - Dongjun Jeong
- 3Soonchunhyang Medical Science Research Institute, Soonchunhyang University, Cheonan, Chungnam Republic of Korea.,4Department of Pathology, College of Medicine, Soonchunhyang University, Room 601, 31 Soonchunhyang 6gil, Dongnam-gu, Cheonan, Chungnam 31151 Republic of Korea
| | - Yoontae Lee
- 1Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk Republic of Korea.,2Division of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology, Pohang, Gyeongbuk Republic of Korea.,POSTECH Biotech Center, Room 388, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673 Republic of Korea
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Paul S, Yang L, Mattingly H, Goyal Y, Shvartsman SY, Veraksa A. Activation-induced substrate engagement in ERK signaling. Mol Biol Cell 2020; 31:235-243. [PMID: 31913744 PMCID: PMC7183763 DOI: 10.1091/mbc.e19-07-0355] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The extracellular signal-regulated kinase (ERK) pathway is an essential component of developmental signaling in metazoans. Previous models of pathway activation suggested that dissociation of activated dually phosphorylated ERK (dpERK) from MAPK/ERK kinase (MEK), a kinase that phosphorylates ERK, and other cytoplasmic anchors, is sufficient for allowing ERK interactions with its substrates. Here, we provide evidence for an additional step controlling ERK’s access to substrates. Specifically, we demonstrate that interaction of ERK with its substrate Capicua (Cic) is controlled at the level of ERK phosphorylation, whereby Cic binds to dpERK much stronger than to unphosphorylated ERK, both in vitro and in vivo. Mathematical modeling suggests that the differential affinity of Cic for dpERK versus ERK is required for both down-regulation of Cic and stabilizing phosphorylated ERK. Preferential association of Cic with dpERK serves two functions: it prevents unproductive competition of Cic with unphosphorylated ERK and contributes to efficient signal propagation. We propose that high-affinity substrate binding increases the specificity and efficiency of signal transduction through the ERK pathway.
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Affiliation(s)
- Sayantanee Paul
- Department of Biology, University of Massachusetts, Boston, Boston, MA 02125
| | - Liu Yang
- Department of Biology, University of Massachusetts, Boston, Boston, MA 02125.,Lewis-Sigler Institute for Integrative Genomics
| | - Henry Mattingly
- Lewis-Sigler Institute for Integrative Genomics.,Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544
| | - Yogesh Goyal
- Lewis-Sigler Institute for Integrative Genomics.,Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544
| | - Stanislav Y Shvartsman
- Lewis-Sigler Institute for Integrative Genomics.,Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544.,Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Alexey Veraksa
- Department of Biology, University of Massachusetts, Boston, Boston, MA 02125
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45
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Establishment of a novel human CIC-DUX 4 sarcoma cell line, Kitra-SRS, with autocrine IGF-1R activation and metastatic potential to the lungs. Sci Rep 2019; 9:15812. [PMID: 31676869 PMCID: PMC6825133 DOI: 10.1038/s41598-019-52143-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 10/14/2019] [Indexed: 02/07/2023] Open
Abstract
Approximately 60–70% of EWSR1-negative small blue round cell sarcomas harbour a rearrangement of CIC, most commonly CIC-DUX4. CIC-DUX4 sarcoma (CDS) is an aggressive and often fatal high-grade sarcoma appearing predominantly in children and young adults. Although cell lines and their xenograft models are essential tools for basic research and development of antitumour drugs, few cell lines currently exist for CDS. We successfully established a novel human CDS cell line designated Kitra-SRS and developed orthotopic tumour xenografts in nude mice. The CIC-DUX4 fusion gene in Kitra-SRS cells was generated by t(12;19) complex chromosomal rearrangements with an insertion of a chromosome segment including a DUX4 pseudogene component. Kitra-SRS xenografts were histologically similar to the original tumour and exhibited metastatic potential to the lungs. Kitra-SRS cells displayed autocrine activation of the insulin-like growth factor 1 (IGF-1)/IGF-1 receptor (IGF-1R) pathway. Accordingly, treatment with the IGF-1R inhibitor, linsitinib, attenuated Kitra-SRS cell growth and IGF-1-induced activation of IGF-1R/AKT signalling both in vitro and in vivo. Furthermore, upon screening 1134 FDA-approved drugs, the responses of Kitra-SRS cells to anticancer drugs appeared to reflect those of the primary tumour. Our model will be a useful modality for investigating the molecular pathology and therapy of CDS.
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46
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Han J, Perez JT, Chen C, Li Y, Benitez A, Kandasamy M, Lee Y, Andrade J, tenOever B, Manicassamy B. Genome-wide CRISPR/Cas9 Screen Identifies Host Factors Essential for Influenza Virus Replication. Cell Rep 2019; 23:596-607. [PMID: 29642015 PMCID: PMC5939577 DOI: 10.1016/j.celrep.2018.03.045] [Citation(s) in RCA: 153] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 01/24/2018] [Accepted: 03/10/2018] [Indexed: 11/13/2022] Open
Abstract
The emergence of influenza A viruses (IAVs) from zoonotic reservoirs poses a great threat to human health. As seasonal vaccines are ineffective against zoonotic strains, and newly transmitted viruses can quickly acquire drug resistance, there remains a need for host-directed therapeutics against IAVs. Here, we performed a genome-scale CRISPR/Cas9 knockout screen in human lung epithelial cells with a human isolate of an avian H5N1 strain. Several genes involved in sialic acid biosynthesis and related glycosylation pathways were highly enriched post-H5N1 selection, including SLC35A1, a sialic acid transporter essential for IAV receptor expression and thus viral entry. Importantly, we have identified capicua (CIC) as a negative regulator of cell-intrinsic immunity, as loss of CIC resulted in heightened antiviral responses and restricted replication of multiple viruses. Therefore, our study demonstrates that the CRISPR/Cas9 system can be utilized for the discovery of host factors critical for the replication of intracellular pathogens.
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Affiliation(s)
- Julianna Han
- Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Jasmine T Perez
- Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Cindy Chen
- Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Yan Li
- Center for Research Informatics, The University of Chicago, Chicago, IL 60637, USA
| | - Asiel Benitez
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Yoontae Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Kyungbuk 790-784, Republic of Korea
| | - Jorge Andrade
- Center for Research Informatics, The University of Chicago, Chicago, IL 60637, USA
| | - Benjamin tenOever
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Balaji Manicassamy
- Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA.
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Simón-Carrasco L, Jiménez G, Barbacid M, Drosten M. The Capicua tumor suppressor: a gatekeeper of Ras signaling in development and cancer. Cell Cycle 2019; 17:702-711. [PMID: 29578365 DOI: 10.1080/15384101.2018.1450029] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Abstract
The transcriptional repressor Capicua (CIC) has emerged as an important rheostat of cell growth regulated by RAS/MAPK signaling. Cic was originally discovered in Drosophila, where it was shown to be inactivated by MAPK signaling downstream of the RTKs Torso and EGFR, which results in signal-dependent responses that are required for normal cell fate specification, proliferation and survival of developing and adult tissues. CIC is highly conserved in mammals, where it is also negatively regulated by MAPK signaling. Here, we review the roles of CIC during mammalian development, tissue homeostasis, tumor formation and therapy resistance. Available data indicate that CIC is involved in multiple biological processes, including lung development, liver homeostasis, autoimmunity and neurobehavioral processes. Moreover, CIC has been shown to be involved in tumor development as a tumor suppressor, both in human as well as in mouse models. Finally, several lines of evidence implicate CIC as a determinant of sensitivity to EGFR and MAPK pathway inhibitors, suggesting that CIC may play a broader role in human cancer than originally anticipated.
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Affiliation(s)
- Lucía Simón-Carrasco
- a Molecular Oncology Programme, Centro Nacional de Investigaciones Oncológicas (CNIO) , Melchor Fernández Almagro 3, Madrid , Spain
| | - Gerardo Jiménez
- b Institut de Biologia Molecular de Barcelona-CSIC , Parc Científic de Barcelona, Barcelona , Spain.,c ICREA , Pg. Lluís Companys 23, Barcelona , Spain
| | - Mariano Barbacid
- a Molecular Oncology Programme, Centro Nacional de Investigaciones Oncológicas (CNIO) , Melchor Fernández Almagro 3, Madrid , Spain
| | - Matthias Drosten
- a Molecular Oncology Programme, Centro Nacional de Investigaciones Oncológicas (CNIO) , Melchor Fernández Almagro 3, Madrid , Spain
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48
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Zhou Y, Wang M, Shuang T, Liu Y, Zhang Y, Shi C. MiR-1307 influences the chemotherapeutic sensitivity in ovarian cancer cells through the regulation of the CIC transcriptional repressor. Pathol Res Pract 2019; 215:152606. [PMID: 31500928 DOI: 10.1016/j.prp.2019.152606] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 08/06/2019] [Accepted: 08/18/2019] [Indexed: 01/26/2023]
Abstract
BACKGROUND Extended from our previously observation that expression of miR-1307 in chemoresistant primary ovarian cancer tissues is elevated, here we are aiming to dissect the function of miR-1307 and its predicted target gene, CIC (capicua transcriptional repressor), in ovarian cancer chemotherapy. METHODS We evaluated the expression of miR-1307 and CIC in chemoresistant and chemosensitive ovarian cancer tissues and cells by real time-PCR and western blot. We used chemoresistant/chemosensitive cells with miR-1307 suppression/overexpression to study the biological effects of miR-1307 by MTT and flow cytometer. Dual luciferase reporter gene assay was used to validate direct binding between miR-1307 and the 3'-UTR of CIC. Real-time PCR and western blot analyses, MTT and flow cytometry were used to reveal the biological effects of miR-1307 and CIC, as well as their regulation. RESULTS We found that miR-1307 affects cell cycle dynamics, cell viability in ovarian cancer cells. In addition, its expression level can influence chemosensitivity to paclitaxel in ovarian cancer cells. We also validate that CIC is a downstream target of miR-1307 via its regulation on 3'-UTR of CIC gene and ETV4 and ETV5 are also regulated by miR-1307/CIC axis. CONCLUSIONS Our data suggested that miR-1307 may be involved in the resistance of ovarian cancer to chemotherapy drugs via regulation of CIC, and should be further explored as a potential therapeutic target.
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Affiliation(s)
- Yingying Zhou
- Department of Obstetrics/Gynecology, Shengjing Hospital, China Medical University, Shenyang, China
| | - Min Wang
- Department of Obstetrics/Gynecology, Shengjing Hospital, China Medical University, Shenyang, China.
| | - Ting Shuang
- Department of Obstetrics/Gynecology, Shengjing Hospital, China Medical University, Shenyang, China; Department of Obstetrics/Gynecology, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shanxi, China
| | - Yisi Liu
- Department of Obstetrics/Gynecology, Shengjing Hospital, China Medical University, Shenyang, China; Cancer Hospital, China Medical University, Shenyang, China
| | - Yongqi Zhang
- Department of Obstetrics/Gynecology, Shengjing Hospital, China Medical University, Shenyang, China; Department of Obstetrics/Gynecology, Roicare Hospital & Clinics, Shenyang, China
| | - Cong Shi
- Department of Obstetrics/Gynecology, Shengjing Hospital, China Medical University, Shenyang, China; Women's and Children's Hospital, Shenyang, China
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The pivotal role of sampling recurrent tumors in the precision care of patients with tumors of the central nervous system. Cold Spring Harb Mol Case Stud 2019; 5:mcs.a004143. [PMID: 31371350 PMCID: PMC6672021 DOI: 10.1101/mcs.a004143] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 05/20/2019] [Indexed: 12/18/2022] Open
Abstract
Effective management of brain and spine tumors relies on a multidisciplinary approach encompassing surgery, radiation, and systemic therapy. In the era of personalized oncology, the latter is complemented by various molecularly targeting agents. Precise identification of cellular targets for these drugs requires comprehensive profiling of the cancer genome coupled with an efficient analytic pipeline, leading to an informed decision on drug selection, prognosis, and confirmation of the original pathological diagnosis. Acquisition of optimal tumor tissue for such analysis is paramount and often presents logistical challenges in neurosurgery. Here, we describe the experience and results of the Personalized OncoGenomics (POG) program with a focus on tumors of the central nervous system (CNS). Patients with recurrent CNS tumors were consented and enrolled into the POG program prior to accrual of tumor and matched blood followed by whole-genome and transcriptome sequencing and processing through the POG bioinformatic pipeline. Sixteen patients were enrolled into POG. In each case, POG analyses identified genomic drivers including novel oncogenic fusions, aberrant pathways, and putative therapeutic targets. POG has highlighted that personalized oncology is truly a multidisciplinary field, one in which neurosurgeons must play a vital role if these programs are to succeed and benefit our patients.
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50
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Taylor CA, Cormier KW, Keenan SE, Earnest S, Stippec S, Wichaidit C, Juang YC, Wang J, Shvartsman SY, Goldsmith EJ, Cobb MH. Functional divergence caused by mutations in an energetic hotspot in ERK2. Proc Natl Acad Sci U S A 2019; 116:15514-15523. [PMID: 31296562 PMCID: PMC6681740 DOI: 10.1073/pnas.1905015116] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The most frequent extracellular signal-regulated kinase 2 (ERK2) mutation occurring in cancers is E322K (E-K). ERK2 E-K reverses a buried charge in the ERK2 common docking (CD) site, a region that binds activators, inhibitors, and substrates. Little is known about the cellular consequences associated with this mutation, other than apparent increases in tumor resistance to pathway inhibitors. ERK2 E-K, like the mutation of the preceding aspartate (ERK2 D321N [D-N]) known as the sevenmaker mutation, causes increased activity in cells and evades inactivation by dual-specificity phosphatases. As opposed to findings in cancer cells, in developmental assays in Drosophila, only ERK2 D-N displays a significant gain of function, revealing mutation-specific phenotypes. The crystal structure of ERK2 D-N is indistinguishable from that of wild-type protein, yet this mutant displays increased thermal stability. In contrast, the crystal structure of ERK2 E-K reveals profound structural changes, including disorder in the CD site and exposure of the activation loop phosphorylation sites, which likely account for the decreased thermal stability of the protein. These contiguous mutations in the CD site of ERK2 are both required for docking interactions but lead to unpredictably different functional outcomes. Our results suggest that the CD site is in an energetically strained configuration, and this helps drive conformational changes at distal sites on ERK2 during docking interactions.
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Affiliation(s)
- Clinton A Taylor
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390
| | - Kevin W Cormier
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390
| | - Shannon E Keenan
- Department of Chemical and Biological Engineering, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Svetlana Earnest
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390
| | - Steve Stippec
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390
| | - Chonlarat Wichaidit
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390
| | - Yu-Chi Juang
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390
| | - Junmei Wang
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390
| | - Stanislav Y Shvartsman
- Department of Chemical and Biological Engineering, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | | | - Melanie H Cobb
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390;
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