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Perycz M, Dabrowski MJ, Jardanowska-Kotuniak M, Roura AJ, Gielniewski B, Stepniak K, Dramiński M, Ciechomska IA, Kaminska B, Wojtas B. Comprehensive analysis of the REST transcription factor regulatory networks in IDH mutant and IDH wild-type glioma cell lines and tumors. Acta Neuropathol Commun 2024; 12:72. [PMID: 38711090 PMCID: PMC11071216 DOI: 10.1186/s40478-024-01779-y] [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: 06/19/2023] [Accepted: 04/09/2024] [Indexed: 05/08/2024] Open
Abstract
The RE1-silencing transcription factor (REST) acts either as a repressor or activator of transcription depending on the genomic and cellular context. REST is a key player in brain cell differentiation by inducing chromatin modifications, including DNA methylation, in a proximity of its binding sites. Its dysfunction may contribute to oncogenesis. Mutations in IDH1/2 significantly change the epigenome contributing to blockade of cell differentiation and glioma development. We aimed at defining how REST modulates gene activation and repression in the context of the IDH mutation-related phenotype in gliomas. We studied the effects of REST knockdown, genome wide occurrence of REST binding sites, and DNA methylation of REST motifs in IDH wild type and IDH mutant gliomas. We found that REST target genes, REST binding patterns, and TF motif occurrence proximal to REST binding sites differed in IDH wild-type and mutant gliomas. Among differentially expressed REST targets were genes involved in glial cell differentiation and extracellular matrix organization, some of which were differentially methylated at promoters or gene bodies. REST knockdown differently impacted invasion of the parental or IDH1 mutant glioma cells. The canonical REST-repressed gene targets showed significant correlation with the GBM NPC-like cellular state. Interestingly, results of REST or KAISO silencing suggested the interplay between these TFs in regulation of REST-activated and repressed targets. The identified gene regulatory networks and putative REST cooperativity with other TFs, such as KAISO, show distinct REST target regulatory networks in IDH-WT and IDH-MUT gliomas, without concomitant DNA methylation changes. We conclude that REST could be an important therapeutic target in gliomas.
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Affiliation(s)
- Malgorzata Perycz
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
- Computational Biology Group, Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland
| | - Michal J Dabrowski
- Computational Biology Group, Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland
| | - Marta Jardanowska-Kotuniak
- Computational Biology Group, Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland
- Doctoral School of Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Adria-Jaume Roura
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Bartlomiej Gielniewski
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Karolina Stepniak
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Michał Dramiński
- Computational Biology Group, Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland
| | - Iwona A Ciechomska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Bozena Kaminska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Bartosz Wojtas
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland.
- Laboratory of Sequencing, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland.
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Parajuli KR, Jung Y, Taichman RS. Abscisic acid signaling through LANCL2 and PPARγ induces activation of p38MAPK resulting in dormancy of prostate cancer metastatic cells. Oncol Rep 2024; 51:39. [PMID: 38624012 PMCID: PMC10804438 DOI: 10.3892/or.2024.8698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/12/2023] [Indexed: 04/17/2024] Open
Abstract
Prostate cancer (PCa) is one the most common malignancies in men. The high incidence of bone metastasis years after primary therapy suggests that disseminated tumor cells must become dormant, but maintain their ability to proliferate in the bone marrow. Abscisic acid (ABA) is a stress response molecule best known for its regulation of seed germination, stomal opening, root shoot growth and other stress responses in plants. ABA is also synthesized by mammalian cells and has been linked to human disease. The aim of the present study was to examine the role of ABA in regulating tumor dormancy via signaling through lanthionine synthetase C‑like protein 2 (LANCL2) and peroxisome proliferator activated receptor γ (PPARγ) receptors. ABA signaling in human PCa cell lines was studied using targeted gene knockdown (KD), western blotting, quantitative PCR, cell proliferation, migration, invasion and soft agar assays, as well as co‑culture assays with bone marrow stromal cells. The data demonstrated that ABA signaling increased the expression of p21, p27 and p16, while inhibiting viability, migration, invasion and colony size in a reversable manner without toxicity. ABA also induced p38MAPK activation and NR2F1 signaling. Targeted gene KD of LANCL2 and PPARγ abrogated the cellular responses to ABA. Taken together, these data demonstrate that ABA may induce dormancy in PCa cell lines through LANCL2 and PPARγ signaling, and suggest novel targets to manage metastatic PCa growth.
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Affiliation(s)
- Keshab Raj Parajuli
- Department of Periodontology, University of Alabama at Birmingham School of Dentistry, Birmingham, AL 35294, USA
| | - Younghun Jung
- Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, MI 48109, USA
| | - Russell S. Taichman
- Department of Periodontology, University of Alabama at Birmingham School of Dentistry, Birmingham, AL 35294, USA
- Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, MI 48109, USA
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Kim Y, Lee HM. CRISPR-Cas System Is an Effective Tool for Identifying Drug Combinations That Provide Synergistic Therapeutic Potential in Cancers. Cells 2023; 12:2593. [PMID: 37998328 PMCID: PMC10670858 DOI: 10.3390/cells12222593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/30/2023] [Accepted: 11/06/2023] [Indexed: 11/25/2023] Open
Abstract
Despite numerous efforts, the therapeutic advancement for neuroblastoma and other cancer treatments is still ongoing due to multiple challenges, such as the increasing prevalence of cancers and therapy resistance development in tumors. To overcome such obstacles, drug combinations are one of the promising applications. However, identifying and implementing effective drug combinations are critical for achieving favorable treatment outcomes. Given the enormous possibilities of combinations, a rational approach is required to predict the impact of drug combinations. Thus, CRISPR-Cas-based and other approaches, such as high-throughput pharmacological and genetic screening approaches, have been used to identify possible drug combinations. In particular, the CRISPR-Cas system (Clustered Regularly Interspaced Short Palindromic Repeats) is a powerful tool that enables us to efficiently identify possible drug combinations that can improve treatment outcomes by reducing the total search space. In this review, we discuss the rational approaches to identifying, examining, and predicting drug combinations and their impact.
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Affiliation(s)
| | - Hyeong-Min Lee
- Department of Computational Biology, St. Jude Research Hospital, Memphis, TN 38105, USA;
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Jin L, Liu Y, Wu Y, Huang Y, Zhang D. REST Is Not Resting: REST/NRSF in Health and Disease. Biomolecules 2023; 13:1477. [PMID: 37892159 PMCID: PMC10605157 DOI: 10.3390/biom13101477] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 09/26/2023] [Accepted: 09/29/2023] [Indexed: 10/29/2023] Open
Abstract
Chromatin modifications play a crucial role in the regulation of gene expression. The repressor element-1 (RE1) silencing transcription factor (REST), also known as neuron-restrictive silencer factor (NRSF) and X2 box repressor (XBR), was found to regulate gene transcription by binding to chromatin and recruiting chromatin-modifying enzymes. Earlier studies revealed that REST plays an important role in the development and disease of the nervous system, mainly by repressing the transcription of neuron-specific genes. Subsequently, REST was found to be critical in other tissues, such as the heart, pancreas, skin, eye, and vascular. Dysregulation of REST was also found in nervous and non-nervous system cancers. In parallel, multiple strategies to target REST have been developed. In this paper, we provide a comprehensive summary of the research progress made over the past 28 years since the discovery of REST, encompassing both physiological and pathological aspects. These insights into the effects and mechanisms of REST contribute to an in-depth understanding of the transcriptional regulatory mechanisms of genes and their roles in the development and progression of disease, with a view to discovering potential therapeutic targets and intervention strategies for various related diseases.
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Affiliation(s)
- Lili Jin
- School of Life Sciences, Liaoning University, Shenyang 110036, China
| | - Ying Liu
- Department of Stem Cells and Regenerative Medicine, Key Laboratory of Cell Biology, National Health Commission of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang 110122, China
| | - Yifan Wu
- Department of Stem Cells and Regenerative Medicine, Key Laboratory of Cell Biology, National Health Commission of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang 110122, China
| | - Yi Huang
- Department of Stem Cells and Regenerative Medicine, Key Laboratory of Cell Biology, National Health Commission of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang 110122, China
| | - Dianbao Zhang
- Department of Stem Cells and Regenerative Medicine, Key Laboratory of Cell Biology, National Health Commission of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang 110122, China
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Idris M, Coussement L, Alves MM, De Meyer T, Melotte V. Promoter hypermethylation of neural-related genes is compatible with stemness in solid cancers. Epigenetics Chromatin 2023; 16:31. [PMID: 37537688 PMCID: PMC10398991 DOI: 10.1186/s13072-023-00505-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/22/2023] [Indexed: 08/05/2023] Open
Abstract
BACKGROUND DNA hypermethylation is an epigenetic feature that modulates gene expression, and its deregulation is observed in cancer. Previously, we identified a neural-related DNA hypermethylation fingerprint in colon cancer, where most of the top hypermethylated and downregulated genes have known functions in the nervous system. To evaluate the presence of this signature and its relevance to carcinogenesis in general, we considered 16 solid cancer types available in The Cancer Genome Atlas (TCGA). RESULTS All tested cancers showed significant enrichment for neural-related genes amongst hypermethylated genes. This signature was already present in two premalignant tissue types and could not be explained by potential confounders such as bivalency status or tumor purity. Further characterization of the neural-related DNA hypermethylation signature in colon cancer showed particular enrichment for genes that are overexpressed during neural differentiation. Lastly, an analysis of upstream regulators identified RE1-Silencing Transcription factor (REST) as a potential mediator of this DNA methylation signature. CONCLUSION Our study confirms the presence of a neural-related DNA hypermethylation fingerprint in various cancers, of genes linked to neural differentiation, and points to REST as a possible regulator of this mechanism. We propose that this fingerprint indicates an involvement of DNA hypermethylation in the preservation of neural stemness in cancer cells.
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Affiliation(s)
- Musa Idris
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, P.O. Box 616, 6229 HX, Maastricht, The Netherlands
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children's Hospital, 3015 GD, Rotterdam, The Netherlands
| | - Louis Coussement
- Department of Data Analysis and Mathematical Modelling, Ghent University, 9000, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, 9000, Ghent, Belgium
| | - Maria M Alves
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children's Hospital, 3015 GD, Rotterdam, The Netherlands
| | - Tim De Meyer
- Department of Data Analysis and Mathematical Modelling, Ghent University, 9000, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, 9000, Ghent, Belgium
| | - Veerle Melotte
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, P.O. Box 616, 6229 HX, Maastricht, The Netherlands.
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children's Hospital, 3015 GD, Rotterdam, The Netherlands.
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Vega-Benedetti AF, Loi E, Moi L, Zavattari P. DNA methylation alterations at RE1-silencing transcription factor binding sites and their flanking regions in cancer. Clin Epigenetics 2023; 15:98. [PMID: 37301955 PMCID: PMC10257853 DOI: 10.1186/s13148-023-01514-9] [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: 01/11/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
BACKGROUND DNA methylation changes, frequent early events in cancer, can modulate the binding of transcription factors. RE1-silencing transcription factor (REST) plays a fundamental role in regulating the expression of neuronal genes, and in particular their silencing in non-neuronal tissues, by inducing chromatin modifications, including DNA methylation changes, not only in the proximity of its binding sites but also in the flanking regions. REST has been found aberrantly expressed in brain cancer and other cancer types. In this work, we investigated DNA methylation alterations at REST binding sites and their flanking regions in a brain cancer (pilocytic astrocytoma), two gastrointestinal tumours (colorectal cancer and biliary tract cancer) and a blood cancer (chronic lymphocytic leukemia). RESULTS Differential methylation analyses focused on REST binding sites and their flanking regions were conducted between tumour and normal samples from our experimental datasets analysed by Illumina microarrays and the identified alterations were validated using publicly available datasets. We discovered distinct DNA methylation patterns between pilocytic astrocytoma and the other cancer types in agreement with the opposite oncogenic and tumour suppressive role of REST in glioma and non-brain tumours. CONCLUSIONS Our results suggest that these DNA methylation alterations in cancer may be associated with REST dysfunction opening the enthusiastic possibility to develop novel therapeutic interventions based on the modulation of this master regulator in order to restore the aberrant methylation of its target regions into a normal status.
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Affiliation(s)
| | - Eleonora Loi
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, 09042, Cagliari, Italy
| | - Loredana Moi
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, 09042, Cagliari, Italy
| | - Patrizia Zavattari
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, 09042, Cagliari, Italy.
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Karapurkar JK, Kim MS, Colaco JC, Suresh B, Sarodaya N, Kim DH, Park CH, Hong SH, Kim KS, Ramakrishna S. CRISPR/Cas9-based genome-wide screening of the deubiquitinase subfamily identifies USP3 as a protein stabilizer of REST blocking neuronal differentiation and promotes neuroblastoma tumorigenesis. J Exp Clin Cancer Res 2023; 42:121. [PMID: 37170124 PMCID: PMC10176696 DOI: 10.1186/s13046-023-02694-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 05/01/2023] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND The repressor element-1 silencing transcription factor (REST), a master transcriptional repressor, is essential for maintenance, self-renewal, and differentiation in neuroblastoma. An elevated expression of REST is associated with impaired neuronal differentiation, which results in aggressive neuroblastoma formation. E3 ligases are known to regulate REST protein abundance through the 26 S proteasomal degradation pathway in neuroblastoma. However, deubiquitinating enzymes (DUBs), which counteract the function of E3 ligase-mediated REST protein degradation and their impact on neuroblastoma tumorigenesis have remained unexplored. METHODS We employed a CRISPR/Cas9 system to perform a genome-wide knockout of ubiquitin-specific proteases (USPs) and used western blot analysis to screen for DUBs that regulate REST protein abundance. The interaction between USP3 and REST was confirmed by immunoprecipitation and Duolink in situ proximity assays. The deubiquitinating effect of USP3 on REST protein degradation, half-life, and neuronal differentiation was validated by immunoprecipitation, in vitro deubiquitination, protein-turnover, and immunostaining assays. The correlation between USP3 and REST expression was assessed using patient neuroblastoma datasets. The USP3 gene knockout in neuroblastoma cells was performed using CRISPR/Cas9, and the clinical relevance of USP3 regulating REST-mediated neuroblastoma tumorigenesis was confirmed by in vitro and in vivo oncogenic experiments. RESULTS We identified a deubiquitinase USP3 that interacts with, stabilizes, and increases the half-life of REST protein by counteracting its ubiquitination in neuroblastoma. An in silico analysis showed a correlation between USP3 and REST in multiple neuroblastoma cell lines and identified USP3 as a prognostic marker for overall survival in neuroblastoma patients. Silencing of USP3 led to a decreased self-renewal capacity and promoted retinoic acid-induced differentiation in neuroblastoma. A loss of USP3 led to attenuation of REST-mediated neuroblastoma tumorigenesis in a mouse xenograft model. CONCLUSION The findings of this study indicate that USP3 is a critical factor that blocks neuronal differentiation, which can lead to neuroblastoma. We envision that targeting USP3 in neuroblastoma tumors might provide an effective therapeutic differentiation strategy for improved survival rates of neuroblastoma patients.
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Affiliation(s)
| | - Min-Seong Kim
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, 04763, South Korea
| | - Jencia Carminha Colaco
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, 04763, South Korea
| | - Bharathi Suresh
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, 04763, South Korea
| | - Neha Sarodaya
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, 04763, South Korea
| | - Dong-Ho Kim
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, 04763, South Korea
| | - Chang-Hwan Park
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, 04763, South Korea
- College of Medicine, Hanyang University, Seoul, 04763, South Korea
| | - Seok-Ho Hong
- Department of Internal Medicine, School of Medicine, Kangwon National University, Chuncheon, South Korea
| | - Kye-Seong Kim
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, 04763, South Korea.
- College of Medicine, Hanyang University, Seoul, 04763, South Korea.
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, 04763, South Korea.
- College of Medicine, Hanyang University, Seoul, 04763, South Korea.
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The NRSF/REST transcription factor in hallmarks of cancer: From molecular mechanisms to clinical relevance. Biochimie 2023; 206:116-134. [PMID: 36283507 DOI: 10.1016/j.biochi.2022.10.012] [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: 08/27/2022] [Revised: 10/07/2022] [Accepted: 10/17/2022] [Indexed: 11/23/2022]
Abstract
The RE-1 silencing transcription factor (REST), or neuron restrictive silencing factor (NRSF), was first identified as a repressor of neuronal genes in non-neuronal tissue. Interestingly, this transcription factor may act as a tumor suppressor or an oncogenic role in developing neuroendocrine and other tumors in patients. The hallmarks of cancer include six biological processes, including proliferative signaling, evasion of growth suppressors, resistance to cell death, replicative immortality, inducing angiogenesis, and activating invasion and metastasis. In addition to two emerging hallmarks, the reprogramming of energy metabolism and evasion of the immune response are all implicated in the development of human tumors. It is essential to know the role of these processes as they will affect the outcome of alternatives for cancer treatment. Various studies in this review demonstrate that NRSF/REST affects the different hallmarks of cancer that could position NRSF/REST as an essential target in the therapy and diagnosis of certain types of cancer.
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Wang G, Yang X, Qi M, Li M, Dong M, Xu R, Zhang C. Systematic analysis identifies REST as an oncogenic and immunological biomarker in glioma. Sci Rep 2023; 13:3023. [PMID: 36810892 PMCID: PMC9944962 DOI: 10.1038/s41598-023-30248-0] [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: 04/18/2022] [Accepted: 02/20/2023] [Indexed: 02/23/2023] Open
Abstract
The repressor element 1 silencing transcription factor (REST) has been proposed to function as a transcription factor to silence gene transcription by binding to repressor element 1 (RE1), a highly conserved DNA motif. The functions of REST in various tumors have been studied, but its role and correlation with immune cell infiltration remains uncertain in gliomas. REST expression was analyzed in datasets of The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) and validated by the Gene Expression Omnibus and Human Protein Atlas databases. The clinical prognosis of REST was evaluated by clinical survival data of TCGA cohort and validated by Chinese Glioma Genome Atlas cohort. MicroRNAs (miRNAs) contributing to REST overexpression in glioma were identified by a combination of a series of in silico analyses, including expression analysis, correlation analysis, and survival analysis. The correlations between immune cell infiltration level and REST expression were analyzed by TIMER2 and GEPIA2 tools. Enrichment analysis of REST was performed using STRING and Metascape tools. The expression and function of predicted upstream miRNAs at REST and their association with glioma malignancy and migration were also confirmed in glioma cell lines. REST was highly expressed and associated with poorer overall survival and disease-specific survival in glioma and some other tumors. MiR-105-5p and miR-9-5p were identified as the most potential upstream miRNAs of REST in glioma patient cohort and experiments in vitro. REST expression was positively correlated with infiltration of immune cells and the expression of immune checkpoints such as PD1/PD-L1 and CTLA-4 in glioma. Furthermore, histone deacetylase 1 (HDAC1) was a potential REST-related gene in glioma. Enrichment analysis of REST found chromatin organization and histone modification were the most significant enriched terms, and Hedgehog-Gli pathway might be involved in the effect of REST on the pathogenesis of glioma. Our study suggests REST to be an oncogenic gene and the biomarker of poor prognosis in glioma. High REST expression might affect the tumor microenvironment of glioma. More basic experiments and large clinical trials aimed at the carcinogenetic study of REST in glioma will be needed in the future.
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Affiliation(s)
- Guan Wang
- grid.452402.50000 0004 1808 3430Department of Pediatrics, Qilu Hospital of Shandong University, No.107 West Wenhua Road, Jinan, 250012 Shandong Province China
| | - Xiaxin Yang
- grid.452402.50000 0004 1808 3430Department of Neurology, Qilu Hospital of Shandong University, No.107 West Wenhua Road, Jinan, 250012 Shandong Province China
| | - Mei Qi
- grid.452402.50000 0004 1808 3430Department of Pathology, Qilu Hospital of Shandong University, No.107 West Wenhua Road, Jinan, 250012 Shandong Province China
| | - Meng Li
- grid.452402.50000 0004 1808 3430Department of Pediatrics, Qilu Hospital of Shandong University, No.107 West Wenhua Road, Jinan, 250012 Shandong Province China
| | - Meng Dong
- grid.452402.50000 0004 1808 3430Department of Pediatrics, Qilu Hospital of Shandong University, No.107 West Wenhua Road, Jinan, 250012 Shandong Province China
| | - Rui Xu
- grid.452402.50000 0004 1808 3430Department of Pediatrics, Qilu Hospital of Shandong University, No.107 West Wenhua Road, Jinan, 250012 Shandong Province China
| | - Chen Zhang
- Department of Pediatrics, Qilu Hospital of Shandong University, No.107 West Wenhua Road, Jinan, 250012, Shandong Province, China.
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Yoshida M, Oda C, Mishima K, Tsuji I, Obika S, Shimojo M. An antisense amido-bridged nucleic acid gapmer oligonucleotide targeting SRRM4 alters REST splicing and exhibits anti-tumor effects in small cell lung cancer and prostate cancer cells. Cancer Cell Int 2023; 23:8. [PMID: 36650528 PMCID: PMC9847160 DOI: 10.1186/s12935-022-02842-1] [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: 10/15/2022] [Accepted: 12/27/2022] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Antisense oligonucleotide (ASO) medicine for clinical applications has been becoming a reality. We previously developed a gapmer ASO targeting Ser/Arg repetitive matrix 4 (SRRM4) that is abnormally expressed in small cell lung cancer (SCLC). However the detailed mechanism of ASO through repressing SRRM4 has not been completely elucidated. Further, effectiveness of SRRM4 ASO to prostate cancer (PCa) cells expressing SRRM4 similar to SCLC remains to be elucidated. RE1-silencing transcription factor (REST) is a tumor suppressor, and its splicing isoform (sREST) is abnormally expressed by SRRM4 and causes carcinogenesis with neuroendocrine phenotype in SCLC. The present study aimed to understand the contribution of REST splicing by SRRM4 ASO administration. METHODS SRRM4 expression and REST splicing were analyzed by RT-qPCR and conventional RT-PCR after treating SRRM4 ASO, and cell viability was analyzed in vitro. Exogenous reconstitution of Flag-tagged REST plasmid in SCLC cells and the splice-switching oligonucleotide (SSO) specific for REST was analyzed for cell viability. Furthermore, we expanded the application of SRRM4 ASO in PCa cells abnormally expressing SRRM4 mRNA in vitro. RESULTS SRRM4 ASO successfully downregulated SRRM4 expression, followed by repressed cell viability of SCLC and PCa cells in a dose-dependent manner. Administration of SRRM4 ASO then modified the alternative splicing of REST, resulting reduced cell viability. REST SSO specifically modified REST splicing increased REST expression, resulting in reduced cell viability. CONCLUSIONS Our data demonstrate that a gapmer ASO targeting SRRM4 (SRRM4 ASO) reduces cell viability through splicing changes of REST, followed by affecting REST-controlled genes in recalcitrant tumors SCLC and PCa cells.
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Affiliation(s)
- Misa Yoshida
- grid.136593.b0000 0004 0373 3971Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Chihiro Oda
- grid.136593.b0000 0004 0373 3971School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Keishiro Mishima
- grid.136593.b0000 0004 0373 3971Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Itsuki Tsuji
- grid.136593.b0000 0004 0373 3971Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Satoshi Obika
- grid.136593.b0000 0004 0373 3971Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871 Japan ,grid.136593.b0000 0004 0373 3971School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871 Japan ,grid.136593.b0000 0004 0373 3971Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Osaka, 565-0871 Japan ,grid.482562.fNational Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Ibaraki, Osaka 567-0085 Japan
| | - Masahito Shimojo
- grid.136593.b0000 0004 0373 3971Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871 Japan
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Loss of the repressor REST affects progesterone receptor function and promotes uterine leiomyoma pathogenesis. Proc Natl Acad Sci U S A 2022; 119:e2205524119. [PMID: 36282915 PMCID: PMC9636955 DOI: 10.1073/pnas.2205524119] [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: 02/01/2023] Open
Abstract
Uterine leiomyomas (UL) are benign tumors that arise in the myometrial layer of the uterus. The standard treatment option for UL is hysterectomy, although hormonal therapies, such as selective progesterone receptor modulators, are often used as temporary treatment options to reduce symptoms or to slow the growth of tumors. However, since the pathogenesis of UL is poorly understood and most hormonal therapies are not based on UL-specific, divergent hormone signaling pathways, hallmarks that predict long-term efficacy and safety of pharmacotherapies remain largely undefined. In a previous study, we reported that aberrant expression of repressor element 1 silencing transcription factor/neuron-restrictive silencing factor (REST/NRSF) target genes activate UL growth due to the near ubiquitous loss of REST. Here, we show that ablation of the Rest gene in mouse uterus leads to UL phenotype and gene-expression patterns analogous to UL, including altered estrogen and progesterone signaling pathways. We demonstrate that many of the genes dysregulated in UL harbor cis-regulatory elements bound by REST and progesterone receptor (PGR) adjacent to each other. Crucially, we identify an interaction between REST and PGR in healthy myometrium and present a putative mechanism for the dysregulation of progesterone-responsive genes in UL ensuing in the loss of REST. Using three Rest conditional knockout mouse lines, we provide a comprehensive picture of the impact loss of REST has in UL pathogenesis and in altering the response of UL to steroid hormones.
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Hu Y, Zhu S, Xu R, Wang M, Chen F, Zhang Z, Feng B, Wang J, Chen Z, Wang J. Delta-catenin attenuates medulloblastoma cell invasion by targeting EMT pathway. Front Genet 2022; 13:867872. [PMID: 36303547 PMCID: PMC9595215 DOI: 10.3389/fgene.2022.867872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 07/08/2022] [Indexed: 11/18/2022] Open
Abstract
Background: Medulloblastoma is the most common pediatric malignant tumor in central nervous system. Although its prognosis has been improved enormously by the combination treatments with surgery, radiotherapy, and chemotherapy, it still could progress via invasion and distant dissemination. We aimed to investigate molecular mechanisms of medulloblastoma invasion in the current work. Methods: The gene expression profile of medulloblastoma were analyzed based on the data deposited in Gene Expression Omnibus (GEO) and filtered according to brain specific proteins in the Uniprot. Delta-catenin was identified and further analyzed about its expression and roles in the prognosis of medulloblastoma patient. The function of delta-catenin on cell invasion and migration were investigated by transwell and wound healing assay. Whether delta-catenin participates in the epithelial-mesenchymal transition (EMT) regulated invasion was also studied. Results: Delta-catenin expression was highly upregulated in tumor tissues compared to normal tissues from medulloblastoma patients in five independent, nonoverlapping cohorts. Furthermore, delta-catenin expression level was upregulated in WNT subgroup, and significantly correlated with better prognosis, and associated with metastasis through GEO database analysis. Functional assays indicated that delta-catenin inhibited medulloblastoma cell invasion and migration through regulating the key factors of EMT pathway, such as E-cadherin and vimentin. Conclusion: Delta-catenin might be a positive predictor for prognosis of medulloblastoma patients, through attenuating medulloblastoma cell invasion by inhibiting EMT pathway.
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Affiliation(s)
- Yuanjun Hu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
- Department of Neurosurgery/Neuro-Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Neurosurgery, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Sihan Zhu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
- Department of Neurosurgery/Neuro-Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Rizhen Xu
- Department of Surgery, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Manxia Wang
- Department of Pharmacology, Guangdong Pharmaceutical University, Guangzhou, China
| | - Furong Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Zeshun Zhang
- Department of Surgery, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Binghong Feng
- Department of Pharmacology, Guangdong Pharmaceutical University, Guangzhou, China
| | - Jian Wang
- Department of Neurosurgery/Neuro-Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
- *Correspondence: Jing Wang, Zhongping Chen, Jian Wang,
| | - Zhongping Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
- Department of Neurosurgery/Neuro-Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
- *Correspondence: Jing Wang, Zhongping Chen, Jian Wang,
| | - Jing Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
- Department of Neurosurgery/Neuro-Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
- *Correspondence: Jing Wang, Zhongping Chen, Jian Wang,
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Long-Distance Repression by Human Silencers: Chromatin Interactions and Phase Separation in Silencers. Cells 2022; 11:cells11091560. [PMID: 35563864 PMCID: PMC9101175 DOI: 10.3390/cells11091560] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/01/2022] [Accepted: 05/02/2022] [Indexed: 12/12/2022] Open
Abstract
Three-dimensional genome organization represents an additional layer in the epigenetic regulation of gene expression. Active transcription controlled by enhancers or super-enhancers has been extensively studied. Enhancers or super-enhancers can recruit activators or co-activators to activate target gene expression through long-range chromatin interactions. Chromatin interactions and phase separation play important roles in terms of enhancer or super-enhancer functioning. Silencers are another major type of cis-regulatory element that can mediate gene regulation by turning off or reducing gene expression. However, compared to active transcription, silencer studies are still in their infancy. This review covers the current knowledge of human silencers, especially the roles of chromatin interactions and phase separation in silencers. This review also proposes future directions for human silencer studies.
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Duly AMP, Kao FCL, Teo WS, Kavallaris M. βIII-Tubulin Gene Regulation in Health and Disease. Front Cell Dev Biol 2022; 10:851542. [PMID: 35573698 PMCID: PMC9096907 DOI: 10.3389/fcell.2022.851542] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 04/07/2022] [Indexed: 11/24/2022] Open
Abstract
Microtubule proteins form a dynamic component of the cytoskeleton, and play key roles in cellular processes, such as vesicular transport, cell motility and mitosis. Expression of microtubule proteins are often dysregulated in cancer. In particular, the microtubule protein βIII-tubulin, encoded by the TUBB3 gene, is aberrantly expressed in a range of epithelial tumours and is associated with drug resistance and aggressive disease. In normal cells, TUBB3 expression is tightly restricted, and is found almost exclusively in neuronal and testicular tissues. Understanding the mechanisms that control TUBB3 expression, both in cancer, mature and developing tissues will help to unravel the basic biology of the protein, its role in cancer, and may ultimately lead to the development of new therapeutic approaches to target this protein. This review is devoted to the transcriptional and posttranscriptional regulation of TUBB3 in normal and cancerous tissue.
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Affiliation(s)
- Alastair M. P. Duly
- Children’s Cancer Institute, Lowy Cancer Research Center, UNSW Sydney, Randwick, NSW, Australia
| | - Felicity C. L. Kao
- Children’s Cancer Institute, Lowy Cancer Research Center, UNSW Sydney, Randwick, NSW, Australia
- Australian Center for NanoMedicine, UNSW Sydney, Sydney, NSW, Australia
- School of Women and Children’s Health, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Wee Siang Teo
- Children’s Cancer Institute, Lowy Cancer Research Center, UNSW Sydney, Randwick, NSW, Australia
- Australian Center for NanoMedicine, UNSW Sydney, Sydney, NSW, Australia
| | - Maria Kavallaris
- Children’s Cancer Institute, Lowy Cancer Research Center, UNSW Sydney, Randwick, NSW, Australia
- Australian Center for NanoMedicine, UNSW Sydney, Sydney, NSW, Australia
- School of Women and Children’s Health, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
- UNSW RNA Institute, UNSW Sydney, Sydney, NSW, Australia
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15
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LaFleur MW, Sharpe AH. CRISPR Screens to Identify Regulators of Tumor Immunity. ANNUAL REVIEW OF CANCER BIOLOGY 2022; 6:103-122. [PMID: 35989706 PMCID: PMC9389862 DOI: 10.1146/annurev-cancerbio-070120-094725] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cancer immunotherapies, such as immune checkpoint blockade (ICB), have been used in a wide range of tumor types with immense clinical benefit. However, ICB does not work in all patients, and attempts to combine ICB with other immune-based therapies have not lived up to their initial promise. Thus, there is a significant unmet need to discover new targets and combination therapies to extend the benefits of immunotherapy to more patients. Systems biology approaches are well suited for addressing this problem because these approaches enable evaluation of many gene targets simultaneously and ranking their relative importance for a phenotype of interest. As such, loss-of-function CRISPR screens are an emerging set of tools being used to prioritize gene targets for modulating pathways of interest in tumor and immune cells. This review describes the first screens performed to discover cancer immunotherapy targets and the technological advances that will enable next-generation screens.
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Affiliation(s)
- Martin W LaFleur
- Department of Immunology and Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Arlene H Sharpe
- Department of Immunology and Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts, USA
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16
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Shyamala N, Kongettira CL, Puranam K, Kupsal K, Kummari R, Padala C, Hanumanth SR. In silico identification of single nucleotide variations at CpG sites regulating CpG island existence and size. Sci Rep 2022; 12:3574. [PMID: 35246549 PMCID: PMC8897451 DOI: 10.1038/s41598-022-05198-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 01/03/2022] [Indexed: 12/20/2022] Open
Abstract
Genetic and epigenetic modifications of genes involved in the key regulatory pathways play a significant role in the pathophysiology and progression of multifactorial diseases. The present study is an attempt to identify single nucleotide variations (SNVs) at CpG sites of promoters of ACAT1, APOB, APOE, CYBA, FAS, FLT1, KSR2, LDLR, MMP9, PCSK9, PHOX2A, REST, SH2B3, SORT1 and TIMP1 genes influencing CpG island (CGI) existence and size associated with the pathophysiology of Diabetes mellitus, Coronary artery disease and Cancers. Promoter sequences located between -2000 to + 2000 bp were retrieved from the EPDnew database and predicted the CpG island using MethPrimer. Further, SNVs at CpG sites were accessed from NCBI, Ensembl while transcription factor (TF) binding sites were accessed using AliBaba2.1. CGI existence and size were determined for each SNV at CpG site with respect to wild type and variant allele by MethPrimer. A total of 200 SNVs at CpG sites were analyzed from the promoters of ACAT1, APOB, APOE, CYBA, FAS, FLT1, KSR2, LDLR, MMP9, PCSK9, PHOX2A, REST, SH2B3, SORT1 and TIMP1 genes. Of these, only 17 (8.5%) SNVs were found to influence the loss of CGI while 70 (35%) SNVs were found to reduce the size of CGI. It has also been found that 59% (10) of CGI abolishing SNVs are showing differences in binding of TFs. The findings of the study suggest that the candidate SNVs at CpG sites regulating CGI existence and size might influence the DNA methylation status and expression of genes involved in molecular pathways associated with several diseases. The insights of the present study may pave the way for new experimental studies to undertake challenges in DNA methylation, gene expression and protein assays.
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Affiliation(s)
- Nivas Shyamala
- Department of Genetics and Biotechnology, University College of Science, Osmania University, Hyderabad, 500007, Telangana State, India
| | - Chaitra Lava Kongettira
- Department of Genetics and Biotechnology, University College of Science, Osmania University, Hyderabad, 500007, Telangana State, India
| | - Kaushik Puranam
- Department of Genetics and Biotechnology, University College of Science, Osmania University, Hyderabad, 500007, Telangana State, India
| | - Keerthi Kupsal
- Department of Genetics and Biotechnology, University College of Science, Osmania University, Hyderabad, 500007, Telangana State, India
| | - Ramanjaneyulu Kummari
- Department of Genetics and Biotechnology, University College of Science, Osmania University, Hyderabad, 500007, Telangana State, India
| | - Chiranjeevi Padala
- Department of Genetics and Biotechnology, University College of Science, Osmania University, Hyderabad, 500007, Telangana State, India
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, Telangana State, India
| | - Surekha Rani Hanumanth
- Department of Genetics and Biotechnology, University College of Science, Osmania University, Hyderabad, 500007, Telangana State, India.
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17
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A reassessment of Jackson's checklist and identification of two Down syndrome sub-phenotypes. Sci Rep 2022; 12:3104. [PMID: 35210468 PMCID: PMC8873406 DOI: 10.1038/s41598-022-06984-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 02/10/2022] [Indexed: 11/08/2022] Open
Abstract
Down syndrome (DS) is characterised by several clinical features including intellectual disability (ID) and craniofacial dysmorphisms. In 1976, Jackson and coll. identified a checklist of signs for clinical diagnosis of DS; the utility of these checklists in improving the accuracy of clinical diagnosis has been recently reaffirmed, but they have rarely been revised. The purpose of this work is to reassess the characteristic phenotypic signs and their frequencies in 233 DS subjects, following Jackson's checklist. 63.77% of the subjects showed more than 12 signs while none showed less than 5, confirming the effectiveness of Jackson's checklist for the clinical diagnosis of DS. An association between three phenotypic signs emerged, allowing us to distinguish two sub-phenotypes: Brachycephaly, short and broad Hands, short Neck (BHN), which is more frequent, and "non-BHN". The strong association of these signs might be interpreted in the context of the growth defects observed in DS children suggesting decreased cell proliferation. Lastly, cognitive assessments were investigated for 114 subjects. The lack of association between the presence of a physical sign or the number of signs present in a subject and cognitive skills disproves the stereotype that physical characteristics are predictive of degree of ID.
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18
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Cloud AS, Vargheese AM, Gunewardena S, Shimak RM, Ganeshkumar S, Kumaraswamy E, Jensen RA, Chennathukuzhi VM. Loss of REST in breast cancer promotes tumor progression through estrogen sensitization, MMP24 and CEMIP overexpression. BMC Cancer 2022; 22:180. [PMID: 35177031 PMCID: PMC8851790 DOI: 10.1186/s12885-022-09280-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 02/08/2022] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Breast cancer is the most common malignancy in women, and is both pathologically and genetically heterogeneous, making early detection and treatment difficult. A subset of breast cancers express normal levels of REST (repressor element 1 silencing transcription factor) mRNA but lack functional REST protein. Loss of REST function is seen in ~ 20% of breast cancers and is associated with a more aggressive phenotype and poor prognosis. Despite the frequent loss of REST, little is known about the role of REST in the molecular pathogenesis of breast cancer. METHODS TCGA data was analyzed for the expression of REST target genes in breast cancer patient samples. We then utilized gene knockdown in MCF-7 cells in the presence or absence of steroid hormones estrogen and/ progesterone followed by RNA sequencing, as well as chromatin immunoprecipitation and PCR in an attempt to understand the tumor suppressor role of REST in breast cancer. RESULTS We show that REST directly regulates CEMIP (cell migration-inducing and hyaluronan-binding protein, KIAA1199) and MMP24 (matrix metallopeptidase 24), genes known to have roles in invasion and metastasis. REST knockdown in breast cancer cells leads to significant upregulation of CEMIP and MMP24. In addition, we found REST binds to RE-1 sites (repressor element-1) within the genes and influences their transcription. Furthermore, we found that the estrogen receptor (ESR1) signaling pathway is activated in the absence of REST, regardless of hormone treatment. CONCLUSIONS We demonstrate a critical role for the loss of REST in aggressive breast cancer pathogenesis and provide evidence for REST as an important diagnostic marker for personalized treatment plans.
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Affiliation(s)
- Ashley S. Cloud
- grid.412016.00000 0001 2177 6375Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS USA
| | - Aditya M. Vargheese
- grid.412016.00000 0001 2177 6375Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS USA ,grid.468219.00000 0004 0408 2680The University of Kansas Cancer Center, Kansas City, KS USA ,grid.266515.30000 0001 2106 0692University of Kansas, Lawrence, KS USA
| | - Sumedha Gunewardena
- grid.412016.00000 0001 2177 6375Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS USA ,grid.412016.00000 0001 2177 6375Department of Biostatistics, University of Kansas Medical Center, Kansas City, KS USA
| | - Raeann M. Shimak
- grid.468219.00000 0004 0408 2680The University of Kansas Cancer Center, Kansas City, KS USA ,grid.412016.00000 0001 2177 6375Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS USA
| | - Sornakala Ganeshkumar
- grid.412016.00000 0001 2177 6375Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS USA
| | - Easwari Kumaraswamy
- grid.468219.00000 0004 0408 2680The University of Kansas Cancer Center, Kansas City, KS USA ,grid.412016.00000 0001 2177 6375Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS USA
| | - Roy A. Jensen
- grid.468219.00000 0004 0408 2680The University of Kansas Cancer Center, Kansas City, KS USA ,grid.266515.30000 0001 2106 0692University of Kansas, Lawrence, KS USA ,grid.412016.00000 0001 2177 6375Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS USA ,grid.412016.00000 0001 2177 6375Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS USA ,grid.412016.00000 0001 2177 6375Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS USA
| | - Vargheese M. Chennathukuzhi
- grid.412016.00000 0001 2177 6375Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS USA ,grid.468219.00000 0004 0408 2680The University of Kansas Cancer Center, Kansas City, KS USA
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Jamali L, Sadeghi H, Ghasemi MR, Mohseni R, Nazemalhosseini-Mojarad E, Yassaee VR, Larki P, Zali MR, Mirfakhraie R. Autophagy ATG16L1 rs2241880 impacts the colorectal cancer risk: A case-control study. J Clin Lab Anal 2021; 36:e24169. [PMID: 34894411 PMCID: PMC8761398 DOI: 10.1002/jcla.24169] [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: 09/20/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 11/29/2022] Open
Abstract
Background Despite many efforts to discover the important role of the autophagy process in the pathogenesis of colorectal cancer (CRC), the exact involved molecular mechanism still remains to be elucidated. Recently, a limited number of studies have been employed to discover the impact of autophagy genes’ variants on the development and progression of CRC. Here, we evaluated the association between two single‐nucleotide polymorphisms (SNPs) in the main components of the autophagy genes, ATG16L1 rs2241880, and ATG5 rs1475270, and the CRC risk in an Iranian population. Methods During this investigation, a total of 369 subjects, including 179 CRC patients and 190 non‐cancer controls have been genotyped using Tetra‐primer amplification refractory mutation system‐polymerase chain reaction (TP‐ARMS‐PCR) method. Result The results demonstrated that the T allele of the ATG16L1 rs2241880 was significantly associated with the increased risk of CRC in the studied population (OR 1.64, 95% CI: 1.21–2.22, p = 0.0015). Moreover, ATG16L1 rs2241880 TT genotype increased the susceptibility to CRC (OR 3.31, 95% CI: 1.64–6.69, p = 0.0008). Furthermore, a significant association was observed under the recessive and dominant inheritance models (p = 0.0015 and p = 0.017, respectively). No statistically significant differences were found in the ATG5 rs1475270 alleles and genotypes between the cases and controls. Conclusion The results of the present study may be helpful concerning the risk stratification in CRC patients based on the genotyping approach of autophagy pathways and emphasize the need for further investigations among different populations and ethnicities to refine our conclusions.
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Affiliation(s)
- Leila Jamali
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Sadeghi
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad-Reza Ghasemi
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Roohollah Mohseni
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Ehsan Nazemalhosseini-Mojarad
- Department of Gastrointestinal Cancer, Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Vahid Reza Yassaee
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Pegah Larki
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Department of Gastrointestinal Cancer, Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Reza Mirfakhraie
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Hematopoietic Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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20
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Gao Y, Kabotyanski EB, Shepherd JH, Villegas E, Acosta D, Hamor C, Sun T, Montmeyor-Garcia C, He X, Dobrolecki LE, Westbrook TF, Lewis MT, Hilsenbeck SG, Zhang XHF, Perou CM, Rosen JM. Tumor suppressor PLK2 may serve as a biomarker in triple-negative breast cancer for improved response to PLK1 therapeutics. CANCER RESEARCH COMMUNICATIONS 2021; 1:178-193. [PMID: 35156101 PMCID: PMC8827906 DOI: 10.1158/2767-9764.crc-21-0106] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
Polo-like kinase (PLK) family members play important roles in cell cycle regulation. The founding member PLK1 is oncogenic and preclinically validated as a cancer therapeutic target. Paradoxically, frequent loss of chromosome 5q11-35 which includes PLK2 is observed in basal-like breast cancer. In this study, we found that PLK2 was tumor suppressive in breast cancer, preferentially in basal-like and triple-negative breast cancer (TNBC) subtypes. Knockdown of PLK1 rescued phenotypes induced by PLK2-loss both in vitro and in vivo. We also demonstrated that PLK2 directly interacted with PLK1 at prometaphase through the kinase but not the polo-box domains of PLK2, suggesting PLK2 functioned at least partially through the interaction with PLK1. Furthermore, an improved treatment response was seen in both Plk2-deleted/low mouse preclinical and PDX TNBC models using the PLK1 inhibitor volasertib alone or in combination with carboplatin. Re-expression of PLK2 in an inducible PLK2-null mouse model reduced the therapeutic efficacy of volasertib. In summary, this study delineates the effects of chromosome 5q loss in TNBC that includes PLK2, the relationship between PLK2 and PLK1, and how this may render PLK2-deleted/low tumors more sensitive to PLK1 inhibition in combination with chemotherapy.
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Affiliation(s)
- Yang Gao
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Elena B. Kabotyanski
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | | | | | - Deanna Acosta
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Clark Hamor
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Tingting Sun
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Verna & Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas
| | | | - Xiaping He
- The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Lacey E. Dobrolecki
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Thomas F. Westbrook
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Verna & Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas
| | - Michael T. Lewis
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Susan G. Hilsenbeck
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Xiang H.-F. Zhang
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- McNair Medical Institute, Baylor College of Medicine, Houston, Texas
| | - Charles M. Perou
- The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jeffrey M. Rosen
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Corresponding Author: Jeffrey M. Rosen, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030. Phone: 832-215-9503; E-mail:
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21
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Chauhan R, Bhat AA, Masoodi T, Bagga P, Reddy R, Gupta A, Sheikh ZA, Macha MA, Haris M, Singh M. Ubiquitin-specific peptidase 37: an important cog in the oncogenic machinery of cancerous cells. J Exp Clin Cancer Res 2021; 40:356. [PMID: 34758854 PMCID: PMC8579576 DOI: 10.1186/s13046-021-02163-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/29/2021] [Indexed: 02/08/2023] Open
Abstract
Protein ubiquitination is one of the most crucial posttranslational modifications responsible for regulating the stability and activity of proteins involved in homeostatic cellular function. Inconsistencies in the ubiquitination process may lead to tumorigenesis. Ubiquitin-specific peptidases are attractive therapeutic targets in different cancers and are being evaluated for clinical development. Ubiquitin-specific peptidase 37 (USP37) is one of the least studied members of the USP family. USP37 controls numerous aspects of oncogenesis, including stabilizing many different oncoproteins. Recent work highlights the role of USP37 in stimulating the epithelial-mesenchymal transition and metastasis in lung and breast cancer by stabilizing SNAI1 and stimulating the sonic hedgehog pathway, respectively. Several aspects of USP37 biology in cancer cells are yet unclear and are an active area of research. This review emphasizes the importance of USP37 in cancer and how identifying its molecular targets and signalling networks in various cancer types can help advance cancer therapeutics.
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Affiliation(s)
- Ravi Chauhan
- Department of Medical Oncology (Lab), All India Institute of Medical Sciences, New Delhi, India
| | - Ajaz A Bhat
- Laboratory of Molecular and Metabolic Imaging, Cancer Research Department, Sidra Medicine, Doha, Qatar
| | - Tariq Masoodi
- Department of Genomic Medicine, Genetikode, Mumbai, India
| | - Puneet Bagga
- Department of Diagnostic Imaging, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ravinder Reddy
- Center for Advanced Metabolic Imaging in Precision Medicine, Department of Radiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, USA
| | - Ashna Gupta
- Department of Medical Oncology (Lab), All India Institute of Medical Sciences, New Delhi, India
| | - Zahoor Ahmad Sheikh
- Department of Surgical Oncology, Sher-I-Kashmir Institute of Medical Sciences, Srinagar, Jammu and Kashmir, India
| | - Muzafar A Macha
- Watson-Crick Centre for Molecular Medicine, Islamic University of Science and Technology, Pulwama, India
| | - Mohammad Haris
- Laboratory of Molecular and Metabolic Imaging, Cancer Research Department, Sidra Medicine, Doha, Qatar.
- Center for Advanced Metabolic Imaging in Precision Medicine, Department of Radiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, USA.
- Laboratory Animal Research Center, Qatar University, Doha, Qatar.
| | - Mayank Singh
- Department of Medical Oncology (Lab), All India Institute of Medical Sciences, New Delhi, India.
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22
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A Monoallelic Variant in REST Is Associated with Non-Syndromic Autosomal Dominant Hearing Impairment in a South African Family. Genes (Basel) 2021; 12:genes12111765. [PMID: 34828371 PMCID: PMC8618167 DOI: 10.3390/genes12111765] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 10/31/2021] [Accepted: 11/02/2021] [Indexed: 01/03/2023] Open
Abstract
Hearing impairment (HI) is a sensory disorder with a prevalence of 0.0055 live births in South Africa. DNA samples from a South African family presenting with progressive, autosomal dominant non-syndromic HI were subjected to whole-exome sequencing, and a novel monoallelic variant in REST [c.1244GC; p.(C415S)], was identified as the putative causative variant. The co-segregation of the variant was confirmed with Sanger Sequencing. The variant is absent from databases, 103 healthy South African controls, and 52 South African probands with isolated HI. In silico analysis indicates that the p.C415S variant in REST substitutes a conserved cysteine and results in changes to the surrounding secondary structure and the disulphide bonds, culminating in alteration of the tertiary structure of REST. Localization studies using ectopically expressed GFP-tagged Wild type (WT) and mutant REST in HEK-293 cells show that WT REST localizes exclusively to the nucleus; however, the mutant protein localizes throughout the cell. Additionally, mutant REST has an impaired ability to repress its known target AF1q. The data demonstrates that the identified mutation compromises the function of REST and support its implication in HI. This study is the second report, worldwide, to implicate REST in HI and suggests that it should be included in diagnostic HI panels.
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23
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He R, Zhang X, Ding L. DBX2 promotes glioblastoma cell proliferation by regulating REST expression. Curr Pharm Biotechnol 2021; 23:1101-1108. [PMID: 34463226 DOI: 10.2174/1389201022666210830142827] [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: 03/06/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Glioblastoma (GBM) is the most common but lethal brain cancer with poor prognosis. The developing brain homeobox 2 (DBX2) has been reported to play important roles in tumor growth. However, the mechanisms of DBX2 in GBM are still unknown. OBJECTIVE This study aims to investigate the function and mechanisms of DBX2 in GBM. METHODS The expressions of DBX2 and REST in GBM were measured by analyzing data from databases, and the results were checked by qPCR and/or western blot of GBM cell lines. Cell proliferation was determined by CCK8 assay, immunohistochemistry and colony formation assay. ChIP-qPCR was used to determine the binding sites of DBX2 on REST. RESULTS In this study, we found that the expression of DBX2 was upregulated in the GBM cell lines. The cell proliferation was damaged after blocking DBX2 expression in U87 and U251 GBM cell lines. The expression level of DBX2 had a positive relationship with that of REST. Our ChIP-qPCR results showed that DBX2 is directly bound to the promoter region of REST. Additionally, the increased GBM cell proliferation caused by DBX2 overexpression can be rescued by REST loss of function. CONCLUSION DBX2 could promote cell proliferation of GBM by binding to the promoter region of REST gene and increasing REST expression.
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Affiliation(s)
- Ruixing He
- Neurosurgery Department, the Affiliated Huai'an No.1 People's Hospital of Nanjing Medical University, Jiangsu. China
| | - Xiaotian Zhang
- Neurosurgery Department, Hongze Huai'an District People's Hospital, Jiangsu. China
| | - Lianshu Ding
- Neurosurgery Department, the Affiliated Huai'an No.1 People's Hospital of Nanjing Medical University, Jiangsu. China
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24
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Drainas AP, Lambuta RA, Ivanova I, Serçin Ö, Sarropoulos I, Smith ML, Efthymiopoulos T, Raeder B, Stütz AM, Waszak SM, Mardin BR, Korbel JO. Genome-wide Screens Implicate Loss of Cullin Ring Ligase 3 in Persistent Proliferation and Genome Instability in TP53-Deficient Cells. Cell Rep 2021; 31:107465. [PMID: 32268084 PMCID: PMC7166082 DOI: 10.1016/j.celrep.2020.03.029] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 11/07/2019] [Accepted: 03/10/2020] [Indexed: 12/22/2022] Open
Abstract
TP53 deficiency is the most common alteration in cancer; however, this alone is typically insufficient to drive tumorigenesis. To identify genes promoting tumorigenesis in combination with TP53 deficiency, we perform genome-wide CRISPR-Cas9 knockout screens coupled with proliferation and transformation assays in isogenic cell lines. Loss of several known tumor suppressors enhances cellular proliferation and transformation. Loss of neddylation pathway genes promotes uncontrolled proliferation exclusively in TP53-deficient cells. Combined loss of CUL3 and TP53 activates an oncogenic transcriptional program governed by the nuclear factor κB (NF-κB), AP-1, and transforming growth factor β (TGF-β) pathways. This program maintains persistent cellular proliferation, induces partial epithelial to mesenchymal transition, and increases DNA damage, genomic instability, and chromosomal rearrangements. Our findings reveal CUL3 loss as a key event stimulating persistent proliferation in TP53-deficient cells. These findings may be clinically relevant, since TP53-CUL3-deficient cells are highly sensitive to ataxia telangiectasia mutated (ATM) inhibition, exposing a vulnerability that could be exploited for cancer treatment. Mixed-effect models with MEMcrispR applied to CRISPR screen analyses Knockout of neddylation genes increases persistent proliferation in TP53−/− cells TP53−/−,CUL3−/− cells exhibit persistent proliferation and partial EMT phenotype TP53−/−,CUL3−/− cells show increased DNA damage and display sensitivity to ATM inhibition
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Affiliation(s)
- Alexandros P Drainas
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Ruxandra A Lambuta
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Irina Ivanova
- BioMed X Innovation Center, 69120 Heidelberg, Germany
| | | | - Ioannis Sarropoulos
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Mike L Smith
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Theocharis Efthymiopoulos
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Benjamin Raeder
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Adrian M Stütz
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Sebastian M Waszak
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | | | - Jan O Korbel
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany.
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25
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Zhang M, Ceyhan Y, Kaftanovskaya EM, Vasquez JL, Vacher J, Knop FK, Nathanson L, Agoulnik AI, Ittmann MM, Agoulnik IU. INPP4B protects from metabolic syndrome and associated disorders. Commun Biol 2021; 4:416. [PMID: 33772116 PMCID: PMC7998001 DOI: 10.1038/s42003-021-01940-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 03/03/2021] [Indexed: 02/01/2023] Open
Abstract
A high fat diet and obesity have been linked to the development of metabolic dysfunction and the promotion of multiple cancers. The causative cellular signals are multifactorial and not yet completely understood. In this report, we show that Inositol Polyphosphate-4-Phosphatase Type II B (INPP4B) signaling protects mice from diet-induced metabolic dysfunction. INPP4B suppresses AKT and PKC signaling in the liver thereby improving insulin sensitivity. INPP4B loss results in the proteolytic cleavage and activation of a key regulator in de novo lipogenesis and lipid storage, SREBP1. In mice fed with the high fat diet, SREBP1 increases expression and activity of PPARG and other lipogenic pathways, leading to obesity and non-alcoholic fatty liver disease (NAFLD). Inpp4b-/- male mice have reduced energy expenditure and respiratory exchange ratio leading to increased adiposity and insulin resistance. When treated with high fat diet, Inpp4b-/- males develop type II diabetes and inflammation of adipose tissue and prostate. In turn, inflammation drives the development of high-grade prostatic intraepithelial neoplasia (PIN). Thus, INPP4B plays a crucial role in maintenance of overall metabolic health and protects from prostate neoplasms associated with metabolic dysfunction.
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Affiliation(s)
- Manqi Zhang
- Department of Medicine, Duke University, Durham, NC, USA
| | - Yasemin Ceyhan
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Elena M Kaftanovskaya
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Judy L Vasquez
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Jean Vacher
- Department of Medicine, Institut de Recherches Cliniques de Montréal, Université de Montréal, Montréal, QC, Canada
| | - Filip K Knop
- Center for Clinical Metabolic Research, Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
| | - Lubov Nathanson
- Institute for Neuro Immune Medicine, Dr. Kiran C. Patel College of Osteopathic Medicine, Nova Southeastern University, Ft. Lauderdale, FL, USA
| | - Alexander I Agoulnik
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
| | - Michael M Ittmann
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
- Michael E. DeBakey Department of Veterans Affairs Medical Center, Houston, TX, USA
| | - Irina U Agoulnik
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA.
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
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26
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Thomas ZV, Wang Z, Zang C. BART Cancer: a web resource for transcriptional regulators in cancer genomes. NAR Cancer 2021; 3:zcab011. [PMID: 33778495 PMCID: PMC7984808 DOI: 10.1093/narcan/zcab011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/09/2021] [Accepted: 03/01/2021] [Indexed: 11/13/2022] Open
Abstract
Dysregulation of gene expression plays an important role in cancer development. Identifying transcriptional regulators, including transcription factors and chromatin regulators, that drive the oncogenic gene expression program is a critical task in cancer research. Genomic profiles of active transcriptional regulators from primary cancer samples are limited in the public domain. Here we present BART Cancer (bartcancer.org), an interactive web resource database to display the putative transcriptional regulators that are responsible for differentially regulated genes in 15 different cancer types in The Cancer Genome Atlas (TCGA). BART Cancer integrates over 10000 gene expression profiling RNA-seq datasets from TCGA with over 7000 ChIP-seq datasets from the Cistrome Data Browser database and the Gene Expression Omnibus (GEO). BART Cancer uses Binding Analysis for Regulation of Transcription (BART) for predicting the transcriptional regulators from the differentially expressed genes in cancer samples compared to normal samples. BART Cancer also displays the activities of over 900 transcriptional regulators across cancer types, by integrating computational prediction results from BART and the Cistrome Cancer database. Focusing on transcriptional regulator activities in human cancers, BART Cancer can provide unique insights into epigenetics and transcriptional regulation in cancer, and is a useful data resource for genomics and cancer research communities.
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Affiliation(s)
- Zachary V Thomas
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
| | - Zhenjia Wang
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Chongzhi Zang
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA
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27
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Ma M, Zhou Y, Sun R, Shi J, Tan Y, Yang H, Zhang M, Shen R, Xu L, Wang Z, Fei J. STAT3 and AKT signaling pathways mediate oncogenic role of NRSF in hepatocellular carcinoma. Acta Biochim Biophys Sin (Shanghai) 2020; 52:1063-1070. [PMID: 32556117 DOI: 10.1093/abbs/gmaa069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/06/2020] [Accepted: 03/09/2020] [Indexed: 02/07/2023] Open
Abstract
Neuron-restrictive silencer factor (NRSF) is a zinc finger protein that acts as a negative transcriptional regulator by recruiting histone deacetylases and other co-factors. It plays a crucial role in nervous system development and is recently reported to be involved in tumorigenesis in a tumor type-dependent manner; however, the role of NRSF in hepatocellular carcinoma (HCC) tumorigenesis remains unclear. Here, we found that NRSF expression was up-regulated in 27 of 49 human HCC tissue samples examined. Additionally, mice with conditional NRSF-knockout in the liver exhibited a higher tolerance against diethylnitrosamine (DEN)-induced acute liver injury and were less sensitive to DEN-induced HCC initiation. Our results showed that silencing NRSF in HepG2 cells using RNAi technology significantly inhibited HepG2 cell proliferation and severely hindered their migration and invasion potentials. Our results demonstrated that NRSF plays a pivotal role in promoting DEN-induced HCC initiation via a mechanism related to the STAT3 and AKT signaling pathways. Thus, NRSF could be a potential therapeutic target for treating human HCC.
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Affiliation(s)
- Ming Ma
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Yunhe Zhou
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
- Sports and Health Research Center, Tongji University, Shanghai 200092, China
| | - Ruilin Sun
- Shanghai Engineering Research Center for Model Organisms, SMOC, Shanghai 201318, China
| | - Jiahao Shi
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Yutong Tan
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Hua Yang
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Mengjie Zhang
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Ruling Shen
- Joint Laboratory for Model Organism, Shanghai Laboratory Animal Research Center, Shanghai 201203, China
| | - Leon Xu
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Zhugang Wang
- Shanghai Engineering Research Center for Model Organisms, SMOC, Shanghai 201318, China
| | - Jian Fei
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
- Shanghai Engineering Research Center for Model Organisms, SMOC, Shanghai 201318, China
- Joint Laboratory for Model Organism, Shanghai Laboratory Animal Research Center, Shanghai 201203, China
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28
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Liu H, Paddock MN, Wang H, Murphy CJ, Geck RC, Navarro AJ, Wulf GM, Elemento O, Haucke V, Cantley LC, Toker A. The INPP4B Tumor Suppressor Modulates EGFR Trafficking and Promotes Triple-Negative Breast Cancer. Cancer Discov 2020; 10:1226-1239. [PMID: 32513774 DOI: 10.1158/2159-8290.cd-19-1262] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 04/22/2020] [Accepted: 06/02/2020] [Indexed: 11/16/2022]
Abstract
Inactivation of the tumor suppressor lipid phosphatase INPP4B is common in triple-negative breast cancer (TNBC). We generated a genetically engineered TNBC mouse model deficient in INPP4B. We found a dose-dependent increase in tumor incidence in INPP4B homozygous and heterozygous knockout mice compared with wild-type (WT), supporting a role for INPP4B as a tumor suppressor in TNBC. Tumors derived from INPP4B knockout mice are enriched for AKT and MEK gene signatures. Consequently, mice with INPP4B deficiency are more sensitive to PI3K or MEK inhibitors compared with WT mice. Mechanistically, we found that INPP4B deficiency increases PI(3,4)P2 levels in endocytic vesicles but not at the plasma membrane. Moreover, INPP4B loss delays degradation of EGFR and MET, while promoting recycling of receptor tyrosine kinases (RTK), thus enhancing the duration and amplitude of signaling output upon growth factor stimulation. Therefore, INPP4B inactivation in TNBC promotes tumorigenesis by modulating RTK recycling and signaling duration. SIGNIFICANCE: Inactivation of the lipid phosphatase INPP4B is frequent in TNBC. Using a genetically engineered mouse model, we show that INPP4B functions as a tumor suppressor in TNBC. INPP4B regulates RTK trafficking and degradation, such that loss of INPP4B prolongs both PI3K and ERK activation.This article is highlighted in the In This Issue feature, p. 1079.
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Affiliation(s)
- Hui Liu
- Department of Pathology and Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts.
| | | | - Haibin Wang
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Charles J Murphy
- Meyer Cancer Center, Weill Cornell Medicine, New York, New York.,Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - Renee C Geck
- Department of Pathology and Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Adrija J Navarro
- Department of Pathology and Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Gerburg M Wulf
- Division of Hematology/Oncology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Olivier Elemento
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - Volker Haucke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Lewis C Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, New York.
| | - Alex Toker
- Department of Pathology and Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts. .,Ludwig Center at Harvard, Boston, Massachusetts
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29
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Gupta R, Malvi P, Parajuli KR, Janostiak R, Bugide S, Cai G, Zhu LJ, Green MR, Wajapeyee N. KLF7 promotes pancreatic cancer growth and metastasis by up-regulating ISG expression and maintaining Golgi complex integrity. Proc Natl Acad Sci U S A 2020; 117:12341-12351. [PMID: 32430335 PMCID: PMC7275752 DOI: 10.1073/pnas.2005156117] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer with a dismal prognosis. Currently, there is no effective therapy for PDAC, and a detailed molecular and functional evaluation of PDACs is needed to identify and develop better therapeutic strategies. Here we show that the transcription factor Krüppel-like factor 7 (KLF7) is overexpressed in PDACs, and that inhibition of KLF7 blocks PDAC tumor growth and metastasis in cell culture and in mice. KLF7 expression in PDACs can be up-regulated due to activation of a MAP kinase pathway or inactivation of the tumor suppressor p53, two alterations that occur in a large majority of PDACs. ShRNA-mediated knockdown of KLF7 inhibits the expression of IFN-stimulated genes (ISGs), which are necessary for KLF7-mediated PDAC tumor growth and metastasis. KLF7 knockdown also results in the down-regulation of Discs Large MAGUK Scaffold Protein 3 (DLG3), resulting in Golgi complex fragmentation, and reduced protein glycosylation, leading to reduced secretion of cancer-promoting growth factors, such as chemokines. Genetic or pharmacologic activation of Golgi complex fragmentation blocks PDAC growth and metastasis similar to KLF7 inhibition. Our results demonstrate a therapeutically amenable, KLF7-driven pathway that promotes PDAC growth and metastasis by activating ISGs and maintaining Golgi complex integrity.
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Affiliation(s)
- Romi Gupta
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35233
| | - Parmanand Malvi
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35233
| | - Keshab Raj Parajuli
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35233
| | - Radoslav Janostiak
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510
| | - Suresh Bugide
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35233
| | - Guoping Cai
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510
| | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Michael R Green
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605;
| | - Narendra Wajapeyee
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35233;
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30
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Shen C, Yan T, Tong T, Shi D, Ren L, Zhang Y, Zhang X, Cao Y, Yan Y, Ma Y, Zhu X, Tian X, Fang JY, Chen H, Ji L, Hong J, Xuan B. ALKBH4 Functions as a Suppressor of Colorectal Cancer Metastasis via Competitively Binding to WDR5. Front Cell Dev Biol 2020; 8:293. [PMID: 32478065 PMCID: PMC7240015 DOI: 10.3389/fcell.2020.00293] [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: 02/02/2020] [Accepted: 04/06/2020] [Indexed: 12/29/2022] Open
Abstract
Background Epithelial-Mesenchymal Transition (EMT) is a major process in the initiation of tumor metastasis, where cancer cells lose sessile epithelial potential and gain mesenchymal phenotype. Large-scale cell identity shifts are often orchestrated on an epigenetic level and the interplay between epigenetic factors and EMT progression was still largely unknown. In this study, we tried to identify candidate epigenetic factors that involved in EMT progression. Methods Colorectal cancer (CRC) cells were transfected with an arrayed shRNA library targeting 384 genes involved in epigenetic modification. Candidate genes were identified by real-time PCR. Western blot, RNA-seq and gene set enrichment analysis were conducted to confirm the suppressive role of ALKBH4 in EMT. The clinical relevance of ALKBH4 in CRC was investigated in two independent Renji Cohorts and a microarray dataset (GSE21510) from GEO database. In vitro transwell assay and in vivo metastatic tumor model were performed to explore the biological function of ALKBH4 in the metastasis of CRC. Co-IP (Co-Immunoprecipitation) and ChIP (Chromatin Immunoprecipitation) assays were employed to uncover the mechanism. Results We screened for candidate epigenetic factors that affected EMT process and identified ALKBH4 as a candidate EMT suppressor gene, which was significantly downregulated in CRC patients. Decreased level of ALKBH4 was associated with metastasis and predicted poor prognosis of CRC patients. Follow-up functional experiments illustrated overexpression of ALKBH4 inhibited the invasion ability of CRC cells in vitro, as well as their metastatic capability in vivo. Mechanistically, CO-IP and ChIP assays indicated that ALKBH4 competitively bound WDR5 (a key component of histone methyltransferase complex) and decreased H3K4me3 histone modification on the target genes including MIR21. Conclusions This study illustrated that ALKBH4 may function as a novel metastasis suppressor of CRC, and inhibits H3K4me3 modification through binding WDR5 during EMT.
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Affiliation(s)
- Chaoqin Shen
- State Key Laboratory of Oncogenes and Related Genes, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Institute of Digestive Disease, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Tingting Yan
- State Key Laboratory of Oncogenes and Related Genes, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Institute of Digestive Disease, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Tianying Tong
- State Key Laboratory of Oncogenes and Related Genes, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Institute of Digestive Disease, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Debin Shi
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Linlin Ren
- State Key Laboratory of Oncogenes and Related Genes, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Institute of Digestive Disease, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Youwei Zhang
- Department of Medical Oncology, Xuzhou Central Hospital, Xuzhou Medical University, Xuzhou, China
| | - Xinyu Zhang
- State Key Laboratory of Oncogenes and Related Genes, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Institute of Digestive Disease, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yingying Cao
- State Key Laboratory of Oncogenes and Related Genes, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Institute of Digestive Disease, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yuqing Yan
- State Key Laboratory of Oncogenes and Related Genes, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Institute of Digestive Disease, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yanru Ma
- State Key Laboratory of Oncogenes and Related Genes, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Institute of Digestive Disease, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoqiang Zhu
- State Key Laboratory of Oncogenes and Related Genes, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Institute of Digestive Disease, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xianglong Tian
- State Key Laboratory of Oncogenes and Related Genes, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Institute of Digestive Disease, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jing-Yuan Fang
- State Key Laboratory of Oncogenes and Related Genes, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Institute of Digestive Disease, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Haoyan Chen
- State Key Laboratory of Oncogenes and Related Genes, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Institute of Digestive Disease, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Linhua Ji
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Hong
- State Key Laboratory of Oncogenes and Related Genes, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Institute of Digestive Disease, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Baoqin Xuan
- State Key Laboratory of Oncogenes and Related Genes, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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31
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Li M, Nopparat J, Aguilar BJ, Chen YH, Zhang J, Du J, Ai X, Luo Y, Jiang Y, Boykin C, Lu Q. Intratumor δ-catenin heterogeneity driven by genomic rearrangement dictates growth factor dependent prostate cancer progression. Oncogene 2020; 39:4358-4374. [PMID: 32313227 PMCID: PMC10493073 DOI: 10.1038/s41388-020-1281-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 03/17/2020] [Accepted: 03/19/2020] [Indexed: 11/09/2022]
Abstract
Only a small number of genes are bona fide oncogenes and tumor suppressors such as Ras, Myc, β-catenin, p53, and APC. However, targeting these cancer drivers frequently fail to demonstrate sustained cancer remission. Tumor heterogeneity and evolution contribute to cancer resistance and pose challenges for cancer therapy due to differential genomic rearrangement and expression driving distinct tumor responses to treatments. Here we report that intratumor heterogeneity of Wnt/β-catenin modulator δ-catenin controls individual cell behavior to promote cancer. The differential intratumor subcellular localization of δ-catenin mirrors its compartmentalization in prostate cancer xenograft cultures as result of mutation-rendered δ-catenin truncations. Wild-type and δ-catenin mutants displayed distinct protein interactomes that highlight rewiring of signal networks. Localization specific δ-catenin mutants influenced p120ctn-dependent Rho GTPase phosphorylation and shifted cells towards differential bFGF-responsive growth and motility, a known signal to bypass androgen receptor dependence. Mutant δ-catenin promoted Myc-induced prostate tumorigenesis while increasing bFGF-p38 MAP kinase signaling, β-catenin-HIF-1α expression, and the nuclear size. Therefore, intratumor δ-catenin heterogeneity originated from genetic remodeling promotes prostate cancer expansion towards androgen independent signaling, supporting a neomorphism model paradigm for targeting tumor progression.
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Affiliation(s)
- Mingchuan Li
- Department of Anatomy and Cell Biology, The Brody school of Medicine, East Carolina University, Greenville, North Carolina, USA 27834
- Department of Urological Surgery, Beijing An Zhen Hospital, Capital Medical University, Beijing, China
| | - Jongdee Nopparat
- Department of Anatomy and Cell Biology, The Brody school of Medicine, East Carolina University, Greenville, North Carolina, USA 27834
- Department of Anatomy, Prince of Songkla University, Songkhla, Thailand
| | - Byron J. Aguilar
- Department of Anatomy and Cell Biology, The Brody school of Medicine, East Carolina University, Greenville, North Carolina, USA 27834
| | - Yan-hua Chen
- Department of Anatomy and Cell Biology, The Brody school of Medicine, East Carolina University, Greenville, North Carolina, USA 27834
| | - Jiao Zhang
- Department of Anatomy and Cell Biology, The Brody school of Medicine, East Carolina University, Greenville, North Carolina, USA 27834
| | - Jie Du
- Beijing Institute of Heart, Lung, and Blood Vessel Diseases, Beijing An Zhen Hospital, Capital Medical University, Beijing, China
| | - Xin Ai
- Dept. of Urology, PLA Army General Hospital, Beijing, China
| | - Yong Luo
- Department of Urological Surgery, Beijing An Zhen Hospital, Capital Medical University, Beijing, China
| | - Yongguang Jiang
- Department of Urological Surgery, Beijing An Zhen Hospital, Capital Medical University, Beijing, China
| | - Christi Boykin
- Department of Anatomy and Cell Biology, The Brody school of Medicine, East Carolina University, Greenville, North Carolina, USA 27834
| | - Qun Lu
- Department of Anatomy and Cell Biology, The Brody school of Medicine, East Carolina University, Greenville, North Carolina, USA 27834
- Department of Urological Surgery, Beijing An Zhen Hospital, Capital Medical University, Beijing, China
- The Harriet and John Wooten Laboratory for Alzheimer’s and Neurodegenerative Diseases Research, The Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA 27834
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32
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Quemener AM, Bachelot L, Forestier A, Donnou-Fournet E, Gilot D, Galibert MD. The powerful world of antisense oligonucleotides: From bench to bedside. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 11:e1594. [PMID: 32233021 PMCID: PMC9285911 DOI: 10.1002/wrna.1594] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 02/12/2020] [Accepted: 02/26/2020] [Indexed: 12/19/2022]
Abstract
Antisense oligonucleotides (ASOs) represent a new and highly promising class of drugs for personalized medicine. In the last decade, major chemical developments and improvements of the backbone structure of ASOs have transformed them into true approved and commercialized drugs. ASOs target both DNA and RNA, including pre‐mRNA, mRNA, and ncRDA, based on sequence complementary. They are designed to be specific for each identified molecular and genetic alteration to restore a normal, physiological situation. Thus, the characterization of the underpinning mechanisms and alterations that sustain pathology is critical for accurate ASO‐design. ASOs can be used to cure both rare and common diseases, such as orphan genetic alterations and cancer. Through pioneering examples, this review shows the versatility of the mechanisms of action that provide ASOs with the potential capacity to achieve custom treatment, revolutionizing personalized medicine. This article is categorized under:RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Small Molecule–RNA Interactions
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Affiliation(s)
- Anaïs M Quemener
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)-UMR6290, ARC Foundation Labellized Team, Rennes, France
| | - Laura Bachelot
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)-UMR6290, ARC Foundation Labellized Team, Rennes, France
| | - Anne Forestier
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)-UMR6290, ARC Foundation Labellized Team, Rennes, France
| | - Emmanuelle Donnou-Fournet
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)-UMR6290, ARC Foundation Labellized Team, Rennes, France
| | - David Gilot
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)-UMR6290, ARC Foundation Labellized Team, Rennes, France
| | - Marie-Dominique Galibert
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)-UMR6290, ARC Foundation Labellized Team, Rennes, France.,Department of Molecular Genetics and Genomic, CHU Rennes, Hospital-University of Rennes, Rennes, France
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33
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Screening Genes Promoting Exit from Naive Pluripotency Based on Genome-Scale CRISPR-Cas9 Knockout. Stem Cells Int 2020; 2020:8483035. [PMID: 32089710 PMCID: PMC7023212 DOI: 10.1155/2020/8483035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 12/31/2019] [Accepted: 01/08/2020] [Indexed: 12/31/2022] Open
Abstract
Two of the main problems of stem cell and regenerative medicine are the exit of pluripotency and differentiation to functional cells or tissues. The answer to these two problems holds great value in the clinical translation of stem cell as well as regenerative medicine research. Although piling researches have revealed the truth about pluripotency maintenance, the mechanisms underlying pluripotent cell self-renewal, proliferation, and differentiation into specific cell lineages or tissues are yet to be defined. To this end, we took full advantage of a novel technology, namely, the genome-scale CRISPR-Cas9 knockout (GeCKO). As an effective way of introducing targeted loss-of-function mutations at specific sites in the genome, GeCKO is able to screen in an unbiased manner for key genes that promote exit from pluripotency in mouse embryonic stem cells (mESCs) for the first time. In this study, we successfully established a model based on GeCKO to screen the key genes in pluripotency withdrawal. Our strategies included lentiviral package and infection technology, lenti-Cas9 gene knockout technology, shRNA gene knockdown technology, next-generation sequencing, model-based analysis of genome-scale CRISPR-Cas9 knockout (MAGeCK analysis), GO analysis, and other methods. Our findings provide a novel approach for large-scale screening of genes involved in pluripotency exit and offer an entry point for cell fate regulation research.
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34
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Ganesh K, Basnet H, Kaygusuz Y, Laughney AM, He L, Sharma R, O'Rourke KP, Reuter VP, Huang YH, Turkekul M, Emrah E, Masilionis I, Manova-Todorova K, Weiser MR, Saltz LB, Garcia-Aguilar J, Koche R, Lowe SW, Pe'er D, Shia J, Massagué J. L1CAM defines the regenerative origin of metastasis-initiating cells in colorectal cancer. ACTA ACUST UNITED AC 2020; 1:28-45. [PMID: 32656539 DOI: 10.1038/s43018-019-0006-x] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Metastasis-initiating cells with stem-like properties drive cancer lethality, yet their origins and relationship to primary-tumor-initiating stem cells are not known. We show that L1CAM+ cells in human colorectal cancer (CRC) have metastasis-initiating capacity, and we define their relationship to tissue regeneration. L1CAM is not expressed in the homeostatic intestinal epithelium, but is induced and required for epithelial regeneration following colitis and in CRC organoid growth. By using human tissues and mouse models, we show that L1CAM is dispensable for adenoma initiation but required for orthotopic carcinoma propagation, liver metastatic colonization and chemoresistance. L1CAMhigh cells partially overlap with LGR5high stem-like cells in human CRC organoids. Disruption of intercellular epithelial contacts causes E-cadherin-REST transcriptional derepression of L1CAM, switching chemoresistant CRC progenitors from an L1CAMlow to an L1CAMhigh state. Thus, L1CAM dependency emerges in regenerative intestinal cells when epithelial integrity is lost, a phenotype of wound healing deployed in metastasis-initiating cells.
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Affiliation(s)
- Karuna Ganesh
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Harihar Basnet
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,These authors contributed equally: Harihar Basnet, Yasemin Kaygusuz, Ashley M. Laughney
| | - Yasemin Kaygusuz
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,These authors contributed equally: Harihar Basnet, Yasemin Kaygusuz, Ashley M. Laughney
| | - Ashley M Laughney
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Present address: Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.,These authors contributed equally: Harihar Basnet, Yasemin Kaygusuz, Ashley M. Laughney
| | - Lan He
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Roshan Sharma
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Applied Physics and Applied Math, Columbia University, New York, NY, USA.,Present address: New York Genome Center, New York, NY, USA
| | - Kevin P O'Rourke
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY, USA
| | - Vincent P Reuter
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yun-Han Huang
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY, USA
| | - Mesruh Turkekul
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ekrem Emrah
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Present address: Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL, USA
| | - Ignas Masilionis
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Katia Manova-Todorova
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Martin R Weiser
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Leonard B Saltz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Julio Garcia-Aguilar
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Richard Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Scott W Lowe
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dana Pe'er
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jinru Shia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joan Massagué
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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35
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Kim JW, Berrios C, Kim M, Schade AE, Adelmant G, Yeerna H, Damato E, Iniguez AB, Florens L, Washburn MP, Stegmaier K, Gray NS, Tamayo P, Gjoerup O, Marto JA, DeCaprio J, Hahn WC. STRIPAK directs PP2A activity toward MAP4K4 to promote oncogenic transformation of human cells. eLife 2020; 9:53003. [PMID: 31913126 PMCID: PMC6984821 DOI: 10.7554/elife.53003] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 01/07/2020] [Indexed: 12/13/2022] Open
Abstract
Alterations involving serine-threonine phosphatase PP2A subunits occur in a range of human cancers, and partial loss of PP2A function contributes to cell transformation. Displacement of regulatory B subunits by the SV40 Small T antigen (ST) or mutation/deletion of PP2A subunits alters the abundance and types of PP2A complexes in cells, leading to transformation. Here, we show that ST not only displaces common PP2A B subunits but also promotes A-C subunit interactions with alternative B subunits (B’’’, striatins) that are components of the Striatin-interacting phosphatase and kinase (STRIPAK) complex. We found that STRN4, a member of STRIPAK, is associated with ST and is required for ST-PP2A-induced cell transformation. ST recruitment of STRIPAK facilitates PP2A-mediated dephosphorylation of MAP4K4 and induces cell transformation through the activation of the Hippo pathway effector YAP1. These observations identify an unanticipated role of MAP4K4 in transformation and show that the STRIPAK complex regulates PP2A specificity and activity. Cells maintain a fine balance of signals that promote or counter cell growth and division. Two sets of enzymes – called kinases and phosphatases – contribute to this balance. In general, kinases “switch on” other proteins by tagging them with a phosphate molecule. This process is called phosphorylation. Phosphatases, on the other hand, dephosphorylate these proteins, switching them off. Cancer cells often have mutations that activate kinases to drive cancer growth. The same cells can have mutations that inactivate the phosphatases or reduce their abundance. The roles of phosphatases in cancer are still being studied. One major hurdle in this research is that it is not always clear how they recognize the proteins they dephosphorylate. Protein phosphatase 2A (or PP2A for short) is one of the phosphatases that is often mutated or deleted in human cancers. Even just reduced levels of PP2A can promote cancer. Kim, Berrios, Kim, Schade et al. used an experimental trick to decrease the phosphatase activity of PP2A in human cells growing in a dish. Biochemical analysis of these cells showed that, as expected, many proteins were now in their phosphorylated states. Unexpectedly, however, some proteins were dephosphorylated under these conditions. One of these proteins was called MAP4K4. In the case of MAP4K4, the dephosphorylated state contributes to the growth of the cancer cell. Kim et al. carried out further genetic and biochemical experiments to show that, in these cells, PP2A and MAP4K4 stay physically connected to one another. This connection was enabled by a group of proteins called the STRIPAK complex. The STRIPAK proteins directed the remaining PP2A towards MAP4K4. Low levels or activity of PP2A could, therefore, promote cancer in a different way. Taken together, PP2A is not a single phosphatase that always turns proteins off, but rather is a dual switch that turns off some proteins while turning on others. Future experiments will explore to what extent these findings also apply in tumors. Information about how mutations in PP2A affect human cancers could suggest new targets for cancer drugs.
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Affiliation(s)
- Jong Wook Kim
- Broad Institute of Harvard and MIT, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Division of Medical Genetics, School of Medicine, University of California, San Diego, San Diego, United States.,Moores Cancer Center, University of California, San Diego, San Diego, United States
| | - Christian Berrios
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Program in Virology, Graduate School of Arts and Sciences, Harvard University, Cambridge, United States
| | - Miju Kim
- Broad Institute of Harvard and MIT, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
| | - Amy E Schade
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Program in Virology, Graduate School of Arts and Sciences, Harvard University, Cambridge, United States
| | - Guillaume Adelmant
- Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, United States.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, United States.,Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, United States
| | - Huwate Yeerna
- Division of Medical Genetics, School of Medicine, University of California, San Diego, San Diego, United States
| | - Emily Damato
- Broad Institute of Harvard and MIT, Cambridge, United States
| | - Amanda Balboni Iniguez
- Broad Institute of Harvard and MIT, Cambridge, United States.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, United States
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, United States
| | - Michael P Washburn
- Stowers Institute for Medical Research, Kansas City, United States.,Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, United States
| | - Kim Stegmaier
- Broad Institute of Harvard and MIT, Cambridge, United States.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, United States
| | - Nathanael S Gray
- Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, United States
| | - Pablo Tamayo
- Division of Medical Genetics, School of Medicine, University of California, San Diego, San Diego, United States.,Moores Cancer Center, University of California, San Diego, San Diego, United States
| | - Ole Gjoerup
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
| | - Jarrod A Marto
- Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, United States.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, United States.,Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, United States
| | - James DeCaprio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Program in Virology, Graduate School of Arts and Sciences, Harvard University, Cambridge, United States.,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, United States
| | - William C Hahn
- Broad Institute of Harvard and MIT, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, United States
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36
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Mangialardi EM, Chen K, Salmon B, Vacher J, Salmena L. Investigating the duality of Inpp4b function in the cellular transformation of mouse fibroblasts. Oncotarget 2019; 10:6378-6390. [PMID: 31695845 PMCID: PMC6824866 DOI: 10.18632/oncotarget.27293] [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: 03/22/2019] [Accepted: 10/19/2019] [Indexed: 11/25/2022] Open
Abstract
Inositol Polyphosphate 4-Phosphatase, Type II (INPP4B) is a tumour suppressor in breast, ovarian, prostate, thyroid and other cancers, attributed to its ability to reduce oncogenic Akt-signaling. However, emerging studies show that INPP4B also has tumour-promoting properties in cancers including acute myeloid leukemia, colon cancer, melanoma and breast cancer. Together these findings suggest that INPP4B may be a context dependent cancer gene. Whether INPP4B functions solely in a tumour suppressing or tumour promoting manner, or both in non-transformed cells is currently not clear. In this study, consequences of deficiency and overexpression of INPP4B on cellular transformation was investigated using a mouse embryonic fibroblast (MEF) model of cellular transformation. We observed that neither deficiency nor overexpression of INPP4B was sufficient to induce neoplastic transformation, alone or in combination with H-Ras V12 or E1A overexpression. However, Inpp4b-deficiency did cooperate with SV40 T-Large-mediated cellular transformation, a finding which was associated with increased phosphorylated-Akt levels. Transformation and phosphorylated-Akt levels were dampened upon overexpression of INPP4B in SV40 T-Large-MEF. Together, our findings support a model where INPP4B function suppresses transformation mediated by SV40 T-Large, but is inconsequential for Ras and E1A mediated transformation.
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Affiliation(s)
| | - Keyue Chen
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Brittany Salmon
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Jean Vacher
- Institut de Recherches Cliniques de Montréal, Département de Médecine, Université de Montréal, Montréal, Québec, Canada
| | - Leonardo Salmena
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
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37
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Malvi P, Janostiak R, Nagarajan A, Cai G, Wajapeyee N. Loss of thymidine kinase 1 inhibits lung cancer growth and metastatic attributes by reducing GDF15 expression. PLoS Genet 2019; 15:e1008439. [PMID: 31589613 PMCID: PMC6797230 DOI: 10.1371/journal.pgen.1008439] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 10/17/2019] [Accepted: 09/19/2019] [Indexed: 12/25/2022] Open
Abstract
Metabolic alterations that are critical for cancer cell growth and metastasis are one of the key hallmarks of cancer. Here, we show that thymidine kinase 1 (TK1) is significantly overexpressed in tumor samples from lung adenocarcinoma (LUAD) patients relative to normal controls, and this TK1 overexpression is associated with significantly reduced overall survival and cancer recurrence. Genetic knockdown of TK1 with short hairpin RNAs (shRNAs) inhibits both the growth and metastatic attributes of LUAD cells in culture and in mice. We further show that transcriptional overexpression of TK1 in LUAD cells is driven, in part, by MAP kinase pathway in a transcription factor MAZ dependent manner. Using targeted and gene expression profiling-based approaches, we then show that loss of TK1 in LUAD cells results in reduced Rho GTPase activity and reduced expression of growth and differentiation factor 15 (GDF15). Furthermore, ectopic expression of GDF15 can partially rescue TK1 knockdown-induced LUAD growth and metastasis inhibition, confirming its important role as a downstream mediator of TK1 function in LUAD. Collectively, our findings demonstrate that TK1 facilitates LUAD tumor and metastatic growth and represents a target for LUAD therapy. Thymidine kinase 1 (TK1) is overexpressed and associated with poor prognosis in a number of different cancers. However, despite these data suggesting an important role for TK1 in cancer pathogenesis, no study thus far has analyzed the functional effect of TK1 inhibition on tumor growth and metastasis. In this study, we performed TK1 knockdown and found that this protein is necessary for lung adenocarcinoma (LUAD) tumor growth and metastasis. Notably, inhibition of another nucleotide kinase, deoxycytidine kinase (DCK), had no effect on LUAD tumor growth and metastatic attributes. We therefore performed experiments to determine if the TK1 mechanism of action in cancer is distinct from its previously reported role in DNA damage, DNA replication, and DNA repair. We found that TK1 can promote LUAD tumor growth and metastasis in a non-canonical manner by activating Rho GTPase activity and growth and differentiation factor 15 (GDF15) expression. Taken together, our data suggest that TK1 may represent a potential target for development of LUAD therapy, due to its critical role in maintaining lung tumor growth and metastasis.
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Affiliation(s)
- Parmanand Malvi
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Radoslav Janostiak
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Arvindhan Nagarajan
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Guoping Cai
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Narendra Wajapeyee
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- * E-mail:
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Liang C, Zhao T, Li H, He F, Zhao X, Zhang Y, Chu X, Hua C, Qu Y, Duan Y, Ming L, Guo J. Long Non-coding RNA ITIH4-AS1 Accelerates the Proliferation and Metastasis of Colorectal Cancer by Activating JAK/STAT3 Signaling. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 18:183-193. [PMID: 31557619 PMCID: PMC6796638 DOI: 10.1016/j.omtn.2019.08.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 08/09/2019] [Accepted: 08/11/2019] [Indexed: 01/18/2023]
Abstract
Accumulating evidence has uncovered long non-coding RNAs (lncRNAs) as central regulators in the pathogenesis of diverse human cancers including colorectal cancer (CRC). The present study discovered that a novel lncRNA ITIH4 antisense RNA 1 (ITHI4-AS1) was frequently under-expressed in most normal human tissues, including colon tissues. Therefore, we aimed to investigate the role of ITHI4-AS1 in CRC. Interestingly, a significant overexpression of ITIH4-AS1 was observed in CRC cell lines relative to normal NCM460 cells. Also, we investigated the facilitating role of ITIH4-AS1 in CRC cell growth and metastasis both in vitro and in vivo. Additionally, we explained that ITIH4-AS1 upregulation in CRC was attributed to downregulation or even depletion of RE1 silencing transcription factor (REST), a presently identified transcriptional repressor for ITIH4-AS1. Meanwhile, the contribution of ITIH4-AS1 to CRC development was validated to rely on the activation of the JAK/STAT3 pathway. More importantly, we verified that FUS interacted with both ITIH4-AS1 and STAT3, and that ITIH4-AS1 evoked nuclear translocation of phosphorylated (p)-STAT3 in CRC through recruiting FUS. In summary, our findings unveiled for the first time that REST downregulation-enhanced ITIH4-AS1 exerts pro-tumor functions in CRC through FUS-dependent activation of the JAK/STAT3 pathway, implying that targeting ITIH4-AS1 may be a novel effective strategy for CRC therapy.
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Affiliation(s)
- Chaojie Liang
- Department of General Surgery, First Hospital/First Clinical College of Shanxi Medical University, No. 85, Jiefangnan Road, Yingze District, Taiyuan 030001, Shanxi, China
| | - Tuanjie Zhao
- Department of Colorectal and Anal Surgery, Beijing Er Long Lu Hospital, Beijing 100032, China
| | - Haijun Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Fucheng He
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Xin Zhao
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Yuan Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Xi Chu
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Chunlan Hua
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Yunhui Qu
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Yu Duan
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Liang Ming
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China.
| | - Jiansheng Guo
- Department of General Surgery, First Hospital/First Clinical College of Shanxi Medical University, No. 85, Jiefangnan Road, Yingze District, Taiyuan 030001, Shanxi, China.
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Cortés-Sarabia K, Medina-Flores Y, Alarcón-Romero LDC, Mata-Ruíz O, Vences-Velázquez A, Rodríguez-Ruíz HA, Valdés J, Ortuño-Pineda C. Production and characterization of monoclonal antibodies against the DNA binding domain of the RE1-silencing transcription factor. J Biochem 2019; 166:393-402. [DOI: 10.1093/jb/mvz046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/06/2019] [Indexed: 12/22/2022] Open
Abstract
Abstract
The use of monoclonal antibodies for the detection of cellular biomarkers during carcinogenesis provides new strategies for cancer diagnosis or prognosis in patients. Loss of the Restrictive Element 1-Silencing Transcription (REST) factor has been observed in previous molecular and immunological approaches in aggressive breast cancer, small cell lung cancer, liver carcinoma, and colo-rectal cancer; however, for clinic diagnosis, monoclonal antibodies for REST recognition are unavailable. The goal of this work was to design, produce and characterize monoclonal antibodies against the REST DNA binding damain (DBD) that would be suitable for immunoassays. We searched for conserved domains, and immunogenic and antigenic sites in the REST structure via in silico analysis. For mice immunization, we used a recombinant REST DBD purified by affinity chromatography, and then Hybridomas were generated by mouse spleen fusion with myeloma cells. Finally, for monoclonal antibody characterization, we performed enzyme-linked immunosorbent (ELISA), western blot, dot blot, immunocytochemistry (ICC) and immunoprecipitation assays. Results showed that the DBD is conserved in REST isoforms and contains immunogenic and antigenic sites. We generated three clones producing monoclonal antibodies against REST DBD, one of them specifically recognized native REST and was suitable for ICC in samples from patients.
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Affiliation(s)
- Karen Cortés-Sarabia
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas s/n, Chilpancingo, Guerrero
| | - Yolanda Medina-Flores
- Instituto de Diagnóstico y Referencia Epidemiológicos “Dr. Manuel Martínez Báez”, Francisco de P. Miranda 177, Lomas de Plateros, Ciudad de México
| | - Luz Del Carmen Alarcón-Romero
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas s/n, Chilpancingo, Guerrero
| | - Olga Mata-Ruíz
- Instituto de Diagnóstico y Referencia Epidemiológicos “Dr. Manuel Martínez Báez”, Francisco de P. Miranda 177, Lomas de Plateros, Ciudad de México
| | - Amalia Vences-Velázquez
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas s/n, Chilpancingo, Guerrero
| | - Hugo Alberto Rodríguez-Ruíz
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas s/n, Chilpancingo, Guerrero
| | - Jesús Valdés
- Departamento de Bioquímica, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Av. Instituto Politécnico Nacional, 2508, Ciudad de México, México
| | - Carlos Ortuño-Pineda
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas s/n, Chilpancingo, Guerrero
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Shimojo M, Kasahara Y, Inoue M, Tsunoda SI, Shudo Y, Kurata T, Obika S. A gapmer antisense oligonucleotide targeting SRRM4 is a novel therapeutic medicine for lung cancer. Sci Rep 2019; 9:7618. [PMID: 31110284 PMCID: PMC6527545 DOI: 10.1038/s41598-019-43100-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 04/16/2019] [Indexed: 12/13/2022] Open
Abstract
Small cell lung cancer (SCLC) is the most aggressive neuroendocrine phenotype of the deadliest human lung cancers. However the therapeutic landscape for SCLC has not changed in over 30 years. Effective treatment and prognosis are needed to combat this aggressive cancer. Herein we report that Ser/Arg repetitive matrix 4 (SRRM4), a splicing activator, is abnormally expressed at high levels in SCLC and thus is a potential therapeutic target. We screened an effective gapmer antisense oligonucleotide (gASO) targeting SRRM4 in vitro which led to cell death of SCLC. Our gASO, which is stabilized by containing artificial nucleotides, effectively represses SRRM4 mRNA. We found that our gASO repressed SRRM4 synthesis leading to a dramatic tumor reduction in a lung cancer mouse model. We also analyzed miRNA microarray and found that the miR-4516 is abnormally increased in exosomes in the blood of SCLC patients. Treating with gASO suppressed tumors in the SCLC model mouse concurrently reduced plasma miR-4516. In conclusion this study reports that administration of an SRRM4-targeted gASO coupled with a novel miRNA diagnostic methodology represents a potential breakthrough in the therapeutic treatment of high mortality SCLC.
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Affiliation(s)
- Masahito Shimojo
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Yuuya Kasahara
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan.,National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan
| | - Masaki Inoue
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan.,The Faculty of Pharmaceutical Sciences, Kobe Gakuin University, 1-1-3 Minatojima, Chuo-ku, Kobe, Hyogo, 650-8586, Japan
| | - Shin-Ichi Tsunoda
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan.,The Faculty of Pharmaceutical Sciences, Kobe Gakuin University, 1-1-3 Minatojima, Chuo-ku, Kobe, Hyogo, 650-8586, Japan
| | - Yoshie Shudo
- Kansai Medical University, 2-5-1 Shin-machi, Hirakata, Osaka, 573-1010, Japan
| | - Takayasu Kurata
- Kansai Medical University, 2-5-1 Shin-machi, Hirakata, Osaka, 573-1010, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan.,National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan
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41
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LaFleur MW, Nguyen TH, Coxe MA, Yates KB, Trombley JD, Weiss SA, Brown FD, Gillis JE, Coxe DJ, Doench JG, Haining WN, Sharpe AH. A CRISPR-Cas9 delivery system for in vivo screening of genes in the immune system. Nat Commun 2019; 10:1668. [PMID: 30971695 PMCID: PMC6458184 DOI: 10.1038/s41467-019-09656-2] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 03/22/2019] [Indexed: 12/26/2022] Open
Abstract
Therapies that target the function of immune cells have significant clinical efficacy in diseases such as cancer and autoimmunity. Although functional genomics has accelerated therapeutic target discovery in cancer, its use in primary immune cells is limited because vector delivery is inefficient and can perturb cell states. Here we describe CHIME: CHimeric IMmune Editing, a CRISPR-Cas9 bone marrow delivery system to rapidly evaluate gene function in innate and adaptive immune cells in vivo without ex vivo manipulation of these mature lineages. This approach enables efficient deletion of genes of interest in major immune lineages without altering their development or function. We use this approach to perform an in vivo pooled genetic screen and identify Ptpn2 as a negative regulator of CD8+ T cell-mediated responses to LCMV Clone 13 viral infection. These findings indicate that this genetic platform can enable rapid target discovery through pooled screening in immune cells in vivo.
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Affiliation(s)
- Martin W LaFleur
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Evergrande Center for Immunological Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Thao H Nguyen
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA
- Evergrande Center for Immunological Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Matthew A Coxe
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA
- Evergrande Center for Immunological Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Kathleen B Yates
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Justin D Trombley
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA
- Evergrande Center for Immunological Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Sarah A Weiss
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Flavian D Brown
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Evergrande Center for Immunological Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Jacob E Gillis
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA
- Evergrande Center for Immunological Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Daniel J Coxe
- School of Energy, Matter, and Transport Engineering at Arizona State University, Tempe, AZ, 85287, USA
| | - John G Doench
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - W Nicholas Haining
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.
| | - Arlene H Sharpe
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA.
- Evergrande Center for Immunological Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, 02115, USA.
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.
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42
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Whole genome sequencing puts forward hypotheses on metastasis evolution and therapy in colorectal cancer. Nat Commun 2018; 9:4782. [PMID: 30429477 PMCID: PMC6235880 DOI: 10.1038/s41467-018-07041-z] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 10/15/2018] [Indexed: 12/23/2022] Open
Abstract
Incomplete understanding of the metastatic process hinders personalized therapy. Here we report the most comprehensive whole-genome study of colorectal metastases vs. matched primary tumors. 65% of somatic mutations originate from a common progenitor, with 15% being tumor- and 19% metastasis-specific, implicating a higher mutation rate in metastases. Tumor- and metastasis-specific mutations harbor elevated levels of BRCAness. We confirm multistage progression with new components ARHGEF7/ARHGEF33. Recurrently mutated non-coding elements include ncRNAs RP11-594N15.3, AC010091, SNHG14, 3’ UTRs of FOXP2, DACH2, TRPM3, XKR4, ANO5, CBL, CBLB, the latter four potentially dual protagonists in metastasis and efferocytosis-/PD-L1 mediated immunosuppression. Actionable metastasis-specific lesions include FAT1, FGF1, BRCA2, KDR, and AKT2-, AKT3-, and PDGFRA-3’ UTRs. Metastasis specific mutations are enriched in PI3K-Akt signaling, cell adhesion, ECM and hepatic stellate activation genes, suggesting genetic programs for site-specific colonization. Our results put forward hypotheses on tumor and metastasis evolution, and evidence for metastasis-specific events relevant for personalized therapy. The evolution and genetic nature of metastatic lesions is not completely characterized. Here the authors perform a comprehensive whole-genome study of colorectal metastases in comparison to matched primary tumors and define a multistage progression model and metastasis-specific changes that, in part, are therapeutically actionable.
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Neuroendocrine Key Regulator Gene Expression in Merkel Cell Carcinoma. Neoplasia 2018; 20:1227-1235. [PMID: 30414538 PMCID: PMC6226622 DOI: 10.1016/j.neo.2018.10.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/07/2018] [Accepted: 10/11/2018] [Indexed: 01/26/2023] Open
Abstract
Merkel cell carcinoma (MCC) is a highly aggressive non-melanoma skin cancer of the elderly which is associated with the Merkel cell polyomavirus (MCPyV). MCC reveals a trilinear differentiation characterized by neuroendocrine, epithelial and pre/pro B-cell lymphocytic gene expression disguising the cellular origin of MCC. Here we investigated the expression of the neuroendocrine key regulators RE1 silencing transcription factor (REST), neurogenic differentiation 1 (NeuroD1) and the Achaete-scute homolog 1 (ASCL1) in MCC. All MCCs were devoid of REST and were positive for NeuroD1 expression. Only one MCC tissue revealed focal ASCL1 expression. This was confirmed in MCPyV-positive MCC cell lines. Of interest, MCPyV-negative cell lines did express REST. The introduction of REST expression in REST-negative, MCPyV-positive MCC cells downregulated the neuroendocrine gene expression. The lack of the neuroendocrine master regulator ASCL1 in almost all tested MCCs points to an important role of the absence of the negative regulator REST towards the MCC neuroendocrine phenotype. This is underlined by the expression of the REST-regulated microRNAs miR-9/9* in REST-negative MCC cell lines. These data might provide the basis for the understanding of neuroendocrine gene expression profile which is expected to help to elucidate the cellular origin of MCC.
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Xie XN, Yu J, Zhang LH, Luo ZY, Ouyang DS, Zheng LJ, Wang CY, Yang L, Chen L, Tan ZR. Relationship between polymorphisms of the lipid metabolism-related gene PLA2G16 and risk of colorectal cancer in the Chinese population. Funct Integr Genomics 2018; 19:227-236. [PMID: 30343388 DOI: 10.1007/s10142-018-0642-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 10/08/2018] [Accepted: 10/16/2018] [Indexed: 01/15/2023]
Abstract
This study aimed to investigate the relationship between polymorphisms in the lipid metabolism-related gene PLA2G16 encoding Group XVI phospholipase A2 and the risk of colorectal cancer (CRC) in the Chinese population. A total of 185 patients with CRC and 313 healthy controls were enrolled. Thirteen single nucleotide polymorphisms (SNPs) of PLA2G16 were genotyped with SNPscan™. Linkage disequilibrium and haplotypes were analysed using Haploview software. Multivariate logistic regression was used to determine the association between the various genotypes and CRC risk. We identified five PLA2G16 SNPs (rs11600655, rs3809072, rs3809073, rs640908 and rs66475048) that were associated with CRC risk after adjusting for age, sex and body mass index. Two haplotypes (CTC and GGA) of rs11600655, rs3809073 and rs3809072, were relevant to CRC risk. The rs11600655 polymorphism was also associated with lymph node metastasis and CRC staging, while rs3809073 and rs3809072 may affect transcriptional regulation of PLA2G16 by altering transcription factor binding. These findings suggest that PLA2G16 polymorphisms-especially CTC and GGA haplotypes-increase CRC susceptibility. Importantly, we showed that the rs11600655 CC, rs640908 CT and rs66475048 GA genotypes are independent risk factors for CRC in the Chinese population.
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Affiliation(s)
- Xiao-Nv Xie
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Xiangya Road 110, Changsha, 410078, China.,Institute of Clinical pharmacology, Human Key Laboratory of Pharmacology, Central South University, Changsha, China
| | - Jing Yu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Xiangya Road 110, Changsha, 410078, China.,Institute of Clinical pharmacology, Human Key Laboratory of Pharmacology, Central South University, Changsha, China
| | - Li-Hua Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Xiangya Road 110, Changsha, 410078, China.,Institute of Clinical pharmacology, Human Key Laboratory of Pharmacology, Central South University, Changsha, China
| | - Zhi-Ying Luo
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Xiangya Road 110, Changsha, 410078, China.,Institute of Clinical pharmacology, Human Key Laboratory of Pharmacology, Central South University, Changsha, China
| | - Dong-Sheng Ouyang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Xiangya Road 110, Changsha, 410078, China.,Institute of Clinical pharmacology, Human Key Laboratory of Pharmacology, Central South University, Changsha, China
| | - Ling-Jie Zheng
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Xiangya Road 110, Changsha, 410078, China.,Institute of Clinical pharmacology, Human Key Laboratory of Pharmacology, Central South University, Changsha, China
| | - Chun-Yang Wang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Xiangya Road 110, Changsha, 410078, China.,Institute of Clinical pharmacology, Human Key Laboratory of Pharmacology, Central South University, Changsha, China
| | - Li Yang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Xiangya Road 110, Changsha, 410078, China.,Institute of Clinical pharmacology, Human Key Laboratory of Pharmacology, Central South University, Changsha, China
| | - Ling Chen
- Xiangya Hospital, Central South University, Changsha, China
| | - Zhi-Rong Tan
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Xiangya Road 110, Changsha, 410078, China. .,Institute of Clinical pharmacology, Human Key Laboratory of Pharmacology, Central South University, Changsha, China.
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45
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Chang YT, Lin TP, Tang JT, Campbell M, Luo YL, Lu SY, Yang CP, Cheng TY, Chang CH, Liu TT, Lin CH, Kung HJ, Pan CC, Chang PC. HOTAIR is a REST-regulated lncRNA that promotes neuroendocrine differentiation in castration resistant prostate cancer. Cancer Lett 2018; 433:43-52. [DOI: 10.1016/j.canlet.2018.06.029] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 06/16/2018] [Accepted: 06/18/2018] [Indexed: 12/23/2022]
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46
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A Druggable Genome Screen Identifies Modifiers of α-Synuclein Levels via a Tiered Cross-Species Validation Approach. J Neurosci 2018; 38:9286-9301. [PMID: 30249792 DOI: 10.1523/jneurosci.0254-18.2018] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 08/08/2018] [Accepted: 08/13/2018] [Indexed: 01/12/2023] Open
Abstract
Accumulation of α-Synuclein (α-Syn) causes Parkinson's disease (PD) as well as other synucleopathies. α-Syn is the major component of Lewy bodies and Lewy neurites, the proteinaceous aggregates that are a hallmark of sporadic PD. In familial forms of PD, mutations or copy number variations in SNCA (the α-Syn gene) result in a net increase of its protein levels. Furthermore, common risk variants tied to PD are associated with small increases of wild-type α-Syn levels. These findings are further bolstered by animal studies which show that overexpression of α-Syn is sufficient to cause PD-like features. Thus, increased α-Syn levels are intrinsically tied to PD pathogenesis and underscore the importance of identifying the factors that regulate its levels. In this study, we establish a pooled RNAi screening approach and validation pipeline to probe the druggable genome for modifiers of α-Syn levels and identify 60 promising targets. Using a cross-species, tiered validation approach, we validate six strong candidates that modulate α-Syn levels and toxicity in cell lines, Drosophila, human neurons, and mouse brain of both sexes. More broadly, this genetic strategy and validation pipeline can be applied for the identification of therapeutic targets for disorders driven by dosage-sensitive proteins.SIGNIFICANCE STATEMENT We present a research strategy for the systematic identification and validation of genes modulating the levels of α-Synuclein, a protein involved in Parkinson's disease. A cell-based screen of the druggable genome (>7,500 genes that are potential therapeutic targets) yielded many modulators of α-Synuclein that were subsequently confirmed and validated in Drosophila, human neurons, and mouse brain. This approach has broad applicability to the multitude of neurological diseases that are caused by mutations in genes whose dosage is critical for brain function.
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47
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Burkholder NT, Mayfield JE, Yu X, Irani S, Arce DK, Jiang F, Matthews WL, Xue Y, Zhang YJ. Phosphatase activity of small C-terminal domain phosphatase 1 (SCP1) controls the stability of the key neuronal regulator RE1-silencing transcription factor (REST). J Biol Chem 2018; 293:16851-16861. [PMID: 30217818 DOI: 10.1074/jbc.ra118.004722] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 08/20/2018] [Indexed: 02/03/2023] Open
Abstract
The RE1-silencing transcription factor (REST) is the major scaffold protein for assembly of neuronal gene silencing complexes that suppress gene transcription through regulating the surrounding chromatin structure. REST represses neuronal gene expression in stem cells and non-neuronal cells, but it is minimally expressed in neuronal cells to ensure proper neuronal development. Dysregulation of REST function has been implicated in several cancers and neurological diseases. Modulating REST gene silencing is challenging because cellular and developmental differences can affect its activity. We therefore considered the possibility of modulating REST activity through its regulatory proteins. The human small C-terminal domain phosphatase 1 (SCP1) regulates the phosphorylation state of REST at sites that function as REST degradation checkpoints. Using kinetic analysis and direct visualization with X-ray crystallography, we show that SCP1 dephosphorylates two degron phosphosites of REST with a clear preference for phosphoserine 861 (pSer-861). Furthermore, we show that SCP1 stabilizes REST protein levels, which sustains REST's gene silencing function in HEK293 cells. In summary, our findings strongly suggest that REST is a bona fide substrate for SCP1 in vivo and that SCP1 phosphatase activity protects REST against degradation. These observations indicate that targeting REST via its regulatory protein SCP1 can modulate its activity and alter signaling in this essential developmental pathway.
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Affiliation(s)
| | | | - Xiaohua Yu
- the Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China, and
| | | | | | - Faqin Jiang
- the School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | | | - Yuanchao Xue
- the Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China, and
| | - Yan Jessie Zhang
- From the Departments of Molecular Biosciences and .,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712
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48
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Yu Y, Li S, Zhang H, Zhang X, Guo D, Zhang J. NRSF/REST levels are decreased in cholangiocellular carcinoma but not hepatocellular carcinoma compared with normal liver tissues: A tissue microarray study. Oncol Lett 2018; 15:6592-6598. [PMID: 29725406 DOI: 10.3892/ol.2018.8169] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 09/15/2017] [Indexed: 01/02/2023] Open
Abstract
The transcription factor neuron-restrictive silencer factor (NRSF), also termed repressor element 1-silencing transcription factor (REST), has been previously demonstrated to repress the expression of neuronal genes in non-neuronal cells, facilitating the controlled development and organization of nerve tissue. However, previous studies have reported NRSF/REST to be upregulated or downregulated in multiple types of carcinoma. Liver diseases are a major global health concern, with cirrhosis and liver carcinoma among the most common causes of mortality worldwide. A previous study demonstrated that there were >400 NRSF/REST target genes in mouse liver cells; however, the expression profile of NRSF/REST in human liver disease remains unclear. The present study examined NRSF/REST expression in human normal and liver carcinoma samples using tissue microarray immunohistochemistry. The results demonstrated that in normal liver tissues, NRSF/REST can be detected in the cytoplasm and nuclei of the cell; whereas in the liver carcinoma tissue, NRSF/REST is only detected in the cytoplasm. Furthermore, the number of samples with high levels of NRSF/REST was significantly lower in cholangiocellular carcinoma samples compared with normal tissues. Additionally, no detectable sex- or age-associated differences were identified in NRSF/REST expression among all the tissues examined. In conclusion, the results of the present study revealed nuclear loss of NRSF/REST in hepatic carcinomas and decreased expression of NRSF/REST in cholangiocellular carcinoma, indicating that the cytoplasmic translocation of NRSF/REST may be involved in liver tumorigenesis. A low expression level of NRSF/REST may be a novel biomarker for cholangiocellular carcinoma.
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Affiliation(s)
- Yanlan Yu
- Department of Neurobiology, Chongqing Key Laboratory of Neurobiology, Third Military Medical University, Chongqing 400038, P.R. China
| | - Shan Li
- Department of Neurobiology, Chongqing Key Laboratory of Neurobiology, Third Military Medical University, Chongqing 400038, P.R. China
| | - Huiyan Zhang
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University, Chongqing 400038, P.R. China
| | - Xuqing Zhang
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University, Chongqing 400038, P.R. China
| | - Deyu Guo
- Department of Pathology, Southwest Hospital, Third Military Medical University, Chongqing 400038, P.R. China
| | - Jiqiang Zhang
- Department of Neurobiology, Chongqing Key Laboratory of Neurobiology, Third Military Medical University, Chongqing 400038, P.R. China
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49
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Suppression of ABHD2, identified through a functional genomics screen, causes anoikis resistance, chemoresistance and poor prognosis in ovarian cancer. Oncotarget 2018; 7:47620-47636. [PMID: 27323405 PMCID: PMC5216966 DOI: 10.18632/oncotarget.9951] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 05/28/2016] [Indexed: 01/06/2023] Open
Abstract
Anoikis resistance is a hallmark of cancer, and relates to malignant phenotypes, including chemoresistance, cancer stem like phenotypes and dissemination. The aim of this study was to identify key factors contributing to anoikis resistance in ovarian cancer using a functional genomics screen. A library of 81 000 shRNAs targeting 15 000 genes was transduced into OVCA420 cells, followed by incubation in soft agar and colony selection. We found shRNAs directed to ABHD2, ELAC2 and CYB5R3 caused reproducible anoikis resistance. These three genes are deleted in many serous ovarian cancers according to The Cancer Genome Atlas data. Suppression of ABHD2 in OVCA420 cells increased phosphorylated p38 and ERK, platinum resistance, and side population cells (p<0.01, respectively). Conversely, overexpression of ABHD2 decreased resistance to anoikis (p<0.05) and the amount of phosphorylated p38 and ERK in OVCA420 and SKOV3 cells. In clinical serous ovarian cancer specimens, low expression of ABHD2 was associated with platinum resistance and poor prognosis (p<0.05, respectively). In conclusion, we found three novel genes relevant to anoikis resistance in ovarian cancer using a functional genomics screen. Suppression of ABHD2 may promote a malignant phenotype and poor prognosis for women with serous ovarian cancer.
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50
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Xiong J, Su T, Qu Z, Yang Q, Wang Y, Li J, Zhou S. Triptolide has anticancer and chemosensitization effects by down-regulating Akt activation through the MDM2/REST pathway in human breast cancer. Oncotarget 2018; 7:23933-46. [PMID: 27004407 PMCID: PMC5029675 DOI: 10.18632/oncotarget.8207] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 03/02/2016] [Indexed: 12/28/2022] Open
Abstract
Triptolide has been shown to exhibit anticancer activity. However, its mechanism of action is not clearly defined. Herein we report a novel signaling pathway, MDM2/Akt, is involved in the anticancer mechanism of triptolide. We observed that triptolide inhibits MDM2 expression in human breast cancer cells with either wild-type or mutant p53. This MDM2 inhibition resulted in decreased Akt activation. More specifically, triptolide interfered with the interaction between MDM2 and the transcription factor REST to increase expression of the regulatory subunit of PI3-kinase p85 and consequently inhibit Akt activation. We further showed that, regardless of p53 status, triptolide inhibited proliferation, induced apoptosis, and caused G1 phase cell cycle arrest. Triptolide also enhanced the cytotoxic effect of doxorubicin. MDM2 inhibition plays a causative role in these effects. The inhibitory effect of triptolide on MDM2-mediated Akt activation was eliminated with MDM2 overexpression. MDM2-overexpressing tumor cells, in turn, were less susceptible to the anticancer and chemosensitization effects of triptolide than control cells. Triptolide also exhibited anticancer and chemosensitization effects in nude mouse xenograft model. When it was administered to tumor-bearing nude mice, triptolide inhibited tumor growth and enhanced the antitumor effects of doxorubicin. In summary, triptolide has anticancer and chemosensitization effects by down-regulating Akt activation through the MDM2/REST pathway in human breast cancer. Our study helps to elucidate the p53-independent regulatory function of MDM2 in Akt signaling, offering a novel view of the mechanism by which triptolide functions as an anticancer agent.
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Affiliation(s)
- Jing Xiong
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Tiefen Su
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zhiling Qu
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Qin Yang
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yu Wang
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jiansha Li
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Sheng Zhou
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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