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Terrazzan A, Vanini R, Ancona P, Bianchi N, Taccioli C, Aguiari G. State-of-the-art in transposable element modulation affected by drugs in malignant prostatic cancer cells. J Cell Biochem 2024; 125:e30557. [PMID: 38501160 DOI: 10.1002/jcb.30557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 02/14/2024] [Accepted: 03/07/2024] [Indexed: 03/20/2024]
Abstract
Over recent years, the investigation of transposable elements (TEs) has granted researchers a deeper comprehension of their characteristics and functions, particularly regarding their significance in the mechanisms contributing to cancer development. This manuscript focuses on prostate carcinoma cell lines and offers a comprehensive review intended to scrutinize the associations and interactions between TEs and genes, as well as their response to treatment using various chemical drugs, emphasizing their involvement in cancer progression. We assembled a compendium of articles retrieved from the PubMed database to construct networks demonstrating correlations with genes and pharmaceuticals. In doing so, we linked the transposition of certain TE types to the expression of specific transcripts directly implicated in carcinogenesis. Additionally, we underline that treatment employing different drugs revealed unique patterns of TE reactivation. Our hypothesis gathers the current understanding and guides research toward evidence-based investigations, emphasizing the association between antiviral drugs, chemotherapy, and the reduced expression of TEs in patients affected by prostate cancer.
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Affiliation(s)
- Anna Terrazzan
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
- Laboratory for Advanced Therapy Technologies (LTTA), University of Ferrara, Ferrara, Italy
| | - Riccardo Vanini
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Pietro Ancona
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Nicoletta Bianchi
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Cristian Taccioli
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Padua, Italy
| | - Gianluca Aguiari
- Department of Neuroscience and Rehabilitation, University of Ferrara, Ferrara, Italy
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2
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Yang JH, Zhao Z, Niu W, Choi HP, Azadzoi KM. Formation of Double Stranded RNA Provokes Smooth Muscle Contractions and Structural Modifications in Bladder Ischemia. Res Rep Urol 2022; 14:399-414. [PMID: 36415310 PMCID: PMC9676006 DOI: 10.2147/rru.s388464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/11/2022] [Indexed: 08/30/2023] Open
Abstract
PURPOSE Growing evidence suggests that ischemia provokes detrusor overactivity and degenerative responses in the bladder. Underlying mechanisms appear to involve modification of smooth muscle contractile rudiments by hypoxia, redox, cellular stress and cell survival signaling. Downstream pathways of cellular stress and stress response molecules eliciting bladder dysfunction in ischemia remain largely elusive. Our goal was to define the role of double stranded RNA (dsRNA), a stress response molecule provoked by redox, in ischemia mediated bladder dysfunction. METHODS A rat model of pelvic ischemia along with a cell culture hypoxia model were used to investigate the expression levels, functional consequences, structural aspects, and regulatory mechanisms of dsRNA in the bladder. Gene and protein expression were examined by reverse transcription polymerase chain reaction (RT-PCR), dot blot, and Western blotting, respectively. Tissue structure and function were assessed using histological staining and organ bath. Regulatory mechanisms were analyzed in cultured bladder smooth muscle cells. RESULTS The data presented here provide the first evidence of the formation of dsRNA in the overactive bladder. dsRNA is a cellular stress response molecule that sensitizes smooth muscle and regulates inflammatory and degenerative rejoinders. Our data suggest that the production of dsRNA in the bladder is provoked by ischemia. Formation of dsRNA appears to augment bladder smooth muscle contractions and provoke fibrotic and apoptotic responses. Downstream actions of dsRNA in the bladder may involve upregulation of dsRNA-activated protein kinase R (PKR) and caspase-3, the executioner of apoptosis. CONCLUSION Activation of dsRNA/PKR pathway may play a role in sensitization of bladder smooth muscle cells to contractile stimuli, whereas dsRNA and caspase-3 crosstalk appear to modulate cellular stress and instigate degenerative responses in bladder ischemia. These observations suggest the role of dsRNA in bladder dysfunction and may open new perspectives to overcome overactive smooth muscle contractions and structural damage in the bladder.
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Affiliation(s)
- Jing-Hua Yang
- Department of Surgery, Boston University School of Medicine and Proteomics Laboratory, VA Boston Healthcare System, Boston, MA, USA
| | - Zuohui Zhao
- Department of Urology, Boston University School of Medicine, Boston, MA, USA
| | - Wanting Niu
- Research Department, VA Boston Healthcare System, Boston, MA, USA
| | - Han-Pil Choi
- Research Department, VA Boston Healthcare System, Boston, MA, USA
| | - Kazem M Azadzoi
- Departments of Urology and Pathology, VA Boston Healthcare System and Boston University School of Medicine, Boston, MA, USA
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3
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mRNA Capture Sequencing and RT-qPCR for the Detection of Pathognomonic, Novel, and Secondary Fusion Transcripts in FFPE Tissue: A Sarcoma Showcase. Int J Mol Sci 2022; 23:ijms231911007. [PMID: 36232302 PMCID: PMC9569610 DOI: 10.3390/ijms231911007] [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: 08/09/2022] [Revised: 09/12/2022] [Accepted: 09/12/2022] [Indexed: 11/17/2022] Open
Abstract
We assess the performance of mRNA capture sequencing to identify fusion transcripts in FFPE tissue of different sarcoma types, followed by RT-qPCR confirmation. To validate our workflow, six positive control tumors with a specific chromosomal rearrangement were analyzed using the TruSight RNA Pan-Cancer Panel. Fusion transcript calling by FusionCatcher confirmed these aberrations and enabled the identification of both fusion gene partners and breakpoints. Next, whole-transcriptome TruSeq RNA Exome sequencing was applied to 17 fusion gene-negative alveolar rhabdomyosarcoma (ARMS) or undifferentiated round cell sarcoma (URCS) tumors, for whom fluorescence in situ hybridization (FISH) did not identify the classical pathognomonic rearrangements. For six patients, a pathognomonic fusion transcript was readily detected, i.e., PAX3-FOXO1 in two ARMS patients, and EWSR1-FLI1, EWSR1-ERG, or EWSR1-NFATC2 in four URCS patients. For the 11 remaining patients, 11 newly identified fusion transcripts were confirmed by RT-qPCR, including COPS3-TOM1L2, NCOA1-DTNB, WWTR1-LINC01986, PLAA-MOB3B, AP1B1-CHEK2, and BRD4-LEUTX fusion transcripts in ARMS patients. Additionally, recurrently detected secondary fusion transcripts in patients diagnosed with EWSR1-NFATC2-positive sarcoma were confirmed (COPS4-TBC1D9, PICALM-SYTL2, SMG6-VPS53, and UBE2F-ALS2). In conclusion, this study shows that mRNA capture sequencing enhances the detection rate of pathognomonic fusions and enables the identification of novel and secondary fusion transcripts in sarcomas.
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Markers of Angiogenesis, Lymphangiogenesis, and Epithelial-Mesenchymal Transition (Plasticity) in CIN and Early Invasive Carcinoma of the Cervix: Exploring Putative Molecular Mechanisms Involved in Early Tumor Invasion. Int J Mol Sci 2020; 21:ijms21186515. [PMID: 32899940 PMCID: PMC7554870 DOI: 10.3390/ijms21186515] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/28/2020] [Accepted: 09/02/2020] [Indexed: 02/01/2023] Open
Abstract
The establishment of a proangiogenic phenotype and epithelial-to-mesenchymal transition (EMT) are considered as critical events that promote the induction of invasive growth in epithelial tumors, and stimulation of lymphangiogenesis is believed to confer the capacity for early dissemination to cancer cells. Recent research has revealed substantial interdependence between these processes at the molecular level as they rely on common signaling networks. Of great interest are the molecular mechanisms of (lymph-)angiogenesis and EMT associated with the earliest stages of transition from intraepithelial development to invasive growth, as they could provide the source of potentially valuable tools for targeting tumor metastasis. However, in the case of early-stage cervical cancer, the players of (lymph-)angiogenesis and EMT processes still remain substantially uncharacterized. In this study, we used RNA sequencing to compare transcriptomes of HPV(+) preinvasive neoplastic lesions and early-stage invasive carcinoma of the cervix and to identify (lymph-)angiogenesis- and EMT-related genes and pathways that may underlie early acquisition of invasive phenotype and metastatic properties by cervical cancer cells. Second, we applied flow cytometric analysis to evaluate the expression of three key lymphangiogenesis/EMT markers (VEGFR3, MET, and SLUG) in epithelial cells derived from enzymatically treated tissue specimens. Overall, among 201 differentially expressed genes, a considerable number of (lymph-)angiogenesis and EMT regulatory factors were identified, including genes encoding cytokines, growth factor receptors, transcription factors, and adhesion molecules. Pathway analysis confirmed enrichment for angiogenesis, epithelial differentiation, and cell guidance pathways at transition from intraepithelial neoplasia to invasive carcinoma and suggested immune-regulatory/inflammatory pathways to be implicated in initiation of invasive growth of cervical cancer. Flow cytometry showed cell phenotype-specific expression pattern for VEGFR3, MET, and SLUG and revealed correlation with the amount of tumor-infiltrating lymphocytes at the early stages of cervical cancer progression. Taken together, these results extend our understanding of driving forces of angiogenesis and metastasis in HPV-associated cervical cancer and may be useful for developing new treatments.
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Evaluating the applicability of mouse SINEs as an alternative normalization approach for RT-qPCR in brain tissue of the APP23 model for Alzheimer’s disease. J Neurosci Methods 2019; 320:128-137. [DOI: 10.1016/j.jneumeth.2019.03.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 02/27/2019] [Accepted: 03/04/2019] [Indexed: 01/04/2023]
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6
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Crans RAJ, Janssens J, Daelemans S, Wouters E, Raedt R, Van Dam D, De Deyn PP, Van Craenenbroeck K, Stove CP. The validation of Short Interspersed Nuclear Elements (SINEs) as a RT-qPCR normalization strategy in a rodent model for temporal lobe epilepsy. PLoS One 2019; 14:e0210567. [PMID: 30629669 PMCID: PMC6328105 DOI: 10.1371/journal.pone.0210567] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 12/26/2018] [Indexed: 01/10/2023] Open
Abstract
Background In gene expression studies via RT-qPCR many conclusions are inferred by using reference genes. However, it is generally known that also reference genes could be differentially expressed between various tissue types, experimental conditions and animal models. An increasing amount of studies have been performed to validate the stability of reference genes. In this study, two rodent-specific Short Interspersed Nuclear Elements (SINEs), which are located throughout the transcriptome, were validated and assessed against nine reference genes in a model of Temporal Lobe Epilepsy (TLE). Two different brain regions (i.e. hippocampus and cortex) and two different disease stages (i.e. acute phase and chronic phase) of the systemic kainic acid rat model for TLE were analyzed by performing expression analyses with the geNorm and NormFinder algorithms. Finally, we performed a rank aggregation analysis and validated the reference genes and the rodent-specific SINEs (i.e. B elements) individually via Gfap gene expression. Results GeNorm ranked Hprt1, Pgk1 and Ywhaz as the most stable genes in the acute phase, while Gusb and B2m were ranked as the most unstable, being significantly upregulated. The two B elements were ranked as most stable for both brain regions in the chronic phase by geNorm. In contrast, NormFinder ranked the B1 element only once as second best in cortical tissue for the chronic phase. Interestingly, using only one of the two algorithms would have led to skewed conclusions. Finally, the rank aggregation method indicated the use of the B1 element as the best option to normalize target genes, independent of the disease progression and brain region. This result was supported by the expression profile of Gfap. Conclusion In this study, we demonstrate the potential of implementing SINEs -notably the B1 element- as a stable normalization factor in a rodent model of TLE, independent of brain region or disease progression.
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Affiliation(s)
- René A. J. Crans
- Laboratory for GPCR Expression and Signal Transduction (L-GEST) - Laboratory of Toxicology, Department of Bioanalysis, Ghent University, Ghent, Belgium
| | - Jana Janssens
- Laboratory of Neurochemistry and Behavior, Department of Biomedical Sciences, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Sofie Daelemans
- Laboratory for Clinical and Experimental Neurophysiology, Neurobiology and Neuropsychology (LCEN3), Department of Internal Medicine, Ghent University Hospital, Ghent, Belgium
| | - Elise Wouters
- Laboratory for GPCR Expression and Signal Transduction (L-GEST) - Laboratory of Toxicology, Department of Bioanalysis, Ghent University, Ghent, Belgium
| | - Robrecht Raedt
- Laboratory for Clinical and Experimental Neurophysiology, Neurobiology and Neuropsychology (LCEN3), Department of Internal Medicine, Ghent University Hospital, Ghent, Belgium
| | - Debby Van Dam
- Laboratory of Neurochemistry and Behavior, Department of Biomedical Sciences, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
- Department of Neurology and Alzheimer Research Center, University Medical Center Groningen (UMCG), Groningen, the Netherlands
| | - Peter P. De Deyn
- Laboratory of Neurochemistry and Behavior, Department of Biomedical Sciences, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
- Department of Neurology and Alzheimer Research Center, University Medical Center Groningen (UMCG), Groningen, the Netherlands
- Department of Neurology and Memory Clinic, Hospital Network Antwerp (ZNA) Middelheim and Hoge Beuken, Antwerp, Belgium
- Biobank, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Kathleen Van Craenenbroeck
- Laboratory for GPCR Expression and Signal Transduction (L-GEST) - Laboratory of Toxicology, Department of Bioanalysis, Ghent University, Ghent, Belgium
| | - Christophe P. Stove
- Laboratory for GPCR Expression and Signal Transduction (L-GEST) - Laboratory of Toxicology, Department of Bioanalysis, Ghent University, Ghent, Belgium
- * E-mail:
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Expressed repetitive elements are broadly applicable reference targets for normalization of reverse transcription-qPCR data in mice. Sci Rep 2018; 8:7642. [PMID: 29769563 PMCID: PMC5955877 DOI: 10.1038/s41598-018-25389-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 04/12/2018] [Indexed: 12/19/2022] Open
Abstract
Reverse transcription quantitative PCR (RT-qPCR) is the gold standard method for gene expression analysis on mRNA level. To remove experimental variation, expression levels of the gene of interest are typically normalized to the expression level of stably expressed endogenous reference genes. Identifying suitable reference genes and determining the optimal number of reference genes should precede each quantification study. Popular reference genes are not necessarily stably expressed in the examined conditions, possibly leading to inaccurate results. Stably and universally expressed repetitive elements (ERE) have previously been shown to be an excellent alternative for normalization using classic reference genes in human and zebrafish samples. Here, we confirm that in mouse tissues, EREs are broadly applicable reference targets for RT-qPCR normalization, provided that the RNA samples undergo a thorough DNase treatment. We identified Orr1a0, Rltr2aiap, and Rltr13a3 as the most stably expressed mouse EREs across six different experimental conditions. Therefore, we propose this set of ERE reference targets as good candidates for normalization of RT-qPCR data in a plethora of conditions. The identification of widely applicable stable mouse RT-qPCR reference targets for normalization has great potential to facilitate future murine gene expression studies and improve the validity of RT-qPCR data.
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8
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Kottorou AE, Antonacopoulou AG, Dimitrakopoulos FID, Diamantopoulou G, Sirinian C, Kalofonou M, Theodorakopoulos T, Oikonomou C, Katsakoulis EC, Koutras A, Makatsoris T, Demopoulos N, Stephanou G, Stavropoulos M, Thomopoulos KC, Kalofonos HP. Deregulation of methylation of transcribed-ultra conserved regions in colorectal cancer and their value for detection of adenomas and adenocarcinomas. Oncotarget 2018; 9:21411-21428. [PMID: 29765549 PMCID: PMC5940382 DOI: 10.18632/oncotarget.25115] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 03/02/2018] [Indexed: 02/06/2023] Open
Abstract
Expression of Transcribed Ultraconserved Regions (T-UCRs) is often deregulated in cancer. The present study assesses the expression and methylation of three T-UCRs (Uc160, Uc283 and Uc346) in colorectal cancer (CRC) and explores the potential of T-UCR methylation in circulating DNA for the detection of adenomas and adenocarcinomas. Expression levels of Uc160, Uc283 and Uc346 were lower in neoplastic tissues from 64 CRC patients (statistically significant for Uc160, p<0.001), compared to non-malignant tissues, while methylation levels displayed the inverse pattern (p<0.001, p=0.001 and p=0.004 respectively). In colon cancer cell lines, overexpression of Uc160 and Uc346 led to increased proliferation and migration rates. Methylation levels of Uc160 in plasma of 50 CRC, 59 adenoma patients, 40 healthy subjects and 12 patients with colon inflammation or diverticulosis predicted the presence of CRC with 35% sensitivity and 89% specificity (p=0.016), while methylation levels of the combination of all three T-UCRs resulted in 45% sensitivity and 74.3% specificity (p=0.013). In conclusion, studied T-UCRs’ expression and methylation status are deregulated in CRC while Uc160 and Uc346 appear to have a complicated role in CRC progression. Moreover their methylation status appears a promising non-invasive screening test for CRC, provided that the sensitivity of the assay is improved.
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Affiliation(s)
- Anastasia E Kottorou
- Clinical and Molecular Oncology Laboratory, Division of Oncology, Medical School, University of Patras, Patras, Greece
| | - Anna G Antonacopoulou
- Clinical and Molecular Oncology Laboratory, Division of Oncology, Medical School, University of Patras, Patras, Greece
| | - Foteinos-Ioannis D Dimitrakopoulos
- Clinical and Molecular Oncology Laboratory, Division of Oncology, Medical School, University of Patras, Patras, Greece.,Division of Oncology, University Hospital of Patras, Patras, Greece
| | | | - Chaido Sirinian
- Clinical and Molecular Oncology Laboratory, Division of Oncology, Medical School, University of Patras, Patras, Greece
| | - Melpomeni Kalofonou
- Clinical and Molecular Oncology Laboratory, Division of Oncology, Medical School, University of Patras, Patras, Greece.,Institute of Biomedical Engineering, Imperial College London, London, UK
| | | | - Chrysa Oikonomou
- Division of Oncology, University Hospital of Patras, Patras, Greece
| | | | - Angelos Koutras
- Clinical and Molecular Oncology Laboratory, Division of Oncology, Medical School, University of Patras, Patras, Greece.,Division of Oncology, University Hospital of Patras, Patras, Greece
| | - Thomas Makatsoris
- Clinical and Molecular Oncology Laboratory, Division of Oncology, Medical School, University of Patras, Patras, Greece.,Division of Oncology, University Hospital of Patras, Patras, Greece
| | - Nikos Demopoulos
- Division of Genetics, Cell and Developmental Biology, Department of Biology, University of Patras, Patras, Greece
| | - Georgia Stephanou
- Division of Genetics, Cell and Developmental Biology, Department of Biology, University of Patras, Patras, Greece
| | | | | | - Haralabos P Kalofonos
- Clinical and Molecular Oncology Laboratory, Division of Oncology, Medical School, University of Patras, Patras, Greece.,Division of Oncology, University Hospital of Patras, Patras, Greece
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9
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Lazzari E, Mondala PK, Santos ND, Miller AC, Pineda G, Jiang Q, Leu H, Ali SA, Ganesan AP, Wu CN, Costello C, Minden M, Chiaramonte R, Stewart AK, Crews LA, Jamieson CHM. Alu-dependent RNA editing of GLI1 promotes malignant regeneration in multiple myeloma. Nat Commun 2017; 8:1922. [PMID: 29203771 PMCID: PMC5715072 DOI: 10.1038/s41467-017-01890-w] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 10/24/2017] [Indexed: 12/12/2022] Open
Abstract
Despite novel therapies, relapse of multiple myeloma (MM) is virtually inevitable. Amplification of chromosome 1q, which harbors the inflammation-responsive RNA editase adenosine deaminase acting on RNA (ADAR)1 gene, occurs in 30–50% of MM patients and portends a poor prognosis. Since adenosine-to-inosine RNA editing has recently emerged as a driver of cancer progression, genomic amplification combined with inflammatory cytokine activation of ADAR1 could stimulate MM progression and therapeutic resistance. Here, we report that high ADAR1 RNA expression correlates with reduced patient survival rates in the MMRF CoMMpass data set. Expression of wild-type, but not mutant, ADAR1 enhances Alu-dependent editing and transcriptional activity of GLI1, a Hedgehog (Hh) pathway transcriptional activator and self-renewal agonist, and promotes immunomodulatory drug resistance in vitro. Finally, ADAR1 knockdown reduces regeneration of high-risk MM in serially transplantable patient-derived xenografts. These data demonstrate that ADAR1 promotes malignant regeneration of MM and if selectively inhibited may obviate progression and relapse. The treatment of multiple myeloma is challenging due to high relapse rates. Here the authors show that expression of ADAR1 correlates with poor patient outcomes, and that ADAR1-mediated editing of GLI1 is a mechanism relevant in the context of multiple myeloma progression and drug resistance.
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Affiliation(s)
- Elisa Lazzari
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Phoebe K Mondala
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Nathaniel Delos Santos
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Amber C Miller
- Department of Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Gabriel Pineda
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA, 92037, USA.,Department of Health Sciences, School of Health and Human Services at National University, San Diego, CA, 92123, USA
| | - Qingfei Jiang
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Heather Leu
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Shawn A Ali
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Anusha-Preethi Ganesan
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Christina N Wu
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Caitlin Costello
- Department of Medicine, Moores Cancer Center at University of California, San Diego, La Jolla, CA, 92093, USA
| | - Mark Minden
- Princess Margaret Hospital, University Health Network, Toronto, ON, Canada, M5G 2M9
| | | | - A Keith Stewart
- Department of Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Leslie A Crews
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA, 92037, USA.
| | - Catriona H M Jamieson
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA, 92037, USA. .,Department of Medicine, Moores Cancer Center at University of California, San Diego, La Jolla, CA, 92093, USA.
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Rihani A, Vandesompele J, Speleman F, Van Maerken T. Inhibition of CDK4/6 as a novel therapeutic option for neuroblastoma. Cancer Cell Int 2015. [PMID: 26225123 PMCID: PMC4518532 DOI: 10.1186/s12935-015-0224-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Background Neuroblastoma is a neural crest-derived tumor and is the most common cancer in children less than 1 year of age. We hypothesized that aberrations in genes that control the cell cycle could play an important role in the pathogenesis of neuroblastoma and could provide a tractable therapeutic target. Methods In this study, we screened 131 genes involved in cell cycle regulation at different levels by analyzing the effect of siRNA-mediated gene silencing on the proliferation of neuroblastoma cells. Results Marked reductions in neuroblastoma cellular proliferation were recorded after knockdown of CCND1 or PLK1. We next showed that pharmacological inhibition of cyclin D1 dependent kinases 4/6 (CDK4/6) with PD 0332991 (palbociclib) reduced the growth of neuroblastoma cell lines, induced G1 cell cycle arrest, and inhibited the cyclin D1-Rb pathway. Conclusion Selective inhibition of CDK4/6 using palbociclib may provide a new therapeutic option for treating neuroblastoma. Electronic supplementary material The online version of this article (doi:10.1186/s12935-015-0224-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ali Rihani
- Center for Medical Genetics, Ghent University, De Pintelaan 185, 9000 Ghent, Belgium
| | - Jo Vandesompele
- Center for Medical Genetics, Ghent University, De Pintelaan 185, 9000 Ghent, Belgium
| | - Frank Speleman
- Center for Medical Genetics, Ghent University, De Pintelaan 185, 9000 Ghent, Belgium
| | - Tom Van Maerken
- Center for Medical Genetics, Ghent University, De Pintelaan 185, 9000 Ghent, Belgium
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11
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Grzincic EM, Yang JA, Drnevich J, Falagan-Lotsch P, Murphy CJ. Global transcriptomic analysis of model human cell lines exposed to surface-modified gold nanoparticles: the effect of surface chemistry. NANOSCALE 2015; 7:1349-62. [PMID: 25491924 PMCID: PMC4411964 DOI: 10.1039/c4nr05166a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Gold nanoparticles (Au NPs) are attractive for biomedical applications not only for their remarkable physical properties, but also for the ease of which their surface chemistry can be manipulated. Many applications involve functionalization of the Au NP surface in order to improve biocompatibility, attach targeting ligands or carry drugs. However, changes in cells exposed to Au NPs of different surface chemistries have been observed, and little is known about how Au NPs and their surface coatings may impact cellular gene expression. The gene expression of two model human cell lines, human dermal fibroblasts (HDF) and prostate cancer cells (PC3) was interrogated by microarray analysis of over 14,000 human genes. The cell lines were exposed to four differently functionalized Au NPs: citrate, poly(allylamine hydrochloride) (PAH), and lipid coatings combined with alkanethiols or PAH. Gene functional annotation categories and weighted gene correlation network analysis were used in order to connect gene expression changes to common cellular functions and to elucidate expression patterns between Au NP samples. Coated Au NPs affect genes implicated in proliferation, angiogenesis, and metabolism in HDF cells, and inflammation, angiogenesis, proliferation apoptosis regulation, survival and invasion in PC3 cells. Subtle changes in surface chemistry, such as the initial net charge, lability of the ligand, and underlying layers greatly influence the degree of expression change and the type of cellular pathway affected.
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Affiliation(s)
- E. M. Grzincic
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - J. A. Yang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - J. Drnevich
- High Performance Biological Computing Group, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - P. Falagan-Lotsch
- Laboratory of Toxicology, Division of Bioengineering, Board of Life Sciences Metrology, National Institute of Metrology, Quality and Technology (INMETRO), Duque de Caxias, Rio de Janeiro 25250-929, Brazil
| | - C. J. Murphy
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
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Vanhauwaert S, Van Peer G, Rihani A, Janssens E, Rondou P, Lefever S, De Paepe A, Coucke PJ, Speleman F, Vandesompele J, Willaert A. Expressed repeat elements improve RT-qPCR normalization across a wide range of zebrafish gene expression studies. PLoS One 2014; 9:e109091. [PMID: 25310091 PMCID: PMC4195698 DOI: 10.1371/journal.pone.0109091] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 09/01/2014] [Indexed: 11/29/2022] Open
Abstract
The selection and validation of stably expressed reference genes is a critical issue for proper RT-qPCR data normalization. In zebrafish expression studies, many commonly used reference genes are not generally applicable given their variability in expression levels under a variety of experimental conditions. Inappropriate use of these reference genes may lead to false interpretation of expression data and unreliable conclusions. In this study, we evaluated a novel normalization method in zebrafish using expressed repetitive elements (ERE) as reference targets, instead of specific protein coding mRNA targets. We assessed and compared the expression stability of a number of EREs to that of commonly used zebrafish reference genes in a diverse set of experimental conditions including a developmental time series, a set of different organs from adult fish and different treatments of zebrafish embryos including morpholino injections and administration of chemicals. Using geNorm and rank aggregation analysis we demonstrated that EREs have a higher overall expression stability compared to the commonly used reference genes. Moreover, we propose a limited set of ERE reference targets (hatn10, dna15ta1 and loopern4), that show stable expression throughout the wide range of experiments in this study, as strong candidates for inclusion as reference targets for qPCR normalization in future zebrafish expression studies. Our applied strategy to find and evaluate candidate expressed repeat elements for RT-qPCR data normalization has high potential to be used also for other species.
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Affiliation(s)
| | - Gert Van Peer
- Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Ali Rihani
- Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Els Janssens
- Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Pieter Rondou
- Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Steve Lefever
- Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Anne De Paepe
- Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Paul J. Coucke
- Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Frank Speleman
- Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Jo Vandesompele
- Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Andy Willaert
- Center of Medical Genetics, Ghent University, Ghent, Belgium
- * E-mail:
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