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Atallah O, Almealawy YF, Awuah WA, Conti A, Chaurasia B. Is simultaneous occurrence of meningioma and glioblastoma a mere coincidence? Clin Neurol Neurosurg 2024; 236:108099. [PMID: 38215500 DOI: 10.1016/j.clineuro.2023.108099] [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: 11/03/2023] [Revised: 12/12/2023] [Accepted: 12/20/2023] [Indexed: 01/14/2024]
Abstract
BACKGROUND It is extremely unusual for multiple tumors to arise from different cell types and occur at the same time inside the brain. It is still unknown whether or not the coexistence of meningioma and glioblastoma is connected in any way or if their simultaneous appearance is merely a coincidence. OBJECTIVE We conduct a comprehensive literature review on cases of concurrent meningioma and glioblastoma occurrence to elucidate the underlying concepts that may constitute this coexistence. METHODS We searched for articles on the topic of glioblastoma coexisting with meningioma in Google Scholar, PubMed, and Scopus. First, the initial literature searches were conducted for study selection and the data collection processes. After evaluating the title and abstract, the papers were selected. RESULTS We analyzed 21 studies describing 23 patients who had both glioblastoma and meningioma. There were ten male patients (47.6 %) and thirteen female patients (61.9 %). The mean age of patients at diagnosis was 61 years old (the range 30 to 86). In 17 cases, both tumors were in the same hemisphere (80.9 %). In 5 cases, they were in the other hemisphere (23.8 %), and in one case, the glioblastoma was in the left hemisphere and the olfactory meningioma was In 5 cases, they were in the other hemisphere (23.8 %), and in one case, the glioblastoma was in the left hemisphere and the olfactory meningioma was in the anterior cranial fossa. In 61.9 % of cases, headache was the predominant symptom. CONCLUSION Understanding the unique challenges posed by the coexistence of glioblastoma and meningioma is crucial for developing effective treatment strategies. Further investigation into the underlying molecular mechanisms and genetic factors involved in this rare occurrence could pave the way for personalized therapies tailored to each patient's specific needs.
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Affiliation(s)
- Oday Atallah
- Departemnt of Neurosurgery, Hannover Medical School, Hannover, Germany.
| | - Yasser F Almealawy
- Department of Neurosurgery, University of Kufa, Kufa, Iraq; Department of Neurosurgery,Global Neurosurgical Alliance, Tucson, AZ, USA.
| | | | - Alfredo Conti
- Department of Neurosurgery, IRCCS Istituto delle Scienze Neurologiche di Bologna Alma Mater Studiorum Universit_a di Bologna, Via Altura 3, 40123 Bologna, Italy
| | - Bipin Chaurasia
- Department of Neurosurgery, Neurosurgery Clinic, Birgunj, Nepal.
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2
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Zhang J, Li Y, Fan TY, Liu D, Zou WD, Li H, Li YK. Identification of bromodomain-containing proteins prognostic value and expression significance based on a genomic landscape analysis of ovarian serous cystadenocarcinoma. Front Oncol 2022; 12:1021558. [PMID: 36276071 PMCID: PMC9579433 DOI: 10.3389/fonc.2022.1021558] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 09/15/2022] [Indexed: 12/24/2022] Open
Abstract
BackgroundOvarian serous cystadenocarcinoma (OSC), a common gynecologic tumor, is characterized by high mortality worldwide. Bromodomain (BRD)-containing proteins are a series of evolutionarily conserved proteins that bind to acetylated Lys residues of histones to regulate the transcription of multiple genes. The ectopic expression of BRDs is often observed in multiple cancer types, but the role of BRDs in OSC is still unclear.MethodsWe performed the differential expression, GO enrichment, GSEA, immune infiltration, risk model, subtype classification, stemness feature, DNA alteration, and epigenetic modification analysis for these BRDs based on multiple public databases.ResultsMost BRDs were dysregulated in OSC tissues compared to normal ovary tissues. These BRDs were positively correlated with each other in OSC patients. Gene alteration and epigenetic modification were significant for the dysregulation of BRDs in OSC patients. GO enrichment suggested that BRDs played key roles in histone acetylation, viral carcinogenesis, and transcription coactivator activity. Two molecular subtypes were classified by BRDs for OSC, which were significantly correlated with stemness features, m6A methylation, ferroptosis, drug sensitivity, and immune infiltration. The risk model constructed by LASSO regression with BRDs performed moderately well in prognostic predictions for OSC patients. Moreover, BRPF1 plays a significant role in these BRDs for the development and progression of OSC patients.ConclusionBRDs are potential targets and biomarkers for OSC patients, especially BRPF1.
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Affiliation(s)
- Juan Zhang
- Department of Assisted Reproductive Centre, Zhuzhou Central Hospital, Xiangya Hospital Zhuzhou Central South University, Central South University, Zhuzhou, China
| | - Yan Li
- Department of Assisted Reproductive Centre, Zhuzhou Central Hospital, Xiangya Hospital Zhuzhou Central South University, Central South University, Zhuzhou, China
| | - Ting-yu Fan
- Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, University of South China, Hengyang, China
| | - Dan Liu
- Department of Assisted Reproductive Centre, Zhuzhou Central Hospital, Xiangya Hospital Zhuzhou Central South University, Central South University, Zhuzhou, China
| | - Wen-da Zou
- Department of Assisted Reproductive Centre, Zhuzhou Central Hospital, Xiangya Hospital Zhuzhou Central South University, Central South University, Zhuzhou, China
| | - Hui Li
- Department of Assisted Reproductive Centre, Zhuzhou Central Hospital, Xiangya Hospital Zhuzhou Central South University, Central South University, Zhuzhou, China
- *Correspondence: Hui Li, ; Yu-kun Li,
| | - Yu-kun Li
- Department of Assisted Reproductive Centre, Zhuzhou Central Hospital, Xiangya Hospital Zhuzhou Central South University, Central South University, Zhuzhou, China
- *Correspondence: Hui Li, ; Yu-kun Li,
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3
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Zhang J, Huang L, Zhang P, Huang X, Yang W, Liu R, Sun Q, Lu Y, Zhang M, Fu Q. Genomic Identification, Evolution, and Expression Analysis of Bromodomain Genes Family in Buffalo. Genes (Basel) 2022; 13:genes13010103. [PMID: 35052443 PMCID: PMC8774554 DOI: 10.3390/genes13010103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/22/2021] [Accepted: 12/28/2021] [Indexed: 02/05/2023] Open
Abstract
Bromodomain (BRD) is an evolutionarily conserved protein-protein interaction module that is critical in gene regulation, cellular homeostasis, and epigenetics. This study aimed to conduct an identification, evolution, and expression analysis of the BRD gene family in the swamp buffalo (Bubalus bubalis). A total of 101 BRD protein sequences deduced from 22 BRD genes were found in the buffalo genome. The BRD proteins were classified into six groups based on phylogenetic relationships, conserved motifs, and conserved domains. The BRD genes were irregularly distributed in 13 chromosomes. Collinearity analysis revealed 20 BRD gene pairs that had remarkable homologous relationships between the buffalo and cattle, although no tandem or segmental duplication event was found in the buffalo BRD genes. Comparative transcriptomics using a 10x sequencing platform analysis showed that 22 BRD genes were identified in the Sertoli cells (SCs) at different developmental stages of buffalo. Further, the mRNA expression levels of bromodomain and the extraterminal (BET) family in SCs at the pubertal stage were higher than that at the prepubertal stage of buffalo. However, the SMARCA2, PHIP, BRD9, and TAF1 genes exhibited the opposite trend. The maturation process of SCs may be regulated by the BRD family members expressed differentially in SCs at different developmental stages of buffalo. In summary, our findings provide an understanding of the evolutionary, structural, and functional properties of the buffalo BRD family members, and further characterize the function of the BRD family in the maturation of SCs. It also provides a theoretical basis for further understanding in the future of the mechanism of SCs regulating spermatogenesis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Qiang Fu
- Correspondence: ; Tel.: +86-771-3237124
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4
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Chamberlin K, Chamberlin G, Saunders K, Khagi S. Next-generation sequencing reveals novel mutations in a collision tumor of glioblastoma and meningioma. CNS Oncol 2021; 10:CNS70. [PMID: 34015961 PMCID: PMC8162195 DOI: 10.2217/cns-2020-0029] [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] [Indexed: 12/26/2022] Open
Abstract
Primary intracranial collision tumors are rare in patients without predisposing factors. We report such a case in a 42-year-old female who presented with headaches and altered mental status. Imaging revealed a single heterogeneous, rim-enhancing lesion in the left parieto-occipital periventricular region, involving the corpus callosum. Stereotactic biopsy demonstrated glioblastoma. Subsequent tumor resection showed histologic evidence of glioblastoma and meningioma. Next-generation sequencing was performed on both tumor components. The glioblastoma exhibited a CDKN2A homozygous deletion and novel missense mutations in TAF1L and CSMD3, while no definitive genetic alterations were identified in the meningioma. Next-generation sequencing may yield insight into molecular drivers of intracranial collision tumors and aid in identifying future therapeutic targets. Next-generation sequencing (NGS) reveals novel mutations in a collision tumor of GBM and meningioma. NGS has the potential to yield insight into molecular drivers of intracranial tumors and identify therapeutic targets.
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Affiliation(s)
- Kelly Chamberlin
- Department of Neurosurgery, UNC Hospitals, Chapel Hill, NC 27514, USA
| | - Gregory Chamberlin
- Department of Pathology & Laboratory Medicine, UNC Hospitals, Chapel Hill, NC 27514, USA
| | - Katherine Saunders
- Department of Pathology & Laboratory Medicine, UNC Hospitals, Chapel Hill, NC 27514, USA
| | - Simon Khagi
- Department of Neurosurgery, UNC Hospitals, Chapel Hill, NC 27514, USA.,Department of Medicine, Division of Medical Oncology, UNC Hospitals, Chapel Hill, NC 27514, USA
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Dubreuil MM, Morgens DW, Okumoto K, Honsho M, Contrepois K, Lee-McMullen B, Traber GM, Sood RS, Dixon SJ, Snyder MP, Fujiki Y, Bassik MC. Systematic Identification of Regulators of Oxidative Stress Reveals Non-canonical Roles for Peroxisomal Import and the Pentose Phosphate Pathway. Cell Rep 2021; 30:1417-1433.e7. [PMID: 32023459 DOI: 10.1016/j.celrep.2020.01.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 10/07/2019] [Accepted: 01/02/2020] [Indexed: 12/13/2022] Open
Abstract
Reactive oxygen species (ROS) play critical roles in metabolism and disease, yet a comprehensive analysis of the cellular response to oxidative stress is lacking. To systematically identify regulators of oxidative stress, we conducted genome-wide Cas9/CRISPR and shRNA screens. This revealed a detailed picture of diverse pathways that control oxidative stress response, ranging from the TCA cycle and DNA repair machineries to iron transport, trafficking, and metabolism. Paradoxically, disrupting the pentose phosphate pathway (PPP) at the level of phosphogluconate dehydrogenase (PGD) protects cells against ROS. This dramatically alters metabolites in the PPP, consistent with rewiring of upper glycolysis to promote antioxidant production. In addition, disruption of peroxisomal import unexpectedly increases resistance to oxidative stress by altering the localization of catalase. Together, these studies provide insights into the roles of peroxisomal matrix import and the PPP in redox biology and represent a rich resource for understanding the cellular response to oxidative stress.
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Affiliation(s)
- Michael M Dubreuil
- Program in Cancer Biology, Stanford University, Stanford, CA 94305-5120, USA; Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - David W Morgens
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Kanji Okumoto
- Department of Biology, Faculty of Sciences, Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan; Division of Organelle Homeostasis, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Masanori Honsho
- Division of Organelle Homeostasis, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kévin Contrepois
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | | | | | - Ria S Sood
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Scott J Dixon
- Program in Cancer Biology, Stanford University, Stanford, CA 94305-5120, USA; Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA; Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA 94305-5120, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Yukio Fujiki
- Division of Organelle Homeostasis, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
| | - Michael C Bassik
- Program in Cancer Biology, Stanford University, Stanford, CA 94305-5120, USA; Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA; Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA 94305-5120, USA.
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6
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Hernández IH, Cabrera JR, Santos-Galindo M, Sánchez-Martín M, Domínguez V, García-Escudero R, Pérez-Álvarez MJ, Pintado B, Lucas JJ. Pathogenic SREK1 decrease in Huntington's disease lowers TAF1 mimicking X-linked dystonia parkinsonism. Brain 2020; 143:2207-2219. [PMID: 32533168 PMCID: PMC7363496 DOI: 10.1093/brain/awaa150] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 02/20/2020] [Accepted: 03/21/2020] [Indexed: 12/04/2022] Open
Abstract
Huntington’s disease and X-linked dystonia parkinsonism are two monogenic basal ganglia model diseases. Huntington’s disease is caused by a polyglutamine-encoding CAG repeat expansion in the Huntingtin (HTT) gene leading to several toxic interactions of both the expanded CAG-containing mRNA and the polyglutamine-containing protein, while X-linked dystonia parkinsonism is caused by a retrotransposon insertion in the TAF1 gene, which decreases expression of this core scaffold of the basal transcription factor complex TFIID. SRSF6 is an RNA-binding protein of the serine and arginine-rich (SR) protein family that interacts with expanded CAG mRNA and is sequestered into the characteristic polyglutamine-containing inclusion bodies of Huntington’s disease brains. Here we report decreased levels of the SRSF6 interactor and regulator SREK1—another SR protein involved in RNA processing—which includes TAF1 as one of its targets. This led us to hypothesize that Huntington’s disease and X-linked dystonia parkinsonism pathogeneses converge in TAF1 alteration. We show that diminishing SRSF6 through RNA interference in human neuroblastoma cells leads to a decrease in SREK1 levels, which, in turn, suffices to cause diminished TAF1 levels. We also observed decreased SREK1 and TAF1 levels in striatum of Huntington’s disease patients and transgenic model mice. We then generated mice with neuronal transgenic expression of SREK1 (TgSREK1 mice) that, interestingly, showed transcriptomic alterations complementary to those in Huntington’s disease mice. Most importantly, by combining Huntington’s disease and TgSREK1 mice we verify that SREK1 overexpression corrects TAF1 deficiency and attenuates striatal atrophy and motor phenotype of Huntington’s disease mice. Our results therefore demonstrate that altered RNA processing upon SREK1 dysregulation plays a key role in Huntington’s disease pathogenesis and pinpoint TAF1 as a likely general determinant of selective vulnerability of the striatum in multiple neurological disorders.
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Affiliation(s)
- Ivó H Hernández
- Center for Molecular Biology 'Severo Ochoa' (CBMSO) CSIC/UAM, Madrid 28049, Spain.,Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid 28031, Spain.,Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Jorge R Cabrera
- Center for Molecular Biology 'Severo Ochoa' (CBMSO) CSIC/UAM, Madrid 28049, Spain.,Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid 28031, Spain
| | - María Santos-Galindo
- Center for Molecular Biology 'Severo Ochoa' (CBMSO) CSIC/UAM, Madrid 28049, Spain.,Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid 28031, Spain
| | - Manuel Sánchez-Martín
- Transgenic Facility, Nucleus platform, Universidad de Salamanca, Salamanca 37007, Spain
| | - Verónica Domínguez
- Center for Molecular Biology 'Severo Ochoa' (CBMSO) CSIC/UAM, Madrid 28049, Spain.,Transgenesis Facility CNB-CBMSO, CSIC-UAM, Madrid 28049, Spain
| | - Ramón García-Escudero
- Molecular Oncology Unit, CIEMAT, Madrid 28040, Spain.,Biomedicine Research Institute, Hospital 12 Octubre, Madrid 28041, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid 28029, Spain
| | - María J Pérez-Álvarez
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Belén Pintado
- Transgenesis Facility CNB-CBMSO, CSIC-UAM, Madrid 28049, Spain
| | - José J Lucas
- Center for Molecular Biology 'Severo Ochoa' (CBMSO) CSIC/UAM, Madrid 28049, Spain.,Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid 28031, Spain
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7
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Yazdani M, Shahdadfar A, Reppe S, Sapkota D, Vallenari EM, Lako M, Connon CJ, Figueiredo FC, Utheim TP. Response of human oral mucosal epithelial cells to different storage temperatures: A structural and transcriptional study. PLoS One 2020; 15:e0243914. [PMID: 33326470 PMCID: PMC7744058 DOI: 10.1371/journal.pone.0243914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 11/30/2020] [Indexed: 11/26/2022] Open
Abstract
PURPOSE Seeking to improve the access to regenerative medicine, this study investigated the structural and transcriptional effects of storage temperature on human oral mucosal epithelial cells (OMECs). METHODS Cells were stored at four different temperatures (4°C, 12°C, 24°C and 37°C) for two weeks. Then, the morphology, cell viability and differential gene expression were examined using light and scanning electron microscopy, trypan blue exclusion test and TaqMan gene expression array cards, respectively. RESULTS Cells stored at 4°C had the most similar morphology to non-stored controls with the highest viability rate (58%), whereas the 37°C group was most dissimilar with no living cells. The genes involved in stress-induced growth arrest (GADD45B) and cell proliferation inhibition (TGFB2) were upregulated at 12°C and 24°C. Upregulation was also observed in multifunctional genes responsible for morphology, growth, adhesion and motility such as EFEMP1 (12°C) and EPHA4 (4°C-24°C). Among genes used as differentiation markers, PPARA and TP53 (along with its associated gene CDKN1A) were downregulated in all temperature conditions, whereas KRT1 and KRT10 were either unchanged (4°C) or downregulated (24°C and 12°C; and 24°C, respectively), except for upregulation at 12°C for KRT1. CONCLUSIONS Cells stored at 12°C and 24°C were stressed, although the expression levels of some adhesion-, growth- and apoptosis-related genes were favourable. Collectively, this study suggests that 4°C is the optimal storage temperature for maintenance of structure, viability and function of OMECs after two weeks.
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Affiliation(s)
- Mazyar Yazdani
- Department of Medical Biochemistry, Oslo University Hospital, Ullevål, Oslo, Norway
- Center for Eye Research, Department of Ophthalmology, Oslo University Hospital, Ullevål, Oslo, Norway
| | - Aboulghassem Shahdadfar
- Center for Eye Research, Department of Ophthalmology, Oslo University Hospital, Ullevål, Oslo, Norway
| | - Sjur Reppe
- Department of Medical Biochemistry, Oslo University Hospital, Ullevål, Oslo, Norway
- Department of Plastic and Reconstructive Surgery, Oslo University Hospital, Oslo, Norway
- Lovisenberg Diaconal Hospital, Unger-Vetlesen Institute, Oslo, Norway
| | - Dipak Sapkota
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Evan M. Vallenari
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Majlinda Lako
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, International Centre for Life, Bioscience West Building, Newcastle upon Tyne, United Kingdom
| | - Che J. Connon
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, International Centre for Life, Bioscience West Building, Newcastle upon Tyne, United Kingdom
| | - Francisco C. Figueiredo
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, International Centre for Life, Bioscience West Building, Newcastle upon Tyne, United Kingdom
- Department of Ophthalmology, Royal Victoria Infirmary & Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Tor Paaske Utheim
- Department of Medical Biochemistry, Oslo University Hospital, Ullevål, Oslo, Norway
- Department of Plastic and Reconstructive Surgery, Oslo University Hospital, Oslo, Norway
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
- Department of Ophthalmology, Stavanger University Hospital, Stavanger, Norway
- Department of Ophthalmology, Sørlandet Hospital Arendal, Arendal, Norway
- Department of Computer Science, Oslo Metropolitan University, Oslo, Norway
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8
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Janakiraman U, Dhanalakshmi C, Yu J, Moutal A, Boinon L, Fukunaga K, Khanna R, Nelson MA. The investigation of the T-type calcium channel enhancer SAK3 in an animal model of TAF1 intellectual disability syndrome. Neurobiol Dis 2020; 143:105006. [PMID: 32622085 PMCID: PMC7422587 DOI: 10.1016/j.nbd.2020.105006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/17/2020] [Accepted: 06/27/2020] [Indexed: 01/21/2023] Open
Abstract
T-type calcium channels, in the central nervous system, are involved in the pathogenesis of many neurodegenerative diseases, including TAF1 intellectual disability syndrome (TAF1 ID syndrome). Here, we evaluated the efficacy of a novel T-type Ca2+ channel enhancer, SAK3 (ethyl 8'-methyl-2', 4-dioxo-2-(piperidin-1-yl)-2'H-spiro [cyclopentane-1, 3'-imidazo [1, 2-a] pyridine]-2-ene-3-carboxylate) in an animal model of TAF1 ID syndrome. At post-natal day 3, rat pups were subjected to intracerebroventricular (ICV) injection of either gRNA-control or gRNA-TAF1 CRISPR/Cas9 viruses. At post-natal day 21 animals were given SAK3 (0.25 mg/kg, p.o.) or vehicle up to post-natal day 35 (i.e. 14 days). Rats were subjected to behavioral, morphological, electrophysiological, and molecular studies. Oral administration of SAK3 (0.25 mg/kg, p.o.) significantly rescued the behavior abnormalities in beam walking test and open field test caused by TAF1 gene editing. We observed an increase in calbindin-positive Purkinje cells and GFAP-positive astrocytes as well as a decrease in IBA1-positive microglia cells in SAK3-treated animals. In addition, SAK3 protected the Purkinje and granule cells from apoptosis induced by TAF-1 gene editing. SAK3 also restored the excitatory post synaptic current (sEPSCs) in TAF1 edited Purkinje cells. Finally, SAK3 normalized the BDNF/AKT signaling axis in TAF1 edited animals. Altogether, these observations suggest that SAK3 could be a novel therapeutic agent for TAF1 ID syndrome.
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Affiliation(s)
- Udaiyappan Janakiraman
- Department of Pathology, University of Arizona College of Medicine, College of Pharmacy, Tucson, AZ, USA
| | - Chinnasamy Dhanalakshmi
- Department of Pathology, University of Arizona College of Medicine, College of Pharmacy, Tucson, AZ, USA
| | - Jie Yu
- Department of Pharmacology, University of Arizona College of Medicine, College of Pharmacy, Tucson, AZ, USA; College of Basic Medical Science, Zhejiang Chinese Medical University, Hangzhou 310058, China
| | - Aubin Moutal
- Department of Pharmacology, University of Arizona College of Medicine, College of Pharmacy, Tucson, AZ, USA
| | - Lisa Boinon
- Department of Pharmacology, University of Arizona College of Medicine, College of Pharmacy, Tucson, AZ, USA
| | - Kohji Fukunaga
- Department of Pharmacology, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Rajesh Khanna
- Department of Pathology, University of Arizona College of Medicine, College of Pharmacy, Tucson, AZ, USA; Department of Pharmacology, University of Arizona College of Medicine, College of Pharmacy, Tucson, AZ, USA; The Center for Innovation in Brain Sciences, The University of Arizona Health Sciences, Tucson, AZ, USA; The BIO5 Institute, University of Arizona, USA
| | - Mark A Nelson
- Department of Pathology, University of Arizona College of Medicine, College of Pharmacy, Tucson, AZ, USA.
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9
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Ding M, Tyrchan C, Bäck E, Östling J, Schubert S, McCrae C. Combined siRNA and Small-Molecule Phenotypic Screening Identifies Targets Regulating Rhinovirus Replication in Primary Human Bronchial Epithelial Cells. SLAS DISCOVERY 2020; 25:634-645. [PMID: 32189556 DOI: 10.1177/2472555220909726] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Human rhinovirus (RV) is the most common cause of acute upper respiratory tract infections and has recently been shown to play a significant role in exacerbations of asthma and chronic obstructive pulmonary disease (COPD). There is a significant unmet medical need for agents for the prevention and/or treatment of exacerbations triggered by human RV infection. Phenotypic drug discovery programs using different perturbation modalities, for example, siRNA, small-molecule compounds, and CRISPR, hold significant value for identifying novel drug targets. We have previously reported the identification of lanosterol synthase as a novel regulator of RV2 replication through a phenotypic screen of a library of siRNAs against druggable genes in normal human bronchial epithelial (NHBE) cells. Here, we describe a follow-up phenotypic screen of small-molecule compounds that are annotated to be pharmacological regulators of target genes that were identified to significantly affect RV2 replication in the siRNA primary screen of 10,500 druggable genes. Two hundred seventy small-molecule compounds selected for interacting with 122 target gene hits were screened in the primary RV2 assay in NHBE cells by quantifying viral replication via in situ hybridization followed by secondary quantitative PCR-based assays for RV2, RV14, and RV16. The described follow-up phenotypic screening allowed us to identify Fms-related tyrosine kinase 4 (FLT4) as a novel target regulating RV replication. We demonstrate that a combination of siRNA and small-molecule compound screening models is a useful phenotypic drug discovery approach for the identification of novel drug targets.
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Affiliation(s)
- Mei Ding
- Discovery Sciences, Research and Early Development, R&D BioPharmaceuticals, AstraZeneca, Gothenburg, Sweden
| | - Christian Tyrchan
- Medicinal Chemistry, Research and Early Development, Respiratory, Inflammation and Autoimmune (RIA), R&D BioPharmaceuticals, AstraZeneca, Gothenburg, Sweden
| | - Elisabeth Bäck
- Discovery Sciences, Research and Early Development, R&D BioPharmaceuticals, AstraZeneca, Gothenburg, Sweden
| | - Jörgen Östling
- Bioscience, Research and Early Development, Respiratory, Inflammation and Autoimmune (RIA), R&D BioPharmaceuticals, AstraZeneca, Gothenburg, Sweden
| | | | - Christopher McCrae
- Translational Science and Experimental Medicine, Research and Early Development, Respiratory, Inflammation and Autoimmune (RIA), R&D BioPharmaceuticals, AstraZeneca, Gaithersburg, MD, USA
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10
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Wang D, Qi H, Zhang H, Zhou W, Li Y, Li A, Liu Q, Wang Y. TAF1L promotes development of oral squamous cell carcinoma via decreasing autophagy-dependent apoptosis. Int J Biol Sci 2020; 16:1180-1193. [PMID: 32174793 PMCID: PMC7053316 DOI: 10.7150/ijbs.41148] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 12/26/2019] [Indexed: 02/07/2023] Open
Abstract
This study focused on investigating the relationships of TAF1L expression and clinical features or pathological stages of oral squamous cell carcinoma (OSCC), and its potential roles of TAF1L on OSCC development. Western blot and immunohistochemical staining were used to detect TAF1L expression in OSCC tissues and cells. Effects of TAF1L on OSCC cells in vitro were examined by cell proliferation assay, wound healing assay, transwell chamber assay, flow cytometry analysis and siRNA technique. Cellular key proteins related to cell autophagy and apoptosis were evaluated by Western blot and immunofluorescent staining. Moreover, functions of TAF1L on OSCC process were observed in nude mouse model. Testing results showed that expression of TAF1L protein was higher in OSCC tissues than that in normal oral epithelial or paracancerous tissues. Additionally, the level of TAF1L protein expression was upregulated in OSCC cell lines, compared to that in normal oral epithelial cells. Furthermore, cell proliferation, migration, autophagy and apoptosis were modulated post siRNA-TAF1L treatment in vitro. Especially, TAF1L knockdown-induced apoptotic activation on OSCC cells could be rescued by autophagic activator (Rapamycin). Moreover, that overexpression of TAF1L protein could promote the growth of OSCC cell xenografts was confirmed in nude mouse model. Taken together, it suggests that TAF1L may facilitate OSCC cells to escape cell apoptosis via autophagic activation for enhancing OSCC development.
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Affiliation(s)
- Daiwei Wang
- Center for Research and Technology of Precision Medicine, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China.,Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, China
| | - Hong Qi
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University. Xi'an, Shanxi, China
| | - Haoxing Zhang
- Center for Research and Technology of Precision Medicine, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
| | - Wei Zhou
- Center for Research and Technology of Precision Medicine, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
| | - Yanpeng Li
- Center for Research and Technology of Precision Medicine, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
| | - Ang Li
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University. Xi'an, Shanxi, China
| | - Qiong Liu
- Center for Research and Technology of Precision Medicine, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China.,Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, China
| | - Yun Wang
- Center for Research and Technology of Precision Medicine, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
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11
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Porter SN, Levine RM, Pruett-Miller SM. A Practical Guide to Genome Editing Using Targeted Nuclease Technologies. Compr Physiol 2019; 9:665-714. [PMID: 30873595 DOI: 10.1002/cphy.c180022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Genome engineering using programmable nucleases is a rapidly evolving technique that enables precise genetic manipulations within complex genomes. Although this technology first surfaced with the creation of meganucleases, zinc finger nucleases, and transcription activator-like effector nucleases, CRISPR-Cas9 has been the most widely adopted platform because of its ease of use. This comprehensive review presents a basic overview of genome engineering and discusses the major technological advances in the field. In addition to nucleases, we discuss CRISPR-derived base editors and epigenetic modifiers. We also delve into practical applications of these tools, including creating custom-edited cell and animal models as well as performing genetic screens. Finally, we discuss the potential for therapeutic applications and ethical considerations related to employing this technology in humans. © 2019 American Physiological Society. Compr Physiol 9:665-714, 2019.
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Affiliation(s)
- Shaina N Porter
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Rachel M Levine
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Shondra M Pruett-Miller
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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12
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Zhong S, Yan H, Chen Z, Li Y, Shen Y, Wang Y, Li L, Sheng S, Wang Y. Overexpression of TAF1L Promotes Cell Proliferation, Migration and Invasion in Esophageal Squamous Cell Carcinoma. J Cancer 2019; 10:979-989. [PMID: 30854104 PMCID: PMC6400815 DOI: 10.7150/jca.26504] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 12/05/2018] [Indexed: 02/05/2023] Open
Abstract
Currently, it reported that TAF1L gene mutation is found in a number of carcinomas, but its pathophysiological function has not been well studied. We focused on investigating expressive levels of TAF1L gene and protein in esophageal squamous cell carcinoma (ESCC) with two tissue microarrays, forty fresh paired ESCC and paracancer samples using immunohistochemistry, real-time PCR or Western blot in this study. Furthermore, we executed TAF1L silence with siRNA in ESCC cell lines to evaluate effects of TAF1L expression on cell proliferation, migration and invasion of ESCC via CCK-8, wound healing and transwell chamber assays. Moreover, key proteins related to ESCC development were also analyzed by Western blot. Results from this study showed that the expression of TAF1L mRNA and protein in ESCC tissues were significantly higher than that in matched paracancer tissues. However, its abnormal expression was not associated with other clinic features, such as the age, gender and pathological grade, except of TNM-N stage. Furthermore, the proliferation, migration and invasion of ESCC cells were inhibited after TAF1L gene silencing. As a consequence, the expression of c-Myc and phosphorylated Akt in esophageal squamous cell line after TAF1L-siRNA treatment were inversely decreased, while p53 was increased significantly, compared those to control group. Taken together, the results from this study suggest that TAF1L gene might be served as an oncogene, and its overexpression could accelerate to the tumorigenesis of ESCC via promoting the malignant cell proliferation and tumor metastasis.
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Affiliation(s)
- Shan Zhong
- Center for Research and Technology of Precision Medicine, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518055, P. R. China
- Laboratory of Molecular Pathology, Shantou University Medical College, Shantou, Guangdong 515041, P. R. China
| | - Hongfei Yan
- Pathology Laboratory, Shantou University Medical College, Cancer Hospital, Shantou, Guangdong 515041, P. R. China
| | - Zhengshan Chen
- Laboratory of Molecular Pathology, Shantou University Medical College, Shantou, Guangdong 515041, P. R. China
| | - Yanpeng Li
- Center for Research and Technology of Precision Medicine, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518055, P. R. China
| | - Yanqin Shen
- Laboratory of Molecular Pathology, Shantou University Medical College, Shantou, Guangdong 515041, P. R. China
| | - Yongyu Wang
- Laboratory of Molecular Pathology, Shantou University Medical College, Shantou, Guangdong 515041, P. R. China
| | - Lan Li
- Laboratory of Molecular Pathology, Shantou University Medical College, Shantou, Guangdong 515041, P. R. China
| | - Sitong Sheng
- Center for Research and Technology of Precision Medicine, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518055, P. R. China
| | - Yun Wang
- Center for Research and Technology of Precision Medicine, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518055, P. R. China
- ✉ Corresponding author: Center for Research and Technology of Precision Medicine, College of Life Sciences and Oceanography, Shenzhen University (Xili Campus), No. 1066, Xueyuan Ave, Nanshan Distract, Shenzhen, Guangdong 518055, P.R. China. Email address:
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13
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Godini R, Fallahi H. Shortening the list of essential genes in the human genome by network analysis. Meta Gene 2018. [DOI: 10.1016/j.mgene.2018.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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14
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Saberi Anvar M, Minuchehr Z, Shahlaei M, Kheitan S. Gastric cancer biomarkers; A systems biology approach. Biochem Biophys Rep 2018; 13:141-146. [PMID: 29556568 PMCID: PMC5857180 DOI: 10.1016/j.bbrep.2018.01.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/12/2017] [Accepted: 01/03/2018] [Indexed: 12/22/2022] Open
Abstract
Gastric cancer is one of the most fatal cancers in the world. Many efforts in recent years have attempted to find effective proteins in gastric cancer. By using a comprehensive list of proteins involved in gastric cancer, scientists were able to retrieve interaction information. The study of protein-protein interaction networks through systems biology based analysis provides appropriate strategies to discover candidate proteins and key biological pathways. In this study, we investigated dominant functional themes and centrality parameters including betweenness as well as the degree of each topological clusters and expressionally active sub-networks in the resulted network. The results of functional analysis on gene sets showed that neurotrophin signaling pathway, cell cycle and nucleotide excision possess the strongest enrichment signals. According to the computed centrality parameters, HNF4A, TAF1 and TP53 manifested as the most significant nodes in the interaction network of the engaged proteins in gastric cancer. This study also demonstrates pathways and proteins that are applicable as diagnostic markers and therapeutic targets for future attempts to overcome gastric cancer. A systematic study of protein-protein interaction networks through comprehensive extracted list of proteins involved in gastric cancer. Dominant functional theme and pathways of each topological clusters and expressionally active subnetworks were reported. The most effective proteins in gastric cancer formation were proposed according to the computed centrality parameters. HNF4A, TAF1and TP53 were mentioned as the key proteins in gastric cancer.
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Affiliation(s)
- Mohammad Saberi Anvar
- Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Zarrin Minuchehr
- Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Mohsen Shahlaei
- Nano Drug Delivery Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Samira Kheitan
- Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
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15
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Blood AJ, Waugh JL, Münte TF, Heldmann M, Domingo A, Klein C, Breiter HC, Lee LV, Rosales RL, Brüggemann N. Increased insula-putamen connectivity in X-linked dystonia-parkinsonism. NEUROIMAGE-CLINICAL 2017. [PMID: 29527488 PMCID: PMC5842648 DOI: 10.1016/j.nicl.2017.10.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Preliminary evidence from postmortem studies of X-linked dystonia-parkinsonism (XDP) suggests tissue loss may occur first and/or most severely in the striatal striosome compartment, followed later by cell loss in the matrix compartment. However, little is known about how this relates to pathogenesis and pathophysiology. While MRI cannot visualize these striatal compartments directly in humans, differences in relative gradients of afferent cortical connectivity across compartments (weighted toward paralimbic versus sensorimotor cortex, respectively) can be used to infer potential selective loss in vivo. In the current study we evaluated relative connectivity of paralimbic versus sensorimotor cortex with the caudate and putamen in 17 individuals with XDP and 17 matched controls. Although caudate and putamen volumes were reduced in XDP, there were no significant reductions in either “matrix-weighted”, or “striosome-weighted” connectivity. In fact, paralimbic connectivity with the putamen was elevated, rather than reduced, in XDP. This was driven most strongly by elevated putamen connectivity with the anterior insula. There was no relationship of these findings to disease duration or striatal volume, suggesting insula and/or paralimbic connectivity in XDP may develop abnormally and/or increase in the years before symptom onset. Previous work suggested striosomes might degenerate preferentially in early XDP. We developed a DTI tractography method to assess striosome and matrix integrity. Striosomal afferents to putamen were elevated in XDP, despite reduced putamen volume. Connectivity was particularly elevated from the insula (two to three-fold). Striosome connectivity strength was not associated with disease duration.
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Affiliation(s)
- Anne J Blood
- Mood and Motor Control Laboratory, Massachusetts General Hospital (MGH), Charlestown, MA, USA; Laboratory of Neuroimaging and Genetics, MGH, Charlestown, MA, USA; Depts. of Neurology, MGH, Boston, MA, USA; Psychiatry, MGH, Boston, MA, USA; Martinos Center for Biomedical Imaging, Dept. of Radiology, MGH, Charlestown, MA, USA; Harvard Medical School, Boston, MA, USA.
| | - Jeff L Waugh
- Mood and Motor Control Laboratory, Massachusetts General Hospital (MGH), Charlestown, MA, USA; Depts. of Neurology, MGH, Boston, MA, USA; Martinos Center for Biomedical Imaging, Dept. of Radiology, MGH, Charlestown, MA, USA; Division of Child Neurology, Boston Children's Hospital, USA; Harvard Medical School, Boston, MA, USA
| | - Thomas F Münte
- Department of Neurology, University of Lübeck, Lübeck, Germany
| | - Marcus Heldmann
- Department of Neurology, University of Lübeck, Lübeck, Germany
| | - Aloysius Domingo
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Hans C Breiter
- Mood and Motor Control Laboratory, Massachusetts General Hospital (MGH), Charlestown, MA, USA; Laboratory of Neuroimaging and Genetics, MGH, Charlestown, MA, USA; Psychiatry, MGH, Boston, MA, USA; Warren Wright Adolescent Center, Department of Psychiatry and Behavioral Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Lillian V Lee
- XDP Study Group, Philippine Children's Medical Center, Quezon City, Philippines
| | - Raymond L Rosales
- XDP Study Group, Philippine Children's Medical Center, Quezon City, Philippines; Department of Neurology and Psychiatry, Faculty of Medicine and Surgery, University of Santo Tomas, Manila, Philippines
| | - Norbert Brüggemann
- Department of Neurology, University of Lübeck, Lübeck, Germany; Institute of Neurogenetics, University of Lübeck, Lübeck, Germany.
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16
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Huang GS, Santin AD. Genetic landscape of clear cell endometrial cancer and the era of precision medicine. Cancer 2017; 123:3216-3218. [PMID: 28485840 DOI: 10.1002/cncr.30743] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 03/29/2017] [Indexed: 11/07/2022]
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17
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Wu Y, Lee S, Bobadilla S, Duan SZ, Liu X. High glucose-induced p53 phosphorylation contributes to impairment of endothelial antioxidant system. Biochim Biophys Acta Mol Basis Dis 2017; 1863:2355-2362. [PMID: 28673515 DOI: 10.1016/j.bbadis.2017.06.022] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 06/14/2017] [Accepted: 06/28/2017] [Indexed: 02/07/2023]
Abstract
High levels of glucose (HG) induce reactive oxygen species-mediated oxidative stress in endothelial cells (ECs), which leads to endothelial dysfunction and tissue damage. However, the molecular mechanisms involved in HG-induced endothelial oxidative stress and damage remain elusive. Here we show that cellular ATP level-modulated p53 Thr55 phosphorylation plays a critical role in the process. Upon HG exposure, the elevated ATP levels induced the kinase activity of TAF1 (TBP-associated factor 1), which leads to p53 Thr55 phosphorylation. The phosphorylation dissociates p53 from the glutathione peroxidase 1 (GPX1) promoter and results in reduction of GPX1 expression. Inhibition of TAF1-mediated p53 Thr55 phosphorylation abolished those events, supporting the role of TAF1 in sensing cellular ATP elevation and in regulating GPX1 expression under the HG condition. Importantly, treating cells with HG increased intracellular H2O2 and cell apoptosis, as well as suppressed nitric oxide (NO) bioavailability and tube network formation. These effects were also remarkably reversed by inhibition of TAF1 and p53 Thr55 phosphorylation. We conclude that HG leads to endothelial dysfunction via TAF1-mediated p53 Thr55 phosphorylation and subsequent GPX1 inactivation. Our study thus revealed a novel mechanism by which HG induces endothelial oxidative stress and damage and possibly provided an avenue for targeted therapy for diabetes-associated cardiovascular diseases.
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Affiliation(s)
- Yong Wu
- Department of Biochemistry, University of California, Riverside, CA 92521, United States
| | - Sangkyu Lee
- Department of Biochemistry, University of California, Riverside, CA 92521, United States
| | - Selene Bobadilla
- Department of Biochemistry, University of California, Riverside, CA 92521, United States
| | - Sheng Zhong Duan
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai, People's Republic of China; Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Xuan Liu
- Department of Biochemistry, University of California, Riverside, CA 92521, United States.
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18
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Fujisawa T, Filippakopoulos P. Functions of bromodomain-containing proteins and their roles in homeostasis and cancer. Nat Rev Mol Cell Biol 2017; 18:246-262. [PMID: 28053347 DOI: 10.1038/nrm.2016.143] [Citation(s) in RCA: 377] [Impact Index Per Article: 53.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Bromodomains (BRDs) are evolutionarily conserved protein-protein interaction modules that are found in a wide range of proteins with diverse catalytic and scaffolding functions and are present in most tissues. BRDs selectively recognize and bind to acetylated Lys residues - particularly in histones - and thereby have important roles in the regulation of gene expression. BRD-containing proteins are frequently dysregulated in cancer, they participate in gene fusions that generate diverse, frequently oncogenic proteins, and many cancer-causing mutations have been mapped to the BRDs themselves. Importantly, BRDs can be targeted by small-molecule inhibitors, which has stimulated many translational research projects that seek to attenuate the aberrant functions of BRD-containing proteins in disease.
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Affiliation(s)
- Takao Fujisawa
- Ludwig Institute for Cancer Research, Old Road Campus Research Building, Roosevelt Drive, Oxford
| | - Panagis Filippakopoulos
- Ludwig Institute for Cancer Research, Old Road Campus Research Building, Roosevelt Drive, Oxford.,Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
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19
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Chu JH, Hart JE, Chhabra D, Garshick E, Raby BA, Laden F. Gene expression network analyses in response to air pollution exposures in the trucking industry. Environ Health 2016; 15:101. [PMID: 27809917 PMCID: PMC5093980 DOI: 10.1186/s12940-016-0187-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 10/24/2016] [Indexed: 05/11/2023]
Abstract
BACKGROUND Exposure to air pollution, including traffic-related pollutants, has been associated with a variety of adverse health outcomes, including increased cardiopulmonary morbidity and mortality, and increased lung cancer risk. METHODS To better understand the cellular responses induced by air pollution exposures, we performed genome-wide gene expression microarray analysis using whole blood RNA sampled at three time-points across the work weeks of 63 non-smoking employees at 10 trucking terminals in the northeastern US. We defined genes and gene networks that were differentially activated in response to PM2.5 (particulate matter ≤ 2.5 microns in diameter) and elemental carbon (EC) and organic carbon (OC). RESULTS Multiple transcripts were strongly associated (padj < 0.001) with pollutant levels (48, 260, and 49 transcripts for EC, OC, and PM2.5, respectively), including 63 that were statistically significantly correlated with at least two out of the three exposures. These genes included many that have been implicated in ischemic heart disease, chronic obstructive pulmonary disease (COPD), lung cancer, and other pollution-related illnesses. Through the combination of Gene Set Enrichment Analysis and network analysis (using GeneMANIA), we identified a core set of 25 interrelated genes that were common to all three exposure measures and were differentially expressed in two previous studies assessing gene expression attributable to air pollution. Many of these are members of fundamental cancer-related pathways, including those related to DNA and metal binding, and regulation of apoptosis and also but include genes implicated in chronic heart and lung diseases. CONCLUSIONS These data provide a molecular link between the associations of air pollution exposures with health effects.
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Affiliation(s)
- Jen-hwa Chu
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT USA
| | - Jaime E. Hart
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Divya Chhabra
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
| | - Eric Garshick
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
- Pulmonary, Allergy, Sleep, and Critical Care Medicine Section, VA Boston Healthcare System, Boston, MA USA
| | - Benjamin A. Raby
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
| | - Francine Laden
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA USA
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA USA
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20
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Azorsa DO, Turnidge MA, Arora S. Data Analysis for High-Throughput RNAi Screening. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2016; 1470:247-60. [PMID: 27581298 DOI: 10.1007/978-1-4939-6337-9_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
High-throughput RNA interference (HT-RNAi) screening is an effective technology to help identify important genes and pathways involved in a biological process. Analysis of high-throughput RNAi screening data is a critical part of this technology, and many analysis methods have been described. Here, we summarize the workflow and types of analyses commonly used in high-throughput RNAi screening.
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Affiliation(s)
- David O Azorsa
- Institute of Molecular Medicine, Phoenix Children's Hospital, Phoenix, AZ, USA. .,Department of Child Health, University of Arizona College of Medicine - Phoenix, Phoenix, AZ, USA.
| | - Megan A Turnidge
- Department of Child Health, University of Arizona College of Medicine - Phoenix, Phoenix, AZ, USA.,School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Shilpi Arora
- Constellation Pharmaceuticals, Cambridge, MA, USA
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21
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Oh HR, An CH, Yoo NJ, Lee SH. Frameshift Mutations in the Mononucleotide Repeats of TAF1 and TAF1L Genes in Gastric and Colorectal Cancers with Regional Heterogeneity. Pathol Oncol Res 2016; 23:125-130. [DOI: 10.1007/s12253-016-0107-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 08/24/2016] [Indexed: 10/21/2022]
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22
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Taylor J, Woodcock S. A Perspective on the Future of High-Throughput RNAi Screening: Will CRISPR Cut Out the Competition or Can RNAi Help Guide the Way? ACTA ACUST UNITED AC 2015; 20:1040-51. [PMID: 26048892 DOI: 10.1177/1087057115590069] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 05/11/2015] [Indexed: 12/18/2022]
Abstract
For more than a decade, RNA interference (RNAi) has brought about an entirely new approach to functional genomics screening. Enabling high-throughput loss-of-function (LOF) screens against the human genome, identifying new drug targets, and significantly advancing experimental biology, RNAi is a fast, flexible technology that is compatible with existing high-throughput systems and processes; however, the recent advent of clustered regularly interspaced palindromic repeats (CRISPR)-Cas, a powerful new precise genome-editing (PGE) technology, has opened up vast possibilities for functional genomics. CRISPR-Cas is novel in its simplicity: one piece of easily engineered guide RNA (gRNA) is used to target a gene sequence, and Cas9 expression is required in the cells. The targeted double-strand break introduced by the gRNA-Cas9 complex is highly effective at removing gene expression compared to RNAi. Together with the reduced cost and complexity of CRISPR-Cas, there is the realistic opportunity to use PGE to screen for phenotypic effects in a total gene knockout background. This review summarizes the exciting development of CRISPR-Cas as a high-throughput screening tool, comparing its future potential to that of well-established RNAi screening techniques, and highlighting future challenges and opportunities within these disciplines. We conclude that the two technologies actually complement rather than compete with each other, enabling greater understanding of the genome in relation to drug discovery.
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Affiliation(s)
- Jessica Taylor
- Global HTS Centre, Discovery Sciences, AstraZeneca, Macclesfield, Cheshire, UK
| | - Simon Woodcock
- Global HTS Centre, Discovery Sciences, AstraZeneca, Macclesfield, Cheshire, UK
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23
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Gaytán BD, Vulpe CD. Functional toxicology: tools to advance the future of toxicity testing. Front Genet 2014; 5:110. [PMID: 24847352 PMCID: PMC4017141 DOI: 10.3389/fgene.2014.00110] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 04/12/2014] [Indexed: 11/16/2022] Open
Abstract
The increased presence of chemical contaminants in the environment is an undeniable concern to human health and ecosystems. Historically, by relying heavily upon costly and laborious animal-based toxicity assays, the field of toxicology has often neglected examinations of the cellular and molecular mechanisms of toxicity for the majority of compounds—information that, if available, would strengthen risk assessment analyses. Functional toxicology, where cells or organisms with gene deletions or depleted proteins are used to assess genetic requirements for chemical tolerance, can advance the field of toxicity testing by contributing data regarding chemical mechanisms of toxicity. Functional toxicology can be accomplished using available genetic tools in yeasts, other fungi and bacteria, and eukaryotes of increased complexity, including zebrafish, fruit flies, rodents, and human cell lines. Underscored is the value of using less complex systems such as yeasts to direct further studies in more complex systems such as human cell lines. Functional techniques can yield (1) novel insights into chemical toxicity; (2) pathways and mechanisms deserving of further study; and (3) candidate human toxicant susceptibility or resistance genes.
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Affiliation(s)
- Brandon D Gaytán
- Department of Nutritional Science and Toxicology, University of California Berkeley Berkeley, CA, USA
| | - Chris D Vulpe
- Department of Nutritional Science and Toxicology, University of California Berkeley Berkeley, CA, USA
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24
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Ribeiro JR, Lovasco LA, Vanderhyden BC, Freiman RN. Targeting TBP-Associated Factors in Ovarian Cancer. Front Oncol 2014; 4:45. [PMID: 24653979 PMCID: PMC3949196 DOI: 10.3389/fonc.2014.00045] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 02/25/2014] [Indexed: 12/11/2022] Open
Abstract
As ovarian tumors progress, they undergo a process of dedifferentiation, allowing adaptive changes in growth and morphology that promote metastasis and chemoresistance. Herein, we outline a hypothesis that TATA-box binding protein associated factors (TAFs), which compose the RNA Polymerase II initiation factor, TFIID, contribute to regulation of dedifferentiation states in ovarian cancer. Numerous studies demonstrate that TAFs regulate differentiation and proliferation states; their expression is typically high in pluripotent cells and reduced upon differentiation. Strikingly, TAF2 exhibits copy number increases or mRNA overexpression in 73% of high-grade serous ovarian cancers (HGSC). At the biochemical level, TAF2 directs TFIID to TATA-less promoters by contact with an Initiator element, which may lead to the deregulation of the transcriptional output of these tumor cells. TAF4, which is altered in 66% of HGSC, is crucial for the stability of the TFIID complex and helps drive dedifferentiation of mouse embryonic fibroblasts to induced pluripotent stem cells. Its ovary-enriched paralog, TAF4B, is altered in 26% of HGSC. Here, we show that TAF4B mRNA correlates with Cyclin D2 mRNA expression in human granulosa cell tumors. TAF4B may also contribute to regulation of tumor microenvironment due to its estrogen-responsiveness and ability to act as a cofactor for NFκB. Conversely, TAF9, a cofactor for p53 in regulating apoptosis, may act as a tumor suppressor in ovarian cancer, since it is downregulated or deleted in 98% of HGSC. We conclude that a greater understanding of mechanisms of transcriptional regulation that execute signals from oncogenic signaling cascades is needed in order to expand our understanding of the etiology and progression of ovarian cancer, and most importantly to identify novel targets for therapeutic intervention.
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Affiliation(s)
| | - Lindsay A Lovasco
- Molecular and Cellular Biology and Biochemistry, Brown University , Providence, RI , USA
| | - Barbara C Vanderhyden
- Cellular and Molecular Medicine, University of Ottawa , Ottawa, ON , Canada ; Centre for Cancer Therapeutics, Ottawa Hospital Research Institute , Ottawa, ON , Canada
| | - Richard N Freiman
- Pathobiology Graduate Program, Brown University , Providence, RI , USA ; Molecular and Cellular Biology and Biochemistry, Brown University , Providence, RI , USA
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Pradhan MP, Nagulapalli K, Palakal MJ. Cliques for the identification of gene signatures for colorectal cancer across population. BMC SYSTEMS BIOLOGY 2012; 6 Suppl 3:S17. [PMID: 23282040 PMCID: PMC3524317 DOI: 10.1186/1752-0509-6-s3-s17] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Background Colorectal cancer (CRC) is one of the most commonly diagnosed cancers worldwide. Studies have correlated risk of CRC development with dietary habits and environmental conditions. Gene signatures for any disease can identify the key biological processes, which is especially useful in studying cancer development. Such processes can be used to evaluate potential drug targets. Though recognition of CRC gene-signatures across populations is crucial to better understanding potential novel treatment options for CRC, it remains a challenging task. Results We developed a topological and biological feature-based network approach for identifying the gene signatures across populations. In this work, we propose a novel approach of using cliques to understand the variability within population. Cliques are more conserved and co-expressed, therefore allowing identification and comparison of cliques across a population which can help researchers study gene variations. Our study was based on four publicly available expression datasets belonging to four different populations across the world. We identified cliques of various sizes (0 to 7) across the four population networks. Cliques of size seven were further analyzed across populations for their commonality and uniqueness. Forty-nine common cliques of size seven were identified. These cliques were further analyzed based on their connectivity profiles. We found associations between the cliques and their connectivity profiles across networks. With these clique connectivity profiles (CCPs), we were able to identify the divergence among the populations, important biological processes (cell cycle, signal transduction, and cell differentiation), and related gene pathways. Therefore the genes identified in these cliques and their connectivity profiles can be defined as the gene-signatures across populations. In this work we demonstrate the power and effectiveness of cliques to study CRC across populations. Conclusions We developed a new approach where cliques and their connectivity profiles helped elucidate the variation and similarity in CRC gene profiles across four populations with unique dietary habits.
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Affiliation(s)
- Meeta P Pradhan
- School of Informatics, Indiana University Purdue University Indianapolis, IN, USA
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Taira N, Mimoto R, Kurata M, Yamaguchi T, Kitagawa M, Miki Y, Yoshida K. DYRK2 priming phosphorylation of c-Jun and c-Myc modulates cell cycle progression in human cancer cells. J Clin Invest 2012; 122:859-72. [PMID: 22307329 PMCID: PMC3287383 DOI: 10.1172/jci60818] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 12/21/2011] [Indexed: 02/06/2023] Open
Abstract
Dysregulation of the G(1)/S transition in the cell cycle contributes to tumor development. The oncogenic transcription factors c-Jun and c-Myc are indispensable regulators at this transition, and their aberrant expression is associated with many malignancies. Degradation of c-Jun/c-Myc is a critical process for the G(1)/S transition, which is initiated upon phosphorylation by glycogen synthase kinase 3 β (GSK3β). However, a specific kinase or kinases responsible for priming phosphorylation events that precede this GSK3β modification has not been definitively identified. Here, we found that the dual-specificity tyrosine phosphorylation-regulated kinase DYRK2 functions as a priming kinase of c-Jun and c-Myc. Knockdown of DYRK2 in human cancer cells shortened the G(1) phase and accelerated cell proliferation due to escape of c-Jun and c-Myc from ubiquitination-mediated degradation. In concert with these results, silencing DYRK2 increased cell proliferation in human cancer cells, and this promotion was completely impeded by codeprivation of c-Jun or c-Myc in vivo. We also found marked attenuation of DYRK2 expression in multiple human tumor samples. Downregulation of DYRK2 correlated with high levels of unphosphorylated c-Jun and c-Myc and, importantly, with invasiveness of human breast cancers. These results reveal that DYRK2 regulates tumor progression through modulation of c-Jun and c-Myc.
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Affiliation(s)
- Naoe Taira
- Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.
Department of Comprehensive Pathology, Aging and Developmental Sciences, Graduate School, Tokyo Medical and Dental University, Tokyo, Japan.
Department of Surgery, The Jikei University School of Medicine, Tokyo, Japan
| | - Rei Mimoto
- Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.
Department of Comprehensive Pathology, Aging and Developmental Sciences, Graduate School, Tokyo Medical and Dental University, Tokyo, Japan.
Department of Surgery, The Jikei University School of Medicine, Tokyo, Japan
| | - Morito Kurata
- Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.
Department of Comprehensive Pathology, Aging and Developmental Sciences, Graduate School, Tokyo Medical and Dental University, Tokyo, Japan.
Department of Surgery, The Jikei University School of Medicine, Tokyo, Japan
| | - Tomoko Yamaguchi
- Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.
Department of Comprehensive Pathology, Aging and Developmental Sciences, Graduate School, Tokyo Medical and Dental University, Tokyo, Japan.
Department of Surgery, The Jikei University School of Medicine, Tokyo, Japan
| | - Masanobu Kitagawa
- Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.
Department of Comprehensive Pathology, Aging and Developmental Sciences, Graduate School, Tokyo Medical and Dental University, Tokyo, Japan.
Department of Surgery, The Jikei University School of Medicine, Tokyo, Japan
| | - Yoshio Miki
- Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.
Department of Comprehensive Pathology, Aging and Developmental Sciences, Graduate School, Tokyo Medical and Dental University, Tokyo, Japan.
Department of Surgery, The Jikei University School of Medicine, Tokyo, Japan
| | - Kiyotsugu Yoshida
- Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.
Department of Comprehensive Pathology, Aging and Developmental Sciences, Graduate School, Tokyo Medical and Dental University, Tokyo, Japan.
Department of Surgery, The Jikei University School of Medicine, Tokyo, Japan
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Abstract
Acetylation of lysine residues is a post-translational modification with broad relevance
to cellular signalling and disease biology. Enzymes that ‘write’
(histone acetyltransferases, HATs) and ‘erase’ (histone deacetylases,
HDACs) acetylation sites are an area of extensive research in current drug development,
but very few potent inhibitors that modulate the ‘reading process’
mediated by acetyl lysines have been described. The principal readers of
ɛ-N-acetyl lysine (Kac) marks are
bromodomains (BRDs), which are a diverse family of evolutionary conserved
protein-interaction modules. The conserved BRD fold contains a deep, largely hydrophobic
acetyl lysine binding site, which represents an attractive pocket for the development of
small, pharmaceutically active molecules. Proteins that contain BRDs have been implicated
in the development of a large variety of diseases. Recently, two highly potent and
selective inhibitors that target BRDs of the BET (bromodomains and extra-terminal) family
provided compelling data supporting targeting of these BRDs in inflammation and in an
aggressive type of squamous cell carcinoma. It is likely that BRDs will emerge alongside
HATs and HDACs as interesting targets for drug development for the large number of
diseases that are caused by aberrant acetylation of lysine residues.
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Identification of Evi-1 as a novel effector of PKCδ in the apoptotic response to DNA damage. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1809:285-94. [DOI: 10.1016/j.bbagrm.2011.02.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Revised: 02/10/2011] [Accepted: 02/22/2011] [Indexed: 12/21/2022]
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Rantala JK, Mäkelä R, Aaltola AR, Laasola P, Mpindi JP, Nees M, Saviranta P, Kallioniemi O. A cell spot microarray method for production of high density siRNA transfection microarrays. BMC Genomics 2011; 12:162. [PMID: 21443765 PMCID: PMC3073923 DOI: 10.1186/1471-2164-12-162] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Accepted: 03/28/2011] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND High-throughput RNAi screening is widely applied in biological research, but remains expensive, infrastructure-intensive and conversion of many assays to HTS applications in microplate format is not feasible. RESULTS Here, we describe the optimization of a miniaturized cell spot microarray (CSMA) method, which facilitates utilization of the transfection microarray technique for disparate RNAi analyses. To promote rapid adaptation of the method, the concept has been tested with a panel of 92 adherent cell types, including primary human cells. We demonstrate the method in the systematic screening of 492 GPCR coding genes for impact on growth and survival of cultured human prostate cancer cells. CONCLUSIONS The CSMA method facilitates reproducible preparation of highly parallel cell microarrays for large-scale gene knockdown analyses. This will be critical towards expanding the cell based functional genetic screens to include more RNAi constructs, allow combinatorial RNAi analyses, multi-parametric phenotypic readouts or comparative analysis of many different cell types.
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Affiliation(s)
- Juha K Rantala
- Medical Biotechnology, VTT Technical Research Centre of Finland, 20521 Turku, Finland.
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30
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Sigoillot FD, King RW. Vigilance and validation: Keys to success in RNAi screening. ACS Chem Biol 2011; 6:47-60. [PMID: 21142076 DOI: 10.1021/cb100358f] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In the 12 years since the process of RNA interference (RNAi) was first discovered, great progress has been made in understanding its mechanism and exploiting its ability to silence gene expression to study gene function at a genome-wide level. Its extensive use as a screening method has yielded many published lists of genes that play novel roles in higher eukaryotes. However, the usefulness of this information is potentially limited by the occurrence of unintended off-target effects. Here we review the potential causes of off-target effects and the impact of this phenomenon in interpreting the results of high-throughput RNAi screens. In addition to targeting the intended gene product, artificial short interfering RNAs (siRNAs) can produce off-target effects by down-regulating the expression of multiple mRNAs through microRNA-like targeting of the 3' untranslated region. We examine why this phenomenon can produce high hit rates in siRNA screens and why independent validation of screening results is critical for the approach to yield new biological insights.
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Affiliation(s)
- Frederic D. Sigoillot
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, United States
| | - Randall W. King
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, United States
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31
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Tuzmen S, Tuzmen P, Arora S, Mousses S, Azorsa D. RNAi-based functional pharmacogenomics. Methods Mol Biol 2011; 700:271-90. [PMID: 21204040 DOI: 10.1007/978-1-61737-954-3_18] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Experimental alteration of gene expression is a powerful technique for functional characterization of disease genes. RNA interference (RNAi) is a naturally occurring mechanism of gene regulation, which is triggered by the introduction of double-stranded RNA into a cell. This phenomenon can be synthetically exploited to down-regulate expression of specific genes by transfecting mammalian cells with synthetic short interfering RNAs (siRNAs). These siRNAs can be designed to silence the expression of specific genes bearing a particular target sequence in high-throughput (HT) siRNA experimental systems and may potentially be presented as a therapeutic strategy for inhibiting transcriptional regulation of genes. This can constitute a strategy that can inhibit targets that are not tractable by small molecules such as chemical compounds. Large-scale experiments using low-dose drug exposure combined with siRNA also represent a promising discovery strategy for the purpose of identifying synergistic targets that facilitate synthetic lethal combination phenotypes. In light of such advantageous applications, siRNA technology has become an ideal research tool for studying gene function. In this chapter, we focus on the application of RNAi, with particular focus on HT siRNA phenotype profiling, to support cellular pharmacogenomics.
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Affiliation(s)
- Sukru Tuzmen
- Pharmaceutical Genomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA.
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32
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North M, Vulpe CD. Functional toxicogenomics: mechanism-centered toxicology. Int J Mol Sci 2010; 11:4796-813. [PMID: 21614174 PMCID: PMC3100848 DOI: 10.3390/ijms11124796] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Revised: 11/22/2010] [Accepted: 11/22/2010] [Indexed: 02/08/2023] Open
Abstract
Traditional toxicity testing using animal models is slow, low capacity, expensive and assesses a limited number of endpoints. Such approaches are inadequate to deal with the increasingly large number of compounds found in the environment for which there are no toxicity data. Mechanism-centered high-throughput testing represents an alternative approach to meet this pressing need but is limited by our current understanding of toxicity pathways. Functional toxicogenomics, the global study of the biological function of genes on the modulation of the toxic effect of a compound, can play an important role in identifying the essential cellular components and pathways involved in toxicity response. The combination of the identification of fundamental toxicity pathways and mechanism-centered targeted assays represents an integrated approach to advance molecular toxicology to meet the challenges of toxicity testing in the 21st century.
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Affiliation(s)
- Matthew North
- Department of Nutritional Science and Toxicology, University of California Berkeley, Berkeley, California 94720, USA; E-Mail:
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33
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Abstract
RNA interference (RNAi) is an effective tool for genome-scale, high-throughput analysis of gene function. In the past five years, a number of genome-scale RNAi high-throughput screens (HTSs) have been done in both Drosophila and mammalian cultured cells to study diverse biological processes, including signal transduction, cancer biology, and host cell responses to infection. Results from these screens have led to the identification of new components of these processes and, importantly, have also provided insights into the complexity of biological systems, forcing new and innovative approaches to understanding functional networks in cells. Here, we review the main findings that have emerged from RNAi HTS and discuss technical issues that remain to be improved, in particular the verification of RNAi results and validation of their biological relevance. Furthermore, we discuss the importance of multiplexed and integrated experimental data analysis pipelines to RNAi HTS.
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Affiliation(s)
- Stephanie Mohr
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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Taira N, Yamamoto H, Yamaguchi T, Miki Y, Yoshida K. ATM augments nuclear stabilization of DYRK2 by inhibiting MDM2 in the apoptotic response to DNA damage. J Biol Chem 2010; 285:4909-19. [PMID: 19965871 PMCID: PMC2836095 DOI: 10.1074/jbc.m109.042341] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Revised: 12/02/2009] [Indexed: 11/06/2022] Open
Abstract
The tumor suppressor p53 is a transcription factor that regulates cell cycle, DNA repair, senescence, and apoptosis in response to DNA damage. Phosphorylation of p53 at Ser-46 is indispensable for the commitment to apoptotic cell death. A previous study has shown that upon exposure to genotoxic stress, DYRK2 translocates into the nucleus and phosphorylates p53 at Ser-46, thereby inducing apoptosis. However, less is known about mechanisms responsible for intracellular control of DYRK2. Here we show the functional nuclear localization signal at N-terminal domain of DYRK2. Under normal conditions, nuclear and not cytoplasmic DYRK2 is ubiquitinated by MDM2, resulting in its constitutive degradation. In the presence of proteasome inhibitors, we detected a stable complex of DYRK2 with MDM2 at the nucleus. Upon exposure to genotoxic stress, ATM phosphorylates DYRK2 at Thr-33 and Ser-369, which enables DYRK2 to escape from degradation by dissociation from MDM2 and to induce the kinase activity toward p53 at Ser-46 in the nucleus. These findings indicate that ATM controls stability and pro-apoptotic function of DYRK2 in response to DNA damage.
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Affiliation(s)
- Naoe Taira
- From the Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University, Yushima 1-5-45, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Hiroyuki Yamamoto
- From the Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University, Yushima 1-5-45, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Tomoko Yamaguchi
- From the Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University, Yushima 1-5-45, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Yoshio Miki
- From the Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University, Yushima 1-5-45, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Kiyotsugu Yoshida
- From the Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University, Yushima 1-5-45, Bunkyo-ku, Tokyo 113-8510, Japan
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