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Angelakakis G, Varkhedi M, Dabkowski TR, Diaz MJ, Yeagley M, Blanck G. B-cell ALL with SOX11 gene amplification associates with a worse outcome. Cell Cycle 2024; 23:36-42. [PMID: 38350028 PMCID: PMC11005798 DOI: 10.1080/15384101.2024.2306756] [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: 04/26/2023] [Accepted: 01/12/2024] [Indexed: 02/15/2024] Open
Abstract
Copy number variation (CNV) of certain genes in pediatric Acute Lymphoblastic Leukemia (ALL) impacts gene expression levels. Here, we aimed to investigate the potential prognostic utility of CNVs in pediatric B-ALL and T-ALL. Using genomics files representing cases from the TARGET-ALL-P2 dataset, genes commonly involved in ALL development were analyzed for CNVs. Case IDs representing increased copy numbers for SOX11, PDGFRB, and MDK represented a worse overall survival probability specifically for B-ALL (logrank p=0.021, p=0.0052, p=0.019, respectively). These data support the continued investigation of using CNVs for clinical prognostic biomarkers for pediatric B-ALL.
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Affiliation(s)
- George Angelakakis
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Mallika Varkhedi
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Toriana R. Dabkowski
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Michael J. Diaz
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | | | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
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Verzeroli C, Hernandez CA, Zoulim F, Parent R. A fluorescent Ponceau S-based total protein normalization method for conventional and challenging immunoblot samples. Anal Biochem 2023; 681:115330. [PMID: 37722522 DOI: 10.1016/j.ab.2023.115330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/11/2023] [Accepted: 09/15/2023] [Indexed: 09/20/2023]
Abstract
Immunoblotting normalization issues have been recently overcome by whole lane staining. Herein, we are taking advantage of these recent advances and of the fluorophore status of the Ponceau S stain in order to combine the advantages of whole lane staining and fluorescence. By Ponceau S excitation at 488 nm, we identify the so-called 'fluorescent Ponceau' method as more linear, more sensitive and more repeatable than the others in protein lysates of distant biochemical profiles (cells, human and mouse tissues). This essentially cost-free method at the single experiment level provides accessible and robust means for post-blot normalization of many types of analytes.
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Affiliation(s)
- Claire Verzeroli
- Hepatitis Viruses and Pathobiology of Chronic Liver Diseases - LabEx DEVweCAN, Inserm U1052, Cancer Research Centre of Lyon, F-69003, Lyon, France; University of Lyon, F-69003, Lyon, France; University of Lyon 1, ISPB, Lyon, F-69622, France; CNRS UMR5286, F-69083, Lyon, France; Centre Léon Bérard, F-69008, Lyon, France
| | - Charlotte A Hernandez
- Hepatitis Viruses and Pathobiology of Chronic Liver Diseases - LabEx DEVweCAN, Inserm U1052, Cancer Research Centre of Lyon, F-69003, Lyon, France; University of Lyon, F-69003, Lyon, France; University of Lyon 1, ISPB, Lyon, F-69622, France; CNRS UMR5286, F-69083, Lyon, France; Centre Léon Bérard, F-69008, Lyon, France
| | - Fabien Zoulim
- Hepatitis Viruses and Pathobiology of Chronic Liver Diseases - LabEx DEVweCAN, Inserm U1052, Cancer Research Centre of Lyon, F-69003, Lyon, France; University of Lyon, F-69003, Lyon, France; University of Lyon 1, ISPB, Lyon, F-69622, France; CNRS UMR5286, F-69083, Lyon, France; Centre Léon Bérard, F-69008, Lyon, France
| | - Romain Parent
- Hepatitis Viruses and Pathobiology of Chronic Liver Diseases - LabEx DEVweCAN, Inserm U1052, Cancer Research Centre of Lyon, F-69003, Lyon, France; University of Lyon, F-69003, Lyon, France; University of Lyon 1, ISPB, Lyon, F-69622, France; CNRS UMR5286, F-69083, Lyon, France; Centre Léon Bérard, F-69008, Lyon, France.
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Wahyuni FS, Syafri S, Permatasari D, Hefni D, Hamidi D, Nomiza NA, Rezti IA. Cowanin induces apoptosis in breast cancer cells via Bcl-2 signaling pathway. JOURNAL OF COMPLEMENTARY & INTEGRATIVE MEDICINE 2023; 20:631-636. [PMID: 37202914 DOI: 10.1515/jcim-2023-0058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/19/2023] [Indexed: 05/20/2023]
Abstract
OBJECTIVES This study aimed to investigate the effect of cowanin the mechanism of cowanin toward cell death and BCL-2 protein (antiapoptotic) expression of T47D breast cancer. METHODS The cell death was evaluated by double staining, namely acridine orange and propidium iodide, and then observed under a fluorescence microscope. Meanwhile, the BCL-2 protein expression was determined by western blotting with measurement of protein area and protein density. RESULTS The result found T47D breast cancer cells were viable, apoptosis, and necrosis after treatment with cowanin. The average viable cells, apoptosis, and necrosis percentages were 54.13 %, 45.43 %, and 0.44 %, respectively. Statistical analysis showed cowanin could significantly induce death in T47D breast cancer cells by apoptosis (p<0.05). It was also revealed that cowanin and positive control (doxorubicin) treatment had a significantly decreased protein area and protein density (p<0.05). CONCLUSIONS It can be concluded that cowanin can induce death in T47D breast cancer cells by apoptosis and affect the expression of Bcl-2 protein in T47D breast cancer cells.
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Affiliation(s)
- Fatma Sri Wahyuni
- Faculty of Pharmacy, Universitas Andalas, Padang, West Sumatra, Indonesia
| | - Suryati Syafri
- Faculty of Pharmacy, Universitas Andalas, Padang, West Sumatra, Indonesia
| | - Dita Permatasari
- Faculty of Pharmacy, Universitas Andalas, Padang, West Sumatra, Indonesia
| | - Dira Hefni
- Faculty of Pharmacy, Universitas Andalas, Padang, West Sumatra, Indonesia
| | - Dachriyanus Hamidi
- Faculty of Pharmacy, Universitas Andalas, Padang, West Sumatra, Indonesia
| | - Nur Azizah Nomiza
- Faculty of Pharmacy, Universitas Andalas, Padang, West Sumatra, Indonesia
| | - Indri Aulia Rezti
- Faculty of Pharmacy, Universitas Andalas, Padang, West Sumatra, Indonesia
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Collins JM, Lester H, Shabnaz S, Wang D. A frequent CYP2D6 variant promotes skipping of exon 3 and reduces CYP2D6 protein expression in human liver samples. Front Pharmacol 2023; 14:1186540. [PMID: 37576811 PMCID: PMC10412816 DOI: 10.3389/fphar.2023.1186540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/17/2023] [Indexed: 08/15/2023] Open
Abstract
CYP2D6 is one of the most polymorphic drug-metabolizing enzymes in the liver. While genetic CYP2D6 variants serve as clinical biomarkers to predict CYP2D6 activity, large inter-person variability in CYP2D6 expression remains unaccounted for. Previous results suggest that there is variable expression of a CYP2D6 splice isoform with an in-frame deletion of exon 3 (CYP2D6ΔE3) encoding a protein lacking numerous active site residues. Here, using fragment analysis and RT-qPCR, we revealed that rs1058164 G (MAF = 27%-43%) is associated with increased formation of CYP2D6∆E3 in human liver samples (1.4-2.5-fold) and transfected cells. Furthermore, western blots showed that rs1058164 G was associated with a 50% decrease in full-length hepatic CYP2D6 protein expression. In addition, by studying a larger liver cohort, we confirmed our previous results that rs16947 (CYP2D6*2) reduces full-length CYP2D6 mRNA by increasing the production of an unstable splice isoform lacking exon 6 (CYP2D6ΔE6) and that the impact of CYP2D6ΔE6 is offset in carriers of the downstream enhancer variant rs5758550. The three frequent SNPs (rs1058164, rs16947, and rs5758550) form various 3-SNP-haplotypes, each with distinct CYP2D6 expression characteristics. Using an expression score (ES) system, we tested the impact of the 3-SNP-haplotype on improving the standard model to predict hepatic CYP2D6 protein expression based on genotype. A model that incorporates the 3-SNP-haplotype provided the best fit for CYP2D6 expression and also accounted for more variability in CYP2D6 protein levels (59%) than a model based on the accepted standard (36%) or one that only adds rs16947 and rs5758550 (42%). Clinical studies are needed to determine whether including the 3-SNP-haplotype alongside current standard CYP2D6 models improves the predictive value of CYP2D6 panels.
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Affiliation(s)
| | | | | | - Danxin Wang
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics, College of Pharmacy, University of Florida, Gainesville, FL, United States
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Tantawy M, Collins JM, Wang D. Genome-wide microRNA profiles identify miR-107 as a top miRNA associating with expression of the CYP3As and other drug metabolizing cytochrome P450 enzymes in the liver. Front Pharmacol 2022; 13:943538. [PMID: 36059981 PMCID: PMC9428441 DOI: 10.3389/fphar.2022.943538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/06/2022] [Indexed: 11/13/2022] Open
Abstract
Cytochrome P450 (CYP) drug metabolizing enzymes are responsible for the metabolism of over 70% of currently used medications with the CYP3A family being the most important CYP enzymes in the liver. Large inter-person variability in expression/activity of the CYP3As greatly affects drug exposure and treatment outcomes, yet the cause of such variability remains elusive. Micro-RNAs (miRNAs) are small noncoding RNAs that negatively regulate gene expression and are involved in diverse cellular processes including metabolism of xenobiotics and therapeutic outcomes. Target prediction and in vitro functional assays have linked several miRNAs to the control of CYP3A4 expression. Yet, their co-expression with CYP3As in the liver remain unclear. In this study, we used genome-wide miRNA profiling in liver samples to identify miRNAs associated with the expression of the CYP3As. We identified and validated both miR-107 and miR-1260 as strongly associated with the expression of CYP3A4, CYP3A5, and CYP3A43. Moreover, we found associations between miR-107 and nine transcription factors (TFs) that regulate CYP3A expression, with estrogen receptor alpha (ESR1) having the largest effect size. Including ESR1 and the other TFs in the regression model either diminished or abolished the associations between miR-107 and the CYP3As, indicating that the role of miR-107 in CYP3A expression may be indirect and occur through these key TFs. Indeed, testing the other nine CYPs previously shown to be regulated by ESR1 identified similar miR-107 associations that were dependent on the exclusion of ESR1 and other key TFs in the regression model. In addition, we found significant differences in miRNA expression profiles in liver samples between race and sex. Together, our results identify miR-107 as a potential epigenetic regulator that is strongly associated with the expression of many CYPs, likely via impacting the CYP regulatory network controlled by ESR1 and other key TFs. Therefore, both genetic and epigenetic factors that alter the expression of miR-107 may have a broad influence on drug metabolism.
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Liang Y, Huang W, Situ Q, Su W, Qiu W, Li S, He L, Chen J. Novel Terpyridine Conjugated Nitrogen Mustard Derivatives: Synthesis, Spectral Properties, and Anticancer Activity. RUSS J GEN CHEM+ 2022. [DOI: 10.1134/s1070363222040144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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