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Lv P, Li J, Yao Y, Fan X, Liu C, Li H, Zhou H. A novel pyrosequencing strategy for RHD zygosity for predicting risk of hemolytic disease of the fetus and newborn. Lab Med 2024; 55:145-152. [PMID: 37307496 DOI: 10.1093/labmed/lmad051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023] Open
Abstract
OBJECTIVE The aim of this study was the development of an accurate and quantitative pyrosequence (PSQ) method for paternal RHD zygosity detection to help risk management of hemolytic disease of the fetus and newborn (HDFN). METHODS Blood samples from 96 individuals were genotyped for RHD zygosity using pyrosequencing assay. To validate the accuracy of pyrosequencing results, all the samples were then detected by the mismatch polymerase chain reaction with sequence-specific primers (PCR-SSP) method and Sanger DNA sequencing. Serological tests were performed to assess RhD phenotypes. RESULTS Serological results revealed that 36 cases were RhD-positive and 60 cases were RhD-negative. The concordance rate between pyrosequencing assay and mismatch PCR-SSP assay was 94.8% (91/96). There were 5 discordant results between pyrosequencing and the mismatch PCR-SSP assay. Sanger sequencing confirmed that the pyrosequencing assay correctly assigned zygosity for the 5 samples. CONCLUSION This DNA pyrosequencing method accurately detect RHD zygosity and will help risk management of pregnancies that are at risk of HDFN.
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Affiliation(s)
- Piao Lv
- Department of Blood Transfusion, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jixin Li
- Department of Blood Transfusion, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yuan Yao
- Department of Blood Transfusion, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xinxin Fan
- Department of Blood Transfusion, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Chixiang Liu
- Department of Blood Transfusion, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hui Li
- Department of Hematology, Guangdong Provincial Hospital of Traditional Chinese Medicine (The Second Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine), Guangzhou, China
| | - Huayou Zhou
- Department of Blood Transfusion, Nanfang Hospital, Southern Medical University, Guangzhou, China
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Zhang H, Wu J, Li R, Kim DH, Bi X, Zhang G, Jiang B, Yong Ng H, Shi X. Novel intertidal wetland sediment-inoculated moving bed biofilm reactor treating high-salinity wastewater: Metagenomic sequencing revealing key functional microorganisms. Bioresour Technol 2022; 348:126817. [PMID: 35134521 DOI: 10.1016/j.biortech.2022.126817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/29/2022] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
In this study, two lab-scale moving bed biofilm reactors (MBBR), seeded with intertidal wetland sediment (IWS) and activated sludge (AS), were constructed to compare their performances in treating high-salinity (3%) wastewater. Under a wide range of influent TOC (178-620 mg/L) and NH4+-N (25-100 mg/L), both the MBBRs (Riws and Ras) exhibited excellent TOC removal efficiencies of >95%. Regarding nitrogen reduction, Riws exhibited a significantly superior TN removal efficiency of 90.2 ± 1.8% than that of Ras (76.8 ± 2.9%). A correlation analysis was innovatively conducted comparing the results between metagenomic sequencing and DNA pyrosequencing, and positive linear relationships were found with R2 values of 0.763-0.945. Meanwhile, for illustration of different TN removal performance, nitrogen metabolic pathways were also assessed. Moreover, a list of functional oxidases (EC: 1.13.11.1, EC: 1.13.11.2, EC: 1.13.11.24, EC: 1.13.12.16, EC: 1.4.3.4, EC: 1.16.3.3, EC: 1.14.14.28) was found in IWS, revealing its potential in degradation of recalcitrant organics.
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Affiliation(s)
- Haifeng Zhang
- School of Environmental and Municipal Engineering, Qingdao University of Technology, 11 Fushun Road, Qingdao 266033, PR China
| | - Jiahua Wu
- School of Environmental and Municipal Engineering, Qingdao University of Technology, 11 Fushun Road, Qingdao 266033, PR China
| | - Ruifeng Li
- School of Environmental and Municipal Engineering, Qingdao University of Technology, 11 Fushun Road, Qingdao 266033, PR China
| | - Dong-Hoon Kim
- Department of Smart City Engineering, Inha University, 100 Inharo, Michuhol-gu, Incheon 22212, South Korea
| | - Xuejun Bi
- School of Environmental and Municipal Engineering, Qingdao University of Technology, 11 Fushun Road, Qingdao 266033, PR China
| | - Guoli Zhang
- School of Environmental and Municipal Engineering, Qingdao University of Technology, 11 Fushun Road, Qingdao 266033, PR China
| | - Bo Jiang
- School of Environmental and Municipal Engineering, Qingdao University of Technology, 11 Fushun Road, Qingdao 266033, PR China
| | - How Yong Ng
- Centre for Water Research, Department of Civil and Environmental Engineering, National University of Singapore, 1 Engineering Dr. 2, 117576, Singapore
| | - Xueqing Shi
- School of Environmental and Municipal Engineering, Qingdao University of Technology, 11 Fushun Road, Qingdao 266033, PR China.
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Hassan HE, Keita JA, Narayan L, Brady SM, Frederick R, Carlson S, C Glass K, Natesan S, Buttolph T, Fandy TE. The combination of dimethoxycurcumin with DNA methylation inhibitor enhances gene re-expression of promoter-methylated genes and antagonizes their cytotoxic effect. Epigenetics 2016; 11:740-749. [PMID: 27588609 DOI: 10.1080/15592294.2016.1226452] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Curcumin and its analogs exhibited antileukemic activity either as single agent or in combination therapy. Dimethoxycurcumin (DMC) is a more metabolically stable curcumin analog that was shown to induce the expression of promoter-methylated genes without reversing DNA methylation. Accordingly, co-treatment with DMC and DNA methyltransferase (DNMT) inhibitors could hypothetically enhance the re-expression of promoter-methylated tumor suppressor genes. In this study, we investigated the cytotoxic effects and epigenetic changes associated with the combination of DMC and the DNMT inhibitor decitabine (DAC) in primary leukemia samples and cell lines. The combination demonstrated antagonistic cytotoxic effects and was minimally cytotoxic to primary leukemia cells. The combination did not affect the metabolic stability of DMC. Although the combination enhanced the downregulation of nuclear DNMT proteins, the hypomethylating activity of the combination was not increased significantly compared to DAC alone. On the other hand, the combination significantly increased H3K27 acetylation (H3K27Ac) compared to the single agents near the promoter region of promoter-methylated genes. Furthermore, sequential chromatin immunoprecipitation (ChIP) and DNA pyrosequencing of the chromatin-enriched H3K27Ac did not show any significant decrease in DNA methylation compared to other regions. Consequently, the enhanced induction of promoter-methylated genes by the combination compared to DAC alone is mediated by a mechanism that involves increased histone acetylation and not through potentiation of the DNA hypomethylating activity of DAC. Collectively, our results provide the mechanistic basis for further characterization of this combination in leukemia animal models and early phase clinical trials.
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Affiliation(s)
- Hazem E Hassan
- a Department of Pharmaceutical Sciences , University of Maryland , Baltimore , MD , USA.,b Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy , Helwan University , Cairo , Egypt
| | - Jean-Arnaud Keita
- c Department of Pharmaceutical Sciences , Albany College of Pharmacy (Vermont Campus) , Colchester , VT , USA
| | - Lawrence Narayan
- c Department of Pharmaceutical Sciences , Albany College of Pharmacy (Vermont Campus) , Colchester , VT , USA
| | - Sean M Brady
- c Department of Pharmaceutical Sciences , Albany College of Pharmacy (Vermont Campus) , Colchester , VT , USA
| | - Richard Frederick
- c Department of Pharmaceutical Sciences , Albany College of Pharmacy (Vermont Campus) , Colchester , VT , USA
| | - Samuel Carlson
- c Department of Pharmaceutical Sciences , Albany College of Pharmacy (Vermont Campus) , Colchester , VT , USA
| | - Karen C Glass
- c Department of Pharmaceutical Sciences , Albany College of Pharmacy (Vermont Campus) , Colchester , VT , USA
| | - Senthil Natesan
- d Department of Experimental and Systems Pharmacology , Washington State University , Spokane , WA , USA
| | - Thomm Buttolph
- e Department of Neurological Sciences , University of Vermont , Burlington , VT , USA
| | - Tamer E Fandy
- c Department of Pharmaceutical Sciences , Albany College of Pharmacy (Vermont Campus) , Colchester , VT , USA
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Wong M, Gertz B, Chestnut BA, Martin LJ. Mitochondrial DNMT3A and DNA methylation in skeletal muscle and CNS of transgenic mouse models of ALS. Front Cell Neurosci 2013; 7:279. [PMID: 24399935 PMCID: PMC3872319 DOI: 10.3389/fncel.2013.00279] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 12/12/2013] [Indexed: 12/13/2022] Open
Abstract
Cytosine methylation is an epigenetic modification of DNA catalyzed by DNA methyltransferases. Cytosine methylation of mitochondrial DNA (mtDNA) is believed to have relative underrepresentation; however, possible tissue and cell differences in mtDNA methylation and relationships to neurodegenerative disease have not been examined. We show by immunoblotting that DNA methyltransferase 3A (Dnmt3a) isoform is present in pure mitochondria of adult mouse CNS, skeletal muscle, and testes, and adult human cerebral cortex. Dnmt1 was not detected in adult mouse CNS or skeletal muscle mitochondria but appeared bound to the outer mitochondrial membrane. Immunofluorescence confirmed the mitochondrial localization of Dnmt3a and showed 5-methylcytosine (5mC) immunoreactivity in mitochondria of neurons and skeletal muscle myofibers. DNA pyrosequencing of two loci (D-loop and 16S rRNA gene) and twelve cytosine-phosphate-guanine (CpG) sites in mtDNA directly showed a tissue differential presence of 5mC. Because mitochondria have been implicated in the pathogenesis of amyotrophic lateral sclerosis (ALS), but the disease mechanisms are uncertain, we evaluated mitochondrial Dnmt3a and 5mC levels in human superoxide dismutase-1 (SOD1) transgenic mouse models of ALS. Mitochondrial Dnmt3a protein levels were reduced significantly in skeletal muscle and spinal cord at presymptomatic or early disease. Immunofluorescence showed that 5mC immunoreactivity was present in mitochondria of neurons and skeletal myofibers, and 5mC immunoreactivity became aggregated in motor neurons of ALS mice. DNA pyrosequencing revealed significant abnormalities in 16S rRNA gene methylation in ALS mice. Immunofluorescence showed that 5mC immunoreactivity can be sequestered into autophagosomes and that mitophagy was increased and mitochondrial content was decreased in skeletal muscle in ALS mice. This study reveals a tissue-preferential mitochondrial localization of Dnmt3a and presence of cytosine methylation in mtDNA of nervous tissue and skeletal muscle and demonstrates that mtDNA methylation patterns and mitochondrial Dnmt3a levels are abnormal in skeletal muscle and spinal cord of presymptomatic ALS mice, and these abnormalities occur in parallel with loss of myofiber mitochondria.
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Affiliation(s)
- Margaret Wong
- Department of Pathology, Division of Neuropathology, Johns Hopkins University School of Medicine Baltimore, MD, USA
| | - Barry Gertz
- Department of Pathology, Division of Neuropathology, Johns Hopkins University School of Medicine Baltimore, MD, USA ; Department of Pathology, Pathobiology Graduate Program, Johns Hopkins University School of Medicine Baltimore, MD, USA
| | - Barry A Chestnut
- Department of Pathology, Division of Neuropathology, Johns Hopkins University School of Medicine Baltimore, MD, USA ; Department of Pathology, Pathobiology Graduate Program, Johns Hopkins University School of Medicine Baltimore, MD, USA
| | - Lee J Martin
- Department of Pathology, Division of Neuropathology, Johns Hopkins University School of Medicine Baltimore, MD, USA ; Department of Pathology, Pathobiology Graduate Program, Johns Hopkins University School of Medicine Baltimore, MD, USA ; Department of Neuroscience, Johns Hopkins University School of Medicine Baltimore, MD, USA
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