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Wang N, Wang T, Ning K. Refining biome labeling for large-scale microbial community samples: Leveraging neural networks and transfer learning. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2024; 17:100304. [PMID: 37635952 PMCID: PMC10457426 DOI: 10.1016/j.ese.2023.100304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 07/09/2023] [Accepted: 07/22/2023] [Indexed: 08/29/2023]
Abstract
Microbiome research has generated an extensive amount of data, resulting in a wealth of publicly accessible samples. Accurate annotation of these samples is crucial for effectively utilizing microbiome data across scientific disciplines. However, a notable challenge arises from the lack of essential annotations, particularly regarding collection location and sample biome information, which significantly hinders environmental microbiome research. In this study, we introduce Meta-Sorter, a novel approach utilizing neural networks and transfer learning, to enhance biome labeling for thousands of microbiome samples in the MGnify database that have incomplete information. Our findings demonstrate that Meta-Sorter achieved a remarkable accuracy rate of 96.7% in classifying samples among the 16,507 lacking detailed biome annotations. Notably, Meta-Sorter provides precise classifications for representative environmental samples that were previously ambiguously labeled as "Marine" in MGnify, thereby elucidating their specific origins in benthic and water column environments. Moreover, Meta-Sorter effectively distinguishes samples derived from human-environment interactions, enabling clear differentiation between environmental and human-related studies. By improving the completeness of biome label information for numerous microbial community samples, our research facilitates more accurate knowledge discovery across diverse disciplines, with particular implications for environmental research.
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Affiliation(s)
| | | | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
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2
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Navarro C, Salazar J, Díaz MP, Chacin M, Santeliz R, Vera I, D′Marco L, Parra H, Bernal MC, Castro A, Escalona D, García-Pacheco H, Bermúdez V. Intrinsic and environmental basis of aging: A narrative review. Heliyon 2023; 9:e18239. [PMID: 37576279 PMCID: PMC10415626 DOI: 10.1016/j.heliyon.2023.e18239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 06/26/2023] [Accepted: 07/12/2023] [Indexed: 08/15/2023] Open
Abstract
Longevity has been a topic of interest since the beginnings of humanity, yet its aetiology and precise mechanisms remain to be elucidated. Aging is currently viewed as a physiological phenomenon characterized by the gradual degeneration of organic physiology and morphology due to the passage of time where both external and internal stimuli intervene. The influence of intrinsic factors, such as progressive telomere shortening, genome instability due to mutation buildup, the direct or indirect actions of age-related genes, and marked changes in epigenetic, metabolic, and mitochondrial patterns constitute a big part of its underlying endogenous mechanisms. On the other hand, several psychosocial and demographic factors, such as diet, physical activity, smoking, and drinking habits, may have an even more significant impact on shaping the aging process. Consequentially, implementing dietary and exercise patterns has been proposed as the most viable alternative strategy for attenuating the most typical degenerative aging changes, thus increasing the likelihood of prolonging lifespan and achieving successful aging.
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Affiliation(s)
- Carla Navarro
- Endocrine and Metabolic Diseases Research Center. School of Medicine. University of Zulia. Maracaibo 4001, Venezuela
| | - Juan Salazar
- Endocrine and Metabolic Diseases Research Center. School of Medicine. University of Zulia. Maracaibo 4001, Venezuela
| | - María P. Díaz
- Endocrine and Metabolic Diseases Research Center. School of Medicine. University of Zulia. Maracaibo 4001, Venezuela
| | - Maricarmen Chacin
- Universidad Simón Bolívar, Facultad de Ciencias de la Salud, Barranquilla 080001, Colombia
| | - Raquel Santeliz
- Endocrine and Metabolic Diseases Research Center. School of Medicine. University of Zulia. Maracaibo 4001, Venezuela
| | - Ivana Vera
- Endocrine and Metabolic Diseases Research Center. School of Medicine. University of Zulia. Maracaibo 4001, Venezuela
| | - Luis D′Marco
- Universidad Cardenal Herrera-CEU Medicine Department, CEU Universities, 46115 Valencia, Spain
| | - Heliana Parra
- Endocrine and Metabolic Diseases Research Center. School of Medicine. University of Zulia. Maracaibo 4001, Venezuela
| | | | - Ana Castro
- Endocrine and Metabolic Diseases Research Center. School of Medicine. University of Zulia. Maracaibo 4001, Venezuela
| | - Daniel Escalona
- Endocrine and Metabolic Diseases Research Center. School of Medicine. University of Zulia. Maracaibo 4001, Venezuela
| | - Henry García-Pacheco
- Universidad del Zulia, Facultad de Medicina, Departamento de Cirugía. Hospital General del Sur “Dr. Pedro Iturbe”. Maracaibo, Venezuela
- Unidad de Cirugía para la Obesidad y Metabolismo (UCOM). Maracaibo, Venezuela
| | - Valmore Bermúdez
- Universidad Simón Bolívar, Facultad de Ciencias de la Salud, Barranquilla 080001, Colombia
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3
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Joseph J, Liu C, Hui Q, Aragam K, Wang Z, Charest B, Huffman JE, Keaton JM, Edwards TL, Demissie S, Djousse L, Casas JP, Gaziano JM, Cho K, Wilson PWF, Phillips LS, O’Donnell CJ, Sun YV. Genetic architecture of heart failure with preserved versus reduced ejection fraction. Nat Commun 2022; 13:7753. [PMID: 36517512 PMCID: PMC9751124 DOI: 10.1038/s41467-022-35323-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
Pharmacologic clinical trials for heart failure with preserved ejection fraction have been largely unsuccessful as compared to those for heart failure with reduced ejection fraction. Whether differences in the genetic underpinnings of these major heart failure subtypes may provide insights into the disparate outcomes of clinical trials remains unknown. We utilize a large, uniformly phenotyped, single cohort of heart failure sub-classified into heart failure with reduced and with preserved ejection fractions based on current clinical definitions, to conduct detailed genetic analyses of the two heart failure sub-types. We find different genetic architectures and distinct genetic association profiles between heart failure with reduced and with preserved ejection fraction suggesting differences in underlying pathobiology. The modest genetic discovery for heart failure with preserved ejection fraction (one locus) compared to heart failure with reduced ejection fraction (13 loci) despite comparable sample sizes indicates that clinically defined heart failure with preserved ejection fraction likely represents the amalgamation of several, distinct pathobiological entities. Development of consensus sub-phenotyping of heart failure with preserved ejection fraction is paramount to better dissect the underlying genetic signals and contributors to this highly prevalent condition.
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Affiliation(s)
- Jacob Joseph
- grid.410370.10000 0004 4657 1992Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA ,Cardiology Section (111A), VA Providence Healthcare System, 830 Chalkstone Avenue, Providence, RI 02908 USA
| | - Chang Liu
- grid.189967.80000 0001 0941 6502Emory University Rollins School of Public Health, Atlanta, GA USA
| | - Qin Hui
- grid.189967.80000 0001 0941 6502Emory University Rollins School of Public Health, Atlanta, GA USA ,grid.484294.7Atlanta VA Health Care System, Decatur, GA USA
| | - Krishna Aragam
- grid.410370.10000 0004 4657 1992Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA USA ,grid.32224.350000 0004 0386 9924Massachusetts General Hospital, Boston, MA USA ,grid.66859.340000 0004 0546 1623Broad Institute of Harvard and MIT, Cambridge, MA USA
| | - Zeyuan Wang
- grid.189967.80000 0001 0941 6502Emory University Rollins School of Public Health, Atlanta, GA USA ,grid.484294.7Atlanta VA Health Care System, Decatur, GA USA
| | - Brian Charest
- grid.410370.10000 0004 4657 1992Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA USA
| | - Jennifer E. Huffman
- grid.410370.10000 0004 4657 1992Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA USA
| | - Jacob M. Keaton
- grid.94365.3d0000 0001 2297 5165Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA ,grid.412807.80000 0004 1936 9916Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA
| | - Todd L. Edwards
- grid.412807.80000 0004 1936 9916Division of Epidemiology, Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN USA
| | - Serkalem Demissie
- grid.410370.10000 0004 4657 1992Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA USA ,grid.189504.10000 0004 1936 7558Boston University School of Medicine, Boston, MA USA
| | - Luc Djousse
- grid.410370.10000 0004 4657 1992Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
| | - Juan P. Casas
- grid.410370.10000 0004 4657 1992Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
| | - J. Michael Gaziano
- grid.410370.10000 0004 4657 1992Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
| | - Kelly Cho
- grid.410370.10000 0004 4657 1992Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
| | - Peter W. F. Wilson
- grid.484294.7Atlanta VA Health Care System, Decatur, GA USA ,grid.189967.80000 0001 0941 6502Emory University School of Medicine, Atlanta, GA USA
| | - Lawrence S. Phillips
- grid.484294.7Atlanta VA Health Care System, Decatur, GA USA ,grid.189967.80000 0001 0941 6502Emory University School of Medicine, Atlanta, GA USA
| | | | - Christopher J. O’Donnell
- grid.410370.10000 0004 4657 1992Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
| | - Yan V. Sun
- grid.189967.80000 0001 0941 6502Emory University Rollins School of Public Health, Atlanta, GA USA ,grid.484294.7Atlanta VA Health Care System, Decatur, GA USA
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The mechanism of BUD13 m6A methylation mediated MBNL1-phosphorylation by CDK12 regulating the vasculogenic mimicry in glioblastoma cells. Cell Death Dis 2022; 13:1017. [PMID: 36463205 PMCID: PMC9719550 DOI: 10.1038/s41419-022-05426-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 12/04/2022]
Abstract
Vasculogenic mimicry (VM) is an endothelium-independent tumor microcirculation that provides adequate blood supply for tumor growth. The presence of VM greatly hinders the treatment of glioblastoma (GBM) with anti-angiogenic drugs. Therefore, targeting VM formation may be a feasible therapeutic strategy for GBM. The research aimed to evaluate the roles of BUD13, CDK12, MBNL1 in regulating VM formation of GBM. BUD13 and CDK12 were upregulated and MBNL1 was downregulated in GBM tissues and cells. Knockdown of BUD13, CDK12, or overexpression of MBNL1 inhibited GBM VM formation. METTL3 enhanced the stability of BUD13 mRNA and upregulated its expression through m6A methylation. BUD13 enhanced the stability of CDK12 mRNA and upregulated its expression. CDK12 phosphorylated MBNL1, thereby regulating VM formation of GBM. The simultaneous knockdown of BUD13, CDK12, and overexpression of MBNL1 reduced the volume of subcutaneously transplanted tumors in nude mice and prolonged the survival period. Thus, the BUD13/CDK12/MBNL1 axis plays a crucial role in regulating VM formation of GBM and provides a potential target for GBM therapy.
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Lukkunaprasit T, Rattanasiri S, Turongkaravee S, Suvannang N, Ingsathit A, Attia J, Thakkinstian A. The association between genetic polymorphisms in ABCG2 and SLC2A9 and urate: an updated systematic review and meta-analysis. BMC MEDICAL GENETICS 2020; 21:210. [PMID: 33087043 PMCID: PMC7580000 DOI: 10.1186/s12881-020-01147-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 10/13/2020] [Indexed: 02/08/2023]
Abstract
Background Replication studies showed conflicting effects of ABCG2 and SLC2A9 polymorphisms on gout and serum urate. This meta-analysis therefore aimed to pool their effects across studies. Methods Studies were located from MEDLINE and Scopus from inception to 17th June 2018. Observational studies in adults with any polymorphism in ABCG2 or SLC2A9, and outcome including gout, hyperuricemia, and serum urate were included for pooling. Data extractions were performed by two independent reviewers. Genotype effects were pooled stratified by ethnicity using a mixed-effect logistic model and a multivariate meta-analysis for dichotomous and continuous outcomes. Results Fifty-two studies were included in the analysis. For ABCG2 polymorphisms, mainly studied in Asians, carrying 1–2 minor-allele-genotypes of rs2231142 and rs72552713 were respectively about 2.1–4.5 and 2.5–3.9 times higher odds of gout than non-minor-allele-genotypes. The two rs2231142-risk-genotypes also had higher serum urate about 11–18 μmol/l. Conversely, carrying 1–2 minor alleles of rs2231137 was about 36–57% significantly lower odds of gout. For SLC2A9 polymorphisms, mainly studied in Caucasians, carrying 1–2 minor alleles of rs1014290, rs6449213, rs6855911, and rs7442295 were about 25–43%, 31–62%, 33–64%, and 35–65% significantly lower odds of gout than non-minor-allele-genotypes. In addition, 1–2 minor-allele-genotypes of the latter three polymorphisms had significantly lower serum urate about 20–49, 21–51, and 18–54 μmol/l than non-minor-allele-genotypes. Conclusions Our findings should be useful in identifying patients at risk for gout and high serum urate and these polymorphisms may be useful in personalized risk scores. Trial registration PROSPERO registration number: CRD42018105275. Supplementary information The online version contains supplementary material available at 10.1186/s12881-020-01147-2.
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Affiliation(s)
- Thitiya Lukkunaprasit
- Department of Clinical Epidemiology and Biostatistics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, 270 Rama VI Rd., Ratchathewi, Bangkok, 10400, Thailand.,Department of Pharmacology, College of Pharmacy, Rangsit University, Pathum Thani, Thailand
| | - Sasivimol Rattanasiri
- Department of Clinical Epidemiology and Biostatistics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, 270 Rama VI Rd., Ratchathewi, Bangkok, 10400, Thailand.
| | - Saowalak Turongkaravee
- Social and Administrative Pharmacy Excellence Research (SAPER) Unit, Department of Pharmacy, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | - Naravut Suvannang
- Department of Clinical Epidemiology and Biostatistics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, 270 Rama VI Rd., Ratchathewi, Bangkok, 10400, Thailand
| | - Atiporn Ingsathit
- Department of Clinical Epidemiology and Biostatistics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, 270 Rama VI Rd., Ratchathewi, Bangkok, 10400, Thailand
| | - John Attia
- Centre for Clincial Epidemiology and Biostatistics, School of Medicine and Public Health, Faculty of Health and Medicine, University of Newcastle, and Hunter Medical Research Institute, Newcastle, NSW, Australia
| | - Ammarin Thakkinstian
- Department of Clinical Epidemiology and Biostatistics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, 270 Rama VI Rd., Ratchathewi, Bangkok, 10400, Thailand
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Fine mapping and identification of serum urate loci in American Indians: The Strong Heart Family Study. Sci Rep 2019; 9:17899. [PMID: 31784582 PMCID: PMC6884539 DOI: 10.1038/s41598-019-52924-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 10/12/2019] [Indexed: 02/07/2023] Open
Abstract
While studies have reported genetic loci affecting serum urate (SU) concentrations, few studies have been conducted in minority populations. Our objective for this study was to identify genetic loci regulating SU in a multigenerational family-based cohort of American Indians, the Strong Heart Family Study (SHFS). We genotyped 162,718 single nucleotide polymorphisms (SNPs) in 2000 SHFS participants using an Illumina MetaboChip array. A genome-wide association analysis of SU was conducted using measured genotype analysis approach accounting for kinships in SOLAR, and meta-analysis in METAL. Our results showed strong association of SU with rs4481233, rs9998811, rs7696092 and rs13145758 (minor allele frequency (MAF) = 25–44%; P < 3 × 10−14) of solute carrier family 2, member 9 (SLC2A9) and rs41481455, rs2231142 and rs1481012 (MAF = 29%; p < 3 × 10−9) of ATP-binding cassette protein, subfamily G, member 2 (ABCG2). Carriers of G alleles of rs9998811, rs4148155 and rs1481012 and A alleles of rs4481233, rs7696092 and rs13145758 and rs2231142 had lower SU concentrations as compared to non-carriers. Genetic analysis of SU conditional on significant SLC2A9 and ABCG2 SNPs revealed new loci, nucleobindin 1 (NUCB1) and neuronal PAS domain protein 4 (NPAS4) (p <6× 10−6). To identify American Indian-specific SNPs, we conducted targeted sequencing of key regions of SLC2A9. A total of 233 SNPs were identified of which 89 were strongly associated with SU (p < 7.1 × 10−10) and 117 were American Indian specific. Analysis of key SNPs in cohorts of Mexican-mestizos, European, Indian and East Asian ancestries showed replication of common SNPs, including our lead SNPs. Our results demonstrate the association of SU with uric acid transporters in a minority population of American Indians and potential novel associations of SU with neuronal-related genes which warrant further investigation.
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Bioinformatic exploration of OLFML2B overexpression in gastric cancer base on multiple analyzing tools. BMC Cancer 2019; 19:227. [PMID: 30866865 PMCID: PMC6416920 DOI: 10.1186/s12885-019-5406-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 02/25/2019] [Indexed: 12/13/2022] Open
Abstract
Background Gastric cancer (GC) is one of the most commonly occuring gastrointestinal tumor types, and early diagnosis and operation have a notable effect on the prognosis of patients. Although certain markers, including HER2, VEGER-2, ERCC1 and Bcl-2, have been utilized in clinical practise to screen out new patients with GC, the results of using these markers remains poor. The role of olfactomedin-like 2B (OLFML2B) in GC, as a member of the olfactomedin domain-containing proteins family, is remain unclear. Methods In the present study, we assessed the expression of OLFML2B, including mRNA and protein level, by using The Cancer Genome Atlas (TCGA) database and 13 pairs of clinical samples between GC and NG tissues. The correlation between expression of OLFML2B and prognosis of GC was evaculated by the Kaplan-Meier plotter and OncoLnc online tools. In addition, mechanism analysis of OLFML2B in GC was explored thought bioinformatic tools, including cBioPortal and FunRich software. Results In our study, the mRNA expression of OLFML2B in GC both TCGA database and clinical samples was consistently revealed to be significantly higher compared with that in NG tissues (P < 0.0001 for TCGA database and P = 0.0034 for clinical samples), and high OLFML2B expression was found in 9 (69.23%) of 13 clinical GC by immunohistochemistry and was positively correlated with the depth of tumor invasion and clinical stage (TNM). In addition, the AUC for a ROC of 0.867 indicated a moderate diagnostic ability of OLFML2B for GC. Survival analysis from the Kaplan-Meier plotter (P = 2.6 × 10− 6) and OncoLnc (P = 0.00276) revealed that the high expression of OLFML2B was associated with a short overall survival. Futhermore, 5% (24/478) alterations of OLFML2B were identified from cBioPortal, and among them, missense mutation (14/478) was the primary type. The results from FunRich revealed that OLFML2B participated in mediating multiple biological processes including cell growth and maintenance, regulation of the cell cycle, apoptosis and cell communication through multiple signaling pathways including the M/G1 transition pathway, post-translational protein modification and DNA replication pre-initiation. Conclusions Taken together, it could be deduced that OLFML2B may act as an oncogene in the development of GC and the overexpression of OLFML2B in GC may be used as a novel diagnostic and prognostic target for GC.
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Zivotić I, Djurić T, Stanković A, Ivančević I, Končar I, Milasinovic D, Stankovic G, Alavantić D, Zivković M. The HACD4 haplotype as a risk factor for atherosclerosis in males. Gene 2018; 641:35-40. [PMID: 29031776 DOI: 10.1016/j.gene.2017.10.030] [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: 05/24/2017] [Revised: 09/15/2017] [Accepted: 10/10/2017] [Indexed: 11/19/2022]
Abstract
The 9p21.3 region is rich in regulatory elements and the variants in this region had been robustly associated with carotid plaque (CP) and coronary artery disease (CAD). Recently, the HACD4 was detected as one of the six 9p21.3 differentially expressed genes associated with accelerated atherosclerosis and greater mean lesion area in the Athsq1 congenic mice. We aimed to investigate association of two potentially regulatory HACD4 variants (rs36212560 I/D, rs2275888 T/C) and their haplotypes with CP occurrence and the level of HACD4 and FOCAD mRNA in human CP tissue. Association study was replicated in CAD patients who suffered the first myocardial infarction. Study included 477 CP patients, 303 healthy controls and replication sample of 224 CAD males from the population of Serbia. Genotypes were determined by polymerase chain reaction (PCR) and real-time PCR using TaqMan® technology. The gene expression was detected with TaqMan® technology. We have found significant and independent association of DT haplotype with CP presence in men (adjusted OR=1.64 CI=1.12-2.42, p=0.011). The result was replicated in CAD males (adjusted OR=1.84 CI=1.21-2.80, p=0.004). We have found significant effect of the HACD4 rs2275888 on FOCAD mRNA level in human CP tissue. Correction for multiple testing was performed. Independent association of HACD4 haplotypes with atherosclerotic phenotypes connotes a further validation and replication in larger cohorts as well as functional studies to enlighten the potential mechanism of its action in pathophysiology of atherosclerosis.
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Affiliation(s)
- Ivan Zivotić
- Laboratory for Radiobiology and Molecular Genetics, VINCA Institute of Nuclear Sciences, University of Belgrade, 11000 Belgrade, Serbia
| | - Tamara Djurić
- Laboratory for Radiobiology and Molecular Genetics, VINCA Institute of Nuclear Sciences, University of Belgrade, 11000 Belgrade, Serbia
| | - Aleksandra Stanković
- Laboratory for Radiobiology and Molecular Genetics, VINCA Institute of Nuclear Sciences, University of Belgrade, 11000 Belgrade, Serbia
| | - Ilija Ivančević
- Laboratory for Radiobiology and Molecular Genetics, VINCA Institute of Nuclear Sciences, University of Belgrade, 11000 Belgrade, Serbia
| | - Igor Končar
- School of Medicine, University of Belgrade, 11000 Belgrade, Serbia; Clinic for the Vascular and Endovascular Surgery, Clinical Center of Serbia, 11000 Belgrade, Serbia
| | - Dejan Milasinovic
- Cardiology Clinic, Clinical Center of Serbia, 11000 Belgrade, Serbia
| | - Goran Stankovic
- School of Medicine, University of Belgrade, 11000 Belgrade, Serbia; Cardiology Clinic, Clinical Center of Serbia, 11000 Belgrade, Serbia
| | - Dragan Alavantić
- Laboratory for Radiobiology and Molecular Genetics, VINCA Institute of Nuclear Sciences, University of Belgrade, 11000 Belgrade, Serbia
| | - Maja Zivković
- Laboratory for Radiobiology and Molecular Genetics, VINCA Institute of Nuclear Sciences, University of Belgrade, 11000 Belgrade, Serbia.
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Li QL, Lei PJ, Zhao QY, Li L, Wei G, Wu M. Epigenomic analysis in a cell-based model reveals the roles of H3K9me3 in breast cancer transformation. Epigenomics 2017; 9:1077-1092. [DOI: 10.2217/epi-2016-0183] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Aim: Epigenetic marks are critical regulators of chromatin and gene activity. Their roles in normal physiology and disease states, including cancer development, still remain elusive. Herein, the epigenomic change of H3K9me3, as well as its potential impacts on gene activity and genome stability, was investigated in an in vitro breast cancer transformation model. Methods: The global H3K9me3 level was studied with western blotting. The distribution of H3K9me3 on chromatin and gene expression was studied with ChIP-Seq and RNA-Seq, respectively. Results: The global H3K9me3 level decreases during transformation and its distribution on chromatin is reprogrammed. By combining with TCGA data, we identified 67 candidate oncogenes, among which five genes are totally novel. Our analysis further links H3K9me3 with transposon activity, and suggests H3K9me3 reduction increases the cell’s sensitivity to DNA damage reagents. Conclusion: H3K9me3 reduction is possibly related with breast cancer transformation by regulating gene expression and chromatin stability during transformation.
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Affiliation(s)
- Qing-Lan Li
- Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Department of Biochemistry & Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Pin-Ji Lei
- Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Department of Biochemistry & Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Quan-Yi Zhao
- Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Department of Biochemistry & Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Lianyun Li
- Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Department of Biochemistry & Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Gang Wei
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute of Computational Biology, Shanghai Institute for Biological Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Min Wu
- Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Department of Biochemistry & Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
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Zhang L, You Y, Wu Y, Zhang Y, Wang M, Song Y, Liu X, Kou C. Association of BUD13 polymorphisms with metabolic syndrome in Chinese population: a case-control study. Lipids Health Dis 2017; 16:127. [PMID: 28659142 PMCID: PMC5490231 DOI: 10.1186/s12944-017-0520-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 06/16/2017] [Indexed: 11/26/2022] Open
Abstract
Background BUD13 homolog (BUD13), one of submits of the retention and splicing complex, was identified in yeast as a splicing factor that affected nuclear pre-mRNA retention. While more and more studies demonstrated that BUD13 played a potential role in the pathogenesis of metabolic syndrome (MetS). This objective was to reassess whether novel locus of BUD13 were linked to MetS and individual complements in the northeast of China. Methods A total of 3850 individuals were recruited in this case-control study, including 1813 MetS cases and 2037 healthy controls. The diagnostic criteria was according to the International Diabetes Federation (IDF). Metabolic complements such as waist circumference (WC), triglyceride, high-density lipoprotein cholesterol (HDL-C), systolic and diastolic blood pressure (SBP and DBP), and fasting glucose were measured. We explored the association between two novel single nucleotide polymorphism (SNPs) of BUD13 (rs7118999 and rs10488698) and MetS and its complements. Results Using binary logistic regression analysis we found that there were no significant associations between SNPs and MetS in different heritance models (all P > 0.05). However, novel locus of BUD13 were linked to individual complements in MetS cases. Rs7118999 conferred to risk of WC (P = 0.016) and the carrier of TT might have higher susceptibility to MetS. While rs10488698 was associated with HDL-C (P = 0.001) and the carrier of TT was significantly associated with higher level of HDL-C. Conclusions We concluded that novel mutations in BUD13 did not confer risk for MetS in our study population, but these mutations changed the level of metabolic complements.
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Affiliation(s)
- Lili Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, No. 1163 Xinmin Street, Changchun, Jilin province, 130021, China
| | - Yueyue You
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, No. 1163 Xinmin Street, Changchun, Jilin province, 130021, China
| | - Yanhua Wu
- Division of Clinical Epidemiology, First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Yangyu Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, No. 1163 Xinmin Street, Changchun, Jilin province, 130021, China
| | - Mohan Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, No. 1163 Xinmin Street, Changchun, Jilin province, 130021, China
| | - Yan Song
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, No. 1163 Xinmin Street, Changchun, Jilin province, 130021, China
| | - Xinyu Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, No. 1163 Xinmin Street, Changchun, Jilin province, 130021, China
| | - Changgui Kou
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, No. 1163 Xinmin Street, Changchun, Jilin province, 130021, China.
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Voruganti VS, Laston S, Haack K, Mehta NR, Cole SA, Butte NF, Comuzzie AG. Serum uric acid concentrations and SLC2A9 genetic variation in Hispanic children: the Viva La Familia Study. Am J Clin Nutr 2015; 101:725-32. [PMID: 25833971 PMCID: PMC4381775 DOI: 10.3945/ajcn.114.095364] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 12/22/2014] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Elevated concentrations of serum uric acid are associated with increased risk of gout and renal and cardiovascular diseases. Genetic studies in adults have consistently identified associations of solute carrier family 2, member 9 (SLC2A9), polymorphisms with variation in serum uric acid. However, it is not known whether the association of serum uric acid with SLC2A9 polymorphisms manifests in children. OBJECTIVE The aim was to investigate whether variation in serum uric acid is under genetic influence and whether the association with SLC2A9 polymorphisms generalizes to Hispanic children of the Viva La Familia Study. DESIGN We conducted a genomewide association study with 1.1 million genetic markers in 815 children. RESULTS We found serum uric acid to be significantly heritable [h(2) ± SD = 0.45 ± 0.08, P = 5.8 × 10(-11)] and associated with SLC2A9 variants (P values between 10(-16) and 10(-7)). Several of the significantly associated polymorphisms were previously identified in studies in adults. We also found positive genetic correlations between serum uric acid and BMI z score (ρG = 0.45, P = 0.002), percentage of body fat (ρG = 0.28, P = 0.04), fat mass (ρG = 0.34, P = 0.02), waist circumference (ρG = 0.42, P = 0.003), and waist-to-height ratio (ρG = 0.46, P = 0.001). CONCLUSIONS Our results show that variation in serum uric acid in Hispanic children is under considerable genetic influence and is associated with obesity-related phenotypes. As in adults, genetic variation in SLC2A9 is associated with serum uric acid concentrations, an important biomarker of renal and cardiovascular disease risk, in Hispanic children.
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Affiliation(s)
- V Saroja Voruganti
- From the Department of Nutrition (VSV) and UNC Nutrition Research Institute (VSV), University of North Carolina at Chapel Hill, Kannapolis, NC; the Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX (SL, KH, SAC, and AGC); and the USDA/Agricultural Research Service Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX (NRM and NFB)
| | - Sandra Laston
- From the Department of Nutrition (VSV) and UNC Nutrition Research Institute (VSV), University of North Carolina at Chapel Hill, Kannapolis, NC; the Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX (SL, KH, SAC, and AGC); and the USDA/Agricultural Research Service Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX (NRM and NFB)
| | - Karin Haack
- From the Department of Nutrition (VSV) and UNC Nutrition Research Institute (VSV), University of North Carolina at Chapel Hill, Kannapolis, NC; the Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX (SL, KH, SAC, and AGC); and the USDA/Agricultural Research Service Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX (NRM and NFB)
| | - Nitesh R Mehta
- From the Department of Nutrition (VSV) and UNC Nutrition Research Institute (VSV), University of North Carolina at Chapel Hill, Kannapolis, NC; the Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX (SL, KH, SAC, and AGC); and the USDA/Agricultural Research Service Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX (NRM and NFB)
| | - Shelley A Cole
- From the Department of Nutrition (VSV) and UNC Nutrition Research Institute (VSV), University of North Carolina at Chapel Hill, Kannapolis, NC; the Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX (SL, KH, SAC, and AGC); and the USDA/Agricultural Research Service Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX (NRM and NFB)
| | - Nancy F Butte
- From the Department of Nutrition (VSV) and UNC Nutrition Research Institute (VSV), University of North Carolina at Chapel Hill, Kannapolis, NC; the Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX (SL, KH, SAC, and AGC); and the USDA/Agricultural Research Service Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX (NRM and NFB)
| | - Anthony G Comuzzie
- From the Department of Nutrition (VSV) and UNC Nutrition Research Institute (VSV), University of North Carolina at Chapel Hill, Kannapolis, NC; the Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX (SL, KH, SAC, and AGC); and the USDA/Agricultural Research Service Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX (NRM and NFB)
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