Abstract:
BACKGROUND:To explore long-non-coding RNA (lncRNA), microRNA (miRNA) and messenger RNA (mRNA) expression profiles and their biological functions in the urine samples in calcium oxalate (CaOx) patients. METHODS:Five CaOx kidney stone patients were recruited in CaOx stone group and six healthy people were included as control group, whose midstream morning urine was collected before the patients were given any medicine on admission. After total RNA was extracted from urine, microarray of miRNA, mRNA and lncRNA were applied to explore their expression variation. Gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed to reveal the gene functions of the dysregulated lncRNA-associated competing endogenous RNA (ceRNA) network. Quantitative real-time PCR were performed on HK-2 cells treated with sodium oxalate (NaOx) to further screen out the differentially expression profiles of these RNAs. RESULTS:A total of nine miRNAs, 883 mRNAs and 1002 lncRNAs were differentially expressed in urine of CaOx patients compared with normal population. GO analysis revealed that most of mRNAs from ceRNA network were enriched in terms of respiratory burst, regulation of mitophagy, and protein kinase regulator activity. KEGG pathway analysis of these genes related to ceRNA network highlight their critical role in pentose phosphate pathway, glyoxylate and dicarboxylate metabolism, and Janus kinase/signal transducer and activator of transcription (JAK-STAT) signaling pathway. Five miRNAs (miR-6796-3p, miR-30d-5p, miR-3192-3p, miR-518b and miR-6776-3p), four mRNAs (NT5E, CDH4, CLEC14A, CCNL1) and six lncRNAs (lnc-TIGD1L2-3, lnc-KIN-1, lnc-FAM72B-4, lnc-EVI5L-1, lnc-SERPINI1-2, lnc-MB-6) from the HK-2 cells induced by NaOx were consistent with the expression changes of microarray results. CONCLUSION:The differential expressed miRNAs, mRNAs and lncRNAs may be associated with numerous variations of the signaling pathways or regulation of metabolism and kinase activity, providing potential biomarkers for early diagnosis of urolithiasis and new basis for further research of urolithiasis mechanism.
journal_name
BMC Med Genomicsjournal_title
BMC medical genomicsauthors
Liang X,Lai Y,Wu W,Chen D,Zhong F,Huang J,Zeng T,Duan X,Huang Y,Zhang S,Li S,Wu Wdoi
10.1186/s12920-019-0502-ysubject
Has Abstractpub_date
2019-04-29 00:00:00pages
57issue
1issn
1755-8794pii
10.1186/s12920-019-0502-yjournal_volume
12pub_type
杂志文章abstract:BACKGROUND:The mechanisms underlying neurodegeneration in the striatum of Huntingon's Disease (HD) brain are currently unknown. While the striatum is massively degenerated in symptomatic individuals, which makes cellular characterization difficult, it is largely intact in asymptomatic HD gene positive (HD+) individuals...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-019-0581-9
更新日期:2019-10-16 00:00:00
abstract:BACKGROUND:Acute erythro- and megakaryoblastic leukaemias are associated with very poor prognoses and the mechanism of blastic transformation is insufficiently elucidated. The murine Graffi leukaemia retrovirus induces erythro- and megakaryoblastic leukaemias when inoculated into NFS mice and represents a good model to...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-3-2
更新日期:2010-01-26 00:00:00
abstract:BACKGROUND:Gulf War Illness (GWI) is a complex multi-symptom disorder that affects up to one in three veterans of this 1991 conflict and for which no effective treatment has been found. Discovering novel treatment strategies for such a complex chronic illness is extremely expensive, carries a high probability of failur...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-015-0111-3
更新日期:2015-07-09 00:00:00
abstract:BACKGROUND:2q37 deletion syndrome is a rare congenital disorder that is characterized by facial dysmorphism, obesity, vascular and skeletal malformations, and a variable degree of intellectual disability. To date, common but variable phenotypes, such as skeletal or digit malformations and obesity, have been associated ...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-7-19
更新日期:2014-04-22 00:00:00
abstract:BACKGROUND:Hypermethylation of promoter CpG islands with associated loss of gene expression, and hypomethylation of CpG-rich repetitive elements that may destabilize the genome are common events in most, if not all, epithelial cancers. METHODS:The methylation of 6,502 CpG-rich sequences spanning the genome was analyze...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-1-47
更新日期:2008-09-30 00:00:00
abstract:BACKGROUND:The collection of viable DNA samples is an essential element of any genetics research programme. Biological samples for DNA purification are now routinely collected in many studies with a variety of sampling methods available. Initial observation in this study suggested a reduced genotyping success rate of s...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-6-20
更新日期:2013-06-10 00:00:00
abstract:BACKGROUND:Glioblastoma is a complex multifactorial disorder that has swift and devastating consequences. Few genes have been consistently identified as prognostic biomarkers of glioblastoma survival. The goal of this study was to identify general and clinical-dependent biomarker genes and biological processes of three...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-4-49
更新日期:2011-06-07 00:00:00
abstract:BACKGROUND:One of the tasks in the 2017 iDASH secure genome analysis competition was to enable training of logistic regression models over encrypted genomic data. More precisely, given a list of approximately 1500 patient records, each with 18 binary features containing information on specific mutations, the idea was f...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-018-0397-z
更新日期:2018-10-11 00:00:00
abstract:BACKGROUND:The opioid use disorder and overdose crisis in the United States affects public health as well as social and economic welfare. While several genetic and non-genetic risk factors for opioid use disorder have been identified, many of the genetic associations have not been independently replicated, and it is no...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-020-00837-3
更新日期:2021-01-07 00:00:00
abstract:BACKGROUND:Nicolaides-Baraitser syndrome (NCBRS) is a neurodevelopmental disorder caused by pathogenic sequence variants in SMARCA2 which encodes the catalytic component of the chromatin remodeling BAF complex. Pathogenic variants in genes that encode epigenetic regulators have been associated with genome-wide changes ...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-019-0555-y
更新日期:2019-07-09 00:00:00
abstract:BACKGROUND:Fat mass and obesity-associated (FTO) gene has been under close investigation since the discovery of its high impact on the obesity status in 2007 by a range of publications. Recent report on its implication in adipocytes underscored its molecular and functional mechanics in pathology. Still, the population ...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-019-0491-x
更新日期:2019-03-13 00:00:00
abstract:BACKGROUND:Balanced reciprocal chromosomal translocations (RCTs) are the ones of the most common structural aberrations in the population, with an incidence of 1:625. RCT carriers usually do not demonstrate changes in phenotype, except when the translocation results in gene interruption. However, these people are at ri...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-018-0384-4
更新日期:2018-08-20 00:00:00
abstract:BACKGROUND:In recent years, high-throughput protein interaction identification methods have generated a large amount of data. When combined with the results from other in vivo and in vitro experiments, a complex set of relationships between biological molecules emerges. The growing popularity of network analysis and da...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-8-S2-S9
更新日期:2015-01-01 00:00:00
abstract:BACKGROUND:Preeclampsia (PE) is a pregnancy-related condition that affects both the infant and the mother. Although the role of various inflammatory molecules in PE has been demonstrated, the importance of pro-inflammatory molecules such as IL-17A, IL-23 is not well understood. In the present investigation, a potential...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-020-00840-8
更新日期:2021-01-06 00:00:00
abstract:BACKGROUND:Integrating multiple data sources is indispensable in improving disease gene identification. It is not only due to the fact that disease genes associated with similar genetic diseases tend to lie close with each other in various biological networks, but also due to the fact that gene-disease associations are...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-8-S3-S2
更新日期:2015-01-01 00:00:00
abstract:BACKGROUND:Recent advances in whole-genome association studies (WGASs) for human cancer risk are beginning to provide the part lists of low-penetrance susceptibility genes. However, statistical analysis in these studies is complicated by the vast number of genetic variants examined and the weak effects observed, as a r...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-1-62
更新日期:2008-12-18 00:00:00
abstract:BACKGROUND:The majority of copy number callers requires high read coverage data that is often achieved with elevated material input, which increases the heterogeneity of tissue samples. However, to gain insights into smaller areas within a tissue sample, e.g. a cancerous area in a heterogeneous tissue sample, less mate...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-020-00731-y
更新日期:2020-06-01 00:00:00
abstract:BACKGROUND:Gene expression studies require appropriate normalization methods. One such method uses stably expressed reference genes. Since suitable reference genes appear to be unique for each tissue, we have identified an optimal set of the most stably expressed genes in human blood that can be used for normalization....
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-2-49
更新日期:2009-08-05 00:00:00
abstract:BACKGROUND:Chiari Type I Malformation (CMI) is characterized by herniation of the cerebellar tonsils through the foramen magnum at the base of the skull, resulting in significant neurologic morbidity. As CMI patients display a high degree of clinical variability and multiple mechanisms have been proposed for tonsillar ...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-7-39
更新日期:2014-06-25 00:00:00
abstract::This editorial summarizes eight research articles included in this supplement issue for the 2020 International Conference on Intelligent Biology and Medicine (ICIBM 2020) conference, that was held on August 9-10, 2020 (virtual conference), with a topic on data-driven analytics in biomedical genomics. These articles co...
journal_title:BMC medical genomics
pub_type: 社论
doi:10.1186/s12920-020-00833-7
更新日期:2020-12-28 00:00:00
abstract:BACKGROUND:Postmenopausal hormone therapy (HT) influences endogenous hormone concentrations and increases the risk of breast cancer. Gene expression profiling may reveal the mechanisms behind this relationship.Our objective was to explore potential associations between sex hormones and gene expression in whole blood fr...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-4-29
更新日期:2011-03-31 00:00:00
abstract:BACKGROUND:The zebrafish is recognized as a versatile cancer and drug screening model. However, it is not known whether the estrogen-responsive genes and signaling pathways that are involved in estrogen-dependent carcinogenesis and human cancer are operating in zebrafish. In order to determine the potential of zebrafis...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-4-41
更新日期:2011-05-16 00:00:00
abstract:BACKGROUND:A Mendelian transmission produces phenotypic and genetic relatedness between family members, giving family-based analytical methods an important role in genetic epidemiological studies-from heritability estimations to genetic association analyses. With the advance in genotyping technologies, whole-genome seq...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-018-0345-y
更新日期:2018-04-20 00:00:00
abstract::In this issue of BMC Medical Genomics Griffin et al. present a user-friendly and freely accessible HIV-associated neurocognitive disorder (HAND) genomic database that compiles viral (HIV-1) genetic sequences and other relevant clinical and treatment data. We discuss the benefits and caveats of public data sharing in N...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-015-0150-9
更新日期:2015-11-11 00:00:00
abstract:BACKGROUND:Currently, diagnosis of affected individuals with rare genetic disorders can be lengthy and costly, resulting in a diagnostic odyssey and in many patients a definitive molecular diagnosis is never achieved despite extensive clinical investigation. The recent advent and use of genomic medicine has resulted in...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-6-32
更新日期:2013-09-17 00:00:00
abstract:BACKGROUND:One of the major goals of genomic medicine is the identification of causal genomic variants in a patient and their relation to the observed clinical phenotypes. Prioritizing the genomic variants by considering only the genotype information usually identifies a few hundred potential variants. Narrowing it dow...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-018-0372-8
更新日期:2018-07-06 00:00:00
abstract:BACKGROUND:Glucocorticoids act on the glucocorticoid receptor (GR; NR3C1) to resolve inflammation and, as inhaled corticosteroids (ICS), are the cornerstone of treatment for asthma. However, reduced efficacy in severe disease or exacerbations indicates a need to improve ICS actions. METHODS:Glucocorticoid-driven trans...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-018-0467-2
更新日期:2019-01-31 00:00:00
abstract:BACKGROUND:DNA methylation levels will be important for detection of epigenetic effects. However, there are few reports showing sex-related differences in the sensitivity to DNA methylation. To evaluate their sex-related individual differences in the sensitivity to methylation rigorously, we performed a systematic anal...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-016-0217-2
更新日期:2016-08-26 00:00:00
abstract:BACKGROUND:Breast cancer comprises multiple tumor entities associated with different biological features and clinical behaviors, making individualized medicine a powerful tool to bring the right drug to the right patient. Next generation sequencing of RNA (RNA-Seq) is a suitable method to detect targets for individuali...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-015-0095-z
更新日期:2015-05-21 00:00:00
abstract:BACKGROUND:Bladder cancer has numerous genomic features that are potentially actionable by targeted agents. Nevertheless, both pre-clinical and clinical research using molecular targeted agents have been very limited in bladder cancer. RESULTS:We created the Genomics of Drug Sensitivity in Bladder Cancer (GDBC) databa...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-018-0406-2
更新日期:2018-10-03 00:00:00