Abstract:
BACKGROUND:Insulin resistance (IR) is accompanied by chronic low grade systemic inflammation, obesity, and deregulation of total body energy homeostasis. We induced inflammation in adipose and liver tissues in vitro in order to mimic inflammation in vivo with the aim to identify tissue-specific processes implicated in IR and to find biomarkers indicative for tissue-specific IR. METHODS:Human adipose and liver tissues were cultured in the absence or presence of LPS and DNA Microarray Technology was applied for their transcriptome analysis. Gene Ontology (GO), gene functional analysis, and prediction of genes encoding for secretome were performed using publicly available bioinformatics tools (DAVID, STRING, SecretomeP). The transcriptome data were validated by proteomics analysis of the inflamed adipose tissue secretome. RESULTS:LPS treatment significantly affected 667 and 483 genes in adipose and liver tissues respectively. The GO analysis revealed that during inflammation adipose tissue, compared to liver tissue, had more significantly upregulated genes, GO terms, and functional clusters related to inflammation and angiogenesis. The secretome prediction led to identification of 399 and 236 genes in adipose and liver tissue respectively. The secretomes of both tissues shared 66 genes and the remaining genes were the differential candidate biomarkers indicative for inflamed adipose or liver tissue. The transcriptome data of the inflamed adipose tissue secretome showed excellent correlation with the proteomics data. CONCLUSIONS:The higher number of altered proinflammatory genes, GO processes, and genes encoding for secretome during inflammation in adipose tissue compared to liver tissue, suggests that adipose tissue is the major organ contributing to the development of systemic inflammation observed in IR. The identified tissue-specific functional clusters and biomarkers might be used in a strategy for the development of tissue-targeted treatment of insulin resistance in patients.
journal_name
BMC Med Genomicsjournal_title
BMC medical genomicsauthors
Szalowska E,Dijkstra M,Elferink MG,Weening D,de Vries M,Bruinenberg M,Hoek A,Roelofsen H,Groothuis GM,Vonk RJdoi
10.1186/1755-8794-4-71subject
Has Abstractpub_date
2011-10-06 00:00:00pages
71issn
1755-8794pii
1755-8794-4-71journal_volume
4pub_type
杂志文章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:Accurate discovery of molecular biomarkers that are prognostic of a clinical outcome is an important yet challenging task, partly due to the combination of the typically weak genomic signal for a clinical outcome and the frequently strong noise due to microarray handling effects. Effective strategies to reso...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-016-0187-4
更新日期:2016-06-10 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: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 clinical overlap exists between mosaic Neurofibromatosis Type 2 and sporadic Schwannomatosis conditions. In these cases a molecular analysis of tumors is recommended for a proper genetic diagnostics. This analysis is challenged by the fact that schwannomas in both conditions bear a somatic double inactivat...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-015-0076-2
更新日期:2015-01-24 00:00:00
abstract:BACKGROUND:Genes do not act in isolation but instead as part of complex regulatory networks. To understand how breast tumors adapt to the presence of the drug letrozole, at the molecular level, it is necessary to consider how the expression levels of genes in these networks change relative to one another. METHODS:Usin...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-6-S2-S2
更新日期:2013-01-01 00:00:00
abstract:BACKGROUND:Genomic data is increasingly collected by a wide array of organizations. As such, there is a growing demand to make summary information about such collections available more widely. However, over the past decade, a series of investigations have shown that attacks, rooted in statistical inference methods, can...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-017-0282-1
更新日期:2017-07-26 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:Testing strategies is crucial for genetics clinics and testing laboratories. In this study, we tried to compare the hit rate between solo and trio and trio plus testing and between trio and sibship testing. Finally, we studied the impact of extended family analysis, mainly in complex and unsolved cases. MET...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-020-00743-8
更新日期:2020-07-17 00:00:00
abstract:BACKGROUND:Neuroblastoma (NB) tumors are well known for their pronounced clinical and molecular heterogeneity. The global gene expression and DNA copy number alterations have been shown to have profound differences in tumors of low or high stage and those with or without MYCN amplification. RNA splicing is an important...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-4-35
更新日期:2011-04-18 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:BACKGROUNDS:Recent large-scale genetic studies often involve clustered phenotypes such as repeated measurements. Compared to a series of univariate analyses of single phenotypes, an analysis of clustered phenotypes can be useful for substantially increasing statistical power to detect more genetic associations. Moreove...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-019-0517-4
更新日期:2019-07-11 00:00:00
abstract:BACKGROUND:The complexity of genome informatics is a recurring challenge for genome exploration and analysis by students and other non-experts. This complexity creates a barrier to wider implementation of experiential genomics education, even in settings with substantial computational resources and expertise. Reducing ...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-019-0615-3
更新日期:2019-11-27 00:00:00
abstract:BACKGROUND:The gene expression profile of cytologically-normal bronchial airway epithelial cells has previously been shown to be altered in patients with lung cancer. Although bronchoscopy is often used for the diagnosis of lung cancer, its sensitivity is imperfect, especially for small and peripheral suspicious lesion...
journal_title:BMC medical genomics
pub_type: 杂志文章,多中心研究
doi:10.1186/s12920-015-0091-3
更新日期:2015-05-06 00:00:00
abstract:BACKGROUND:Colon adenocarcinoma (COAD) is one of the most common gastrointestinal cancers globally. Molecular aberrations of tumor suppressors and/or oncogenes are the main contributors to tumorigenesis. However, the exact underlying mechanisms of COAD pathogenesis are clearly not known yet. In this regard, there is an...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-020-00757-2
更新日期:2020-07-29 00:00:00
abstract:BACKGROUND:Cardiac pathological hypertrophy is associated with a significantly increased risk of coronary heart disease and has been observed in diabetic patients treated with rosiglitazone whereas most published studies do not suggest a similar increase in risk of cardiovascular events in pioglitazone-treated diabetic...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-7-35
更新日期:2014-06-17 00:00:00
abstract:BACKGROUND:Childhood leukemia is characterized by the presence of balanced chromosomal translocations or by other structural or numerical chromosomal changes. It is well know that leukemias with specific molecular abnormalities display profoundly different global gene expression profiles. However, it is largely unknown...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-3-6
更新日期:2010-03-08 00:00:00
abstract:BACKGROUND:Epithelial to mesenchymal transition, and mimicking processes, contribute to cancer invasion and metastasis, and are known to be responsible for resistance to various therapeutic agents in many cancers. While a number of studies have proposed molecular signatures that characterize the spectrum of such transi...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-017-0252-7
更新日期:2017-03-09 00:00:00
abstract:BACKGROUND:Glaucoma is the largest cause of irreversible blindness affecting more than 60 million people globally. The disease is defined as a gradual loss of peripheral vision due to death of Retinal Ganglion Cells (RGC). The RGC death is largely influenced by the rate of aqueous humor production by ciliary processes ...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-016-0177-6
更新日期:2016-03-22 00:00:00
abstract:BACKGROUND:The right dataset is essential to obtain the right insights in data science; therefore, it is important for data scientists to have a good understanding of the availability of relevant datasets as well as the content, structure, and existing analyses of these datasets. While a number of efforts are underway ...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-018-0411-5
更新日期:2018-11-20 00:00:00
abstract:BACKGROUND:Genomic copy number alterations are widely associated with a broad range of human tumors and offer the potential to be used as a diagnostic tool. Especially in the emerging era of personalized medicine medical informatics tools that allow the fast visualization and analysis of genomic alterations of a patien...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-3-11
更新日期:2010-04-09 00:00:00
abstract:BACKGROUND:With 15,949 markers, the low-density Infinium QC Array-24 BeadChip enables linkage analysis, HLA haplotyping, fingerprinting, ethnicity determination, mitochondrial genome variations, blood groups and pharmacogenomics. It represents an attractive independent QC option for NGS-based diagnostic laboratories, a...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-017-0297-7
更新日期:2017-10-06 00:00:00
abstract:BACKGROUND:Gene expression profiling has shown its ability to identify with high accuracy low cytogenetic risk acute myeloid leukemia such as acute promyelocytic leukemia and leukemias with t(8;21) or inv(16). The aim of this gene expression profiling study was to evaluate to what extent suboptimal samples with low leu...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-5-6
更新日期:2012-01-30 00:00:00
abstract:BACKGROUND:Cancer shows a great diversity in its clinical behavior which cannot be easily predicted using the currently available clinical or pathological markers. The identification of pathways associated with lymph node metastasis (N+) and recurrent head and neck squamous cell carcinoma (HNSCC) may increase our under...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-4-33
更新日期:2011-04-13 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:BACKGROUND:Host protein-protein interaction networks are altered by invading virus proteins, which create new interactions, and modify or destroy others. The resulting network topology favors excessive amounts of virus production in a stressed host cell network. Short linear peptide motifs common to both virus and host...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-2-27
更新日期:2009-05-18 00:00:00
abstract:BACKGROUND:Gastric emptying is impaired in patients with gastroparesis whereas it is either unchanged or accelerated in obese individuals. The goal of the current study was to identify changes in gene expression in the stomach muscularis that may be contributing to altered gastric motility in idiopathic gastroparesis a...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-019-0550-3
更新日期:2019-06-20 00:00:00
abstract:BACKGROUND:While most pediatric sarcomas respond to front-line therapy, some bone sarcomas do not show radiographic response like soft-tissue sarcomas (rhabdomyosarccomas) but do show 90% necrosis. Though, new therapies are urgently needed to improve survival and quality of life in pediatric patients with sarcomas. Com...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-018-0456-5
更新日期:2019-01-31 00:00:00
abstract:BACKGROUND:Preterm birth (PTB), defined as infant delivery before 37 weeks of completed gestation, results from the interaction of both genetic and environmental components and constitutes a complex multifactorial syndrome. Transcriptome analysis of PTB has proven challenging because of the multiple causes of PTB and t...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-019-0498-3
更新日期:2019-04-01 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