Scandiatransplant acceptable mismatch program-10 years with an effective strategy for transplanting highly sensitized patients

In March 2009, the Scandiatransplant acceptable mismatch program (STAMP) was introduced as a strategy toward improving kidney allocation to highly sensitized patients. Patients with a transplantability scorePeer reviewe

Genetic and epigenetic regulation of gene expression in fetal and adult human livers

Background: The liver plays a central role in the maintenance of homeostasis and health in general. However, there is substantial inter-individual variation in hepatic gene expression, and although numerous genetic factors have been identified, less is known about the epigenetic factors. Results: By analyzing the methylomes and transcriptomes of 14 fetal and 181 adult livers, we identified 657 differentially methylated genes with adult-specific expression, these genes were enriched for transcription factor binding sites of HNF1A and HNF4A. We also identified 1,000 genes specific to fetal liver, which were enriched for GATA1, STAT5A, STAT5B and YY1 binding sites. We saw strong liver-specific effects of single nucleotide polymorphisms on both methylation levels (28,447 unique CpG sites (meQTL)) and gene expression levels (526 unique genes (eQTL)), at a false discovery rate (FDR) <0.05. Of the 526 unique eQTL associated genes, 293 correlated significantly not only with genetic variation but also with methylation levels. The tissue-specificities of these associations were analyzed in muscle, subcutaneous adipose tissue and visceral adipose tissue. We observed that meQTL were more stable between tissues than eQTL and a very strong tissue-specificity for the identified associations between CpG methylation and gene expression. Conclusions: Our analyses generated a comprehensive resource of factors involved in the regulation of hepatic gene expression, and allowed us to estimate the proportion of variation in gene expression that could be attributed to genetic and epigenetic variation, both crucial to understanding differences in drug response and the etiology of liver diseases

Methylation Markers of Early-Stage Non-Small Cell Lung Cancer

Despite of intense research in early cancer detection, there is a lack of biomarkers for the reliable detection of malignant tumors, including non-small cell lung cancer (NSCLC). DNA methylation changes are common and relatively stable in various types of cancers, and may be used as diagnostic or prognostic biomarkers.We performed DNA methylation profiling of samples from 48 patients with stage I NSCLC and 18 matching cancer-free lung samples using microarrays that cover the promoter regions of more than 14,500 genes. We correlated DNA methylation changes with gene expression levels and performed survival analysis.We observed hypermethylation of 496 CpGs in 379 genes and hypomethylation of 373 CpGs in 335 genes in NSCLC. Compared to adenocarcinoma samples, squamous cell carcinoma samples had 263 CpGs in 223 hypermethylated genes and 513 CpGs in 436 hypomethylated genes. 378 of 869 (43.5%) CpG sites discriminating the NSCLC and control samples showed an inverse correlation between CpG site methylation and gene expression levels. As a result of a survival analysis, we found 10 CpGs in 10 genes, in which the methylation level differs in different survival groups.We have identified a set of genes with altered methylation in NSCLC and found that a minority of them showed an inverse correlation with gene expression levels. We also found a set of genes that associated with the survival of the patients. These newly-identified marker candidates for the molecular screening of NSCLC will need further analysis in order to determine their clinical utility

Inimese tervete kudede ja mitteväikerakulise kopsuvähi võrdlevad ülegenoomsed DNA metülatsiooni uuringud

Väitekirja elektrooniline versioon ei sisalda publikatsioone.Metüleeritud tsütosiinil on suur roll imetajate organismi arengus. CpG dinukleotiidis asuvad tsütosiinid võivad olla kas metüleeritud või metüleerimata olekus. Kuna DNA metülatsioon on eluliselt vajalik organismi funktsioneerimiseks, tekitavad muutused epigenoomis erinevaid haiguslikke seisundeid, näiteks vähki. Ka põhjustab erinev metüleerimise tase inimestevahelist varieeruvust ravimite metaboliseerimises, mis võib kaasa tuua ebasoovitavaid ravimite kõrvaltoimeid. Töös kirjeldati ülegenoomseid DNA metülatsioonimustreid ning nende mõju geeniekspressioonile erinevates inimkudedes, nii tervetes kui ka tuumoris. Inimese tervete kudede uuringute põhjal järeldasime, et promootorpiirkonna metülatsiooni ning geeniekspressiooni vahel on negatiivne seos ja DNA metülatsiooni mustrid peegeldasid kudede funktsioone. Koe-spetsiifiliste erinevalt metüleeritud regioonide (tDMR) analüüs leidis suurel hulgal piirkondi, mis paiknesid geenisiseselt, kuid ei suudetud leida seoseid, kuidas need tDMR-d põhjustavad koe-spetsiifilist transkriptsiooni. Geenide, mis on seotud absorbtsiooni, jaotuse, metabolismi ning väljutusega (ADME) ekspressioonis on leitud suur indiviidide vaheline varieeruvus, mis omakorda mõjutab ravimvastust ja toksilisust. Uurides spetsiifiliselt maksakude, püüdsime määrata, kui suurel hulgal SNP-d ning DNA metülatsioon on võimelised üheskoos kirjeldama ADME geenide ekspressiooni varieeruvust maksas. Ootuspäraselt leidsime, et SNP genotüübi ning CpG metülatsioonitaseme kombineerimine võimaldab kirjeldada ekspressiooni variatsiooni paremini, kui kasutades ainult SNP-d või CpG metülatsiooni taset eraldiseisvalt. Töö viimane osa keskendus DNA metülatsiooni kirjeldamisele varajase staadiumi mitteväikerakulise kopsuvähi (NSCLC) patsientidel. Leidsime suurel hulgal erinevalt metüleeritud CpG saite. Mitmed neist on tuntud vähiseoselised biomarkerid, kuid enamik kirjeldatud geenidest on uued kopsuvähi markerid. Leitud geenide ontoloogiaanalüüs näitas, et nende geenide funktsioonid olid seotud vähi progresseerumisega. Elulemusanalüüsi tulemusel leidsime CpG saite, mille metülatsiooni tasemed erinesid erinevates elulemusgruppides. Mõned neist geenidest võivad olla head prognostiliste markerite kandidaadid.Methylated cytosines have a crucial role in mammalian development, and the proportion of methylated CpG sites can vary greatly over a genome. As DNA methylation is vital for the normal functioning of organism, changes in the epigenome can account for individual differences in drug responses or the incidence of severe diseases, especially cancer. The aim of the experimental work presented in this thesis was to describe methylation patterns and their effect on gene expression in different tissue types, both healthy and cancerous. Studies of healthy human tissues confirmed a clear correlation between DNA methylation in promoter regions and gene expression. The DNA methylation patterns also clearly reflected tissue-specific functions as demonstrated with hierarchical clustering and GO analyses of hypomethylated tissue-specific differentially methylated regions (tDMRs). The tDMR analysis revealed that a large number of methylated regions were within gene body regions, yet we were not able to show how these tDMRs mechanistically contribute to tissue-specific functions. Based on the observation that inter-individual variability in ADME gene expression affects drug efficacy, toxicity, and susceptibility to environmental toxins, we determined to what extent SNPs and DNA methylation can jointly explain variations in ADME gene expression in liver. As expected, the combination of SNP genotype and CpG site methylation levels data explained more of the observed expression variations than the use of SNP or methylation levels alone. The third part of the thesis concentrated on describing DNA methylation patterns in early-stage non-small cell lung cancer (NSCLC) patients. A number of differentially methylated CpG sites were found, most of the identified genes represent novel markers for NSCLC. GO analysis revealed that differentially methylated genes were closely related to cancer progression. Furthermore, a survival analysis identified a number of CpG sites whose methylation levels differed according to patient survival. Accordingly, the latter sites represent CpGs that could potentially serve as prognostic markers

Mutation analysis and copy number alterations of KIF23 in non-small-cell lung cancer exhibiting KIF23 over-expression

KIF23 was recently suggested to be a potential molecular target for the treatment of lung cancer. This proposal is based on elevated expression of KIF23 in several tumors affecting breast, lung, brain, and liver, and also on the presence of KIF23 mutations in melanoma and colorectal cancer. Recently, we identified a mutation in the KIF23 gene causing a rare hereditary form of dyserythropoietic anemia (CDA III) with predisposition to blood cancer. We suggested that KIF23 overexpression in tumors might be due to the presence of activating somatic mutations, and therefore, mutation screening of the KIF23 in 15 non-small-cell lung cancer (NSCLC) cases with elevated expression level of KIF23 was undertaken. Eight sequence variants were found in all samples. Furthermore, one variant was present in two cases, and one variant was case specific. Nine variants were previously reported while one variant lacks frequency information. Nine of ten cases available for single nucleotide polymorphism-array analysis demonstrated aberrant karyotypes with additional copy of entire chromosome 15. Thus, no activating somatic mutations in coding regions of the KIF23 were found. Furthermore, no mutations were detected in cell cycle genes homology region in KIF23 promoter responsible for p53-dependent repression of KIF23 expression. We showed that the elevated level of KIF23 could be due to additional copy of chromosome 15 demonstrated in 90% of NSCLC cases analyzed in this study. Considering the crucial role of KIF23 in the final step of mitosis, the gene is a potential molecular marker, and for better understanding of its role in cancer development, more tumors should be analyzed

DNA methylome profiling of human tissues identifies global and tissue-specific methylation patterns

BACKGROUND: DNA epigenetic modifications, such as methylation, are important regulators of tissue differentiation, contributing to processes of both development and cancer. Profiling the tissue-specific DNA methylome patterns will provide novel insights into normal and pathogenic mechanisms, as well as help in future epigenetic therapies. In this study, 17 somatic tissues from four autopsied humans were subjected to functional genome analysis using the Illumina Infinium HumanMethylation450 BeadChip, covering 486 428 CpG sites. RESULTS: Only 2% of the CpGs analyzed are hypermethylated in all 17 tissue specimens; these permanently methylated CpG sites are located predominantly in gene-body regions. In contrast, 15% of the CpGs are hypomethylated in all specimens and are primarily located in regions proximal to transcription start sites. A vast number of tissue-specific differentially methylated regions are identified and considered likely mediators of tissue-specific gene regulatory mechanisms since the hypomethylated regions are closely related to known functions of the corresponding tissue. Finally, a clear inverse correlation is observed between promoter methylation within CpG islands and gene expression data obtained from publicly available databases. CONCLUSIONS: This genome-wide methylation profiling study identified tissue-specific differentially methylated regions in 17 human somatic tissues. Many of the genes corresponding to these differentially methylated regions contribute to tissue-specific functions. Future studies may use these data as a reference to identify markers of perturbed differentiation and disease-related pathogenic mechanisms

DNA methylome profiling of human tissues identifies global and tissue-specific methylation patterns

BACKGROUND: DNA epigenetic modifications, such as methylation, are important regulators of tissue differentiation, contributing to processes of both development and cancer. Profiling the tissue-specific DNA methylome patterns will provide novel insights into normal and pathogenic mechanisms, as well as help in future epigenetic therapies. In this study, 17 somatic tissues from four autopsied humans were subjected to functional genome analysis using the Illumina Infinium HumanMethylation450 BeadChip, covering 486 428 CpG sites. RESULTS: Only 2% of the CpGs analyzed are hypermethylated in all 17 tissue specimens; these permanently methylated CpG sites are located predominantly in gene-body regions. In contrast, 15% of the CpGs are hypomethylated in all specimens and are primarily located in regions proximal to transcription start sites. A vast number of tissue-specific differentially methylated regions are identified and considered likely mediators of tissue-specific gene regulatory mechanisms since the hypomethylated regions are closely related to known functions of the corresponding tissue. Finally, a clear inverse correlation is observed between promoter methylation within CpG islands and gene expression data obtained from publicly available databases. CONCLUSIONS: This genome-wide methylation profiling study identified tissue-specific differentially methylated regions in 17 human somatic tissues. Many of the genes corresponding to these differentially methylated regions contribute to tissue-specific functions. Future studies may use these data as a reference to identify markers of perturbed differentiation and disease-related pathogenic mechanisms

Correction: Methylation Markers of Early-Stage Non-Small Cell Lung Cancer.

[This corrects the article DOI: 10.1371/journal.pone.0039813.]