Identification of epigenetic modulators in human breast cancer by integrated analysis of DNA methylation and RNA-Seq data

<p>Human tumors undergo massive changes in DNA methylation. Recent studies showed that site-specific methylation of CpG sites is determined by the DNA sequence context surrounding the CpG site, which alludes to a possible mechanism for site-specific aberrant DNA methylation in cancer through DNA-binding proteins. In this paper, DNA methylation data and RNA-Seq data of breast tumors and normal tissues in the database of The Cancer Genome Atlas (TCGA) were integrated with information of DNA motifs in seven databases to find DNA-binding proteins and their binding motifs that were involved in aberrant DNA methylation in breast cancer. A total of 42,850 differentially methylated regions (DMRs) that include 77,298 CpG sites were detected in breast cancer. One hundred eight DNA motifs were found to be enriched in DMRs, and 109 genes encoding proteins binding to these motifs were determined. Based on these motifs and genes, 63 methylation modulator genes were identified to regulate differentially methylated CpG sites in breast cancer. A network of these 63 modulator genes and 645 transcription factors was constructed, and 20 network modules were determined. A number of pathways and gene sets related to breast cancer were found to be enriched in these network modules. The 63 methylation modulator genes identified may play an important role in aberrant methylation of CpG sites in breast cancer. They may help to understand site-specific dysregulation of DNA methylation and provide epigenetic markers for breast cancer.</p

Selected examples of the detected SREs.

<p># Occ. is abbreviation for number of occurrences.</p

Real-World Efficiency of Pharmacogenetic Screening for Carbamazepine-Induced Severe Cutaneous Adverse Reactions

<div><p>Objectives</p><p>We evaluated the cost and efficiency of routine HLA-B*15∶02 screening to prevent carbamazepine-induced Stevens-Johnson syndrome and toxic epidermal necrolysis (CBZ-SJS/TEN) in Hong Kong.</p><p>Methods</p><p>Data were extracted from patients who commenced CBZ as the first-ever AED treatment or tested for HLA-B*15∶02 allele in three years before policy implementation (pre-policy: 16 September 2005 to 15 September 2008) and three years after (post-policy: 16 September 2008 to 15 September 2011). Using published unit costs, we estimated the cost of screening by comparing the costs to prevent and treat CBZ-SJS/TEN. We compared the number of person-tests needed and the cost to prevent resultant death with cancer screening programs.</p><p>Results</p><p>The number of screening tests needed to prevent one case of CBZ-SJS/TEN was 442, and to prevent one resultant death was 1,474 to 8,840. The screening cost was $332 per person, of which 42$146,749 to prevent a case of CBZ-SJS/TEN, and $489,386–$2,934,986 to prevent a resultant death. The corresponding numbers of tests and costs for mammography and Pap smear to prevent death due to breast and cervical cancers were 7,150 and 7,000, and $614,900 and$273,000, respectively. Comparing to the SJS/TEN treatment cost, HLA-B*15∶02 screening would become cost saving if a point-of-care test of less than $37 was available.</p><p>Conclusions</p><p>HLA-B*15∶02 screening is as efficient as mammography and Pap smear in preventing death. Development of point-of-care testing will vastly improve efficiency.</p></div

Illustration of equation (12).

<p>Two possible SREs are considered in this example, one for SF1, and the other one for SF2. Four different conditions are shown. Binding of either SF can affect the probability of spliceosome assembly. The arrow connecting two SFs indicates the interaction between two SFs. The contribution to spliceosome assembly from SFs is represented by , and .</p

Illustration of Proposition 1.

<p>The dashed curve is for and the dashed lines with arrows define the region where or . The dash-dot curve is for and the dash-dot lines with arrows define the region where or . The solid lines define the decision region of described in Proposition 1.</p

Cost of HLA-B*15∶02 screening compared with mammography and Pap smear.

1<p>Upper-limit cost of HLA-B*15∶02 screening to prevent one death was estimated from overall SJS/TEN mortality rate at 5%, and 30% mortality rate was used for lower-limit.</p>2<p>Costs were converted from UK sterling to US dollars using the May 2004 exchange rate of £0.56 to $1.</p>†<p>Excluded costs of diagnostic screening, biopsy and all subsequent procedures if any abnormality was found.</p>#<p>Cost for an additional consultation was included based on the observed 98.6% non-same-day test turnaround rate.</p><p>SJS, Stevens-Johnson Syndrome; TEN, toxic epidermal necrolysis.</p

Five regions around ASEs used to extract SREs and the model inference framework.

<p>(<b>A</b>) All hexamers in the five regions around ASEs are considered as candidate SREs. UU (upstream/upstream) stands for the 5′ end of the upstream intron. UD (upstream/downstream) denotes the 3′ end of the upstream intron. DU and DD are defined in a similar way. EXON stands for the ASE region. (<b>B</b>) The inference framework for detecting active SREs and SRE pairs. RCV: refitted cross-validation; OLS: ordinary least squares regression.</p

Expression level of several splicing factors in 9 tissues.

<p>The expression levels are calculated from the RNA-Seq data <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054885#pone.0054885-Wang1" target="_blank">[1]</a> as reads per kilobases per million mapped reads (RPKM).</p

Number of person-tests of HLA-B*15∶02 screening compared to mammography and Pap smear.

1<p>Overall SJS/TEN mortality rate ranged from 5% to 30%.</p>2<p>Based on the recommended biennial screening for 20 years from aged 50 years and detection of one case per 715 persons screened over this period. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096990#pone.0096990-Warner1" target="_blank">[25]</a> Number excluded 20% non-compliance rate that was assumed in the original report.</p>3<p>Based on the recommended quinquennial screening for 35 years from aged 24 years and detection of one case per 1000 persons screened over this period. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096990#pone.0096990-Raffle1" target="_blank">[26]</a>.</p

Percentage of different types of SRE pairs.

<p>Two hundred and forty-one SRE pairs are detected in different or same regions. This figure shows breakdown of the SRE pairs in different regions.</p