Radiation Exposure in Pediatric Intensive Care Unit Patients: How Much Is Too Much?

We aimed to determine median cumulative radiation exposure in pediatric intensive care unit (PICU) patients, proportion of patients with high radiation exposure (above annual average radiation per person of 6.2 mSv), and determine risk factors for high exposure. This was a retrospective chart review of PICU patients up to 18 years of age admitted to a large community hospital over 2 years. Radiologic studies and radiation exposure were determined for each patient, and total hospital radiation exposure was classified as high (>6.2 mSv) or not (≤6.2 mSv). Median radiation exposure per patient was 0.2 mSv (interquartile range = 2.1) and 11.7% of patients received >6.2 mSv radiation during their hospitalization. Factors associated with high radiation exposure included admission for trauma or surgery, number of computed tomography scans, age, and PICU length of stay (all P < .0001). We concluded that subsets of PICU patients are at risk of high radiation exposure. Policies and protocols may help minimize radiation exposure among PICU patients.

Nutritional risk factors predict severe acute graft-versus-host disease and early mortality in pediatric allogeneic hematopoietic stem cell transplantation.

BACKGROUND: Malnutrition is a pro-inflammatory state, yet data on nutritional risk factors and development of acute graft-versus-host disease (aGVHD) are extremely limited. PROCEDURE: We conducted a retrospective cohort analysis of pediatric patients up to age 21 years who underwent allogeneic hematopoietic stem cell transplantation (HSCT) at the Children's Hospital of Philadelphia from January 2011 to September 2014 to determine whether malnutrition was associated with development of aGVHD and early mortality. We identified body mass index (BMI) percentile and serum albumin levels as potential markers of malnutrition and defined two composite nutritional risk variables as any of the following: albumin < 2.8 g/dl, weight loss ≥10% from baseline, and low BMI [<25th (NUT25) or <5th percentile (NUT5)]. Nutritional markers and GVHD grade were assessed at baseline, 30, 60, and 90 days post-HSCT, and patients were censored upon development of GVHD. RESULTS: BMI <25th or <5th percentile, NUT25, and NUT5 at the beginning of any 30-day period predicted a three- to fourfold risk of developing of severe (grade III-IV) aGVHD in the subsequent 30 days in models adjusted for age, sex, donor source, and degree of human leukocyte antigen matching. Mortality at day 100 was low, but NUT25 risk at baseline conferred an increased risk of death (7.9% vs. 1%, P = 0.035). CONCLUSIONS: Malnutrition is a targetable risk factor in pediatric HSCT; prospective trials are needed to investigate this relationship further and identify effective nutritional interventions.

Epigenetic deregulation of TCF21 inhibits metastasis suppressor KISS1 in metastatic melanoma.

Metastatic melanoma is a fatal disease due to the lack of successful therapies and biomarkers for early detection and its incidence has been increasing. Genetic studies have defined recurrent chromosomal aberrations, suggesting the location of either tumor suppressor genes or oncogenes. Transcription factor 21 (TCF21) belongs to the class A of the basic helix-loop-helix family with reported functions in early lung and kidney development as well as tumor suppressor function in the malignancies of the lung and head and neck. In this study, we combined quantitative DNA methylation analysis in patient biopsies and in their derived cell lines to demonstrate that TCF21 expression is downregulated in metastatic melanoma by promoter hypermethylation and TCF21 promoter DNA methylation is correlated with decreased survival in metastatic skin melanoma patients. In addition, the chromosomal location of TCF21 on 6q23-q24 coincides with the location of a postulated metastasis suppressor in melanoma. Functionally, TCF21 binds the promoter of the melanoma metastasis-suppressing gene, KiSS1, and enhances its gene expression through interaction with E12, a TCF3 isoform and with TCF12. Loss of TCF21 expression results in loss of KISS1 expression through loss of direct interaction of TCF21 at the KISS1 promoter. Finally, overexpression of TCF21 inhibits motility of C8161 melanoma cells. These data suggest that epigenetic downregulation of TCF21 is functionally involved in melanoma progression and that it may serve as a biomarker for aggressive tumor behavior.

Quantitative analysis of slurry sample by laser-induced breakdown spectroscopy.

Laser-induced breakdown spectroscopy (LIBS) has been employed for the analysis of slurry samples. Quantitative analysis of slurry samples is crucial and challenging. The problems associated with slurry samples include splashing, surface turbulence, and the difficulties of obtaining reproducible samples due to sedimentation. The LIBS analysis has achieved limited success due to inherent disadvantages when applied to slurry samples. In order to achieve improved measurement precision and accuracy, a spin-on-glass sampling method was evaluated. Five elements (Al, Ca, Fe, Ni, and Si) were examined in five slurry simulants containing varying amounts of each ion. Three calibration models were developed by using univariate calibration, multiple linear regression, and partial least square regression. LIBS analysis results obtained from the partial least square regression model were determined to be the best fit to results obtained from inductively coupled plasma optical emission spectroscopy analysis.

Epigenetic regulation of beta2-adrenergic receptor expression in T(H)1 and T(H)2 cells.

We showed previously that murine naive CD4(+) T cells and T(H)1 cell clones express the beta2-adrenergic receptor (ß(2)AR), while T(H)2 cell clones do not. We report here that naive CD4(+) T cells that differentiated for 1-5 days under T(H)1 driving conditions increased ß(2)AR gene expression, while cells cultured under T(H)2 driving conditions decrease ß(2)AR gene expression. Chromatin immunoprecipitation revealed that the increase in ß(2)AR gene expression in T(H)1 cells is mediated by an increase in histone 3 (H3) and H4 acetylation, as well as an increase in histone 3 lysine 4 (H3K4) methylation. Conversely, the decrease in ß(2)AR gene expression in T(H)2 cells is mediated by a decrease in H3 and H4 acetylation and a decrease in H3K4 methylation, as well as an increase H3K9 and H3K27 methylation. The histone changes could be detected as early as 3 days of differentiating conditions. Genomic bisulfite sequencing showed that the level of methylated CpG dinucleotides within the promoter of the ß(2)AR gene was increased in T(H)2 cells as compared to naive and T(H)1 cells. Collectively, these results suggest that epigenetic mechanisms mediate maintenance and repression, respectively, of the ß(2)AR gene expression in T(H)1- and T(H)2-driven cells, providing a potential mechanism by which the level of ß(2)AR expression might be modulated pharmacologically within immune cells and other cell types in which the expression profile may change during a disease process.

Restriction landmark genomic scanning (RLGS) spot identification by second generation virtual RLGS in multiple genomes with multiple enzyme combinations.

BACKGROUND: Restriction landmark genomic scanning (RLGS) is one of the most successfully applied methods for the identification of aberrant CpG island hypermethylation in cancer, as well as the identification of tissue specific methylation of CpG islands. However, a limitation to the utility of this method has been the ability to assign specific genomic sequences to RLGS spots, a process commonly referred to as "RLGS spot cloning." RESULTS: We report the development of a virtual RLGS method (vRLGS) that allows for RLGS spot identification in any sequenced genome and with any enzyme combination. We report significant improvements in predicting DNA fragment migration patterns by incorporating sequence information into the migration models, and demonstrate a median Euclidian distance between actual and predicted spot migration of 0.18 centimeters for the most complex human RLGS pattern. We report the confirmed identification of 795 human and 530 mouse RLGS spots for the most commonly used enzyme combinations. We also developed a method to filter the virtual spots to reduce the number of extra spots seen on a virtual profile for both the mouse and human genomes. We demonstrate use of this filter to simplify spot cloning and to assist in the identification of spots exhibiting tissue-specific methylation. CONCLUSION: The new vRLGS system reported here is highly robust for the identification of novel RLGS spots. The migration models developed are not specific to the genome being studied or the enzyme combination being used, making this tool broadly applicable. The identification of hundreds of mouse and human RLGS spot loci confirms the strong bias of RLGS studies to focus on CpG islands and provides a valuable resource to rapidly study their methylation.

Unraveling the epigenetic code of cancer for therapy.

Alterations in the genome and the epigenome are common in most cancers. Changes in epigenetic signatures, including aberrant DNA methylation and histone deacetylation, are among the most prevalent modifications in cancer and lead to dramatic changes in gene expression patterns. Because DNA methylation and histone deacetylation are reversible processes, they have become attractive as targets for cancer epigenetic therapy, both as single agents and as 'enhancing' agents for other treatment strategies. In this review we discuss our current view of the mammalian epigenome, this view has changed over the years because of the availability of novel technologies. We further demonstrate how the profound understanding of epigenetic alterations in cancer will help develop novel strategies for epigenetic therapies.

Tumor suppressor activity of CCAAT/enhancer binding protein alpha is epigenetically down-regulated in head and neck squamous cell carcinoma.

Tumor suppressor CCAAT enhancer binding protein alpha (C/EBPalpha) is a transcription factor involved in cell cycle control and cellular differentiation. In a recent study, microarray expression profiling on head and neck squamous cell carcinoma (HNSCC) samples identified significant C/EBPalpha down-regulation, correlating with poor prognosis. However, the mechanisms of C/EBPalpha down-regulation remained elusive. C/EBPalpha has been previously found to provide an antiproliferative role in lung cancer, and our laboratory showed that its down-regulation involves epigenetic mechanisms. This prompted us to investigate the involvement of epigenetics in down-regulating C/EBPalpha in HNSCC. Here, we show that C/EBPalpha is down-regulated in HNSCC by loss of heterozygosity and DNA methylation, but not by gene mutation. We found a consistently methylated upstream regulatory region (-1,399 bp to -1,253 bp in relation to the transcription start site) in 68% of the HNSCC tumor samples, and DNA demethylation using 5-aza-2'-deoxycytidine treatment was able to significantly restore C/EBPalpha mRNA expression in the HNSCC cell lines we tested. In addition, C/EBPalpha overexpression in a HNSCC cell line (SCC22B) revealed its ability to provide tumor suppressor activity in HNSCC in vitro and in vivo. In conclusion, we showed for the first time not only that C/EBPalpha has tumor suppressor activity in HNSCC, but also that it is down-regulated by DNA promoter methylation.

Diverse histone modifications on histone 3 lysine 9 and their relation to DNA methylation in specifying gene silencing.

BACKGROUND: Previous studies of individual genes have shown that in a self-enforcing way, dimethylation at histone 3 lysine 9 (dimethyl-H3K9) and DNA methylation cooperate to maintain a repressive mode of inactive genes. Less clear is whether this cooperation is generalized in mammalian genomes, such as mouse genome. Here we use epigenomic tools to simultaneously interrogate chromatin modifications and DNA methylation in a mouse leukemia cell line, L1210. RESULTS: Histone modifications on H3K9 and DNA methylation in L1210 were profiled by both global CpG island array and custom mouse promoter array analysis. We used chromatin immunoprecipitation microarray (ChIP-chip) to examine acetyl-H3K9 and dimethyl-H3K9. We found that the relative level of acetyl-H3K9 at different chromatin positions has a wider range of distribution than that of dimethyl-H3K9. We then used differential methylation hybridization (DMH) and the restriction landmark genome scanning (RLGS) to analyze the DNA methylation status of the same targets investigated by ChIP-chip. The results of epigenomic profiling, which have been independently confirmed for individual loci, show an inverse relationship between DNA methylation and histone acetylation in regulating gene silencing. In contrast to the previous notion, dimethyl-H3K9 seems to be less distinct in specifying silencing for the genes tested. CONCLUSION: This study demonstrates in L1210 leukemia cells a diverse relationship between histone modifications and DNA methylation in the maintenance of gene silencing. Acetyl-H3K9 shows an inverse relationship between DNA methylation and histone acetylation in regulating gene silencing as expected. However, dimethyl-H3K9 seems to be less distinct in relation to promoter methylation. Meanwhile, a combination of epigenomic tools is of help in understanding the heterogeneity of epigenetic regulation, which may further our vision accumulated from single-gene studies.

20q11.1 amplification in giant-cell tumor of bone: Array CGH, FISH, and association with outcome.

The goal of this study was to identify recurrent regions of genomic gain or loss in giant-cell tumor of bone (GCTb). Array comparative genomic hybridization (aCGH) was performed for 20 frozen tumor samples of GCTb. A separate subset of 59 GCTb with outcome data was used for validation. The most frequent region of change identified by aCGH was gain of a 1-Mbp region at 20q11.1. In the validation arm of 59 cases the minimal common region of copy number gain at 20q11.1, seen in 54% of the samples, was BAC clone RP11-4O9, which contained the genes TPX2 and BCL2L1. For most cases, amplification was restricted to the mononuclear component and was not present in the multinucleated giant cells. Southern blot for TPX2 and BCL2L1 identified the former as the gene with the highest level of amplification for these two proposed candidate genes of importance. Immunohistochemistry for TPX2 expression correlated with amplification, while BCL2L1 expression was not identified. Kaplan-Meier curves for progression-free survival showed a statistically significant difference for cases with 20q11.1 amplification (P = 0.0001). Univariate analysis involving Cox proportional hazards models did not show a significant difference for initial treatment type (curettage versus resection) (P = 0.575), age (50) (P = 0.543), or sex (P = 0.268), but did correlate with 20q11.1 amplification (P = 0.001). By multivariate analysis, it was found that 20q11.1 amplification (P = 0.001) was the only factor to reach statistical significance. 20q11.1 amplification can be used as a marker of prognostic importance in GCTb. We propose TPX2 as a candidate oncogene in the core-amplified region at 20q11.1.

ChIP-chip comes of age for genome-wide functional analysis.

In the post-genome era, attention has focused on the functions of genome sequences and how they are regulated. The emerging epigenomic changes and the interactions between cis-acting elements and protein factors may play a central role in gene regulation. To understand the crosstalk between DNA and protein on a genome-wide scale, one emerging technique, called ChIP-chip, takes the strategy of combining chromatin immunoprecipitation with microarray. This new high-throughput strategy helps screen the targets of critical transcription factors and profile the genome-wide distribution of histone modifications, which will enable the feasibility of conducting a large-scale study, such as the Human Epigenome Project.

Combinatorial analysis of transcription factor partners reveals recruitment of c-MYC to estrogen receptor-alpha responsive promoters.

In breast cancer and normal estrogen target tissues, estrogen receptor-alpha (ERalpha) signaling results in the establishment of spatiotemporal patterns of gene expression. Whereas primary target gene regulation by ERalpha involves recruitment of coregulatory proteins, coactivators, or corepressors, activation of these downstream promoters by receptor signaling may also involve partnership of ERalpha with other transcription factors. By using an integrated, genome-wide approach that involves ChIP-chip and computational modeling, we uncovered 13 ERalpha-responsive promoters containing both ERalpha and c-MYC binding elements located within close proximity (13-214 bp) to each other. Estrogen stimulation enhanced the c-MYC-ERalpha interaction and facilitated the association of ERalpha, c-MYC, and the coactivator TRRAP with these estrogen-responsive promoters, resulting in chromatin remodeling and increased transcription. These results suggest that ERalpha and c-MYC physically interact to stabilize the ERalpha-coactivator complex, thereby permitting other signal transduction pathways to fine-tune estrogen-mediated signaling networks.

Epigenetic regulation of the tumor suppressor gene TCF21 on 6q23-q24 in lung and head and neck cancer.

The identification of tumor suppressor genes has classically depended on their localization within recurrent regions of loss of heterozygosity. According to Knudson's two-hit hypothesis, the remaining allele is lost, either genetically or, more recently identified, through epigenetic events. To date, retrospective analyses have determined promoter methylation as a common alternative alteration in cancer cells to silence cancer-related genes. Here we report an application of restriction landmark genomic scanning that allows for DNA methylation profiling along a region of recurrent loss of heterozygosity at chromosome 6q23-q24. This approach resulted in the identification of a tumor suppressor gene, TCF21, which is frequently lost in human malignancies. We demonstrate that TCF21 is expressed in normal lung airway epithelial cells and aberrantly methylated and silenced in the majority of head and neck squamous cell carcinomas and non-small-cell lung cancers analyzed. TCF21 is known to regulate mesenchymal cell transition into epithelial cells, a property that has been shown to be deficient in carcinomas. We further demonstrate that exogenous expression of TCF21 in cells that have silenced the endogenous TCF21 locus resulted in a reduction of tumor properties in vitro and in vivo.

Global assessment of promoter methylation in a mouse model of cancer identifies ID4 as a putative tumor-suppressor gene in human leukemia.

DNA methylation is associated with malignant transformation, but limitations imposed by genetic variability, tumor heterogeneity, availability of paired normal tissues and methodologies for global assessment of DNA methylation have limited progress in understanding the extent of epigenetic events in the initiation and progression of human cancer and in identifying genes that undergo methylation during cancer. We developed a mouse model of T/natural killer acute lymphoblastic leukemia that is always preceded by polyclonal lymphocyte expansion to determine how aberrant promoter DNA methylation and consequent gene silencing might be contributing to leukemic transformation. We used restriction landmark genomic scanning with this mouse model of preleukemia reproducibly progressing to leukemia to show that specific genomic methylation is associated with only the leukemic phase and is not random. We also identified Idb4 as a putative tumor-suppressor gene that is methylated in most mouse and human leukemias but in only a minority of other human cancers.

Direct observation of the luminescence from the (3)deltadelta excited state of Re(2)Cl(2)(p-OCH(3)form)(4).

There are only a few reports on the measurement of the energy of the low-lying (3)deltadelta state of quadruply bonded bimetallic complexes, and the direct observation of the (1)deltadelta excited electronic state was only recently reported. In the quadruply bonded bimetallic complexes reported to date, luminescence arises from their (1)deltadelta excited state, and the (3)deltadelta state is nonemissive. Here we report the luminescence of Re(2)Cl(2)(p-OCH(3)form)(4) [p-OCH(3)form = (p-CH(3)OC(6)H(4))NCHN(p-CH(3)OC(6)H(4))(-)] observed upon 400-460 nm excitation with maxima at 820 nm (CH(2)Cl(2), tau = 1.4 micros) and 825 nm (CH(3)CN, tau = 1.3 micros) at 298 K. From the large Stokes shift, the vibronic progression at 77 K, the quenching by O(2), the long lifetime, and the calculated energy of the (3)deltadelta state, the luminescence of Re(2)Cl(2)(p-OCH(3)form)(4) and the corresponding transient absorption signal are assigned as arising from the (3)deltadelta ((3)A(2u)) excited state of the complex.

An AscI boundary library for the studies of genetic and epigenetic alterations in CpG islands.

Knudson's two-hit hypothesis postulates that genetic alterations in both alleles are required for the inactivation of tumor-suppressor genes. Genetic alterations include small or large deletions and mutations. Over the past years, it has become clear that epigenetic alterations such as DNA methylation are additional mechanisms for gene silencing. Restriction Landmark Genomic Scanning (RLGS) is a two-dimensional gel electrophoresis that assesses the methylation status of thousands of CpG islands. RLGS has been applied successfully to scan cancer genomes for aberrant DNA methylation patterns. So far, the majority of this work was done using NotI as the restriction landmark site. Here, we describe the development of RLGS using AscI as the restriction landmark site for genome-wide scans of cancer genomes. The availability of AscI as a restriction landmark for RLGS allows for scanning almost twice as many CpG islands in the human genome compared with using NotI only. We describe the development of an AscI-EcoRV boundary library that supports the cloning of novel methylated genes. Feasibility of this system is shown in three tumor types, medulloblastomas, lung cancers, and head and neck cancers. We report the cloning of 178 AscI RLGS fragments via two methods by use of this library.

Regulation of DNA methylation of Rasgrf1.

In mammals, DNA is methylated at cytosines within CpG dinucleotides. Properly regulated methylation is crucial for normal development. Inappropriate methylation may contribute to tumorigenesis by silencing tumor-suppressor genes or by activating growth-stimulating genes. Although many genes have been identified that acquire methylation and whose expression is methylation-sensitive, little is known about how DNA methylation is controlled. We have identified a DNA sequence that regulates establishment of DNA methylation in the male germ line at Rasgrf1. In mice, the imprinted Rasgrf1 locus is methylated on the paternal allele within a differentially methylated domain (DMD) 30 kbp 5' of the promoter. Expression is exclusively from the paternal allele in neonatal brain. Methylation is regulated by a repeated sequence, consisting of a 41-mer repeated 40 times, found immediately 3' of the DMD. This sequence is present in organisms in which Rasgrf1 is imprinted. In addition, DMD methylation is required for imprinted Rasgrf1 expression. Together the DMD and repeat element constitute a binary switch that regulates imprinting at the locus.

Preparation and Structure of Two Ditungsten Compounds Synthesized with the 3,5-Dichlorophenylformamidinate Ligand.

The structure, preparation, and spectroscopy of a W(2)(II, II) paddlewheel complex with four formamidinate ligands is reported. Upon exposure to air and moisture in solution, the W(2)(II, II) core undergoes an oxidative addition reaction to form a W(2)(III, III) edge-sharing bioctahedral (ESBO) complex with two bridging hydroxides. The products, W(2)(&mgr;-DCPF)(4) (1) and W(2)(&mgr;-OH)(2)(&mgr;-DCPF)(2)(eta(2)-DCPF)(2) (2) where DCPF is [(3,5-Cl(2)C(6)H(3))NC(H)N(3,5-Cl(2)C(6)H(3))(-)], were characterized by UV-vis and (1)H NMR spectroscopy. Structural data are presented for W(2)(&mgr;-DCPF)(4) with four bridging formamidinate ligands and W(2)(&mgr;-OH)(2)(&mgr;-DCPF)(2)(eta(2)-DCPF)(2) with the formamidinate ligands in both chelating and bridging positions. Crystallographic data for W(2)(&mgr;-DCPF)(4) (1) and W(2)(&mgr;-OH)(2)(&mgr;-DCPF)(2)(eta(2)-DCPF)(2) (2) are as follows: (1), C(68)H(60)Cl(16)N(8)O(4)W(2), a = 12.6906(3) Å, b = 12.7818(4) Å, c = 13.0450(3) Å, alpha = 109.173(1) degrees, beta = 93.865(1) degrees, gamma = 103.746(1) degrees, triclinic, P&onemacr; (No. 2), and Z = 1 and (2), C(59)H(35)Cl(16)N(8)O(2)W(2), a = 17.1524(1) Å, b = 20.6568(3) Å, c = 19.3959(3) Å, beta = 102.791(1) degrees, monoclinic, C2/c (No. 15), and Z = 4.