Increased incidence of neonatal respiratory distress in infants with mucopolysaccharidosis type II (MPS II, Hunter syndrome).

Records were reviewed on all patients with mucopolysaccharidosis type II (Hunter syndrome) seen at a single institution from 1999 to 2013 to identify those with a history of neonatal intensive care. Eleven of 34 patients were in a neonatal intensive care unit and all had respiratory distress with 8 diagnoses of respiratory distress syndrome and 3 of transient tachypnea of the newborn. None of the infants were premature; four were delivered by cesarean section. These findings suggest that respiratory distress is more commonly observed in neonates with MPS II than in the general population. This may reflect airway disease already present in this disorder at the time of birth.

High dose genistein aglycone therapy is safe in patients with mucopolysaccharidoses involving the central nervous system.

Genistein (4,5,7-trihydroexyisoflavone), a soy derived isoflavone, has been proposed as a substrate reduction therapy in patients with mucopolysaccharidoses (MPS) disorders with central nervous system involvement based on studies in cultured fibroblasts demonstrating that this agent inhibits glycosaminoglycan synthesis. Several studies have reported treatment of MPS III patients with low dose genistein (5-15mg/kg/day) with no serious adverse effects and variable neurocognitive outcomes. Mice with MPS IIIB treated with high dose (160mg/kg/day) genistein exhibited a significant decrease in heparan sulfate accumulation and neuroinflammation in the brain and improvement of the behavioral phenotype. No study to date has been performed using high dose genistein treatment in MPS patients. We initiated an open label study to assess the safety of high dose genistein treatment in MPS patients with neurological impairment. Twenty-two eligible patients were treated at least 12months with pure synthetic genistein at a dose of 150mg/kg/day. Safety labs, urine GAG levels, clinical status and history of adverse events were obtained every 3months and physical examination was performed by single examiner at least every 12months. While neurocognitive level was not a primary endpoint, participants were asked to obtain annual neurocognitive testing if available and a 9 point disability scale (FPSS) was recorded at each study visit. In the course of 12months of treatment, we observed no serious adverse events that were unexplained by the underlying condition and no severe adverse events that were felt to be potentially related to the genistein therapy. Two male subjects developed Tanner II breast development not present at baseline which could be related to the mild estrogenic effects of genistein. We observed no consistent decline in urine GAG levels; however, urinary GAG excretion was erratic. After 12months, the FPSS remained unchanged in 16 patients and declined by 1 point in 2 patients. Based on the results obtained so far, high dose oral genistein therapy appears to be safe in MPS patients and additional testing in a larger randomized placebo controlled trial is needed to further assess safety and efficacy.

A genome-wide study of cytogenetic changes in colorectal cancer using SNP microarrays: opportunities for future personalized treatment.

In colorectal cancer (CRC), chromosomal instability (CIN) is typically studied using comparative-genomic hybridization (CGH) arrays. We studied paired (tumor and surrounding healthy) fresh frozen tissue from 86 CRC patients using Illumina's Infinium-based SNP array. This method allowed us to study CIN in CRC, with simultaneous analysis of copy number (CN) and B-allele frequency (BAF)--a representation of allelic composition. These data helped us to detect mono-allelic and bi-allelic amplifications/deletion, copy neutral loss of heterozygosity, and levels of mosaicism for mixed cell populations, some of which can not be assessed with other methods that do not measure BAF. We identified associations between CN abnormalities and different CRC phenotypes (histological diagnosis, location, tumor grade, stage, MSI and presence of lymph node metastasis). We showed commonalities between regions of CN change observed in CRC and the regions reported in previous studies of other solid cancers (e.g. amplifications of 20q, 13q, 8q, 5p and deletions of 18q, 17p and 8p). From Therapeutic Target Database, we identified relevant drugs, targeted to the genes located in these regions with CN changes, approved or in trials for other cancers and common diseases. These drugs may be considered for future therapeutic trials in CRC, based on personalized cytogenetic diagnosis. We also found many regions, harboring genes, which are not currently targeted by any relevant drugs that may be considered for future drug discovery studies. Our study shows the application of high density SNP arrays for cytogenetic study in CRC and its potential utility for personalized treatment.

Interpretation of genome-wide infinium methylation data from ligated DNA in formalin-fixed, paraffin-embedded paired tumor and normal tissue.

BACKGROUND: Formalin-fixed, paraffin-embedded (FFPE) samples are a highly desirable resource for epigenetic studies, but there is no suitable platform to assay genome-wide methylation in these widely available resources. Recently, Thirlwell et al. (2010) have reported a modified ligation-based DNA repair protocol to prepare FFPE DNA for the Infinium methylation assay. In this study, we have tested the accuracy of methylation data obtained with this modification by comparing paired fresh-frozen (FF) and FFPE colon tissue (normal and tumor) from colorectal cancer patients. We report locus-specific correlation and concordance of tumor-specific differentially methylated loci (DML), both of which were not previously assessed. METHODS: We used Illumina's Infinium Methylation 27K chip for 12 pairs of FF and 12 pairs of FFPE tissue from tumor and surrounding healthy tissue from the resected colon of the same individual, after repairing the FFPE DNA using Thirlwell's modified protocol. RESULTS: For both tumor and normal tissue, overall correlation of ß values between all loci in paired FF and FFPE was comparable to previous studies. Tissue storage type (FF or FFPE) was found to be the most significant source of variation rather than tissue type (normal or tumor). We found a large number of DML between FF and FFPE DNA. Using ANOVA, we also identified DML in tumor compared to normal tissue in both FF and FFPE samples, and out of the top 50 loci in both groups only 7 were common, indicating poor concordance. Likewise, while looking at the correlation of individual loci between FFPE and FF across the patients, less than 10% of loci showed strong correlation (r ≥ 0.6). Finally, we checked the effect of the ligation-based modification on the Infinium chemistry for SNP genotyping on an independent set of samples, which also showed poor performance. CONCLUSION: Ligation of FFPE DNA prior to the Infinium genome-wide methylation assay may detect a reasonable number of loci, but the numbers of detected loci are much fewer than in FF samples. More importantly, the concordance of DML detected between FF and FFPE DNA is suboptimal, and DML from FFPE tissues should be interpreted with great caution.

A genome-wide DNA methylation study in colorectal carcinoma.

BACKGROUND: We performed a genome-wide scan of 27,578 CpG loci covering 14,475 genes to identify differentially methylated loci (DML) in colorectal carcinoma (CRC). METHODS: We used Illumina's Infinium methylation assay in paired DNA samples extracted from 24 fresh frozen CRC tissues and their corresponding normal colon tissues from 24 consecutive diagnosed patients at a tertiary medical center. RESULTS: We found a total of 627 DML in CRC covering 513 genes, of which 535 are novel DML covering 465 genes. We also validated the Illumina Infinium methylation data for top-ranking genes by non-bisulfite conversion q-PCR-based methyl profiler assay in a subset of the same samples. We also carried out integration of genome-wide copy number and expression microarray along with methylation profiling to see the functional effect of methylation. Gene Set Enrichment Analysis (GSEA) showed that among the major "gene sets" that are hypermethylated in CRC are the sets: "inhibition of adenylate cyclase activity by G-protein signaling", "Rac guanyl-nucleotide exchange factor activity", "regulation of retinoic acid receptor signaling pathway" and "estrogen receptor activity". Two-level nested cross validation showed that DML-based predictive models may offer reasonable sensitivity (around 89%), specificity (around 95%), positive predictive value (around 95%) and negative predictive value (around 89%), suggesting that these markers may have potential clinical application. CONCLUSION: Our genome-wide methylation study in CRC clearly supports most of the previous findings; additionally we found a large number of novel DML in CRC tissue. If confirmed in future studies, these findings may lead to identification of genomic markers for potential clinical application.