A fatal case of Degos' disease which presented with recurrent intestinal perforation

Degos’ disease,otherwise known as "malignant atrophic papulosis" is a rare vasculopathy with an unknown etiology characterized by typical cutaneous lesions.Involvement of the gastrointestinal(GI) tract is observed in approximately half of patients and small infarctions in the mucosa can cause perforation and resulting peritonitis,the leading cause of death.We present a fatal case of Degos’ disease with skin and GI involvement,manifesting as recurrent intestinal perforations and peritonitis,in a 15-year-old Iranian boy.     

A comprehensive assay for targeted multiplex amplification of human DNA sequences

We developed a robust and reproducible methodology to amplify human sequences in parallel for use in downstream multiplexed sequence analyses. We call the methodology SMART (Spacer Multiplex Amplification Reaction), and it is based, in part, on padlock probe technology. As a proof of principle, we used SMART technology to simultaneously amplify 485 human exons ranging from 100 to 500 bp from human genomic DNA. In multiple repetitions, >90% of the targets were successfully amplified with a high degree of uniformity, with 70% of targets falling within a 10-fold range and all products falling within a 100-fold range of each other in abundance. We used long padlock probes (LPPs) >300 bases in length for the assay, and the increased length of these probes allowed for the capture of human sequences up to 500 bp in length, which is optimal for capturing most human exons. To engineer the LPPs, we developed a method that generates ssDNA molecules with precise ends, using an appropriately designed dsDNA template. The template has appropriate restriction sites engineered into it that can be digested to generate nucleotide overhangs that are suitable for lambda exonuclease digestion, producing a single-stranded probe from dsDNA. The SMART technology is flexible and can be easily adapted to multiplex tens of thousands of target sequences in a single reaction.     

Ag-bearing liposomes engrafted with peptides that interact with CD11c/CD18 induce potent Ag-specific and antitumor immunity

Dendritic cells (DCs) play key role in eliciting antigen (Ag)-specific immune responses, and crucial to this is the uptake of Ag via surface receptors including the heterodimeric integrin CD11c/CD18. Here we report that CD11c/CD18-interacting peptides can be used as targeting moieties to deliver liposomal Ag to antigen presenting cells (APCs) and elicit Ag-specific and antitumor immunity. Two peptides of sequence related to human ICAM-4 and previously reported to bind CD11c/CD18, and a 12-mer cyclic peptide previously identified by phage display to bind CD11c/CD18, were produced synthetically, and tested for their ability to target liposomal Ag. The three peptides were designed to contain a shorter spacer to reduce steric hindrance, and a His-tag to enable engraftment onto liposomes incorporated with chelator lipid. Our results show that the three peptides, denoted as p17, p18 and p30, promote strong binding of liposomes to CD11c(+) and CD11b(+) cells in vitro and in vivo. Vaccination of mice with Ag-bearing liposomes engrafted with the peptides, particularly p18 and p30, induced Ag-specific T cell priming and antibody production. Importantly, the vaccination of C57BL/6 mice with syngeneic B16-OVA-derived plasma membrane vesicles (PMVs) engrafted with p18 and p30 peptide showed dramatic antitumor responses, inhibiting tumor growth/metastasis in both the lung and subcutaneous tumor models, with a high proportion of the mice apparently being "cured" of their tumors. The engraftment of p18 and p30 peptides onto liposomes and PMVs, thus provides an effective means to target Ags to DCs in vivo, for the development of effective cancer vaccines and immunotherapies.     

Calycopterin, an immunoinhibitory compound from the extract of Dracocephalum kotschyi

Medicinal plants have been widely investigated for their various effects. Dracocephalum kotschyi Boiss (Labiatae) is used in Iranian traditional medicine for the treatment of rheumatoid diseases. The inhibitory effect of D. kotschyi on the lectin-induced cellular immune response has been demonstrated previously. In this study, mitogen-treated lymphocytes were exposed to the extract of D. kotschyi and analysed for the induction of apoptosis using flow cytometry and gel electrophoresis. The data obtained indicated a dose-dependent increase of cells in the sub-G1 phase of cell cycle. Study of internucleosomal DNA fragmentation showed a typical DNA laddering in agarose gels. A bioactivity-guided fractionation assay to find the active components responsible for the inhibitory effect of D. kotschyi on mitogen-induced lymphocyte proliferation led to the isolation of calycopterin from the ethyl acetate extract of D. kotschyi. Its structure was identified by spectroscopic methods including( 1)H-NMR, (13)C-NMR, MS and UV spectra. Calycopterin inhibited lymphocyte proliferation in a dose-dependent manner with an IC(50) value of 1.7 microg/mL. In conclusion, the results of this study suggest that D. kotschyi extract has the capacity to induce apoptosis in the lymphocytes and that isolated calycopterin is responsible for the inhibitory effect of D. kotschyi on lymphocyte proliferation.     

High-throughput method for analyzing methylation of CpGs in targeted genomic regions

A unique microarray-based method for determining the extent of DNA methylation has been developed. It relies on a selective enrichment of the regions to be assayed by target amplification by capture and ligation (mTACL). The assay is quantitatively accurate, relatively precise, and lends itself to high-throughput determination using nanogram amounts of DNA. The measurements using mTACLs are highly reproducible and in excellent agreement with those obtained by sequencing (r = 0.94). In the present work, the methylation status of >145,000 CpGs from 5,472 promoters in 221 samples was measured. The methylation levels of nearby CpGs are correlated, but the correlation falls off dramatically over several hundred base pairs. In some instances, nearby CpGs have very different levels of methylation. Comparison of normal and tumor samples indicates that in tumors, the promoter regions of genes involved in differentiation and signaling are preferentially hypermethylated, whereas those of housekeeping genes remain hypomethylated. mTACL is a platform for profiling the state of methylation of a large number of CpG in many samples in a cost-effective fashion, and is capable of scaling to much larger numbers of CpGs than those collected here.     

Mismatch repair detection (MRD): high-throughput scanning for DNA variations

Although there are several methods for genotyping previously identified single nucleotide polymorphisms (SNPs), there is a paucity of approaches for high-throughput scanning for unknown variations. Mismatch repair detection (MRD) utilizes a bacterial mismatch repair system in vivo to detect sequence variants in human DNA samples. We describe modifications in MRD that allow a high degree of parallel processing, and use this modified version to accurately scan for variations in 35 different human DNA fragments simultaneously. MRD's potential for high-throughput scanning can be used to identify new SNPs and to comprehensively compare sequences between patients and controls for identifying disease susceptibility alleles.     

Rapid identification of somatic mutations in colorectal and breast cancer tissues using mismatch repair detection (MRD)

Mismatch repair detection (MRD) was used to screen 93 matched tumor-normal sample pairs and 22 cell lines for somatic mutations in 30 cancer relevant genes. Using a starting amount of only 150 ng of genomic DNA, we screened 102 kb of sequence for somatic mutations in colon and breast cancer. A total of 152 somatic mutations were discovered, encompassing previously reported mutations, such as BRAF V600E and KRAS G12S, G12V, and G13D, as well as novel mutations, including some in genes in which somatic mutations have not previously been reported, such as MAP2K1 and MAP2K2. The distribution of mutations ranged widely within and across tumor types. The functional significance of many of these mutations is not understood, with patterns of selection only evident in KRAS and BRAF in colon cancer. These results present a novel approach to high-throughput mutation screening using small amounts of starting material and reveal a mutation spectrum across 30 genes in a large cohort of breast and colorectal cancers.     

Liposomal Ag engrafted with peptides of sequence derived from HMGB1 induce potent Ag-specific and anti-tumour immunity

High-mobility group box 1 (HMGB1) protein is a nuclear binding protein which is released by monocytes and macrophages and is a potent maturation signal for dendritic cells (DCs). Synthetic HMGB1-related peptides are reported to be potent DC stimulants. Two HMGB1-related peptides, denoted as pHMGB-89 and pHMGB-106, were explored for their ability to enhance the immunogenicity of Ag-containing liposomes. pHMGB-engrafted liposomes targeted murine CD11c⁺ and CD11b⁺ cells in vitro and in vivo. Vaccination of mice with OVA-containing liposomes engrafted with pHMGB-89 and pHMGB-106 induced OVA-specific T cell priming and production of IgG₁, IgG_2a and IgG_2b antibodies. Importantly, vaccination of mice with B16-OVA-derived plasma membrane vesicles (PMVs) engrafted with pHMGB-89 and pHMGB-106 inhibited tumour growth and metastasis, in syngeneic mice challenged with highly metastatic B16-OVA melanoma. The results show that vaccination with Ag-containing liposomes/PMVs engrafted with HMGB1 peptides could be an effective approach for developing novel vaccines and cancer immunotherapies.