Bacterial Feature Finder (BaFF)-a system for extracting features overrepresented in sets of prokaryotic organisms.

MOTIVATION: The results of some experimental and computational techniques are given in terms of large sets of organisms, especially prokaryotic. While their distinctive features can provide useful data regarding specific phenomenon, there are no automated tools for extracting them. RESULTS: We present here the Bacterial Feature Finder web server, a tool to automatically interrogate sets of prokaryotic organisms provided by the user to evaluate their specific biological features. At the core of the system is a searchable database of qualitative and quantitative features compiled for more than 23 000 prokaryotic organisms. Both the input set of organisms and the background set used to calculate the enriched features can be directly provided by the user, or they can be obtained by searching the database. The results are presented via an interactive graphical interface, with links to external resources. AVAILABILITY AND IMPLEMENTATION: The web server is freely available at http://csbg.cnb.csic.es/BaFF. It has been tested in the main web browsers and does not require any especial plug-ins or additional software. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Risk of solid subsequent malignant neoplasms after childhood Hodgkin lymphoma-Identification of high-risk populations to guide surveillance: A report from the Late Effects Study Group.

BACKGROUND: Survivors of Hodgkin lymphoma (HL) in childhood have an increased risk of subsequent malignant neoplasms (SMNs). Herein, the authors extended the follow-up of a previously reported Late Effects Study Group cohort and identified patients at highest risk for SMNs to create evidence for risk-based screening recommendations. METHODS: The standardized incidence ratio was calculated using rates from the Surveillance, Epidemiology, and End Results program as a reference. The risk of SMN was estimated using proportional subdistribution hazards regression. The cohort included 1136 patients who were diagnosed with HL before age 17 years between 1955 and 1986. The median length of follow-up was 26.6 years. RESULTS: In 162 patients, a total of 196 solid SMNs (sSMNs) were identified. Compared with the general population, the cohort was found to be at a 14-fold increased risk of developing an sSMN (95% confidence interval, 12.0-fold to 16.3-fold). The cumulative incidence of any sSMN was 26.4% at 40 years after a diagnosis of HL. Risk factors for breast cancer among females were an HL diagnosis between ages 10 years and 16 years and receipt of chest radiotherapy. Males treated with chest radiotherapy at age <10 years were found to be at highest risk of developing lung cancer. Survivors of HL who were treated with abdominal/pelvic radiotherapy and high-dose alkylating agents were found to be at highest risk of developing colorectal cancer and females exposed to neck radiotherapy at age <10 years were at highest risk of thyroid cancer. By age 50 years, the cumulative incidence of breast, lung, colorectal, and thyroid cancer was 45.3%, 4.2%, 9.5%, and 17.3%, respectively, among those at highest risk. CONCLUSIONS: Survivors of childhood HL remain at an increased risk of developing sSMNs. In the current study, subgroups of survivors of HL at highest risk of specific sSMNs were identified, and evidence for screening provided.

Comparative proteomic profiling of dystroglycan-associated proteins in wild type, mdx, and Galgt2 transgenic mouse skeletal muscle.

Dystroglycan is a major cell surface glycoprotein receptor for the extracellular matrix in skeletal muscle. Defects in dystroglycan glycosylation cause muscular dystrophy and alterations in dystroglycan glycosylation can impact extracellular matrix binding. Here we describe an immunoprecipitation technique that allows isolation of beta dystroglycan with members of the dystrophin-associated protein complex (DAPC) from detergent-solubilized skeletal muscle. Immunoprecipitation, coupled with shotgun proteomics, has allowed us to identify new dystroglycan-associated proteins and define changed associations that occur within the DAPC in dystrophic skeletal muscles. In addition, we describe changes that result from overexpression of Galgt2, a normally synaptic muscle glycosyltransferase that can modify alpha dystroglycan and inhibit the development of muscular dystrophy when it is overexpressed. These studies identify new dystroglycan-associated proteins that may participate in dystroglycan's roles, both positive and negative, in muscular dystrophy.

Induction of a regenerative microenvironment in skeletal muscle is sufficient to induce embryonal rhabdomyosarcoma in p53-deficient mice.

We have previously reported that mice with muscular dystrophy, including mdx mice, develop embryonal rhabdomyosarcoma (eRMS) with a low incidence after 1 year of age and that almost all such tumours contain cancer-associated p53 mutations. To further demonstrate the relevance of p53 inactivation, we created p53-deficient mdx mice. Here we demonstrate that loss of one or both p53 (Trp53) alleles accelerates eRMS incidence in the mdx background, such that almost all Trp53(-/-) mdx animals develop eRMS by 5 months of age. To ascertain whether increased tumour incidence was due to the regenerative microenvironment found in dystrophic skeletal muscles, we induced muscle regeneration in Trp53(+/+) and Trp53(-/-) animals using cardiotoxin (Ctx). Wild-type (Trp53(+/+) ) animals treated with Ctx, either once every 7 days or once every 14 days from 1 month of age onwards, developed no eRMS; however, all similarly Ctx-treated Trp53(-/-) animals developed eRMS by 5 months of age at the site of injection. Most of these tumours displayed markers of human eRMS, including over-expression of Igf2 and phosphorylated Akt. These data demonstrate that the presence of a regenerative microenvironment in skeletal muscle, coupled with Trp53 deficiency, is sufficient to robustly induce eRMS in young mice. These studies further suggest that consideration should be given to the potential of the muscle microenvironment to support tumourigenesis in regenerative therapies for myopathies.

Mice lacking dystrophin or alpha sarcoglycan spontaneously develop embryonal rhabdomyosarcoma with cancer-associated p53 mutations and alternatively spliced or mutant Mdm2 transcripts.

Altered expression of proteins in the dystrophin-associated glycoprotein complex results in muscular dystrophy and has more recently been implicated in a number of forms of cancer. Here we show that loss of either of two members of this complex, dystrophin in mdx mice or alpha sarcoglycan in Sgca(-/-) mice, results in the spontaneous development of muscle-derived embryonal rhabdomyosarcoma (RMS) after 1 year of age. Many mdx and Sgca(-/-) tumors showed increased expression of insulin-like growth factor 2, retinoblastoma protein, and phosphorylated Akt and decreased expression of phosphatase and tensin homolog gene, much as is found in a human RMS. Further, all mdx and Sgca(-/-) RMS analyzed had increased expression of p53 and murine double minute (mdm)2 protein and contained missense p53 mutations previously identified in human cancers. The mdx RMS also contained missense mutations in Mdm2 or alternatively spliced Mdm2 transcripts that lacked an exon encoding a portion of the p53-binding domain. No Pax3:Fkhr or Pax7:Fkhr translocation mRNA products were evident in any tumor. Expression of natively glycosylated alpha dystroglycan and alpha sarcoglycan was reduced in mdx RMS, whereas dystrophin expression was absent in almost all human RMS, both for embryonal and alveolar RMS subtypes. These studies show that absence of members of the dystrophin-associated glycoprotein complex constitutes a permissive environment for spontaneous development of embryonal RMS associated with mutation of p53 and mutation or altered splicing of Mdm2.

Altered expression of natively glycosylated alpha dystroglycan in pediatric solid tumors.

Altered glycosylation and/or expression of dystroglycan have been reported in forms of congenital muscular dystrophy as well as in cancers of the breast, colon, and oral epithelium. To date, however, there has been no study of the expression of dystroglycan in pediatric solid tumors. Using a combination of immunostaining on tissue microarrays and immunoblotting of snap-frozen unfixed tissues, we demonstrate a significant reduction in native alpha dystroglycan expression in pediatric alveolar rhabdomyosarcoma (RMS), embryonal RMS, neuroblastoma (NBL), and medulloblastoma, whereas expression of beta dystroglycan, which is cotranslated with alpha dystroglycan, is largely unchanged. Loss of native alpha dystroglycan expression was significantly more pronounced in stage 4 NBL than in pooled samples of stage 1 and stage 2 NBL, suggesting that loss of native alpha dystroglycan expression increases with advancing tumor stage. Neuroblastoma and RMS samples with reduced expression of native alpha dystroglycan also showed reduced laminin binding in laminin overlay experiments. Expression of natively glycosylated alpha dystroglycan was not altered in several other pediatric tumor types when compared with appropriate normal tissue controls. These data provide the first evidence that alpha dystroglycan glycosylation and laminin binding to alpha dystroglycan are altered in certain pediatric solid tumors and suggest that aberrant dystroglycan glycosylation may contribute to tumor cell biology in patients with RMS, medulloblastoma, and NBL.

Genetically altered mice with different sialyltransferase deficiencies show tissue-specific alterations in sialylation and sialic acid 9-O-acetylation.

Glycan chains on glycoconjugates traversing the Golgi apparatus are often terminated by sialic acid residues, which can also be 9-O-acetylated. This process involves competition between multiple Golgi enzymes. Expression levels of Golgi enzyme mRNAs do not always correlate with enzyme activity, which in turn cannot accurately predict glycan sequences found on cell surfaces. Here we examine the cell type-specific expression of terminal glycans in tissues of normal mice in comparison with animals deficient in ST6Gal-I (transfers alpha2-6-linked sialic acid to Galbeta1-4GlcNAc) or ST3Gal-I (transfers alpha2-3-linked sialic acid to Galbeta1-3GalNAc). Tissues of ST6Gal-I null mice showed minimal binding of an alpha2-6-sialic acid-specific lectin, indicating that no other enzyme generates Siaalpha2-6Galbeta1-4GlcNAc and that Siaalpha2-6GalNAc (sialyl-Tn) is rare in mice. However, exposed Galbeta1-4GlcNAc termini were only moderately increased, indicating that these can be partially capped by other enzymes. Indeed, Galalpha1-3Galbeta1-4GlcNAc and Fucalpha1-2Galbeta1-4GlcNAc termini were enhanced in some tissues. Many tissues of ST3Gal-I null animals showed increases in Galbeta1-3GalNAc termini, and some increases in poly-N-acetyllactosamines. However, overall expression of alpha2-3-linked sialic acid was selectively reduced only in a few instances, indicating that other ST3Gal enzymes can generate this linkage in most tissues. Highly selective losses of 9-O-acetylation of sialic acid residues were also observed, with ST6Gal-I deficiency causing loss on endothelium and ST3Gal-I deficiency giving a marked decrease on CD4(+) lymphocytes. These data demonstrate selective regulation of sialylation and 9-O-acetylation, point to cell types with potential physiological defects in null animals, and show in vivo evidence for competition between Golgi enzymes.