Detailed gene copy number and RNA expression analysis of the 17q12-23 region in primary breast cancers

Chromosome region 17q12-23 commonly shows an increase in DNA copy number in breast cancers, suggesting that several oncogenes are located at this site. We performed a high-resolution expression array and comparative genomic hybridization analysis of genes mapped to the entire 17q12-23 region, to identify novel candidate oncogenes. We identified 24 genes that showed significant overexpression in breast cancers with gain of 17q12-23, compared to cancers without gain. These genes included previously identified oncogenes, together with several novel candidate oncogenes. FISH analysis using specific gene probes hybridized to tissue arrays confirmed the underlying amplification of overexpressed genes. This high-resolution analysis of the 17q12-23 region indicates that several established and novel candidate oncogenes, including a Wnt-signaling pathway member, are amplified and overexpressed within individual primary breast cancer samples. We were also able to confirm the presence of two apparently separate and reciprocally amplified groups of genes within this region. Investigation of these genes and their functional interactions will facilitate our understanding of breast oncogenesis and optimal management of this disease.     

Two-center collaborative evaluation of the performance of the BD Phoenix automated microbiology system for identification and antimicrobial susceptibility testing of Enterococcus spp. and Staphylococcus spp

The performance of the BD Phoenix Automated Microbiology System (BD Diagnostic Systems, Sparks, Md.) was assessed for identification (ID) and antimicrobial susceptibility testing (AST) for the majority of clinically encountered bacterial isolates in a European collaborative two-center trial. A total of 469 bacterial isolates of the genera Staphylococcus (275 isolates), Enterococcus (179 isolates), and Streptococcus (15 isolates, for ID only) were investigated; of these, 367 were single patient isolates, and 102 were challenge strains tested at one center. Sixty-four antimicrobial drugs were tested, including the following drug classes: aminoglycosides, beta-lactam antibiotics, beta-lactam-beta-lactamase inhibitors, carbapenems, cephems, folate antagonists, quinolones, glycopeptides, macrolides-lincosamides-streptogramin B (MLS), and others. Phoenix ID results were compared to those of the laboratories' routine ID systems (API 32 Staph, API 32 Strep, and VITEK 2 [bioMérieux, Marcy l'Etoile, France]); Phoenix AST results were compared to those of frozen standard broth microdilution (SBM) panels according to NCCLS guidelines (NCCLS document M 100-S 9, approved standard M 7-A 4). Discrepant results were repeated in duplicate. Concordant IDs of 97.1, 98.9, and 100% were observed for staphylococci, enterococci, and streptococci, respectively. For AST results the overall essential agreement was 93.3%; the category agreement was 97.3%; and the very major error rate, major error rate, and minor error rate were 1.2, 1.9, and 1.3%, respectively. In conclusion, the Phoenix ID results showed high agreement with results of the systems to which they were being compared; the AST performance was highly equivalent to that of the SBM reference method.     

Additional chromosomal abnormalities in patients with a previously detected abnormal karyotype, mental retardation, and dysmorphic features

The detection of chromosomal abnormalities in patients with mental retardation (MR) and dysmorphic features increases with improvements of molecular cytogenetic methods. We report on six patients referred for detailed characterization of chromosomal abnormalities (four translocations, one inversion, one deletion) detected by conventional cytogenetics, in whom metaphase CGH revealed imbalances not involved in the initially detected rearrangements. The detected abnormalities were validated by real-time PCR. Parents were investigated by CGH in four cases. The genomic screening revealed interstitial deletions of 2q33.2-q34, 3p21, 4q12-q13.1, 6q25, 13q22.2-q31.1, and 14q12. The estimated minimum sizes of the deletions ranged from 2.65 to 9.27 Mb. The CGH assay did not reveal imbalances that colocalized with the breakpoints of the inversion or the translocations. The deletion of 6q included ESR1, in which polymorphisms are associated with variation of adult height. FOXG1B, known to be involved in cortical development, was located in the 14q deletion. The results illustrate that whole-genome molecular cytogenetic analysis of phenotypically affected patients with abnormal conventional karyotypes may detect inapparent molecular cytogenetic abnormalities in patients with microscopic chromosomal abnormalities and that these data provide additional information of clinical importance.     

Two-center collaborative evaluation of performance of the BD phoenix automated microbiology system for identification and antimicrobial susceptibility testing of gram-negative bacteria

The performance of the BD Phoenix Automated Microbiology System (BD Diagnostic Systems, Sparks, MD) was assessed for identification (ID) and antimicrobial susceptibility testing (AST) of the majority of clinically encountered bacterial isolates in a European collaborative two-center trial. A total of 494 bacterial isolates including various species of the Enterobacteriaceae and 110 nonfermentative gram-negative bacteria were investigated: of these, 385 were single patient isolates, and 109 were challenge strains tested at one center. The performance of the Phoenix extended-spectrum beta-lactamase (ESBL) test was also evaluated for 203 strains of Escherichia coli, Klebsiella pneumoniae, and Klebsiella oxytoca included in the study. Forty-two antimicrobial drugs were tested, including members of the following drug classes: aminoglycosides, beta-lactam antibiotics, beta-lactam/beta-lactamase inhibitors, carbapenems, cephems, monobactams, folate antagonists, quinolones, and others. Phoenix system ID results were compared to those of the laboratories' routine ID systems (API 20E and API CHE, ATB ID32E, ID32GN, and VITEK 2 [bioMérieux, Marcy l'Etoile, France]); Phoenix AST results were compared to those of frozen standard broth microdilution (SBM) panels according to NCCLS (now CLSI) guidelines (NCCLS document M100-S9, approved standard M7-A4). Discrepant results were repeated in duplicate. Concordant IDs of 98.4 and 99.1% were observed for the Enterobacteriaceae and the nonfermentative group, respectively. For AST results, the overall essential agreement was 94.2%; the category agreement was 97.3%; and the very major error rate, major error rate, and minor error rate were 1.6, 0.6, and 1.9%, respectively. In terms of ESBL detection, Phoenix results were 98.5% concordant with those of the reference system, with 98.0% sensitivity and 98.7% specificity. In conclusion, the Phoenix ID results showed high agreement with results of the systems to which they were being compared: the AST performance was highly equivalent to that of the SBM reference method, and the system proved to be very accurate for the detection of ESBL producers.     

Costimulation blockade induces tolerance to HESC transplanted to the testis and induces regulatory T-cells to HESC transplanted into the heart

In order to study the ability of costimulation blockade to induce tolerance to human embryonic stem cells (HESC), severe combined immunodeficient (SCID), and immunocompetent C57BL/6 mice treated with costimulation blockade received intratesticular and intramyocardial HESC transplants. All SCID mice with intratesticular HESC transplants developed teratoma. When SCID mice were transplanted intramyocardially, only two of five mice developed teratoma-like tumors. C57BL/6 mice transplanted intratesticularly and treated with costimulation blockade all developed teratoma and were surrounded by CD4(+)CD25(+)Foxp3(+) T-cells, while isotype control treated recipients rejected their grafts. Most C57BL/6 mice transplanted intramyocardially and treated with costimulation blockade demonstrated lymphocytic infiltrates 1 month after transplantation, whereas one maintained its graft. Isolation of regulatory T-cells from intramyocardial transplanted recipients treated with costimulation blockade demonstrated specificity toward undifferentiated HESC and down-regulated naive T-cell activation toward HESC. These results demonstrate that costimulation blockade is sufficiently robust to induce tolerance to HESC in the immune-privileged environment of the testis. HESC specific regulatory T-cells developed to HESC transplanted to the heart and the success of transplantation was similar to that seen in SCID mice.     

Structural and kinetic basis for low affinity cross-reactivity in T cell allorecognition

The alloreactive BM3.3TCR interacts with high affinity with H-2Kb loaded with the endogenous peptide pBM1 (INFDFNTI), and shows low affinity cross-reactivity for H-2Kb loaded with a viral peptide VSV8 (RGYVYQGL), CTL activity requiring 10(3)-fold higher peptide concentration and being highly sensitive to inhibition by anti-CD8 monoclonal antibody. VSV8 peptides substituted with pBM1/TCR contact residues (N6 and T7) retained low affinity characteristics and among pBM1 peptides substituted with residues Q6 and/or G7 present in VSV8, only pBM1(G7) was recognized, albeit with characteristics akin to those of VSV8. Despite the difference in KD values and the faster dissociation rate of multimeric VSV8/H-2Kb as compared to pBM1/H-2Kb complexes, similar TCR occupancy could be achieved with both multimers either at 4 or 37 degrees C. Only TCR engagement with pBM1/H-2Kb, however, resulted in early (Ca2+ flux) and late (CD69 expression) activation events in naive BM3.3TCR CD8 T cells. CD8 coreceptor, essential for binding of the weak agonists, was dispensable for binding of pBM1/H-2Kb multimers and their induction of signaling in naive T cells. Hence, high number of TCR and coreceptor engagement by weak agonists fail to substitute for strong agonist TCR engagement that can be coreceptor-independent and involve a limited number of TCR.     

A reflection on the challenge of protecting confidentiality of participants while disseminating research results locally

Background

Researchers studying health systems in low-income countries face a myriad of ethical challenges throughout the entire research process. In this article, we discuss one of the greatest ethical challenges that we encountered during our fieldwork in West Africa: the difficulty of protecting the confidentiality of participants (or groups of participants) while locally disseminating results of health systems research to stakeholders.

Methods

This reflection is based on experiences of authors involved in conducting evaluative research of interventions aimed at improving health systems in West Africa. Our observation and collaboration with the research projects’ stakeholders informed our analysis. Examples from two research projects illustrate the issues raised.

Results

We found that in some cases there is a risk that local stakeholders may be able to identify research participants, or at least groups of participants, during the dissemination of results, even if they are anonymized. Four factors can interact and influence this challenge: 1) hierarchical structure, 2) small milieu, 3) immersion in a few sites, and 4) vested interests of decision-makers. For example, local stakeholders can sometimes find out when and where the data were collected. Moreover, health systems, especially rural healthcare centres, in West African countries can be small settings, so people often know each other. Some types of participants have unique characteristics or positions in the health system that may make them more easily identifiable by local stakeholders familiar with the environment. We identified a number of potential strategies that can help researchers minimize this difficulty and improve ethical research practices. These strategies pertain to the development of the study design, the process of obtaining informed consent, the dissemination of results, and the researchers’ reflexivity.

Conclusion

Researchers must develop and adopt strategies that enable them to respect their promise of confidentiality while effectively disseminating sometimes sensitive results. Reflections surrounding ethical issues in global health research should be deepened to better address how to manage competing ethical responsibilities while promoting valuable research uptake.

     

Carriage of methicillin-resistant Staphylococci and their SCCmec types in a long-term-care facility

Following an outbreak caused by staphylococcal cassette chromosome mec (SCCmec) type V methicillin (meticillin)-resistant Staphylococcus aureus (MRSA), a point-prevalence survey of the nasal carriage of staphylococci was conducted in a long-term-care facility in northern Finland in 2004. The focus was directed at methicillin-resistant coagulase-negative staphylococci (MR-CNS) and their SCCmec elements. A nasal swab was taken from 76 of the 80 residents 6 months after the onset of the outbreak. Staphylococcal isolates were identified by conventional methods and the GenoType Staphylococcus test, and their SCCmec elements were analyzed. Of the 76 individuals, 24 (32%) carried S. aureus and 67 (88%) CNS in their nostrils. Of the CNS carriers, 41 (61%) had at least one mecA-positive MR-CNS, and two individuals (3%) had both MRSA and methicillin-resistant Staphylococcus epidermidis (MRSE). Among the 61 MR-CNS isolates identified, 49 (80%) were MRSE. The distribution of the SCCmec types was diverse: 20 (33%) were of type IV, 11 (18%) of type V, 4 (6%) of type I or IA, 3 (4%) of type II, and 23 (38%) of new types (with six different combinations of ccr and other mec genes or only mecA). Both of the individuals with MRSA and MRSE shared SCCmec type V among their isolates. Nasal MR-CNS carriage was common among the residents of this long-term-care facility. A variety of SCCmec types, including many new types, were identified among the MR-CNS strains. The horizontal transfer of SCCmec elements is speculated based on the sharing of SCCmec type V between MRSA and MRSE.     

Variability in dentofacial phenotypes in four families with WNT10A mutations

This article describes the inter- and intra-familial phenotypic variability in four families with WNT10A mutations. Clinical characteristics of the patients range from mild to severe isolated tooth agenesis, over mild symptoms of ectodermal dysplasia, to more severe syndromic forms like odonto-onycho-dermal dysplasia (OODD) and Schöpf–Schulz–Passarge syndrome (SSPS). Recurrent WNT10A mutations were identified in all affected family members and the associated symptoms are presented with emphasis on the dentofacial phenotypes obtained with inter alia three-dimensional facial stereophotogrammetry. A comprehensive overview of the literature regarding WNT10A mutations, associated conditions and developmental defects is presented. We conclude that OODD and SSPS should be considered as variable expressions of the same WNT10A genotype. In all affected individuals, a dished-in facial appearance was observed which might be helpful in the clinical setting as a clue to the underlying genetic etiology.