The Clinical Impact and Molecular Biology of del(17p) in Multiple Myeloma Treated with Conventional or Thalidomide-Based Therapy

Hemizygous deletion of 17p (del(17p)) has been identified as a variable associated with poor prognosis in myeloma, although its impact in the context of thalidomide therapy is not well described. The clinical outcome of 85 myeloma patients with del(17p) treated in a clinical trial incorporating both conventional and thalidomide-based induction therapies was examined. The clinical impact of deletion, low expression, and mutation of TP53 was also determined. Patients with del(17p) did not have inferior response rates compared to patients without del(17p), but, despite this, del(17p) was associated with impaired overall survival (OS) (median OS 26.6 vs. 48.5 months, P <0.001). Within the del(17p) group, thalidomide induction therapy was associated with improved response rates compared to conventional therapy, but there was no impact on OS. Thalidomide maintenance was associated with impaired OS, although our analysis suggests that this effect may have been due to confounding variables. A minimally deleted region on 17p13.1 involving 17 genes was identified, of which only TP53 and SAT2 were underexpressed. TP53 was mutated in <1% in patients without del(17p) and in 27% of patients with del(17p). The higher TP53 mutation rate in samples with del(17p) suggests a role for TP53 in these clinical outcomes. In conclusion, del(17p) defined a patient group associated with short survival in myeloma, and although thalidomide induction therapy was associated with improved response rates, it did not impact OS, suggesting that alternative therapeutic strategies are required for this group. (C) 2011 Wiley-Liss, Inc.

Personalized cancer medicine: molecular diagnostics, predictive biomarkers, and drug resistance.

The progressive elucidation of the molecular pathogenesis of cancer has fueled the rational development of targeted drugs for patient populations stratified by genetic characteristics. Here we discuss general challenges relating to molecular diagnostics and describe predictive biomarkers for personalized cancer medicine. We also highlight resistance mechanisms for epidermal growth factor receptor (EGFR) kinase inhibitors in lung cancer. We envisage a future requiring the use of longitudinal genome sequencing and other omics technologies alongside combinatorial treatment to overcome cellular and molecular heterogeneity and prevent resistance caused by clonal evolution.

Molecular characterization of complete and incomplete immunoglobulin heavy chain gene rearrangements in hairy cell leukemia.

PURPOSE: We analyzed patients with hairy cell leukemia (HCL) to achieve a better understanding of the differentiation stage reached by HCL cells and to define the key role of the diversification of cell surface makers, especially CD25 expression. PATIENTS AND METHODS: We analyzed 38 previously untreated patients with HCL to characterize their complete (VDJ(H)) and incomplete (DJ(H)) immunoglobulin (Ig) heavy chain (IgH) rearrangements, including somatic hypermutation pattern and gene segment use. RESULTS: A correlation between immunophenotypic profile and molecular data was seen. All 38 cases showed monoclonal amplifications: VDJ(H) in 97%, DJ(H) in 42%, and both in 39%. Segments from the D(H)3 family were used more in complete compared with incomplete rearrangements (45% vs. 12%; P <.005). Furthermore, comparison between molecular and immunophenotypic characteristics disclosed differences in the expression of CD25 antigen; CD25(-) cases, a phenotype associated with HCL variant, showed complete homology to the germline in 3 of 5 cases (60%), whereas this characteristic was never observed in CD25(+) cases (P <.005). Moreover, V(H)4-34, V(H)1-08, and J(H)3 segments appeared in 2, 1, and 2 CD25(-) cases, respectively, whereas they were absent in all CD25(+) cases. CONCLUSION: These results support that HCL is a heterogeneous entity including subgroups with different molecular characteristics, which reinforces the need for additional studies with a larger number of patients to clarify the real role of gene rearrangements in HCL.

Self-refraction, ready-made glasses and quality of life among rural myopic Chinese children: a non-inferiority randomized trial.

PURPOSE: To study, for the first time, the effect of wearing ready-made glasses and glasses with power determined by self-refraction on children's quality of life. METHODS: This is a randomized, double-masked non-inferiority trial. Children in grades 7 and 8 (age 12-15 years) in nine Chinese secondary schools, with presenting visual acuity (VA) ≤6/12 improved with refraction to ≥6/7.5 bilaterally, refractive error ≤-1.0 D and <2.0 D of anisometropia and astigmatism bilaterally, were randomized to receive ready-made spectacles (RM) or identical-appearing spectacles with power determined by: subjective cycloplegic retinoscopy by a university optometrist (U), a rural refractionist (R) or non-cycloplegic self-refraction (SR). Main study outcome was global score on the National Eye Institute Refractive Error Quality of Life-42 (NEI-RQL-42) after 2 months of wearing study glasses, comparing other groups with the U group, adjusting for baseline score. RESULTS: Only one child (0.18%) was excluded for anisometropia or astigmatism. A total of 426 eligible subjects (mean age 14.2 years, 84.5% without glasses at baseline) were allocated to U [103 (24.2%)], RM [113 (26.5%)], R [108 (25.4%)] and SR [102 (23.9%)] groups, respectively. Baseline and endline score data were available for 398 (93.4%) of subjects. In multiple regression models adjusting for baseline score, older age (p = 0.003) and baseline spectacle wear (p = 0.016), but not study group assignment, were significantly associated with lower final score. CONCLUSION: Quality of life wearing ready-mades or glasses based on self-refraction did not differ from that with cycloplegic refraction by an experienced optometrist in this non-inferiority trial.

Mapping Protein-DNA Interactions Using ChIP-exo and Illumina-Based Sequencing

Chromatin immunoprecipitation (ChIP) provides a means of enriching DNA associated with transcription factors, histone modifications, and indeed any other proteins for which suitably characterized antibodies are available. Over the years, sequence detection has progressed from quantitative real-time PCR and Southern blotting to microarrays (ChIP-chip) and now high-throughput sequencing (ChIP-seq). This progression has vastly increased the sequence coverage and data volumes generated. This in turn has enabled informaticians to predict the identity of multi-protein complexes on DNA based on the overrepresentation of sequence motifs in DNA enriched by ChIP with a single antibody against a single protein. In the course of the development of high-throughput sequencing, little has changed in the ChIP methodology until recently. In the last three years, a number of modifications have been made to the ChIP protocol with the goal of enhancing the sensitivity of the method and further reducing the levels of nonspecific background sequences in ChIPped samples. In this chapter, we provide a brief commentary on these methodological changes and describe a detailed ChIP-exo method able to generate narrower peaks and greater peak coverage from ChIPped material.

Genetic analyses reveal high levels of seed and pollen flow in hawthorn (Crataegus monogyna Jacq.), a key component of hedgerows

Hedgerows represent important components of agri-environment landscapes that are increasingly coming under threat from climate change, emergent diseases, invasive species and land use change. Given that population genetic data can be used to inform best-practice management strategies for woodland and hedgerow tree species, we carried out a study on hawthorn (Crataegus monogyna Jacq.), a key component of hedgerows, on a regional basis using a combination of nuclear and chloroplast microsatellite markers. We found that levels of genetic diversity were high and comparable to, or slightly higher than, other tree species from the same region. Levels of population differentiation for both sets of markers, however, were extremely low, suggesting extensive gene flow via both seed and pollen. These findings suggest that a holistic approach to woodland management, one which does not necessarily rely on the concept of “seed zones” previously suggested, but which also takes into account populations with high and/or rare chloroplast (i.e. seed-specific) genetic variation, might be the best approach to restocking and replanting.