A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers

Somatic rearrangements contribute to the mutagenized landscape of cancer genomes. Here, we systematically interrogated rearrangements in 560 breast cancers by using a piecewise constant fitting approach. We identified 33 hotspots of large (>100 kb) tandem duplications, a mutational signature associated with homologous-recombination-repair deficiency. Notably, these tandem-duplication hotspots were enriched in breast cancer germline susceptibility loci (odds ratio (OR) = 4.28) and breast-specific 'super-enhancer' regulatory elements (OR = 3.54). These hotspots may b

Mutational processes molding the genomes of 21 breast cancers

All cancers carry somatic mutations. The patterns of mutation in cancer genomes reflect the DNA damage and repair processes to which cancer cells and their precursors have been exposed. To explore these mechanisms further, we generated catalogs of somatic mutation from 21 breast cancers and applied mathematical methods to extract mutational signatures of the underlying processes. Multiple distinct single- and double-nucleotide substitution signatures were discernible. Cancers with BRCA1 or BRCA2 mutations exhibited a characteristic combination of substitution mutation signatures and a distinctive profile of deletions. Complex relationships between somatic mutation prevalence and transcription were detected. A remarkable phenomenon of localized hypermutation, termed "kataegis," was observed. Regions of kataegis differed between cancers but usually colocalized with somatic rearrangements. Base substitutions in these regions were almost exclusively of cytosine at TpC dinucleotides. The mechanisms underlying most of these mutational signatures are unknown. However, a role for the APOBEC family of cytidine deaminases is proposed

Partially methylated domains are hypervariable in breast cancer and fuel widespread CpG island hypermethylation

Global loss of DNA methylation and CpG island (CGI) hypermethylation are key epigenomic aberrations in cancer. Global loss manifests itself in partially methylated domains (PMDs) which extend up to megabases. However, the distribution of PMDs within and between tumor types, and their effects on key functional genomic elements including CGIs are poorly defined. We comprehensively show that loss of methylation in PMDs occurs in a large fraction of the genome and represents the prime source of DNA methylation variation. PMDs are hypervariable in methylation level, size and distribution, and display elevated mutation rates. They impose intermediate DNA methylation levels incognizant of functional genomic elements including CGIs, underpinning a CGI methylator phenotype (CIMP). Repression effects on tumor suppressor genes are negligible as they are generally excluded from PMDs. The genomic distribution of PMDs reports tissue-of-origin and may represent tissue-specific silent regions which tolerate instability at the epigenetic, transcriptomic and genetic level

Antimicrobial innovation: combining commitment, creativity and coherence

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Myc phosphorylation in its basic helix–loop–helix region destabilizes transient α-helical structures, disrupting Max and DNA binding

Myelocytomatosis proto-oncogene transcription factor (Myc) is an intrinsically disordered protein with critical roles in cellular homeostasis and neoplastic transformation. It is tightly regulated in the cell, with Myc phosphorylation playing a major role. In addition to the well-described tandem phosphorylation of Thr-52 and Ser-62 in the Myc transactivation domain linked to its degradation, P21 (RAC1)–activated kinase 2 (PAK2)–mediated phosphorylation of serine and threonine residues in the C-terminal basic helix–loop–helix leucine zipper (bHLH-LZ) region regulates Myc transcriptional activity. Here we report that PAK2 preferentially phosphorylates Myc twice, at Thr-358 and Ser-373, with only a minor fraction being modified at the previously identified Thr-400 site. For transcriptional activity, Myc binds E-box DNA elements, requiring its heterodimerization with Myc-associated factor X (Max) via the bHLH-LZ regions. Using isothermal calorimetry (ITC), we found that Myc phosphorylation destabilizes this ternary protein–DNA complex by decreasing Myc's affinity for Max by 2 orders of magnitude, suggesting a major effect of phosphorylation on this complex. Phosphomimetic substitutions revealed that Ser-373 dominates the effect on Myc–Max heterodimerization. Moreover, a T400D substitution disrupted Myc's affinity for Max. ITC, NMR, and CD analyses of several Myc variants suggested that the effect of phosphorylation on the Myc–Max interaction is caused by secondary structure disruption during heterodimerization rather than by a change in the structurally disordered state of Myc or by phosphorylation-induced electrostatic repulsion in the heterodimer. Our findings provide critical insights into the effects of PAK2-catalyzed phosphorylation of Myc on its interactions with Max and DNA

Bias towards dementia: are hip fracture trials excluding too many patients? A systematic review

Item does not contain fulltextPatients with hip fractures are older and often present many co-morbidities, including dementia. These patients cannot answer quality of life questionnaires and are generally excluded from trials. We hypothesized that a significant number of patients are being excluded from these studies and this may impact outcomes. This was a two part study; the first analyzing databases of two ongoing large-scale multi-centred hip fracture trials and the second being a systematic review. The FAITH and HEALTH studies were analyzed for exclusion incidence directly related to dementia. The second part consisted of a systematic search of all relevant studies within the last 20 years. In the FAITH study, a total of 1690 subjects were excluded, 375 (22.2%) of which were due to dementia or cognitive impairment. In the HEALTH study, 575 were excluded with dementia/cognitive impairment representing 207 patients (36%). Following the systematic review, 251 articles were identified 17 of which were retained. The overall prevalence of dementia was 27.9% (range 2-51%). Only two studies compared demented and non-demented groups. In these studies significant increases in both mortality and complications were found. In summary, when investigating hip fractures, choosing appropriate objective endpoints is essential to ensure results are also applicable to patients with dementia

Mutational signatures impact the breast cancer transcriptome and distinguish mitotic from immune response pathways

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Professionals' perceptions of their patients' experiences with fertility care

Item does not contain fulltextBACKGROUND: Patient-centredness is one of the core dimensions of quality of care. It can be monitored with surveys measuring patients' experiences with care. The objective of the present study was to determine to what extent gynaecologists, physicians specializing in infertility and nurses can estimate the level of patient-centredness of their clinic. METHODS: A random sample of 1189 couples with fertility problems and 194 physicians and nurses from 29 Dutch fertility clinics participated in this cross-sectional study. Differences between patients' experiences with fertility care and professionals' perceptions of these experiences as measured with the patient-centredness questionnaire-infertility (PCQ-infertility) were calculated. The questionnaire's structure, comprising one total scale (level 1), seven subscales (level 2) and 46 single items (level 3), was used as a framework. RESULTS: Response rates were 75% (n = 888) in the patient sample and 83% (n = 160) in the professional sample. Independent sample t-tests, corrected for multiple comparisons with the Bonferroni correction method (P < 0.05), showed no significant differences in mean scores on the total scale of patient-centredness for either professionals or patients. At level 2, professionals underestimated most subscales, namely, 'Accessibility', 'Communication', 'Patient involvement' and 'Competence', whereas 'Continuity of care' was overestimated. Professionals significantly and clinically relevantly misjudged 29 care aspects. CONCLUSIONS: Professionals within fertility care cannot adequately evaluate their performance regarding patient-centredness, and specifically the care aspects to which their own patients attribute the greatest improvement potential. Providing detailed feedback might start improvement of patient-centredness and quality of care