DNA mismatch repair-dependent DNA damage responses and cancer

Canonical DNA mismatch repair (MMR) excises base-base mismatches to increase the fidelity of DNA replication. Thus, loss of MMR leads to increased spontaneous mutagenesis. MMR genes also are involved in the suppression of mutagenic, and the induction of protective, responses to various types of DNA damage. In this review we describe these non-canonical roles of MMR at different lesion types. Loss of non-canonical MMR gene functions may have important ramifications for the prevention, development and treatment of colorectal cancer associated with inherited MMR gene defects in Lynch syndrome. This graphical review pays tribute to Samuel H. Wilson. Sam not only made seminal contributions to understanding base excision repair, particularly with respect to structure-function relationships in DNA polymerase beta but also, as Editor of DNA Repair, has maintained a high standard of the journal.Genome Instability and Cance

Thirty years of heart transplantation at the University Medical Centre Utrecht.

PURPOSE: To analyse patient demographics, indications, survival and donor characteristics for heart transplantation (HTx) during the past 30 years at the University Medical Centre Utrecht (UMCU). METHODS: Data have been prospectively collected for all patients who underwent HTx at the UMCU from 1985 until 2015. Patients who were included underwent orthotopic HTx at an age >14 years. RESULTS: In total, 489 hearts have been transplanted since 1985; 120 patients (25%) had left ventricular assist device (LVAD) implantation prior to HTx. A shift from ischaemic heart disease to dilated cardiomyopathy has been seen as the leading indication for HTx since the year 2000. Median age at HTx was 49 years (range 16-68). Median waiting time and donor age have also increased from 40 to 513 days and from 27 to 44 years respectively (range 11-65). Donor cause of death is now primarily stroke, in contrast to head and brain injury in earlier years. Estimated median survival is 15.4 years (95% confidence interval 14.2-16.6) There is better survival throughout these years. CONCLUSION: Over the past 30 years, patient and donor demographics and underlying diseases have shifted substantially. Furthermore, the increase in waiting time due to lack of available donor hearts has led to a rise in the use of LVADs as bridge to transplant. Importantly, an improvement in survival rates is found over time which could be explained by better immunosuppressive therapy and improvements in follow-up care

Clinical utility of circulating tumor DNA as a response and follow-up marker in cancer therapy

Response evaluation for cancer treatment consists primarily of clinical and radiological assessments. In addition, a limited number of serum biomarkers that assess treatment response are available for a small subset of malignancies. Through recent technological innovations, new methods for measuring tumor burden and treatment response are becoming available. By utilization of highly sensitive techniques, tumor-specific mutations in circulating DNA can be detected and circulating tumor DNA (ctDNA) can be quantified. These so-called liquid biopsies provide both molecular information about the genomic composition of the tumor and opportunities to evaluate tumor response during therapy. Quantification of tumor-specific mutations in plasma correlates well with tumor burden. Moreover, with liquid biopsies, it is also possible to detect mutations causing secondary resistance during treatment. This review focuses on the clinical utility of ctDNA as a response and follow-up marker in patients with non-small cell lung cancer, melanoma, colorectal cancer, and breast cancer. Relevant studies were retrieved from a literature search using PubMed database. An overview of the available literature is provided and the relevance of ctDNA as a response marker in anti-cancer therapy for clinical practice is discussed. We conclude that the use of plasma-derived ctDNA is a promising tool for treatment decision-making based on predictive testing, detection of resistance mechanisms, and monitoring tumor response. Necessary steps for translation to daily practice and future perspectives are discussed

Prostaglandin E2 stimulates progression-related gene expression in early colorectal adenoma cells

Upregulation of cyclooxygenase-2 (COX-2) and prostaglandin-dependent vascularisation in small adenomatous polyps is an essential part of colon carcinogenesis. To study the underlying cellular mechanisms, LT97 and Caco2 human colorectal tumour cells not expressing endogenous COX-2 were exposed to 1 μM prostaglandin E2 (PGE2) in their medium. At 30 min after addition, expression of c-fos was stimulated 5-fold and 1.3-fold, respectively, depending on the activation of both extracellular signal-regulated kinase and p38. The amount of c-jun in nuclear extracts was increased 20% in LT97 cells. Expression of COX-2 was upregulated 1.7-fold in LT97 cells and 1.5-fold in Caco2 2 h after prostaglandin (PG) addition by a p38-mediated pathway. The known PGE2 target gene vascular endothelial growth factor (VEGF) was not modulated. Effects of sustained PGE2 production were studied in VACO235 cells that have high endogenous COX-2 and in LT97 cells infected with an adenovirus expressing COX-2. Prostaglandin E2 secretion into the medium was 1–2 nM and 250 pM, respectively. Expression of both VEGF and c-fos was high in VACO235 cells. In LT97 cells, COX-2 upregulated c-fos expression and c-jun content in nuclear extracts 1.7- and 1.2-fold, respectively, in a PG-dependent way. This shows that exogenous PGE2 as well as COX-2 overexpression affect signalling and gene expression in a way that enhances tumour progression

A high density linkage map of the bovine genome

<p>Abstract</p> <p>Background</p> <p>Recent technological advances have made it possible to efficiently genotype large numbers of single nucleotide polymorphisms (SNPs) in livestock species, allowing the production of high-density linkage maps. Such maps can be used for quality control of other SNPs and for fine mapping of quantitative trait loci (QTL) via linkage disequilibrium (LD).</p> <p>Results</p> <p>A high-density bovine linkage map was constructed using three types of markers. The genotypic information was obtained from 294 microsatellites, three milk protein haplotypes and 6769 SNPs. The map was constructed by combining genetic (linkage) and physical information in an iterative mapping process. Markers were mapped to 3,155 unique positions; the 6,924 autosomal markers were mapped to 3,078 unique positions and the 123 non-pseudoautosomal and 19 pseudoautosomal sex chromosome markers were mapped to 62 and 15 unique positions, respectively. The linkage map had a total length of 3,249 cM. For the autosomes the average genetic distance between adjacent markers was 0.449 cM, the genetic distance between unique map positions was 1.01 cM and the average genetic distance (cM) per Mb was 1.25.</p> <p>Conclusion</p> <p>There is a high concordance between the order of the SNPs in our linkage map and their physical positions on the most recent bovine genome sequence assembly (Btau 4.0). The linkage maps provide support for fine mapping projects and LD studies in bovine populations. Additionally, the linkage map may help to resolve positions of unassigned portions of the bovine genome.</p

Rev1 deficiency induces a metabolic shift in MEFs that can be manipulated by the NAD plus precursor nicotinamide riboside

Replication stress, caused by Rev1 deficiency, is associated with mitochondrial dysfunction, and metabolic stress. However, the overall metabolic alterations and possible interventions to rescue the deficits due to Rev1 loss remain unclear. Here, we report that loss of Rev1 leads to intense changes in metabolites and that this can be manipulated by NAD + supplementation. Autophagy decreases in Rev1-/- mouse embryonic fibroblasts (MEFs) and can be restored by supplementing the NAD+ precursor nicotinamide riboside (NR). The abnormal mitochondrial morphology in Rev1-/-MEFs can be partially reversed by NR supplementation, which also protects the mito-chondrial cristae from rotenone-induced degeneration. In nematodes rev-1 deficiency causes sensitivity to oxidative stress but this cannot be rescued by NR supplementation. In conclusion, Rev1 deficiency leads to metabolic dysregulation of especially lipid and nucleotide metabolism, impaired autophagy, and mitochondrial anomalies, and all of these phenotypes can be improved by NR replenishment in MEFs.Genome Instability and Cance

The course of traumatic pancreatitis in a patient with pancreas divisum: a case report

BACKGROUND: The peculiar anatomy of pancreatic ducts in pancreas divisum (PD) may interfere with the development of acute chronic pancreatitis. In the presented case, PD influenced the evolution of lesions after pancreatic trauma. CASE PRESENTATION: A 38 years old patient refferred to our hospital with recurrent episodes of mild pancreatitis during the last two years. The first episode occurred four months after blunt abdominal trauma. Endoscopic Retrograde Cholangiopancreatography, Magnetic Resonance Imaging of upper abdomen and Magnetic Resonance Cholangiopancreatography disclosed pancreas divisum, changes consistent with chronic pancreatitis in the dorsal pancreatic duct, atrophy in the body and tail of the pancreas and a pseudocyst in the pancreatic head, that was drained endoscopically. CONCLUSION: Pancreas Divisum may interfere with the evolution of posttraumatic changes in the pancreas after blunt abdominal trauma

Two integrated and highly predictive functional analysis-based procedures for the classification of MSH6 variants in Lynch syndrome

Purpose: Variants in the DNA mismatch repair (MMR) gene MSH6, identified in individuals suspected of Lynch syndrome, are difficult to classify owing to the low cancer penetrance of defects in that gene. This not only obfuscates personalized health care but also the development of a rapid and reliable classification procedure that does not require clinical data. Methods: The complete in vitro MMR activity (CIMRA) assay was calibrated against clinically classified MSH6 variants and, employing Bayes’ rule, integrated with computational predictions of pathogenicity. To enable the validation of this two-component classification procedure we have employed a genetic screen to generate a large set of inactivating Msh6 variants, as proxies for pathogenic variants. Results: The genetic screen-derived variants established that the two-component classification procedure displays high sensitivities and specificities. Moreover, these inactivating variants enabled the direct reclassification of human variants of uncertain significance (VUS) as (likely) pathogenic. Conclusion: The two-component classification procedure and the genetic screens provide complementary approaches to rapidly and cost-effectively classify the large majority of human MSH6 variants. The approach followed here provides a template for the classification of variants in other disease-predisposing genes, facilitating the translation of personalized genomics into personalized health care

Patterns in sedentary and exercise behaviors and associations with overweight in 9–14-year-old boys and girls - a cross-sectional study.

BACKGROUND: Before starting interventions addressing energy-balance related behaviors, knowledge is needed about the prevalence of sedentary behaviors and low physical exercise, their interrelationships, possible gender differences. Therefore this study aimed to describe gender differences in sedentary and physical exercise behaviors and their association with overweight status in children from nine European countries. Additionally, to identify clusters of children sharing the same pattern regarding sedentary and physical exercise behavior and compare these groups regarding overweight status. METHODS: Cross-sectional study among 11-year-old children in nine countries (n = 12538). Self-administered questionnaires assessed the time spent on TV viewing during dinner and during the day, PC use and on physical exercise. The parents reported children's weight and height. Descriptive statistics, cluster analyses, and logistic regression analyses were used for data analyses. RESULTS: Boys spent more time on sedentary behaviors but also more on physical exercise than girls. High TV viewing and low exercise behavior independently increased the risk of being overweight. Based on the behaviors, five clusters were identified. Among boys, clear associations with being overweight were found, with the most unhealthy behavior pattern having the highest risks of being overweight. Among girls, high TV viewers and high PC users had increased risk of being overweight. In girls sedentary behaviors seemed more important than physical exercise with regard to overweight status. CONCLUSION: Despite selective non-response on BMI and reliance on self-reports, the associations between clusters and overweight in boys were clear, and differences between boys and girls regarding the behaviors and risks for overweight are noteworthy. These differences need to be considered when developing tailored intervention strategies for prevention of overweight