Biomarkers of mismatch repair deficiency in colorectal cancer and cancer predisposition syndromes

PhD ThesisColorectal cancer (CRC) is the third most common cancer in Western societies and approximately 15% are mismatch repair deficient (MMRd). MMRd CRCs have a distinct prognosis, respond to immunotherapy, and occur at a high rate in patients with Lynch syndrome or constitutional mismatch repair deficiency (CMMRD). Detection of MMR deficiency, therefore, guides treatment and identification of associated cancerpredisposition syndromes. However, there is a need for novel biomarkers to detect MMRd CRC, and innovative assays to improve Lynch syndrome and CMMRD diagnosis. I assessed autoantibodies generated against MMRd CRCs as a liquid-biopsy biomarker for cancer detection, by analysing the sera of 464 Lynch syndrome gene carriers using a recently published, multiplex method. Although autoantibodies correlated with a history of CRC, a lack of signal from patients who developed CRC shortly after sampling suggests the method has poor sensitivity. Microsatellite instability (MSI) is an established biomarker of MMR deficiency. I used single molecule molecular inversion probes to develop a sequencing-based MSI assay with an automated results analysis, suitable as a companion diagnostic for immunotherapy, and for streamlined Lynch syndrome screening. The assay achieved 100% accuracy in 197 CRCs, and was robust to sample variables, including quantity, quality, and tumour cell content. Subsequently, I adapted the MSI assay to detect low-level MSI in non-neoplastic tissues of CMMRD patients. The assay separated all 32 CMMRD patients from 94 controls. For both CRC and CMMRD diagnostics, the MSI assay is cheaper and faster than current methods, and is scalable to large cohorts. These results suggest that the humoral immune response to MMRd CRCs cannot readily be used as a biomarker to detect disease, and that alternatives should be sought. However, the MSI assay could be deployed into clinical practice to meet the high demand for MMR deficiency testing of CRCs and to improve CMMRD diagnostics.the Barbour Foundatio

Umbilical Deployment Device

The landing scheme for NASA's next-generation Mars rover will encompass a novel landing technique (see figure). The rover will be lowered from a rocket-powered descent stage and then placed onto the surface while hanging from three bridles. Communication between the rover and descent stage will be maintained through an electrical umbilical cable, which will be deployed in parallel with structural bridles. The -inch (13-mm) umbilical cable contains a Kevlar rope core, around which wires are wrapped to create a cable. This cable is helically coiled between two concentric truncated cones. It is deployed by pulling one end of the cable from the cone. A retractable mechanism maintains tension on the cable after deployment. A break-tie tethers the umbilical end attached to the rover even after the cable is cut after touchdown. This break-tie allows the descent stage to develop some velocity away from the rover prior to the cable releasing from the rover deck, then breaks away once the cable is fully extended. The descent stage pulls the cable up so that recontact is not made. The packaging and deployment technique can store a long length of cable in a relatively small volume while maintaining compliance with the minimum bend radius requirement for the cable being deployed. While the packaging technique could be implemented without the use of break-ties, they were needed in this design due to the vibratory environment and the retraction required by the cable. The break-ties used created a series of load-spikes in the deployment signature. The load spikes during the deployment of the initial three coils of umbilical showed no increase between the different temperature trials. The cold deployment did show an increased load requirement for cable extraction in the region where no break-ties were used. This increase in cable drag was superimposed on the loads required to rupture the last set of break-ties, and as such, these loads saw significant increase when compared to their ambient counterparts. While the loads showed spikes of high magnitude, they were of short duration. Because of this, neither the deployment of the rover, nor the motion of the descent stage, would be adversely affected. In addition, the umbilical was found to have a maximum of 1.2 percent chance for recontact with the ultra-high frequency antenna due to the large margin of safety built in

Pyrotechnic Actuator for Retracting Tubes Between MSL Subsystems

An apparatus, denoted the "retractuator" (a contraction of "retracting actuator"), was designed to help ensure clean separation between the cruise stage and the entry-vehicle subsystem of the Mars Science Laboratory (MSL) mission. The retractuator or an equivalent mechanism is needed because of tubes that (1) transport a heat-transfer fluid between the stages during flight and (2) are cut immediately prior to separation of the stages retractuator. The role of the retractuator is to retract the tubes, after they are cut and before separation of the subsystem, so that cut ends of the tubes do not damage thermal-protection coats on the entry vehicle and do not contribute to uncertainty of drag and consequent uncertainty in separation velocity

Circulating Cell-Free DNA Captures the Intratumor Heterogeneity in Multinodular Hepatocellular Carcinoma.

PURPOSE Hepatocellular carcinoma (HCC) is a highly heterogeneous disease, with more than 40% of patients initially diagnosed with multinodular HCCs. Although circulating cell-free DNA (cfDNA) has been shown to effectively detect somatic mutations, little is known about its utility to capture intratumor heterogeneity in patients with multinodular HCC undergoing systemic treatment. MATERIALS AND METHODS Tumor biopsies and plasma were synchronously collected from seven prospectively recruited patients with HCC before and during systemic therapy. Plasma-derived cfDNA and matched germline were subjected to high-depth targeted sequencing with molecular barcoding. The mutational profile of the cfDNA was compared with whole-exome sequencing from matched tumor biopsies. RESULTS Genomic data revealed that out of the seven patients, five were considered intrahepatic metastasis and two multicentric HCCs. cfDNA captured the majority of mutations in the tumors and detected significantly more mutations than tumor biopsies. Driver mutations such as CTNNB1 S33C, NRAS Q61R, ARID1A R727fs, and NF1 E2368fs as well as standard-of-care biomarkers of response to targeted therapy were detected only in cfDNA. In the two patients with multicentric HCC, cfDNA detected mutations derived from the genetically independent and spatially distinct nodules. Moreover, cfDNA was not only able to capture clonal mutations but also the subclonal mutations detected in only one of the multiple biopsied nodules. Furthermore, serial cfDNA detected variants of tumor origin emerging during treatment. CONCLUSION This study revealed that the genetic analysis of cfDNA captures the intratumor heterogeneity in multinodular HCC highlighting the potential for cfDNA as a sensitive and noninvasive tool for precision medicine

The Role of Chronic Liver Diseases in the Emergence and Recurrence of Hepatocellular Carcinoma: An Omics Perspective.

Hepatocellular carcinoma (HCC) typically develops from a background of cirrhosis resulting from chronic inflammation. This inflammation is frequently associated with chronic liver diseases (CLD). The advent of next generation sequencing has enabled extensive analyses of molecular aberrations in HCC. However, less attention has been directed to the chronically inflamed background of the liver, prior to HCC emergence and during recurrence following surgery. Hepatocytes within chronically inflamed liver tissues present highly activated inflammatory signaling pathways and accumulation of a complex mutational landscape. In this altered environment, cells may transform in a stepwise manner toward tumorigenesis. Similarly, the chronically inflamed environment which persists after resection may impact the timing of HCC recurrence. Advances in research are allowing an extensive epigenomic, transcriptomic and proteomic characterization of CLD which define the emergence of HCC or its recurrence. The amount of data generated will enable the understanding of oncogenic mechanisms in HCC from the CLD perspective and provide the possibility to identify robust biomarkers or novel therapeutic targets for the treatment of primary and recurrent HCC. Importantly, biomarkers defined by the analysis of CLD tissue may permit the early detection or prevention of HCC emergence and recurrence. In this review, we compile the current omics based evidence of the contribution of CLD tissues to the emergence and recurrence of HCC

PI5P4Kα supports prostate cancer metabolism and exposes a survival vulnerability during androgen receptor inhibition.

Phosphatidylinositol (PI)regulating enzymes are frequently altered in cancer and have become a focus for drug development. Here, we explore the phosphatidylinositol-5-phosphate 4-kinases (PI5P4K), a family of lipid kinases that regulate pools of intracellular PI, and demonstrate that the PI5P4Kα isoform influences androgen receptor (AR) signaling, which supports prostate cancer (PCa) cell survival. The regulation of PI becomes increasingly important in the setting of metabolic stress adaptation of PCa during androgen deprivation (AD), as we show that AD influences PI abundance and enhances intracellular pools of PI-4,5-P2. We suggest that this PI5P4Kα-AR relationship is mitigated through mTORC1 dysregulation and show that PI5P4Kα colocalizes to the lysosome, the intracellular site of mTORC1 complex activation. Notably, this relationship becomes prominent in mouse prostate tissue following surgical castration. Finally, multiple PCa cell models demonstrate marked survival vulnerability following stable PI5P4Kα inhibition. These results nominate PI5P4Kα as a target to disrupt PCa metabolic adaptation to castrate resistance

GEOTRACES IC1 (BATS) contamination-prone trace element isotopes Cd, Fe, Pb, Zn, Cu, and Mo intercalibration

International audienceWe report data on the isotopic composition of cadmium, copper, iron, lead, zinc, and molybdenum at the GEOTRACES IC1 BATS Atlantic intercalibration station. In general, the between lab and within-lab precisions are adequate to resolve global gradients and vertical gradients at this station for Cd, Fe, Pb, and Zn. Cd and Zn isotopes show clear variations in the upper water column and more subtle variations in the deep water; these variations are attributable, in part, to progressive mass fractionation of isotopes by Rayleigh distillation from biogenic uptake and/or adsorption. Fe isotope variability is attributed to heavier crustal dust and hydrothermal sources and light Fe from reducing sediments. Pb isotope variability results from temporal changes in anthropogenic source isotopic compositions and the relative contributions of U.S. and European Pb sources. Cu and Mo isotope variability is more subtle and close to analytical precision. Although the present situation is adequate for proceeding with GEOTRACES, it should be possible to improve the within-lab and between-lab precisions for some of these properties

Standardizing Patient-Derived Organoid Generation Workflow to Avoid Microbial Contamination From Colorectal Cancer Tissues.

The use of patient-derived organoids (PDO) as a valuable alternative to in vivo models significantly increased over the last years in cancer research. The ability of PDOs to genetically resemble tumor heterogeneity makes them a powerful tool for personalized drug screening. Despite the extensive optimization of protocols for the generation of PDOs from colorectal tissue, there is still a lack of standardization of tissue handling prior to processing, leading to microbial contamination of the organoid culture. Here, using a cohort of 16 patients diagnosed with colorectal carcinoma (CRC), we aimed to test the efficacy of phosphate-buffered saline (PBS), penicillin/streptomycin (P/S), and Primocin, alone or in combination, in preventing organoid cultures contamination when used in washing steps prior to tissue processing. Each CRC tissue was divided into 5 tissue pieces, and treated with each different washing solution, or none. After the washing steps, all samples were processed for organoid generation following the same standard protocol. We detected contamination in 62.5% of the non-washed samples, while the use of PBS or P/S-containing PBS reduced the contamination rate to 50% and 25%, respectively. Notably, none of the organoid cultures washed with PBS/Primocin-containing solution were contaminated. Interestingly, addition of P/S to the washing solution reduced the percentage of living cells compared to Primocin. Taken together, our results demonstrate that, prior to tissue processing, adding Primocin to the tissue washing solution is able to eliminate the risk of microbial contamination in PDO cultures, and that the use of P/S negatively impacts organoids growth. We believe that our easy-to-apply protocol might help increase the success rate of organoid generation from CRC patients

DNA Methylation Landscapes of Prostate Cancer Brain Metastasis Are Shaped by Early Driver Genetic Alterations

UNLABELLED Metastases from primary prostate cancers to rare locations, such as the brain, are becoming more common due to longer life expectancy resulting from improved treatments. Epigenetic dysregulation is a feature of primary prostate cancer, and distinct DNA methylation profiles have been shown to be associated with the mutually exclusive SPOP-mutant or TMPRSS2-ERG fusion genetic backgrounds. Using a cohort of prostate cancer brain metastases (PCBM) from 42 patients, with matched primary tumors for 17 patients, we carried out a DNA methylation analysis to examine the epigenetic distinction between primary prostate cancer and PCBM, the association between epigenetic alterations and mutational background, and particular epigenetic alterations that may be associated with PCBM. Multiregion sampling of PCBM revealed epigenetic stability within metastases. Aberrant methylation in PCBM was associated with mutational background and PRC2 complex activity, an effect that is particularly pronounced in SPOP-mutant PCBM. While PCBM displayed a CpG island hypermethylator phenotype, hypomethylation at the promoters of genes involved in neuroactive ligand-receptor interaction and cell adhesion molecules such as GABRB3, CLDN8, and CLDN4 was also observed, suggesting that cells from primary tumors may require specific reprogramming to form brain metastasis. This study revealed the DNA methylation landscapes of PCBM and the potential mechanisms and effects of PCBM-associated aberrant DNA methylation. SIGNIFICANCE DNA methylation analysis reveals the molecular characteristics of PCBM and may serve as a starting point for efforts to identify and target susceptibilities of these rare metastases

Effect of sirolimus on malignancy and survival after kidney transplantation: systematic review and meta-analysis of individual patient data

Objective To examine risk of malignancy and death in patients with kidney transplant who receive the immunosuppressive drug sirolimus.Design Systematic review and meta-analysis of individual patient data.Data sources Medline, Embase, and the Cochrane Central Register of Controlled Trials from inception to March 2013.Eligibility Randomized controlled trials comparing immunosuppressive regimens with and without sirolimus in recipients of kidney or combined pancreatic and renal transplant for which the author was willing to provide individual patient level data. Two reviewers independently screened titles/abstracts and full text reports of potentially eligible trials to identify studies for inclusion. All eligible trials reported data on malignancy or survival.Results the search yielded 2365 unique citations. Patient level data were available from 5876 patients from 21 randomized trials. Sirolimus was associated with a 40% reduction in the risk of malignancy (adjusted hazard ratio 0.60, 95% confidence interval 0.39 to 0.93) and a 56% reduction in the risk of non-melanoma skin cancer (0.44, 0.30 to 0.63) compared with controls. the most pronounced effect was seen in patients who converted to sirolimus from an established immunosuppressive regimen, resulting in a reduction in risk of malignancy (0.34, 0.28 to 0.41), non-melanoma skin cancer (0.32, 0.24 to 0.42), and other cancers (0.52, 0.38 to 0.69). Sirolimus was associated with an increased risk of death (1.43, 1.21 to 1.71) compared with controls.Conclusions Sirolimus was associated with a reduction in the risk of malignancy and non-melanoma skin cancer in transplant recipients. the benefit was most pronounced in patients who converted from an established immunosuppressive regimen to sirolimus. Given the risk of mortality, however, the use of this drug does not seem warranted for most patients with kidney transplant. Further research is needed to determine if different populations, such as those at high risk of cancer, might benefit from sirolimus.PfizerOttawa Hosp, Res Inst, Ottawa, ON K1H 7W9, CanadaUniv Ottawa, Ottawa, ON, CanadaCairo Univ, Cairo Kidney Ctr, Cairo, EgyptLimites Med Res, Vacallo, SwitzerlandUniv Manitoba, Dept Pediat & Childs Hlth, Winnipeg, MB, CanadaLund Univ, Dept Nephrol & Transplantat, Malmo, SwedenUniversidade Federal de São Paulo, Hosp Rim & Hipertensao, São Paulo, BrazilAddenbrookes Hosp, Dept Renal Med, Cambridge, EnglandNorthwestern Univ, Feinberg Sch Med, Chicago, IL 60611 USAMaastricht Univ, Med Ctr, Maastricht, NetherlandsSt Louis Hosp, Dept Nephrol, Paris, FranceHosp JW Goethe, Div Nephrol, Frankfurt, GermanyUniv Munich, Dept Surg, Munich, GermanyGoethe Univ Frankfurt, JW Goethe Clin, Clin Dermatol Venerol & Allergol, Frankfurt, GermanyInst Klin Expt Med, Dept Nephrol, Prague, Czech RepublicUniv Cambridge, Addenbrookes Hosp, Dept Surg, NIHR Cambridge Biomed Res Ctr, Cambridge CB2 2QQ, EnglandUniversidade Federal de São Paulo, Hosp Rim & Hipertensao, São Paulo, BrazilWeb of Scienc