Entwicklung von DNA- und Expressions-Markern zum Nachweis von menschlichen künstlichen Chromosomen und in vivo Transfektionsanalyse verbesserter HAC Vektoren

Für die stabile, regulierte Expression eines therapeutischen Gens in Zielzellen stellen künstliche menschliche Chromosomen (HACs) derzeit das einzige Konzept dar, das hohe Sicherheit und technische Realisierbarkeit bietet. Künstliche Chromosomen (HACs) mit dem CFTR-Gen sollen sich durch den Transfer definierter HAC-Konstrukte effizient formieren, ohne dabei die Zielzellen zu stören. Im Augenblick werden künstliche Chromosomen zur Klärung vieler grundlegender Fragen auf dem Gebiet der Chromosomenstruktur und -funktion sowie der Genregulation konstruiert. In der vorliegenden Arbeit sollte die zugrundeliegende de novo HAC-Technologie der Arbeitsgruppe, die sich auf die Konstruktion und den intakten Transfer von PACs mit den funktionellen Komponenten menschlicher Chromosomen (zentromerische, telomerische und genomische Sequenzen mit oris und Gene) konzentriert, weiterentwickelt werden. Die Verwendung von PACs als Kloniervektoren erlaubt die stabile Klonierung langer, genomischer DNA, die biochemische Verknüpfung über lox/Cre vermittelte Rekombination, sowie die Darstellung grosser Mengen intakter, supercoiled PAC DNA durch Anwendung einer in der Arbeitsgruppe entwickelten Technik (Reinigung der supercoiled DNA Fraktion in Agaroseplugs von gebrochener und genickter DNA im elektrischen Feld). Eine Verbesserung der Vektoren ist nötig, da die Effizienz der HAC Formierung bisheriger Vektoren für eine klinische Anwendung nicht ausreicht. Dafür wurden zunächst Marker benötigt, die Anzeigen können wieviele Zellen mit wievielen Vektormolekülen transfiziert wurden und wieviele der physikalisch erfolgreich transfizierten Zellen stabile HACs bilden (genetische Funktion). Im Rahmen dieser Arbeit wurden Expressionsmarker entwickelt, die eine Formierung stabiler HAC-Linien durch grüne Fluoreszenz anzeigen können. So wurde ein tetratelomerischer PAC-Vektor „pTT“ konstruiert, der stabil eine EGFP-Kassette exprimiert, ein funktionelles Zentromer trägt (TTE1), und für die Klonierung weiterer genomischer Komponenten eine weiss/blau selektionierbare Sal I Stelle enthält. Ausserdem wurde ein CFTR-Gen-basierender „genomischer“ Marker (159 kb) vorgestellt, der den intakten Transfer langer, genomischer DNA und die Expression vom CFTR Promoter anzeigen kann. Besonders hervorzuhebende Ergebnisse aus der Arbeit sind: 1) Kopiezahlabhängigkeit bei der transienten Expression. Einzelne Markergen-Kopien genügen nicht, um Anwesenheit der transfizierten DNA mittels transienter Expression nachzuweisen. 2) Sichtbar transient exprimierende HAC Konstrukte (große Zahl) führen nicht zu stabilen Linien, was nahelegt, dass ein „low copy“ HAC Transfer benötigt wird. Für eine Optimierung und besseres „low copy“ HAC-Monitoring wurden multimere Marker (EGFP Array) und DNA-tags (Gal4-BD, Lac-Operator) entwickelt und stehen nun für einen Einsatz bereit. 3) Für den „low copy“ Transfer wurden neben Lipofektionsassays und der Mikroinjektion insbesondere eine neue Methode, die Baktofektion, eingesetzt, bei der die DNA nicht aus Bakterien isoliert werden muss: Modifizierte Transferbakterien dringen in die Zelle ein und geben die DNA-Konstrukte nach Autolyse frei („suicidal transfer“). Dabei wurde ein funktioneller Transfer genomischer DNA nachgewiesen. Es konnte zum einen gezeigt werden, dass Zentromer tragende Konstrukte effizient de novo HACs bildeten, und zum anderen, dass das lange genomische CFTR Expressionskonstrukt CGT21 stabil vom CFTR Promoter exprimiert wird. Damit steht nun die Baktofektion als effizienteste Methode zur HAC Optimierung zur Verfügung. 4) Durch Auszählung der stabilen Klone, Isolierung von Stichproben klonaler Linien und einem HAC-Formierungsassay mittels FISH Analyse, wurden folgende grundlegende Beobachtungen gemacht: Die Rate der Formierung stabiler Klone mit HAC Konstrukten hängt nicht von a) der Zahl der im einzelnen Konstrukt vorhandenen, oder cotransfizierten Zahl der BS Marker, b) nicht von der Orientierung der alpha-sat DNA relativ zum BS-Gen oder dem entgegengesetzt gerichteten EGFP-Gen, und c) nicht absolut von der Verwendung unterschiedlicher alpha-sat Sequenzen der zwei homogenen Array Typen auf Chr.5 ab, wobei der Vektor pTT mit dem Zentromer E1 die besten Ergebnisse der HAC Bildung erzielte und die höchsten Klonzahlen in Cotransfektionen mit einem telomerisierten Genkonstrukt erhalten wurden, nicht aber in Cotransfektionen mit dem Telomervektor ohne einklonierte genomische DNA. Diese Erkenntnisse haben direkte Relevanz für die Weiterentwicklung CFTR exprimierender HAC Vektoren. Mit den Konstrukten pTTE1 und CGT21, und den zukünftig erweiterten Konstrukten mit multimeren Markern bzw. Tags und einem kompletten CFTR Gen, kann nun auch der physikalische Transfer der HAC Konstrukte in Zielzellen, sowie deren Funktion effizient untersucht werden. Damit konnten wichtige Voraussetzungen für die Weiterentwicklung einer stabilen CFTR Gentherapie geschaffen werden

Low-level APC mutational mosaicism is the underlying cause in a substantial fraction of unexplained colorectal adenomatous polyposis cases

Background In 30-50% of patients with colorectal adenomatous polyposis, no germline mutation in the known genes APC, causing familial adenomatous polyposis, MUTYH, causing MUTYH-associated polyposis, or POLE or POLD1, causing polymerase-proofreading-associated polyposis can be identified, although a hereditary aetiology is likely. This study aimed to explore the impact of APC mutational mosaicism in unexplained polyposis. Methods To comprehensively screen for somatic low-level APC mosaicism, high-coverage next-generation sequencing of the APC gene was performed using DNA from leucocytes and a total of 53 colorectal tumours from 20 unrelated patients with unexplained sporadic adenomatous polyposis. APC mosaicism was assumed if the same loss-of-function APC mutation was present in 2 anatomically separated colorectal adenomas/carcinomas per patient. All mutations were validated using diverse methods. Results In 25% (5/20) of patients, somatic mosaicism of a pathogenic APC mutation was identified as underlying cause of the disease. In 2/5 cases, the mosaic level in leucocyte DNA was slightly below the sensitivity threshold of Sanger sequencing;while in 3/5 cases, the allelic fraction was either very low (0.1-1%) or no mutations were detectable. The majority of mosaic mutations were located outside the somatic mutation cluster region of the gene. Conclusions The present data indicate a high prevalence of pathogenic mosaic APC mutations below the detection thresholds of routine diagnostics in adenomatous polyposis, even if high-coverage sequencing of leucocyte DNA alone is taken into account. This has important implications for both routine work-up and strategies to identify new causative genes in this patient group

Gene-specific ACMG/AMP classification criteria for germline APC variants: recommendations from the ClinGen InSIGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel

Purpose The Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (VCEP) was established by the International Society for Gastrointestinal Hereditary Tumours and the Clinical Genome Resource, who set out to develop recommendations for the interpretation of germline APC variants underlying Familial Adenomatous Polyposis, the most frequent hereditary polyposis syndrome. Methods Through a rigorous process of database analysis, literature review, and expert elicitation, the APC VCEP derived gene-specific modifications to the ACMG/AMP (American College of Medical Genetics and Genomics and Association for Molecular Pathology) variant classification guidelines and validated such criteria through the pilot classification of 58 variants. Results The APC-specific criteria represented gene- and disease-informed specifications, including a quantitative approach to allele frequency thresholds, a stepwise decision tool for truncating variants, and semiquantitative evaluations of experimental and clinical data. Using the APC-specific criteria, 47% (27/58) of pilot variants were reclassified including 14 previous variants of uncertain significance (VUS). Conclusion The APC-specific ACMG/AMP criteria preserved the classification of well-characterized variants on ClinVar while substantially reducing the number of VUS by 56% (14/25). Moving forward, the APC VCEP will continue to interpret prioritized lists of VUS, the results of which will represent the most authoritative variant classification for widespread clinical use

Highly sensitive liquid biopsy Duplex sequencing complements tissue biopsy to enhance detection of clinically relevant genetic variants

BackgroundLiquid biopsy (LB) is a promising complement to tissue biopsy for detection of clinically relevant genetic variants in cancer and mosaic diseases. A combined workflow to enable parallel tissue and LB analysis is required to maximize diagnostic yield for patients.MethodsWe developed and validated a cost-efficient combined next-generation sequencing (NGS) workflow for both tissue and LB samples, and applied Duplex sequencing technology for highly accurate detection of low frequency variants in plasma. Clinically relevant cutoffs for variant reporting and quantification were established.ResultsWe investigated assay performance characteristics for very low amounts of clinically relevant variants. In plasma, the assay achieved 100% sensitivity and 92.3% positive predictive value (PPV) for single nucleotide variants (SNVs) and 91.7% sensitivity and 100% PPV for insertions and deletions (InDel) in clinically relevant hotspots with 0.5-5% variant allele frequencies (VAFs). We further established a cutoff for reporting variants (i.e. Limit of Blank, LOB) at 0.25% VAF and a cutoff for quantification (i.e. Limit of Quantification, LOQ) at 5% VAF in plasma for accurate clinical interpretation of analysis results. With our LB approach, we were able to identify the molecular cause of a clinically confirmed asymmetric overgrowth syndrome in a 10-year old child that would have remained undetected with tissue analysis as well as other molecular diagnostic approaches.ConclusionOur flexible and cost-efficient workflow allows analysis of both tissue and LB samples and provides clinically relevant cutoffs for variant reporting and precise quantification. Complementing tissue analysis by LB is likely to increase diagnostic yield for patients with molecular diseases

Identification of new molecular targets for PET imaging of the microglial anti-inflammatory activation state

Microglia are potential targets for therapeutic intervention in neurological and neurodegenerative diseases affecting the central nervous system. In order to assess the efficacy of therapies aimed to reduce the tissue damaging activities of microglia and/or to promote the protective potential of these cells, suitable pre-clinical and clinical tools for the in vivo analysis of microglia activities and dynamics are required. The aim of this work was to identify new translational markers of the anti-inflammatory/protective state of microglia for the development of novel PET tracers.Methods: New translational markers of the anti-inflammatory/protective activation state of microglia were selected by bioinformatic approaches and were in vitro and ex vivo validated by qPCR and immunohistochemistry in rodent and human samples. Once a viable marker was identified, a novel PET tracer was developed. This tracer was subsequently confirmed by autoradiography experiments in murine and human brain tissues.Results: Here we provide evidence that P2RYI2 expression increases in murine and human microglia following exposure to anti-inflammatory stimuli, and that its expression is modulated in the reparative phase of experimental and clinical stroke. We then synthesized a novel carbon-II labeled tracer targeting P2RYI2, showing increased binding in brain sections of mice treated with IL4, and low binding to brain sections of a murine stroke model and of a stroke patient.Conclusion: This study provides new translational targets for PET tracers for the anti-inflammatory/protective activation state of microglia and shows the potential of a rationale-based approach. It therefore paves the way for the development of novel non-invasive methodologies aimed to monitor the success of therapeutic approaches in various neurological diseases.</div

Optimasi Portofolio Resiko Menggunakan Model Markowitz MVO Dikaitkan dengan Keterbatasan Manusia dalam Memprediksi Masa Depan dalam Perspektif Al-Qur`an

Risk portfolio on modern finance has become increasingly technical, requiring the use of sophisticated mathematical tools in both research and practice. Since companies cannot insure themselves completely against risk, as human incompetence in predicting the future precisely that written in Al-Quran surah Luqman verse 34, they have to manage it to yield an optimal portfolio. The objective here is to minimize the variance among all portfolios, or alternatively, to maximize expected return among all portfolios that has at least a certain expected return. Furthermore, this study focuses on optimizing risk portfolio so called Markowitz MVO (Mean-Variance Optimization). Some theoretical frameworks for analysis are arithmetic mean, geometric mean, variance, covariance, linear programming, and quadratic programming. Moreover, finding a minimum variance portfolio produces a convex quadratic programming, that is minimizing the objective function ðð¥with constraintsð ð 𥠥 ðandð´ð¥ = ð. The outcome of this research is the solution of optimal risk portofolio in some investments that could be finished smoothly using MATLAB R2007b software together with its graphic analysis

Measurement of the Splitting Function in &ITpp &ITand Pb-Pb Collisions at root&ITsNN&IT=5.02 TeV

Data from heavy ion collisions suggest that the evolution of a parton shower is modified by interactions with the color charges in the dense partonic medium created in these collisions, but it is not known where in the shower evolution the modifications occur. The momentum ratio of the two leading partons, resolved as subjets, provides information about the parton shower evolution. This substructure observable, known as the splitting function, reflects the process of a parton splitting into two other partons and has been measured for jets with transverse momentum between 140 and 500 GeV, in pp and PbPb collisions at a center-of-mass energy of 5.02 TeV per nucleon pair. In central PbPb collisions, the splitting function indicates a more unbalanced momentum ratio, compared to peripheral PbPb and pp collisions.. The measurements are compared to various predictions from event generators and analytical calculations.Peer reviewe

Measurement of nuclear modification factors of gamma(1S)), gamma(2S), and gamma(3S) mesons in PbPb collisions at root s(NN)=5.02 TeV

The cross sections for ϒ(1S), ϒ(2S), and ϒ(3S) production in lead-lead (PbPb) and proton-proton (pp) collisions at √sNN = 5.02 TeV have been measured using the CMS detector at the LHC. The nuclear modification factors, RAA, derived from the PbPb-to-pp ratio of yields for each state, are studied as functions of meson rapidity and transverse momentum, as well as PbPb collision centrality. The yields of all three states are found to be significantly suppressed, and compatible with a sequential ordering of the suppression, RAA(ϒ(1S)) > RAA(ϒ(2S)) > RAA(ϒ(3S)). The suppression of ϒ(1S) is larger than that seen at √sNN = 2.76 TeV, although the two are compatible within uncertainties. The upper limit on the RAA of ϒ(3S) integrated over pT, rapidity and centrality is 0.096 at 95% confidence level, which is the strongest suppression observed for a quarkonium state in heavy ion collisions to date. © 2019 The Author(s). Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). Funded by SCOAP3.Peer reviewe

Electroweak production of two jets in association with a Z boson in proton-proton collisions root s =13 TeV

A measurement of the electroweak (EW) production of two jets in association with a Z boson in proton-proton collisions at root s = 13 TeV is presented, based on data recorded in 2016 by the CMS experiment at the LHC corresponding to an integrated luminosity of 35.9 fb(-1). The measurement is performed in the lljj final state with l including electrons and muons, and the jets j corresponding to the quarks produced in the hard interaction. The measured cross section in a kinematic region defined by invariant masses m(ll) > 50 GeV, m(jj) > 120 GeV, and transverse momenta P-Tj > 25 GeV is sigma(EW) (lljj) = 534 +/- 20 (stat) fb (syst) fb, in agreement with leading-order standard model predictions. The final state is also used to perform a search for anomalous trilinear gauge couplings. No evidence is found and limits on anomalous trilinear gauge couplings associated with dimension-six operators are given in the framework of an effective field theory. The corresponding 95% confidence level intervals are -2.6 <cwww/Lambda(2) <2.6 TeV-2 and -8.4 <cw/Lambda(2) <10.1 TeV-2. The additional jet activity of events in a signal-enriched region is also studied, and the measurements are in agreement with predictions.Peer reviewe

Search for supersymmetry in events with one lepton and multiple jets in proton-proton collisions at root s=13 TeV

Peer reviewe