Bacteria tracking by in vivo magnetic resonance imaging

Background: Different non-invasive real-time imaging techniques have been developed over the last decades to study bacterial pathogenic mechanisms in mouse models by following infections over a time course. In vivo investigations of bacterial infections previously relied mostly on bioluminescence imaging (BLI), which is able to localize metabolically active bacteria, but provides no data on the status of the involved organs in the infected host organism. In this study we established an in vivo imaging platform by magnetic resonance imaging (MRI) for tracking bacteria in mouse models of infection to study infection biology of clinically relevant bacteria. Results: We have developed a method to label Gram-positive and Gram-negative bacteria with iron oxide nano particles and detected and pursued these with MRI. The key step for successful labeling was to manipulate the bacterial surface charge by producing electro-competent cells enabling charge interactions between the iron particles and the cell wall. Different particle sizes and coatings were tested for their ability to attach to the cell wall and possible labeling mechanisms were elaborated by comparing Gram-positive and -negative bacterial characteristics. With 5-nm citrate-coated particles an iron load of 0.015 ± 0.002 pg Fe/bacterial cell was achieved for Staphylococcus aureus. In both a subcutaneous and a systemic infection model induced by iron-labeled S. aureus bacteria, high resolution MR images allowed for bacterial tracking and provided information on the morphology of organs and the inflammatory response. Conclusion: Labeled with iron oxide particles, in vivo detection of small S. aureus colonies in infection models is feasible by MRI and provides a versatile tool to follow bacterial infections in vivo. The established cell labeling strategy can easily be transferred to other bacterial species and thus provides a conceptual advance in the field of molecular MRI.<br

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts.The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that -80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAFPeer reviewe

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Zur Versorgungssituation und konservativen Therapie des okulären vernarbenden Schleimhautpemphigoids in Deutschland

$\bf Hintergrund:$ Die okuläre Beteiligung bei vernarbendem Schleimhautpemphigoid (SHP) ist mit einer Prävalenz von 25 Fällen je 1 Mio. Einwohner und damit ca. 2100 Patienten in ganz Deutschland selten. Die Diagnosestellung kann – besonders in Abwesenheit anderer Beteiligungen – schwierig und die Therapie komplex und langwierig sein. Nicht selten kommen Immunsuppressiva zum Einsatz. Aufgrund der Komplexität von Diagnose und Therapie sind SHP-Patienten meist an entsprechend spezialisierte Zentren angebunden. Ziel dieses Projektes war die Erfassung der aktuellen augenärztlichen Versorgungssituation von Patienten mit SHP in Deutschland. $\bf Methoden:$ Eine papierbasierte Umfrage wurde konzipiert und im April 2020 an alle Universitätsaugenkliniken und weitere potenzielle Zentren versandt. Gefragt wurde nach dem Bestehen einer spezialisierten Sprechstunde, der jährlichen Gesamtzahl der betreuten Patienten, der jährlichen Anzahl von neu diagnostizierten Patienten, den klinischen Kooperationspartnern in Diagnostik und Therapie sowie nach der angewendeten lokalen und systemischen Therapie. $\bf Ergebnisse:$ Von insgesamt 44 angeschrieben Kliniken erfolgten 28 (64%) vollständige Rückmeldungen. Im Mittel werden in den Kliniken 27 $\pm$ 42 (0–200) Patienten betreut und jährlich pro Zentrum 3,6 $\pm$ 2,2 (0–10) neue Fälle diagnostiziert. Dies entspricht einer Gesamtpatientenzahl von 741 Patienten. Lediglich 9 (32%) der antwortenden Kliniken bieten eine spezialisierte SHP-Sprechstunde an. 93% der Zentren kooperieren mit der lokalen Klinik für Dermatologie. 79% führen die serologische und histologische Diagnostik intern durch. Etwa die Hälfte der Zentren (n = 16) wendet ein standardisiertes Therapieschema an. Systemisch werden Glukokortikoide (66,7%) am häufigsten verwendet, gefolgt von Mycophenolatmofetil und Dapson (57,1 %), Rituximab (33,3%), Azathioprin und Cyclophosphamid (28,6%) sowie Methotrexat (19,0%). Am seltensten werden i.v. Immunoglobuline eingesetzt (14,3 %). $\bf Schlussfolgerung:$ Mit dieser Umfrage unter deutschen augenärztlichen Zentren wurden Daten von etwa einem Drittel der geschätzten Gesamtzahl aller in Deutschland an einem SHP erkrankten Menschen erhoben. Dabei handelt es sich vermutlich ausschließlich um Patienten mit mindestens einer okulären Beteiligung. Aktuell wird eine augenärztliche SHP-Registerstudie etabliert, um die Epidemiologie und Versorgungssituation besser zu erfassen und langfristig zu verbessern

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts