Single cell proteomics characterization of bone marrow hematopoiesis with distinct Ras pathway lesions

Normal hematopoiesis requires constant prolific production of different blood cell lineages by multipotent hematopoietic stem cells (HSC). Stem- and progenitor- cells need to balance dormancy with proliferation. How genetic alterations impact frequency, lineage potential, and metabolism of HSC is largely unknown. Here, we compared induced expression of KRAS G12D or RasGRP1 to normal hematopoiesis. At low-resolution, both Ras pathway lesions result in skewing towards myeloid lineages. Single-cell resolution CyTOF proteomics unmasked an expansion of HSC- and progenitor- compartments for RasGRP1, contrasted by a depletion for KRAS G12D . SCENITH™ quantitates protein synthesis with single-cell precision and corroborated that immature cells display low metabolic SCENITH™ rates. Both RasGRP1 and KRAS G12D elevated mean SCENITH™ signals in immature cells. However, RasGRP1-overexpressing stem cells retain a metabolically quiescent cell-fraction, whereas this fraction diminishes for KRAS G12D . Our temporal single cell proteomics and metabolomics datasets provide a resource of mechanistic insights into altered hematopoiesis at single cell resolution.

SARS-CoV-2 infection of airway organoids reveals conserved use of Tetraspanin-8 by Ancestral, Delta, and Omicron variants

Ancestral SARS coronavirus-2 (SARS-CoV-2) and variants of concern (VOC) caused a global pandemic with a spectrum of disease severity. The mechanistic explaining variations related to airway epithelium are relatively understudied. Here, we biobanked airway organoids (AO) by preserving stem cell function. We optimized viral infection with H1N1/PR8 and comprehensively characterized epithelial responses to SARS-CoV-2 infection in phenotypically stable AO from 20 different subjects. We discovered Tetraspanin-8 (TSPAN8) as a facilitator of SARS-CoV-2 infection. TSPAN8 facilitates SARS-CoV-2 infection rates independently of ACE2-Spike interaction. In head-to-head comparisons with Ancestral SARS-CoV-2, Delta and Omicron VOC displayed lower overall infection rates of AO but triggered changes in epithelial response. All variants shared highest tropism for ciliated and goblet cells. TSPAN8-blocking antibodies diminish SARS-CoV-2 infection and may spur novel avenues for COVID-19 therapy.

KS01.6.A Comparative analysis of the immune compartment in human glioblastoma and IDH-mutant WHO grade 4 astrocytoma reveals profound differences in microglia phenotypes

BACKGROUND

Glioblastoma (GBM) are the most common primary brain tumors. If untreated the average survival is around 12–18 months. Unfortunately, despite extensive research efforts, the therapeutic options remain limited. One major aspect complicating therapeutic development is an immunosuppressive tumor microenvironment. Isocitrate dehydrogenase (IDH)-mutant, WHO grade 4 astrocytomas appear histologically indistinguishable from GBM, but show significantly longer survival times. IDH mutations lead to changes in the tumor microenvironment with accrual of the neometabolite R-2-hydroxyglutarate. Previous studies on bulk transcriptomes have shown differences in the immune compartment of both tumor entities that were linked to the differences in clinical behavior.

MATERIAL AND METHODS

We have conducted high-dimensional comparative analyses of the myeloid compartment in surgically resected human GBM and IDH-mutant WHO grade 4 astrocytomas using single-cell RNA-Sequencing and immunohistochemistry. Histologically normal brain regions from epilepsy patients were used as controls. For analysis, whole-cell suspensions were prepared from freshly resected tumors or controls. Fluorescence activated cell sorting was used for myeloid cell enrichment. Samples were processed using the high-sensitivity single-cell RNA sequencing protocol CEL-Seq2. Seurat and StemID2 algorithms were used for clustering, differential gene expression and pseudotime analysis. Protein validation was achieved using immunohistochemistry.

RESULTS

We identified profound transcriptional changes of glioma-associated microglia in GBM with respect to control brain samples. Namely, we observed a global upregulation of major histocompatibility complex associated genes in GBM across all clusters. Additionally, we identified distinct myeloid subsets with phagocytic, hypoxia-associated and chemotactic transcriptomic signatures. Pseudotime analysis finely resolved transitional cell states. These changes were dramatically attenuated in IDH-mutant WHO grade 4 astrocytomas. The myeloid cells in these tumors resembled homeostatic microglia and showed an increased expression of cytokine and chemokine genes.

CONCLUSION

Here, we present a high-dimensional transcriptomic atlas of the myeloid compartment in human GBM and IDH-mutant WHO grade 4 astrocytomas. The identified differences point towards targeted therapeutic options via the modulation of the tumor microenvironment.

Einfluss der Entblätterung vor der Blüte auf Traubenqualität und Ertrag von “Riesling” und “Zweigelt”

Die Auswirkungen verschiedener Entblätterungsmaßnahmen auf das Auftreten von Sonnenbrand und Botrytis, Traubendichte, Ertrag, Traubengewicht, Wildverbiss, Beerengewicht, Mostgewicht, Säuregehalt, pH-Wert und die Gehalte an Phenolen und Stickstoff im Most wurden in einem zweijährigen Versuch an den Rebsorten ‘Riesling' und ‘Zweigelt' erhoben. Im Jahr 2012 wurden bei ‘Riesling' die Sonnenbrandschäden durch die Entblätterung und im Besonderen durch die frühe Entfernung der untersten sechs Blätter und Geiztriebe vor der Blüte zum Entwicklungsstadium BBCH 57 erhöht. Im Jahr 2013 waren die Sonnenbrandschäden witterungsbedingt deutlich geringer und traten wie bei der Rebsorte ‘Zweigelt' nur an einzelnen Beeren auf. Dieselbe Maßnahme hatte bei ‘Riesling' einen signifikant reduzierenden Effekt auf das Auftreten von Botrytis, hingegen war der Befall in jener Variante, in der keine Blätter entfernt wurden, am signifikant höchsten. Bei “Zweigelt” war der Befall mit Botrytis sehr gering und trat nur an einzelnen Beeren auf. Eine Reduktion der Traubendichte durch die Entblätterung vor der Blüte konnte bei “Riesling” nicht ermittelt werden. Die Traubendichte war als “mittel” bis “dicht” einzustufen. Bei “Zweigelt” wurde die Traubendichte durch die frühe Entblätterung und Geiztriebentfernung hingegen signifikant verringert, und zwar von “dicht” auf “mittel”. Bei beiden Rebsorten waren Ertrag und Traubengewicht in jener Variante, in der vor der Blüte die Blätter und Geiztriebe entfernt wurden, signifikant verringert. Die Ertragsreduktion betrug jahresabhängig bei “Riesling” 16% beziehungsweise 21% und bei “Zweigelt” 28% beziehungsweise 35%. Das Traubengewicht verringerte sich jahresabhängig um 20% und 15% bei “Riesling´beziehungsweise 24% und 29% bei “Zweigelt”. Das Mostgewicht wurde bei der Rebsorte ‘Riesling' in jener Variante, in der die untersten sechs Blätter und Geiztriebe zum Entwicklungsstadium BBCH 83 (Beerenverfärbung) entfernt wurden, in beiden Jahren signifikant verringert, und zwar um 0.8 bis 1 ∘KMW beziehungsweise um 0.4 bis 0.7 ∘KMW, nicht jedoch bei der Rebsorte ‘Zweigelt'. Durch die frühe Entfernung der untersten sechs Blätter und Geiztriebe vor der Blüte wurde das Mostgewicht bei keiner der beiden Rebsorten beeinflusst. Nur im Jahr 2012 und nur bei der Rebsorte ‘Riesling' war der Gehalt an Gesamtphenolen im Most der vor der Blüte entblätterten Variante mit 0.039 g/l signifikant erhöht. Die Stickstoffwerte im Most streuten innerhalb der Versuchsvarianten bei beiden Rebsorten stark ohne signifikante Unterschiede zwischen den Versuchsvarianten. Die sensorische Bewertung der Weine der Rebsorte “Riesling” erbrachte in beiden Jahren keine signifikanten Unterschiede.

Establishing an International Reference Image Database for Research and Development in Medical Image Processing

Introduction: The lack of comparability of evaluation results is one of the major obstacles of research and development in Medical Image Processing (MIP). The main reason for that is the usage of different image datasets with different quality, size and Gold standard.

Objectives: Therefore, one of the goals of the Working Group on Medical Image Processing of the European Federation for Medical Informatics (EFMI WG MIP) is to develop first parts of a Reference Image Database.

Methods: Kernel of the concept is to identify highly relevant medical problems with significant potential for improvement by MIP, and then to provide respective reference datasets. The EFMI WG MIP has primarily the role of a specifying group and an information broker, while the provider user relationships are defined by bilateral co-operation or license agreements.

Results: An explorative database prototype has been implemented using the MySQL database software on the Web. Templates for provider user agreements have been worked out and already applied for own ‘pre-RID-MIP’ co-operations of the authors.

Discussion and Conclusion: First steps towards a comprehensive reference image database have been done. Issues like funding, motivation, management, provision of Gold standards and evaluation guidelines are to be solved. Due to the interest from research groups and industry the efforts will be continued.

HIV encephalopathy: glial activation and hippocampal neuronal apoptosis, but limited neural repair

OBJECTIVES

HIV infection affects the central nervous system (CNS), frequently causing cognitive impairment. Hippocampal injury impedes the ability to transfer information into memory. Therefore, we aimed to examine neuronal injury and repair in the hippocampal formation in HIV encephalopathy.

METHODS

We compared neuropathological findings in 14 autopsy cases after death from systemic complications of HIV infection and in 15 age-matched HIV-negative control cases after sudden death from nonneurological causes using immunohistochemistry.

RESULTS

The density of apoptotic granule cells in the dentate gyrus was higher in HIV-infected than in control cases (P = 0.048). Proliferation of neural progenitor cells in the dentate gyrus was increased in HIV infection (P = 0.028), whereas the density of recently generated TUC-4 [TOAD (turned on after division)/Ulip/CRMP family 4]-expressing neurons in this region was not significantly elevated in HIV-infected cases (P = 0.13). HIV infection caused microglial activation and astrocytosis in the neocortex and hippocampal formation. Conversely, we were unable to detect more pronounced axonal injury in HIV-infected than in control cases.

CONCLUSIONS

As in other infections involving the CNS, apoptosis of hippocampal neurons accompanied by microglial activation and astrocytosis is a prominent feature of HIV encephalopathy. The regenerative potential, assessed using the density of young neurons in the hippocampal dentate gyrus, in HIV infection appears to be lower than in acute bacterial meningitis and septic encephalitis.

DNA commission of the International Society of Forensic Genetics: Recommendations on the evaluation of STR typing results that may include drop-out and/or drop-in using probabilistic methods

DNA profiling of biological material from scenes of crimes is often complicated because the amount of DNA is limited and the quality of the DNA may be compromised. Furthermore, the sensitivity of STR typing kits has been continuously improved to detect low level DNA traces. This may lead to (1) partial DNA profiles and (2) detection of additional alleles. There are two key phenomena to consider: allelic or locus 'drop-out', i.e. 'missing' alleles at one or more genetic loci, while 'drop-in' may explain alleles in the DNA profile that are additional to the assumed main contributor(s). The drop-in phenomenon is restricted to 1 or 2 alleles per profile. If multiple alleles are observed at more than two loci then these are considered as alleles from an extra contributor and analysis can proceed as a mixture of two or more contributors. Here, we give recommendations on how to estimate probabilities considering drop-out, Pr(D), and drop-in, Pr(C). For reasons of clarity, we have deliberately restricted the current recommendations considering drop-out and/or drop-in at only one locus. Furthermore, we offer recommendations on how to use Pr(D) and Pr(C) with the likelihood ratio principles that are generally recommended by the International Society of Forensic Genetics (ISFG) as measure of the weight of the evidence in forensic genetics. Examples of calculations are included. An Excel spreadsheet is provided so that scientists and laboratories may explore the models and input their own data.