New Proteomic Signatures to Distinguish Between Zika and Dengue Infections.

Distinguishing between Zika and dengue virus infections is critical for accurate treatment, but we still lack detailed understanding of their impact on their host. To identify new protein signatures of the two infections, we used next-generation proteomics to profile 122 serum samples from 62 Zika and dengue patients. We quantified >500 proteins and identified 13 proteins that were significantly differentially expressed (adjusted p-value < 0.05). These proteins typically function in infection and wound healing, with several also linked to pregnancy and brain function. We successfully validated expression differences with Carbonic Anhydrase 2 in both the original and an independent sample set. Three of the differentially expressed proteins, i.e., Fibrinogen Alpha, Platelet Factor 4 Variant 1, and Pro-Platelet Basic Protein, predicted Zika virus infection at a ∼70% true-positive and 6% false-positive rate. Further, we showed that intraindividual temporal changes in protein signatures can disambiguate diagnoses and serve as indicators for past infections. Taken together, we demonstrate that serum proteomics can provide new resources that serve to distinguish between different viral infections.

[Development and progress of the National Autopsy Network (NATON)]. / Entwicklung und Fortschritte des Nationalen Obduktionsnetzwerks (NATON).

BACKGROUND: Autopsies have long been considered the gold standard for quality assurance in medicine, yet their significance in basic research has been relatively overlooked. The COVID-19 pandemic underscored the potential of autopsies in understanding pathophysiology, therapy, and disease management. In response, the German Registry for COVID-19 Autopsies (DeRegCOVID) was established in April 2020, followed by the DEFEAT PANDEMIcs consortium (2020-2021), which evolved into the National Autopsy Network (NATON). DEREGCOVID: DeRegCOVID collected and analyzed autopsy data from COVID-19 deceased in Germany over three years, serving as the largest national multicenter autopsy study. Results identified crucial factors in severe/fatal cases, such as pulmonary vascular thromboemboli and the intricate virus-immune interplay. DeRegCOVID served as a central hub for data analysis, research inquiries, and public communication, playing a vital role in informing policy changes and responding to health authorities. NATON: Initiated by the Network University Medicine (NUM), NATON emerged as a sustainable infrastructure for autopsy-based research. NATON aims to provide a data and method platform, fostering collaboration across pathology, neuropathology, and legal medicine. Its structure supports a swift feedback loop between research, patient care, and pandemic management. CONCLUSION: DeRegCOVID has significantly contributed to understanding COVID-19 pathophysiology, leading to the establishment of NATON. The National Autopsy Registry (NAREG), as its successor, embodies a modular and adaptable approach, aiming to enhance autopsy-based research collaboration nationally and, potentially, internationally.

Re-mining serum proteomics data reveals extensive post-translational modifications upon Zika and dengue infection.

Zika virus (ZIKV) and dengue virus (DENV) are two closely related flaviviruses with similar symptoms. However, due to the implications of ZIKV infections for pregnancy outcomes, understanding differences in their molecular impact on the host is of high interest. Viral infections change the host proteome, including post-translational modifications. As modifications are diverse and of low abundance, they typically require additional sample processing which is not feasible for large cohort studies. Therefore, we tested the potential of next-generation proteomics data in its ability to prioritize specific modifications for later analysis. We re-mined published mass spectra from 122 serum samples from ZIKV and DENV patients for the presence of phosphorylated, methylated, oxidized, glycosylated/glycated, sulfated, and carboxylated peptides. We identified 246 modified peptides with significantly differential abundance in ZIKV and DENV patients. Amongst these, methionine-oxidized peptides from apolipoproteins and glycosylated peptides from immunoglobulin proteins were more abundant in ZIKV patient serum and generate hypotheses on the potential roles of the modification in the infection. The results demonstrate how data-independent acquisition techniques can help prioritize future analyses of peptide modifications.

Determinants of public interest in emerging and re-emerging arboviral diseases in Europe: A spatio-temporal analysis of cross-sectional time series data.

Introduction: Climate change, the resulting geographical expansion of arthropod disease vectors, and increasing international mobility are contributing to the emergence of arboviral diseases in Europe. Public interest in vector-borne diseases and a subsequent gain of awareness and knowledge are essential to control outbreaks but had not yet been systematically assessed prior to this analysis. Methods: Trends, patterns, and determinants of public interest in six emerging and re-emerging arboviral diseases were assessed in a spatio-temporal analysis of Google Trends data from 30 European countries between 2008 and 2020 while controlling for potential confounders. Results: Only public interest in endemic arboviral diseases in Europe displays seasonal patterns and has been increasing since 2008, while no significant patterns or trends could be determined for public interest in non-endemic diseases. The main drivers for public interest in all six analysed arboviral diseases are reported case rates, and public interest drops rapidly as soon as cases decline. For Germany, the correlation of public interest and the geographical distribution of locally-acquired reported cases of endemic arboviral infections could be shown on a sub-country level. Conclusions: The results of the analysis indicate that public interest in arboviral diseases in Europe is heavily impacted by perceived susceptibility on a temporal as well as on a spatial level. This result may be crucial for the design of future public health interventions to alert the public to the increasing risk of infection with arboviral diseases.

Ectopic Expression of Hematopoietic SHIP1 in Human Colorectal Cancer.

Colorectal cancer (CRC) is a heterogeneous disease that results from the accumulation of mutations in colonic mucosa cells. A subclass of CRC is characterized by microsatellite instability, which is thought to occur mainly through inactivation of the DNA mismatch repair genes MLH1 and MSH2. The inositol 5-phosphatase SHIP1 is expressed predominantly in hematopoietic cells. In this study, the expression of SHIP1 in carcinomas and its putative correlation with clinicopathologic parameters, expression of DNA repair genes and microsatellite instability was investigated. By analyzing a multi-tumor tissue microarray, expression of SHIP1 was detected in 48 out of 72 cancer entities analyzed. The expression of SHIP1 protein of 145 kDa was confirmed by Western blot analysis in 7 out of 14 carcinoma cell lines. Analysis of a large colorectal cancer tissue microarray with 1009 specimens revealed SHIP1 expression in 62% of the samples analyzed. SHIP1 expression was inversely correlated with lymph node metastasis, vascular invasion and tumor grade, and it was positively associated with left-sided tumor localization. Interestingly, a strong relationship between the expression of SHIP1 and nuclear and membranous beta-catenin and the DNA repair genes MLH1 and MSH2 was observed.

New insights into the cellular temporal response to proteostatic stress.

Maintaining a healthy proteome involves all layers of gene expression regulation. By quantifying temporal changes of the transcriptome, translatome, proteome, and RNA-protein interactome in cervical cancer cells, we systematically characterize the molecular landscape in response to proteostatic challenges. We identify shared and specific responses to misfolded proteins and to oxidative stress, two conditions that are tightly linked. We reveal new aspects of the unfolded protein response, including many genes that escape global translation shutdown. A subset of these genes supports rerouting of energy production in the mitochondria. We also find that many genes change at multiple levels, in either the same or opposing directions, and at different time points. We highlight a variety of putative regulatory pathways, including the stress-dependent alternative splicing of aminoacyl-tRNA synthetases, and protein-RNA binding within the 3' untranslated region of molecular chaperones. These results illustrate the potential of this information-rich resource.