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Background SARS-CoV-2 infection causes acute respiratory distress, which may progress to multiorgan failure and death. Severe COVID-19 disease is accompanied by reduced erythrocyte turnover, low hemoglobin levels along with increased total bilirubin and ferritin serum concentrations. Moreover, expansion of erythroid progenitors in peripheral blood together with hypoxia, anemia, and coagulopathies highly correlates with severity and mortality. We demonstrate that SARS-CoV-2 directly infects erythroid precursor cells, impairs hemoglobin homeostasis and aggravates COVID-19 disease. Methods Erythroid precursor cells derived from peripheral CD34+ blood stem cells of healthy donors were infected in vitro with SARS-CoV-2 alpha variant and differentiated into red blood cells (RBCs). Hemoglobin and iron metabolism in hospitalized COVID-19 patients and controls were analyzed in plasma-depleted whole blood samples. Raman trapping spectroscopy rapidly identified diseased cells. Results RBC precursors express ACE2 receptor and CD147 at day 5 of differentiation, which makes them susceptible to SARS-CoV-2 infection. qPCR analysis of differentiated RBCs revealed increased HAMP mRNA expression levels, encoding for hepcidin, which inhibits iron uptake. COVID-19 patients showed impaired hemoglobin biosynthesis, enhanced formation of zinc-protoporphyrine IX, heme-CO2, and CO-hemoglobin as well as degradation of Fe-heme. Moreover, significant iron dysmetablolism with high serum ferritin and low serum iron and transferrin levels occurred, explaining disturbances of oxygen-binding capacity in severely ill COVID-19 patients. Conclusions Our data identify RBC precursors as a direct target of SARS-CoV-2 and suggest that SARS-CoV-2 induced dysregulation in hemoglobin- and iron-metabolism contributes to the severe systemic course of COVID-19. This opens the door for new diagnostic and therapeutic strategies. Graphical Abstract

Tissue health is regulated by a myriad of exogenous or endogenous factors. Here we investigated the role of the conserved Kynurenine pathway (KP) in maintaining retinal homeostasis in the context of light stress in Drosophila melanogaster. cinnabar, cardinal and, scarlet, are fly genes that encode different steps in the KP. Along with white, these genes are known regulators of brown pigment (ommochrome) biosynthesis. Using white as a sensitized genetic background, we showed that mutations in cinnabar, cardinal, and scarlet differentially modulate light-induced retinal damage. Mass Spectrometric measurements of KP metabolites in flies with different genetic combinations support the notion that increased levels of 3-hydroxykynurenine (3OH-K) and Xanthurenic acid (XA) enhance retinal damage, whereas Kynurenic Acid (KYNA) and Kynurenine (K) are neuro-protective. This conclusion was corroborated by showing that feeding 3OH-K results in enhanced retinal damage, whereas feeding KYNA protects the retina in sensitized genetic backgrounds. Interestingly, the harmful effects of free 3OH-K are diminished by its sub-cellular compartmentalization within the cell. Sequestering of 3OH-K enables the quenching of its toxicity through conversion to brown pigment or conjugation to proteins. This work enabled us to decouple the role of these KP genes in ommochrome formation from their role in retinal homeostasis. Additionally, it puts forward new hypotheses on the importance of the balance of KP metabolites and their compartmentalization in disease alleviation.

Neanderthal brains were similar in size to those of modern humans. We sought to investigate potential differences in neurogenesis during neocortex development. Modern human transketolase-like 1 (TKTL1) differs from Neanderthal TKTL1 by a lysine-to-arginine amino acid substitution. Using overexpression in developing mouse and ferret neocortex, knockout in fetal human neocortical tissue, and genome-edited cerebral organoids, we found that the modern human variant, hTKTL1, but not the Neanderthal variant, increases the abundance of basal radial glia (bRG) but not that of intermediate progenitors (bIPs). bRG generate more neocortical neurons than bIPs. The hTKTL1 effect requires the pentose phosphate pathway and fatty acid synthesis. Inhibition of these metabolic pathways reduces bRG abundance in fetal human neocortical tissue. Our data suggest that neocortical neurogenesis in modern humans differs from that in Neanderthals.

Upon exposure to excessive reactive oxygen species (ROS), organismal survival depends on the strength of the endogenous antioxidant defense barriers that prevent mitochondrial and cellular deterioration. Previously, we showed that glycolic acid can restore the mitochondrial membrane potential of C. elegans treated with paraquat, an oxidant that produces superoxide and other ROS species, including hydrogen peroxide. Here, we demonstrate that glycolate fully suppresses the deleterious effects of peroxide on mitochondrial activity and growth in worms. This endogenous compound acts by entering serine/glycine metabolism. In this way, conversion of glycolate into glycine and serine ameliorates the drastically decreased NADPH/NADP+ and GSH/GSSG ratios induced by H2O2 treatment. Our results reveal the central role of serine/glycine metabolism as a major provider of reducing equivalents to maintain cellular antioxidant systems and the fundamental function of glycolate as a natural antioxidant that improves cell fitness and survival., Diez et al. show that glycolate suppresses deleterious effects of peroxide on mitochondrial activity and growth of worms. They find that the conversion of glycolate into glycine and serine helps worms maintain cellular antioxidants following oxidative stress. This study suggests that glycolate serves as a natural antioxidant improving organismal fitness under stress.

Nine mammalian adenylyl cyclases (AC) are pseudoheterodimers with two hexahelical membrane domains which are isoform-specifically conserved. Previously we proposed that these membrane domains are orphan receptors (10.7554/eLife.13098; 10.1016/j.cellsig.2020.109538). Lipids extracted from fetal bovine serum at pH 1 inhibited several mAC activities. Guided by a lipidomic analysis we tested glycerophospholipids as potential ligands. Contrary to expectations we surprisingly discovered that 1-stearoyl-2-docosahexaenoyl-phosphatidic acid (SDPA) potentiated Gsα-activated activity of human AC isoform 3 seven-fold. The specificity of fatty acyl esters at glycerol positions 1 and 2 was rather stringent. 1-Stearoyl-2-docosahexaenoyl-phosphatidylserine and 1-stearoyl-2-docosahexaenoyl-phosphatidylethanolamine significantly potentiated several Gsα-activated mAC isoforms to different extents. SDPA appears not interact with forskolin activation of AC isoform 3. SDPA enhanced Gsα-activated AC activities in membranes from mouse brain cortex. The action of SDPA was reversible. Unexpectedly, SDPA did not affect cAMP generation in HEK293 cells stimulated by isoproterenol, PGE2 and adenosine, virtually excluding a role as an extracellular ligand and, instead, suggesting an intracellular role. In summary, we discovered a new dimension of intracellular AC regulation by chemically defined glycerophospholipids.

Recognition of pathogen-derived foreign nucleic acids is central to innate immune defense. This requires discrimination between structurally highly similar self and nonself nucleic acids to avoid aberrant inflammatory responses as in the autoinflammatory disorder Aicardi-Goutières syndrome (AGS). How vast amounts of self RNA are shielded from immune recognition to prevent autoinflammation is not fully understood. Here we show that SAM domain and HD domain-containing protein 1 (SAMHD1), one of the AGS-causing genes, functions as a single-stranded RNA (ssRNA) 3’exonuclease, the lack of which causes cellular RNA accumulation. Increased ssRNA in cells leads to dissolution of RNA-protein condensates, which sequester immunogenic double-stranded RNA (dsRNA). Release of sequestered dsRNA from condensates triggers activation of antiviral type I interferon via retinoic acid-inducible gene I-like receptors. Our results establish SAMHD1 as a key regulator of cellular RNA homeostasis and demonstrate that buffering of immunogenic self RNA by condensates regulates innate immune responses.

All organisms encounter abiotic stress but only certain organisms are able to cope with extreme conditions and enter into cryptobiosis (hidden life). Previously, we have shown that C. elegans dauer larvae can survive severe desiccation (anhydrobiosis), a specific form of cryptobiosis. Entry into anhydrobiosis is preceded by activation of a set of biochemical pathways by exposure to mild desiccation. This process called preconditioning induces elevation of trehalose, intrinsically disordered proteins, polyamines and some other pathways that allow the preservation of cellular functionality in the absence of water. Here, we demonstrate that another stress factor, high osmolarity, activates similar biochemical pathways. The larvae that acquired resistance to high osmotic pressure can also withstand desiccation. In addition, high osmolarity significantly increases the biosynthesis of glycerol making larva tolerant to freezing. Thus, to survive abiotic stress, C. elegans activates a combination of genetic and biochemical pathways that serve as a general survival program.

Shotgun analysis provides a quantitative snapshot of the lipidome composition of cells, tissues, or model organisms; however, it does not elucidate the spatial distribution of lipids. Here we demonstrate that shotgun analysis could quantify low-picomole amounts of lipids isolated by laser capture microdissection (LCM) of hundred micrometer-sized histological zones visualized at the cryosections of tissues. We identified metabolically distinct periportal (pp) and pericentral (pc) zones by immunostaining of 20 μm thick cryosections of a healthy mouse liver. LCM was used to ablate, catapult, and collect the tissue material from 10 to 20 individual zones covering a total area of 0.3-0.5 mm2 and containing ca. 500 cells. Top-down shotgun profiling relying upon computational stitching of 61 targeted selective ion monitoring ( t-SIM) spectra quantified more than 200 lipid species from 17 lipid classes including glycero- and glycerophospholipids, sphingolipids, cholesterol esters, and cholesterol. Shotgun LCM revealed the overall commonality of the full lipidome composition of pp and pc zones along with significant ( p < 0.001) difference in the relative abundance of 13 lipid species. Follow-up proteomics analyses of pellets recovered from an aqueous phase saved after the lipid extraction identified 13 known and 7 new protein markers exclusively present in pp or in pc zones and independently validated the specificity of their visualization, isolation, and histological assignment.

Loss of heterozygosity (LOH) is detectable in many forms of cancer, including leukaemia. LOH contributes to tumorigenesis through the loss of one of the two alleles of one tumor suppressor gene at a given locus, caused by deletion or uniparental disomy (UPD). In this study, we analysed 146 patients with primary AML, using high-density single nucleotide polymorphisms (SNPs) arrays. Leukemic cells and healthy T-cells from each patient were obtained using FACS-Vantage cell sorting. The genome wide SNP analysis was carried out using Human Mapping 10K Arrays (Affymetrix). So far LOH was identified in 27 cases with normal karyotype (18.5%). Potential LOH regions were confirmed by analysis of short tandem repeat (STR) markers using DNA samples from T-cells and blasts. In 21 of these cases, STR-analysis of T-cells representing the corresponding tumor-free material confirmed the regions of UPD. This aberration affected different chromosomes, but most frequently chromosome 2, 6, 11, 13, 21, and covered between 11.5 and 88 Mb. In the remaining 6 LOH cases, long stretches of homozygosity occurring at identical positions in the T-cells and in the leukemic blasts were found. These cases were detected and separated from those with UPD. So far, correlation of clinical variables and LOH results in this cohort did not indicate significant differences based on age, WBC-counts, sex and FAB-subtype. Additionally, we did not detect any proven correlation between FLT3-ITD, MLL-PTD, NPM1 mutations and UPD. Interestingly, 80% of the patients with UPD that had achieved CR after chemotherapy relapsed within 6 months. In contrast, the rate of relapse in patients without UPD was only 54% . Furthermore, we were able to confirm the relationship between UPD and gene aberrations. We demonstrated that the UPD cases found in chromosomes 21, 19, and 11 were correlated with point mutations in the RUNX1, CEBPA and WT1 genes, respectively. Furthermore, AML cases with and without UPD showed different gene expression profiles, revealing different expression levels for some genes involved in double strand brake repair. In conclusion, the use of the SNP array technology allowed the identification and mapping of LOH in 18.5% of AML patients with normal karyotype. Our data also underline the necessity of analysing tumour-free material in order to confirm the somatic origin of the alteration. Furthermore, our results indicate a higher relapse rate in patients with UPD.

Loss of heterozygosity (LOH) is detectable in many forms of cancer including leukemia and contributes to tumorigenesis through the deletion of tumor suppressor genes. It derives from the loss of one of the two alleles at a given locus caused by deletion or uniparental disomy (UPD). In this study we describe the genome wide analysis of LOH in purified leukemic blasts from acute myeloid leukemia (AML) samples with normal karyotype using a novel technique based on single nucleotide polymorphisms (SNP). In total we selected 50 peripheral blood samples of de novo AML patients with normal karyotype at the time of diagnosis. Patients were treated according to the AML-96 multi-center protocol of the DSIL. Pure leukemic cells and tumor free material (T cells) from each patient were obtained using FACS-Vantage cell-sorting (BD Sciences, Germany). DNA was isolated from sorted cells. Genome wide SNP analysis was carried out according to the standard GeneChip Mapping Assay protocol (Affymetrix, USA) with pre-amplified DNA (Repli-g™ Kit; Molecular Staging Inc. USA) using the Human Mapping 10K Arrays XbaI 131 (Affymetrix). Individual regions of potential LOH identified by the Affymetrix® GeneChip® Chromosome Copy Number Analysis tool were confirmed by microsatellite analysis of short tandem repeat (STR) markers using the matched non-manipulated original DNA samples. Genome wide analysis of SNP in pre amplified DNA of FACS sorted cells from AML samples with normal karyotype detected long stretches of hemizygosity, indicative of LOH in 8/49 evaluable patients (16%). In 6 of these cases STR-analysis of T cells representing the corresponding tumor free material confirmed the regions of partial UPD. UPD affected four different chromosomes (chromosome 2p and 11q, in each case twice; chromosome 8q, and 13q) and covered between 11.5 and 88 Mb. To our surprise in the healthy material of the remaining two cases no heterozygote loci were identified at the affected chromosomal regions (chromosome 3 14.5 Mb; chromosome 20 29.3 Mb) and consequently identified as unusual long stretches of homozygosity present in both the malignant and the healthy cells. These cases might reflect genotypes with high susceptibility to malignant mutations. No differences were observed for any clinical factors, including age, WBC-counts, sex and FAB-subtype. Also, several of the mutations frequently identified in patients with normal karyotype (FLT3-ITD, MLL-PTD, NPM1) had a comparable prevalence in patients with and without UPD. Interestingly, although 5/6 patients with UPD achieved complete remission after induction chemotherapy, 4/5 (80%) relapsed within the first 6 months. In contrast the rate of relapse in patients without UPD was only 54% (15/28). The only patient positive for UPD and alive in remission received an allogeneic stem cell transplantation. In conclusion, the combination of whole genome amplification method and SNP array technology allows the identification and mapping of LOH in AML patients with normal karyotype. Our data also point to the necessity to analyze tumor free material to confirm the somatic origin of the alteration. Although small numbers of patients were investigated, our data might indicate that patients with UPD have a high rate of treatment failure. This should be further investigated in larger cohorts of patients.