Detecting expressed genes in cell populations at the single-cell level with scGeneXpress.

Determining whether genes are expressed or not remains a challenge in single-cell RNAseq experiments due to their different expression spectra, which are influenced by genetics, the microenvironment and gene length. Current approaches for addressing this issue fail to provide a comprehensive landscape of expressed genes, since they neglect the inherent differences in the expression ranges and distributions of genes. Here, we present scGeneXpress, a method for detecting expressed genes in cell populations of single-cell RNAseq samples based on gene-specific reference distributions. We demonstrate that scGeneXpress accurately detects expressed cell markers and identity genes in 34 human and mouse tissues and can be employed to improve differential expression analysis of single-cell RNAseq data.

A Catalogus Immune Muris of the mouse immune responses to diverse pathogens.

Immunomodulation strategies are crucial for several biomedical applications. However, the immune system is highly heterogeneous and its functional responses to infections remains elusive. Indeed, the characterization of immune response particularities to different pathogens is needed to identify immunomodulatory candidates. To address this issue, we compiled a comprehensive map of functional immune cell states of mouse in response to 12 pathogens. To create this atlas, we developed a single-cell-based computational method that partitions heterogeneous cell types into functionally distinct states and simultaneously identifies modules of functionally relevant genes characterizing them. We identified 295 functional states using 114 datasets of six immune cell types, creating a Catalogus Immune Muris. As a result, we found common as well as pathogen-specific functional states and experimentally characterized the function of an unknown macrophage cell state that modulates the response to Salmonella Typhimurium infection. Thus, we expect our Catalogus Immune Muris to be an important resource for studies aiming at discovering new immunomodulatory candidates.

Dysregulated pathways and differentially expressed proteins associated with adverse transfusion reactions in different types of platelet components.

Platelet components (PCs) are occasionally associated with adverse transfusion reactions (ATRs). ATRs can occur regardless of the type of PC being transfused, whether it is a single-donor apheresis PC (SDA-PC) or a pooled PC (PPCs). The purpose of this study was to investigate the proteins and dysregulated pathways in both of the main types of PCs. The proteomic profiles of platelet pellets from SDA-PCs and PPCs involved in ATRs were analysed using the label-free LC-MS/MS method. Differentially expressed proteins with fold changes >|1.5| in clinical cases versus controls were characterised using bioinformatic tools (RStudio, GeneCodis3, and Ingenuity Pathways Analysis (IPA). The proteins were confirmed by western blotting. The common primary proteins found to be dysregulated in both types of PCs were the mitochondrial carnitine/acylcarnitine carrier protein (SLC25A20), multimerin-1 (MMRN1), and calumenin (CALU), which are associated with the important enrichment of platelet activation, platelet degranulation, and mitochondrial activity. Furthermore, this analysis revealed the involvement of commonly dysregulated canonical pathways, particularly mitochondrial dysfunction, platelet activation, and acute phase response. This proteomic analysis provided an interesting contribution to our understanding of the meticulous physiopathology of PCs associated with ATR. A larger investigation would assist in delineating the most relevant proteins to target within preventive transfusion safety strategies. BIOLOGICAL SIGNIFICANCE: Within platelet transfusion strategies, the two primary types of PCs predominantly processed in Europe, include (i) single donor apheresis PCs (SDA-PCs) from one donor and (ii) pooled PCs (PPCs). The current study used PCs from five buffy coats derived from five whole blood donations that were identical in ABO, RH1 and KEL1 groups. Both PC types were shown to be associated with the onset of an ATR in the transfused patient. Several common platelet proteins were found to be dysregulated in bags associated with ATR occurrences regardless of the type of PCs transfused and of their process. The dysregulated proteins included mitochondrial carnitine/acylcarnitine carrier protein (SLC25A20), which is involved in a fatty acid oxidation disorder; calumenin (CALU); and multimerin-1 (MMRN1), which is chiefly involved in platelet activation and degranulation. Dysregulated platelet protein pathways for ATRs that occurred with SDA-PCs and PPCs could support the dysregulated functions found in association with those three proteins. Those common platelet proteins may become candidates to define biomarkers associated with the onset of an ATR from PC transfusions, including monitoring during the quality steps of PC manufacturing, provided that the results are confirmed in larger cohorts. This study enriches our knowledge of platelet proteomics in PCs under pathological conditions.

Data from differentially expressed proteins in platelet components associated with adverse transfusion reactions.

The presented dataset was used for the study focused on the search for differentially expressed proteins in blood platelet components (PCs) associated with adverse transfusion reactions (ATRs). Pellets of ATR platelet components and their controls were subjected to high-throughput proteomics analysis using a Q Exactive high-resolution tandem mass spectrometer. The data reported here constitutes an extension of "Differential protein expression of blood platelet components associated with adverse transfusion reactions" article Aloui et al., 2018. The reported data herein have been deposited into the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD003510 for the pooled platelet components (PPCs) and PXD008886 for the apheresis platelet components (SDA-PCs) associated with ATRs.

Differential protein expression of blood platelet components associated with adverse transfusion reactions.

Platelets found within platelet components (PCs) intended for transfusion release inflammatory molecules. Despite the implementation of leukoreduction, some of these PCs are occasionally associated with adverse transfusion reactions (ATRs). The aim of this study was to decipher the platelet proteome in two types of PCs, buffy-coat-derived pooled PCs (PPCs) and single-donor apheresis PCs (SDA-PCs), associated with ATRs. A label-free LC-MS/MS method was used for the proteomic analysis of washed platelet pellets from 3 PPCs and 3 SDA-PCs associated with ATRs, compared to matched controls. Bioinformatics tools allowed us to characterise the differentially expressed (DE) proteins between cases (ATR-PCs) and controls (no.ATR-PCs). From the PPCs and SDA-PCs, 473 and 146 proteins were DE, respectively. The functional interpretation of these proteins revealed enrichment in platelet activation and degranulation as the most important biological process. The most dysregulated pathways were integrin signaling for PPCs and acute phase response signaling for SDA-PCs. Interestingly, inflammatory disorders were found to be enriched in both PC types. Profound proteome changes were found in the platelets of PCs that led to clinical ATRs in patients. This study presents the first exploration of the platelet proteomic signature associated with ATRs and could provide clues to improving transfusion medicine. BIOLOGICAL SIGNIFICANCE: Adverse transfusion reactions (ATRs) can still occur after transfusion of platelet components (PC). This is the first report on the proteomic analysis of PCs associated with ATR. In this study, the contents of PC bags implicated in ATRs were examined. The aims of this study were to characterise molecules that could be central to the inflammation of ATRs and to highlight dysregulated mechanisms to explain the onset of ATRs. Two types of PCs were used: 3 PPCs (each from 5 donors) and 3 SDA-PCs (each from one donor). We have shown that the two types of PCs, from bags undergoing different processing (i.e., sampling, preparation), involve two types of dysregulated - pathophysiological mechanisms associated with the onset of ATRs. The most dysregulated signaling pathways were cytoskeleton and integrin regulation for PPCs, acute phase response signaling and remodelling of adherens junctions for SDA-PCs. Inflammation, platelet activation and degranulation processes were present in both PC types but were more important for PPCs. This proteomics analysis provides a better understanding of the pathophysiological mechanisms involved in ATRs and may lead to novel steps to ensure safe PC transfusion.

Molecular genetic diagnosis of Tunisian Glanzmann thrombasthenia patients reveals a common nonsense mutation in the ITGA2B gene that seems to be specific for the studied population.

: Glanzmann thrombasthenia is an inherited severe bleeding disease. Mutations associated with Glanzmann thrombasthenia are highly heterogeneous and occur across the two genes coding for the platelet αIIbß3 integrin. This study was aimed at identifying Glanzmann thrombasthenia-associated novel mutations in Tunisian patients. Seven unrelated Glanzmann thrombasthenia patients issued from high consanguineous families (86%; 6/7 of the patients) were studied. Glanzmann thrombasthenia diagnoses were based on patients' bleeding histories and platelet aggregation tests. Screening of ITGA2B and ITGB3 genes was performed by denaturing high-performance liquid chromatography (DHPLC) analysis. Amplicons with abnormal elution profiles were subjected to direct sequencing. DHPLC/sequencing analysis identified a pathogenic homozygous mutation in exon 26 at position c.2702C>A, inducing a substitution of a serine to a stop codon (p.S901*) in the ITGA2B gene, in three patients. This mutation was only previously reported in a Glanzmann thrombasthenia patient of a Tunisian origin and not in other populations. We diagnosed a pathogenic Glanzmann thrombasthenia mutation in ITGA2B screened by DHPLC that appears to be specific to individuals of Tunisian heritage and that deserves to be investigated in first intention. As a result, we determined that performing prenatal diagnosis and setting a prevention strategy via counselling for affected heterozygote individuals will be helpful for Tunisian Glanzmann thrombasthenia families where there is still a high rate of consanguinity.