Effect of Neutralizing Monoclonal Antibody Treatment on Early Trajectories of Virologic and Immunologic Biomarkers in Patients Hospitalized With COVID-19

BACKGROUND: Neutralizing monoclonal antibodies (nmAbs) failed to show clear benefit for hospitalized patients with coronavirus disease 2019 (COVID-19). Dynamics of virologic and immunologic biomarkers remain poorly understood. METHODS: Participants enrolled in the Therapeutics for Inpatients with COVID-19 trials were randomized to nmAb versus placebo. Longitudinal differences between treatment and placebo groups in levels of plasma nucleocapsid antigen (N-Ag), anti-nucleocapsid antibody, C-reactive protein, interleukin-6, and D-dimer at enrollment, day 1, 3, and 5 were estimated using linear mixed models. A 7-point pulmonary ordinal scale assessed at day 5 was compared using proportional odds models. RESULTS: Analysis included 2149 participants enrolled between August 2020 and September 2021. Treatment resulted in 20% lower levels of plasma N-Ag compared with placebo (95% confidence interval, 12%-27%; P \u3c .001), and a steeper rate of decline through the first 5 days (P \u3c .001). The treatment difference did not vary between subgroups, and no difference was observed in trajectories of other biomarkers or the day 5 pulmonary ordinal scale. CONCLUSIONS: Our study suggests that nmAb has an antiviral effect assessed by plasma N-Ag among hospitalized patients with COVID-19, with no blunting of the endogenous anti-nucleocapsid antibody response. No effect on systemic inflammation or day 5 clinical status was observed. CLINICAL TRIALS REGISTRATION: NCT04501978

Genome-Wide Interrogation of Mammalian Stem Cell Fate Determinants by Nested Chromosome Deletions

Understanding the function of important DNA elements in mammalian stem cell genomes would be enhanced by the availability of deletion collections in which segmental haploidies are precisely characterized. Using a modified Cre-loxP–based system, we now report the creation and characterization of a collection of ∼1,300 independent embryonic stem cell (ESC) clones enriched for nested chromosomal deletions. Mapping experiments indicate that this collection spans over 25% of the mouse genome with good representative coverage of protein-coding genes, regulatory RNAs, and other non-coding sequences. This collection of clones was screened for in vitro defects in differentiation of ESC into embryoid bodies (EB). Several putative novel haploinsufficient regions, critical for EB development, were identified. Functional characterization of one of these regions, through BAC complementation, identified the ribosomal gene Rps14 as a novel haploinsufficient determinant of embryoid body formation. This new library of chromosomal deletions in ESC (DelES: http://bioinfo.iric.ca/deles) will serve as a unique resource for elucidation of novel protein-coding and non-coding regulators of ESC activity

Ι – TRANSLATION AS INTERPRETATION ΙΙ – ON JOSEPH MARGOLIS’ AESTHETICS. A SYMPOSIUM

This issue of the journal JoLMA is divided in two parts: Ι – TRANSLATION AS INTERPRETATION ed. by Francesco Camera and Gian Luigi Paltrinieri ΙΙ – ON JOSEPH MARGOLIS’ AESTHETICS. A SYMPOSIUM ed. by Alessandro Cavazzan

HIV-1 Antisense Transcription Is Preferentially Activated in Primary Monocyte-Derived Cells

International audienceIn this study, an antisense luciferase-expressing human immunodeficiency virus type 1 (HIV-1) molecular clone was used to infect primary cells. We found that antisense transcription activity from the 3' long terminal repeat (LTR) was significantly more abundant in monocyte-derived cells than in activated T lymphocytes. Moreover, by analyzing antisense transcription in infected monocyte-derived dendritic cells (MDDCs), we observed that the majority of HIV-1-infected MDDCs with significant antisense transcription activity did not produce Gag. We also confirmed that the negative-strand-encoded antisense protein (ASP) was expressed in monocyte-derived cells

Proteogenomic characterization of 5-azacytidine effects on acute myeloid leukemia immunopeptidome

peer reviewedBackground: Hypomethylating agents like 5-azacytidine (AZA) are licensed for the treatment of acute myeloid leukemia (AML) patients ineligible for allogeneic hematopoietic cell transplantation. While previous reports suggested that AZA promotes the recognition of AML blasts by cytotoxic T cells, the mechanism behind this improved recognition is not fully understood. Specifically, AZA is assumed to promote the expression of transcripts repressed by genomic methylation, namely cancer-testis antigens (CTA) and endogenous retroelements (ERE), resulting in the presentation of immunogenic MHC-I-associated peptides (MAPs, collectively referred to as the immunopeptidome) derived from the translation of these transcripts. However, the presentation of such MAPs after AZA treatment has not been firmly demonstrated thus far. Aims: Our study aims to characterize how AZA treatment shapes the identity of MAPs presented by AML cells. Methods: Four different AML cell lines, THP-1, OCI-AML3, SKM-1, and MOLM-13 were treated with a non-cytotoxic dose of AZA for 3 days. Their transcriptome has been characterized by high-coverage RNA sequencing (RNA-seq) and their immunopeptidome by shotgun mass spectrometry (MS). To identify MAPs deriving from unannotated genomic regions, we have designed a cutting-edge proteogenomic pipeline using the RNA-seq data to build personalized MS databases that enabled the identification of non-canonical MAPs such as ERE-derived MAPs. Results: Paired transcriptomic comparisons between treated and untreated cells showed that AZA induces a large-scale gene upregulation (87% differentially-expressed transcripts were upregulated). Among them, 38% were EREs and 6% were CTAs, suggesting that AZA-induced MAPs have greater chances of deriving from EREs than from CTAs. However, we could not identify a single ERE-derived upregulated MAP among the immunopeptidome of AZA-treated AML cells while multiple CTA-derived MAPs (0.4 - 0.7% of the upregulated MAPs) were presented at greater levels by AZA. Because a GO-term analysis of the upregulated protein-coding genes evidenced a robust innate immune response in AZA-treated cells, we conclude that AZA-induced enhanced CTL recognition is more dependent on CTA- than on ERE-derived MAP presentation and that ERE enhanced expression could rather trigger the observed innate immune response. An in-depth analysis of the immunopeptidome showed that MAPs having an altered presentation following AZA treatment derived only partially from transcripts whose expression was affected by AZA. The analysis of the other AZA-induced MAPs showed that they resulted preferentially from the activity of the constitutive proteasome (vs the immunoproteasome) and derived preferentially from proteins having less aromatic residues (and therefore more prone to misfolding). Because the degradation of misfolded proteins by the constitutive proteasome can indicate that AZA induces an unfolded protein response, we have examined whether AZA stimulates autophagy, a process frequently triggered in association with such stress. Accordingly, flow cytometry assays on AML cells treated with AZA for 24h evidenced a robust autophagy induction. Summary/Conclusion: Altogether our results show that AZA promotes the presentation of CTA-derived rather than ERE-derived MAPs and that autophagy induction could enable the survival of AML cells to AZA-induced proteotoxic stress. Our findings suggest that autophagy inhibitors could synergize with AZA in AML therapy

NLRC4 GOF Mutations, a Challenging Diagnosis from Neonatal Age to Adulthood

International audienceThe NLRC4 inflammasome is part of the human immune innate system. Its activation leads to the cleavage of pro-inflammatory cytokines IL-1β and IL-18, promoting inflammation. NLRC4 gain-of-function (GOF) mutations have been associated with early-onset recurrent fever, recurrent macrophagic activation syndrome and enterocolitis. Herein, we describe two new patients with NLRC4 mutations. The first case presented with recurrent fever and vasoplegic syndrome, gut symptoms and urticarial rashes initially misdiagnosed as a severe protein-induced enterocolitis syndrome. The second case had recurrent macrophage activation syndrome (MAS) and shock, suggesting severe infection. We identified two NLRC4 mutations, on exon 4, within the nucleotide-binding protein domain (NBD). After a systematic review of NLRC4 GOF mutations, we highlight the wide spectrum of this disease with a limited genotype-phenotype correlation. Vasoplegic shock was only reported in patients with mutation in the NBD. Diagnosing this new entity combined with gastrointestinal symptoms and vasoplegic shocks is challenging. It mimics severe allergic reaction or sepsis. The plasma IL-18 level and genetic screening are instrumental to make a final diagnosis