SARS-CoV-2 variants evolve convergent strategies to remodel the host response.

SARS-CoV-2 variants of concern (VOCs) emerged during the COVID-19 pandemic. Here, we used unbiased systems approaches to study the host-selective forces driving VOC evolution. We discovered that VOCs evolved convergent strategies to remodel the host by modulating viral RNA and protein levels, altering viral and host protein phosphorylation, and rewiring virus-host protein-protein interactions. Integrative computational analyses revealed that although Alpha, Beta, Gamma, and Delta ultimately converged to suppress interferon-stimulated genes (ISGs), Omicron BA.1 did not. ISG suppression correlated with the expression of viral innate immune antagonist proteins, including Orf6, N, and Orf9b, which we mapped to specific mutations. Later Omicron subvariants BA.4 and BA.5 more potently suppressed innate immunity than early subvariant BA.1, which correlated with Orf6 levels, although muted in BA.4 by a mutation that disrupts the Orf6-nuclear pore interaction. Our findings suggest that SARS-CoV-2 convergent evolution overcame human adaptive and innate immune barriers, laying the groundwork to tackle future pandemics.

Structures of SARS-CoV-2 N7-methyltransferase with DOT1L and PRMT7 inhibitors provide a platform for new antivirals.

The RNA N7-methyltransferase (MTase) activity of SARS-CoV-2's nsp14 protein is essential for viral replication and is a target for the development of new antivirals. Nsp14 uses S-adenosyl methionine (SAM) as the methyl donor to cap the 5' end of the SARS-CoV-2 mRNA and generates S-adenosyl homocysteine (SAH) as the reaction byproduct. Due to the central role of histone MTases in cancer, many SAM/SAH analogs with properties of cell permeability have recently been developed for the inhibition of these MTases. We have succeeded in identifying two such compounds (SGC0946 and SGC8158) that display significant antiviral activity and bind to the SARS-CoV-2 nsp14 N7-MTase core. Unexpectedly, crystal structures of SGC0946 and SGC8158 with the SARS-CoV-2 nsp14 N7-MTase core identify them as bi-substrate inhibitors of the viral MTase, co-occupying both the SAM and RNA binding sites; positing novel features that can be derivatized for increased potency and selectivity for SARS-CoV-2 nsp14. Taken together, the high-resolution structures and the accompanying biophysical and viral replication data provide a new avenue for developing analogs of SGC0946 and SGC8158 as antivirals.

Structure-Based Discovery of Inhibitors of the SARS-CoV-2 Nsp14 N7-Methyltransferase.

An under-explored target for SARS-CoV-2 is the S-adenosyl methionine (SAM)-dependent methyltransferase Nsp14, which methylates the N7-guanosine of viral RNA at the 5'-end, allowing the virus to evade host immune response. We sought new Nsp14 inhibitors with three large library docking strategies. First, up to 1.1 billion lead-like molecules were docked against the enzyme's SAM site, leading to three inhibitors with IC50 values from 6 to 50 µM. Second, docking a library of 16 million fragments revealed 9 new inhibitors with IC50 values from 12 to 341 µM. Third, docking a library of 25 million electrophiles to covalently modify Cys387 revealed 7 inhibitors with IC50 values from 3.5 to 39 µM. Overall, 32 inhibitors encompassing 11 chemotypes had IC50 values < 50 µM and 5 inhibitors in 4 chemotypes had IC50 values < 10 µM. These molecules are among the first non-SAM-like inhibitors of Nsp14, providing starting points for future optimization.

SARS-CoV-2 Inhibitors Identified by Phenotypic Analysis of a Collection of Viral RNA-Binding Molecules.

Antiviral agents are needed for the treatment of SARS-CoV-2 infections and to control other coronavirus outbreaks that may occur in the future. Here we report the identification and characterization of RNA-binding compounds that inhibit SARS-CoV-2 replication. The compounds were detected by screening a small library of antiviral compounds previously shown to bind HIV-1 or HCV RNA elements with a live-virus cellular assay detecting inhibition of SARS-CoV-2 replication. These experiments allowed detection of eight compounds with promising anti-SARS-CoV-2 activity in the sub-micromolar to micromolar range and wide selectivity indexes. Examination of the mechanism of action of three selected hit compounds excluded action on the entry or egress stages of the virus replication cycle and confirmed recognition by two of the molecules of conserved RNA elements of the SARS-CoV-2 genome, including the highly conserved S2m hairpin located in the 3'-untranslated region of the virus. While further studies are needed to clarify the mechanism of action responsible for antiviral activity, these results facilitate the discovery of RNA-targeted antivirals and provide new chemical scaffolds for developing therapeutic agents against coronaviruses.

Preclinical and randomized phase I studies of plitidepsin in adults hospitalized with COVID-19.

Plitidepsin, a marine-derived cyclic-peptide, inhibits SARS-CoV-2 replication at nanomolar concentrations by targeting the host protein eukaryotic translation elongation factor 1A. Here, we show that plitidepsin distributes preferentially to lung over plasma, with similar potency against across several SARS-CoV-2 variants in preclinical studies. Simultaneously, in this randomized, parallel, open-label, proof-of-concept study (NCT04382066) conducted in 10 Spanish hospitals between May and November 2020, 46 adult hospitalized patients with confirmed SARS-CoV-2 infection received either 1.5 mg (n = 15), 2.0 mg (n = 16), or 2.5 mg (n = 15) plitidepsin once daily for 3 d. The primary objective was safety; viral load kinetics, mortality, need for increased respiratory support, and dose selection were secondary end points. One patient withdrew consent before starting procedures; 45 initiated treatment; one withdrew because of hypersensitivity. Two Grade 3 treatment-related adverse events were observed (hypersensitivity and diarrhea). Treatment-related adverse events affecting more than 5% of patients were nausea (42.2%), vomiting (15.6%), and diarrhea (6.7%). Mean viral load reductions from baseline were 1.35, 2.35, 3.25, and 3.85 log10 at days 4, 7, 15, and 31. Nonmechanical invasive ventilation was required in 8 of 44 evaluable patients (16.0%); six patients required intensive care support (13.6%), and three patients (6.7%) died (COVID-19-related). Plitidepsin has a favorable safety profile in patients with COVID-19.

Epitope spreading driven by the joint action of CART cells and pharmacological STING stimulation counteracts tumor escape via antigen-loss variants.

BACKGROUND: Target antigen (Ag) loss has emerged as a major cause of relapse after chimeric antigen receptor T (CART)-cell therapy. We reasoned that the combination of CART cells, with the consequent tumor debulking and release of Ags, together with an immunomodulatory agent, such as the stimulator of interferon gene ligand (STING-L) 2'3'-cyclic GMP-AMP (2'3'-cGAMP), may facilitate the activation of an endogenous response to secondary tumor Ags able to counteract this tumor escape mechanism. METHODS: Mice bearing B16-derived tumors expressing prostate-specific membrane Ag or gp75 were treated systemically with cognate CART cells followed by intratumoral injections of 2'3'-cGAMP. We studied the target Ag inmunoediting by CART cells and the effect of the CART/STING-L combination on the control of STING-L-treated and STING-L-non-treated tumors and on the endogenous antitumor T-cell response. The role of Batf3-dependent dendritic cells (DCs), stimulator of interferon gene (STING) signaling and perforin (Perf)-mediated killing in the efficacy of the combination were analyzed. RESULTS: Using an immune-competent solid tumor model, we showed that CART cells led to the emergence of tumor cells that lose the target Ag, recreating the cancer immunoediting effect of CART-cell therapy. In this setting, the CART/STING-L combination, but not the monotherapy with CART cells or STING-L, restrained tumor progression and enhanced overall survival, showing abscopal effects on distal STING-L-non-treated tumors. Interestingly, a secondary immune response against non-chimeric antigen receptor-targeted Ags (epitope spreading), as determined by major histocompatibility complex-I-tetramer staining, was fostered and its intensity correlated with the efficacy of the combination. This was consistent with the oligoclonal expansion of host T cells, as revealed by in-depth T-cell receptor repertoire analysis. Moreover, only in the combination group did the activation of endogenous T cells translate into a systemic antitumor response. Importantly, the epitope spreading and the antitumor effects of the combination were fully dependent on host STING signaling and Batf3-dependent DCs, and were partially dependent on Perf release by CART cells. Interestingly, the efficacy of the CART/STING-L treatment also depended on STING signaling in CART cells. CONCLUSIONS: Our data show that 2'3'-cGAMP is a suitable adjuvant to combine with CART-cell therapy, allowing the induction of an endogenous T-cell response that prevents the outgrowth of Ag-loss tumor variants.

Análisis genético, clínico y molecular de una familia afectada con una malformación del esmalte dental / Genetic, clinical and molecular analysis of a family affected by amelogenesis imperfecta

Background: Amelogenesis Imperfecta (AI) is a group of conditions where there is an abnormal formation of enamel in terms of quantity, structure and composition. AI is clinically and genetically heterogeneous, there are sex linked and autosomal versions, dominant and/or recessive, with phenotypes of hypoplastic, hypocalcified or hypomature enamel. Only recently, through clinical, genetic and molecular studies of affected families, phenotypic-genotypic correlations are being established in this group of anomalies. Aim: To carry out a genetic, clinical and molecular analysis of a Chilean family affected with an enamel malformation, which probably would correspond to Amelogenesis Imperfecta Dominant Autosomal (AIDA), of hypoplastic type, resulting from g.6395G>A mutation in the enamelin gene. Patients and Methods: A genealogical pattern was created for five generations. Five members of this family group were clinically examined, and four of them had a molecular analysis that consisted of the detection of a mutation in the enamelin gene using PCR. Results: In this family, the enamel malformation presents a dominant autosomal pattern of inheritance. The clinical examination of the group allowed a diagnosis of Amelogenesis Imperfecta, of the hypoplastic local type. However, the molecular analysis revealed that the members analyzed did not exhibit the g.6395G>A mutation reported for the enamelin gene (ENAM). Conclusions: The enamel phenotype in this family could be explained by the presence of one of four other mutations recently described in this or another gene, thereby supporting the findings of allelic heterogeneity reported in the literature.

[Genetic, clinical and molecular analysis of a family affected by amelogenesis imperfecta]. / Análisis genético, clínico y molecular de una familia afectada con una malformación del esmalte dental.

BACKGROUND: Amelogenesis Imperfecta (AI) is a group of conditions where there is an abnormal formation of enamel in terms of quantity, structure and composition. AI is clinically and genetically heterogeneous, there are sex linked and autosomal versions, dominant and/or recessive, with phenotypes of hypoplastic, hypocalcified or hypomature enamel. Only recently, through clinical, genetic and molecular studies of affected families, phenotypic-genotypic correlations are being established in this group of anomalies. AIM: To carry out a genetic, clinical and molecular analysis of a Chilean family affected with an enamel malformation, which probably would correspond to Amelogenesis Imperfecta Dominant Autosomal (AIDA), of hypoplastic type, resulting from g.6395G>A mutation in the enamelin gene. PATIENTS AND METHODS: A genealogical pattern was created for five generations. Five members of this family group were clinically examined, and four of them had a molecular analysis that consisted of the detection of a mutation in the enamelin gene using PCR. RESULTS: In this family, the enamel malformation presents a dominant autosomal pattern of inheritance. The clinical examination of the group allowed a diagnosis of Amelogenesis Imperfecta, of the hypoplastic local type. However, the molecular analysis revealed that the members analyzed did not exhibit the g.6395G>A mutation reported for the enamelin gene (ENAM). CONCLUSIONS: The enamel phenotype in this family could be explained by the presence of one of four other mutations recently described in this or another gene, thereby supporting the findings of allelic heterogeneity reported in the literature.

Cáncer mamario factores de riesgo / Risk factors of breast cancer

El cáncer mamario presenta una gran incidencia en nuestra población de mujeres aun con los avances actuales, su curación depende principalmente de su detección précoz, para lograr dicho objetivo se requiere de una adecuada clasificación de las mujeres con alto riesgo de padecer ésta patología por medio de la identificación de los factores de riesgo que presentan una asociación importante con dicho cáncer. En éste estudio retrospectivo o de casos y controles tratamos de establecer el comportamiento de los factores que mas se postulan como de mayor asociación causal con cáncer mamario (edad, edad del primer parto, hiperfunción tiroidea, ingesta de A.C.O. y antecedentes familiares de cáncer), dentro del grupo de estudio. Finalmente concluimos que los factores con asociación importante con dicha patología son: edad, uso de anticonceptivos orales, edad tardia del primer parto y nuliparidad. Ademas encontramos que no existe una asociacion importante entre la aparición de dicho cáncer y antecedentes familiares de cáncer e hiperfunción tiroide