Characterization of SARS-CoV-2 Mutational Signatures from 1.5+ Million Raw Sequencing Samples

We present a large-scale analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) substitutions, considering 1,585,456 high-quality raw sequencing samples, aimed at investigating the existence and quantifying the effect of mutational processes causing mutations in SARS-CoV-2 genomes when interacting with the human host. As a result, we confirmed the presence of three well-differentiated mutational processes likely ruled by reactive oxygen species (ROS), apolipoprotein B editing complex (APOBEC), and adenosine deaminase acting on RNA (ADAR). We then evaluated the activity of these mutational processes in different continental groups, showing that some samples from Africa present a significantly higher number of substitutions, most likely due to higher APOBEC activity. We finally analyzed the activity of mutational processes across different SARS-CoV-2 variants, and we found a significantly lower number of mutations attributable to APOBEC activity in samples assigned to the Omicron variant

Liquid Biopsy in Cancer: Focus on Lymphoproliferative Disorders

Within the context of precision medicine, the scientific community is giving particular attention to early diagnosis and intervention, guided by non-invasive methodologies. Liquid biopsy (LBx) is a recent laboratory approach consisting of a non-invasive blood draw, which allows the detection of information about potential prognostic factors, or markers to be used for diagnostic purposes; it might also allow the clinician to establish a treatment regimen and predict a patient’s response. Since the discovery of circulating tumor cells (CTCs) in the nineteenth century, the possibility of integrating LBx into clinical practice has been explored, primarily because of its safeness and easy execution: indeed, compared to solid biopsy, sampling-related risks are less of a concern, and the quickness and repeatability of the process could help confirm a prompt diagnosis or to further corroborate the existence of a metastatic spreading of the disease. LBx’s usefulness has been consolidated in a narrow range of oncological settings, first of all, non-small cell lung carcinoma (NSCLC), and it is now gradually being assessed also in lymphoproliferative diseases, such as acute lymphocytic leukemia (ALL), B-cell lymphomas, and multiple myeloma. The present review aims to summarize LBx’s overall characteristics (such as its advantages and flaws, collection and analysis methodologies, indications, and targets of the test), and to highlight the applications of this technique within the specific field of B-cell malignancies. The perspectives on how such a simple and convenient technique could improve hemato-oncological clinical practice are broadly encouraging, yet far from a complete integration in routine clinical settings

Balanced SET levels favor the correct enhancer repertoire during cell fate acquisition

Abstract Within the chromatin, distal elements interact with promoters to regulate specific transcriptional programs. Histone acetylation, interfering with the net charges of the nucleosomes, is a key player in this regulation. Here, we report that the oncoprotein SET is a critical determinant for the levels of histone acetylation within enhancers. We disclose that a condition in which SET is accumulated, the severe Schinzel-Giedion Syndrome (SGS), is characterized by a failure in the usage of the distal regulatory regions typically employed during fate commitment. This is accompanied by the usage of alternative enhancers leading to a massive rewiring of the distal control of the gene transcription. This represents a (mal)adaptive mechanism that, on one side, allows to achieve a certain degree of differentiation, while on the other affects the fine and corrected maturation of the cells. Thus, we propose the differential in cis-regulation as a contributing factor to the pathological basis of SGS and possibly other the SET-related disorders in humans

Binding of Fng to phage particles in the presence and in the absence of inhibitors.

<p><b>A</b>. Binding to Fng of increasing numbers of 5p or 6p lambda phage (λ5p or λ6p) particles. Plates were coated with Fng, and phage particles were added at the indicated PFU numbers followed by anti-lambda phage rabbit IgG and alkaline phosphatase-labeled goat anti-rabbit IgG. Error bars represent means ± standard deviations from three independent experiments; *, p<0.05 by analysis of variance followed by the Student Newman Keuls test. <b>B</b> and <b>C</b>. Inhibition of binding of 5p or 6p lambda phage particles (λ5p or λ6p, 10⁸ PFU) to immobilized Fng in the presence of increasing concentrations of recombinant FbsA fragments (5pGST and 6pGST in panels B and C, respectively) used as inhibitors. Data are from one experiment, representative of three producing similar results.</p

Interaction of Fng with recombinant FbsA fragments.

<p><b>A</b>. Dose-dependent binding of Fng to recombinant FbsA fragments. 5pGST and 6pGST were coated onto microtiter plates (500 ng/well) and incubated with increasing amounts of Fng, followed by mouse anti-Fng IgG and HRP-conjugated rabbit anti-mouse IgG. Values represent the means of triplicate samples ± S.E. This experiment was performed three times with similar results. <b>B</b> and <b>C</b>. Surface Plasmon Resonance analysis of the interaction of 5pGST and 6pGST with Fng. 5pGST (panel B) and 6pGST (panel C) were captured on a BIAcore sensor chip coated with goat anti-GST IgG. Human Fng (2.92 nM to 750 nM) was then flowed over the chip surface. The data shown are representative of three individual experiments.</p

Effects of active immunoprotection with the 6pGST FbsA fragment in adult and neonatal mouse models of GBS sepsis.

<p><b>A</b>. Immunoprotection in adult mice. Five-week-old CD1 mice underwent three immunizations with the 6p FbsA fragment fused to GST (6pGST) or with GST alone. At 3 weeks after the last immunizations mice were challenged by the i.p. injection of GBS strain COH1 (5x10⁷ CFUs) and lethality was observed daily. *, p<0.05 relative to GST-immunized mice by Kaplan-Meier survival plots. Shown are the cumulative results of two independent experiments. <b>B</b>. Effect of maternal immunization on survival of experimentally infected pups. Female CD1 mice (5 wk old) were immunized three times with the 6p FbsA fragment fused to GST (6pGST) or with GST alone. Mice were then time-mated and two-day-old pups were infected s.c. with 250 CFUs of GBS strain 6313. *, p<0.05 relative to GST-immunized mice by Kaplan-Meier survival plots.</p

ETNK1 mutations induce a mutator phenotype that can be reverted with phosphoethanolamine

Recurrent somatic mutations in ETNK1 (Ethanolamine-Kinase-1) were identified in several myeloid malignancies and are responsible for a reduced enzymatic activity. Here, we demonstrate in primary leukemic cells and in cell lines that mutated ETNK1 causes a significant increase in mitochondrial activity, ROS production, and Histone H2AX phosphorylation, ultimately driving the increased accumulation of new mutations. We also show that phosphoethanolamine, the metabolic product of ETNK1, negatively controls mitochondrial activity through a direct competition with succinate at mitochondrial complex II. Hence, reduced intracellular phosphoethanolamine causes mitochondria hyperactivation, ROS production, and DNA damage. Treatment with phosphoethanolamine is able to counteract complex II hyperactivation and to restore a normal phenotype