A highly potent antibody effective against SARS-CoV-2 variants of concern

Control of the ongoing SARS-CoV-2 pandemic is endangered by the emergence of viral variants with increased transmission efficiency, resistance to marketed therapeutic antibodies, and reduced sensitivity to vaccine-induced immunity. Here, we screen B cells from COVID-19 donors and identify P5C3, a highly potent and broadly neutralizing monoclonal antibody with picomolar neutralizing activity against all SARS-CoV-2 variants of concern (VOCs) identified to date. Structural characterization of P5C3 Fab in complex with the spike demonstrates a neutralizing activity defined by a large buried surface area, highly overlapping with the receptor-binding domain (RBD) surface necessary for ACE2 interaction. We further demonstrate that P5C3 shows complete prophylactic protection in the SARS-CoV-2-infected hamster challenge model. These results indicate that P5C3 opens exciting perspectives either as a prophylactic agent in immunocompromised individuals with poor response to vaccination or as combination therapy in SARS-CoV-2-infected individuals.

Heterochromatic genes undergo epigenetic changes and escape silencing in immunodeficiency, centromeric instability, facial anomalies (ICF) syndrome

Immunodeficiency, Centromeric Instability, Facial Anomalies (ICF) syndrome is a rare autosomal recessive disorder that is characterized by a marked immunodeficiency, severe hypomethylation of the classical satellites 2 and 3 associated with disruption of constitutive heterochromatin, and facial anomalies. Sixty percent of ICF patients have mutations in the DNMT3B (DNA methyltransferase 3B) gene, encoding a de novo DNA methyltransferase. In the present study, we have shown that, in ICF lymphoblasts and peripheral blood, juxtacentromeric heterochromatic genes undergo dramatic changes in DNA methylation, indicating that they are bona fide targets of the DNMT3B protein. DNA methylation in heterochromatic genes dropped from about 80% in normal cells to approximately 30% in ICF cells. Hypomethylation was observed in five ICF patients and was associated with activation of these silent genes. Although DNA hypomethylation occurred in all the analyzed heterochromatic genes and in all the ICF patients, gene expression was restricted to some genes, every patient having his own group of activated genes. Histone modifications were preserved in ICF patients. Heterochromatic genes were associated with histone modifications that are typical of inactive chromatin: they had low acetylation on H3 and H4 histones and were slightly enriched in H3K9Me(3), both in ICF and controls. This was also the case for those heterochromatic genes that escaped silencing. This finding suggests that gene activation was not generalized to all the cells, but rather was restricted to a clonal cell population that may contribute to the phenotypic variability observed in ICF syndrome. A slight increase in H3K27 monomethylation was observed both in heterochromatin and active euchromatin in ICF patients; however, no correlation between this modification and activation of heterochromatic genes was found.

Analysis of factors associated with mortality of heavy slaughter pigs during transport and lairage

The study was based on data collected during 5 yr (2003-2007) and was aimed at assessing the effects of the month, slaughter house of destination (differing for stocking density, openings, brightness, and cooling device types), length of the journey, and temperature-humidity index (THI) on mortality of heavy slaughter pigs (approximately 160 kg live weight) during transport and lairage. Data were obtained from 24,098 journeys and 3,676,153 pigs transported from 1,618 farms to 3 slaughter houses. Individual shipments were the unit of observation. The terms dead on arrival (DOA) and dead in pen (DIP) refer to pigs that died during transport and in lairage at the abattoir before slaughtering, respectively. These 2 variables were assessed as the dependent counts in separate univariate Poisson regressions. The independent variables assessed univariately in each set of regressions were month of shipment, slaughter house of destination, time traveled, and each combination of the month with the time traveled. Two separate piecewise regressions were done. One used DOA counts within THI levels over pigs transported as a dependent ratio and the second used DIP counts within THI levels over pigs from a transport kept in lairage as a dependent ratio. The THI was the sole independent variable in each case. The month with the greatest frequency of deaths was July with a risk ratio of 1.22 (confidence interval: 1.06-1.36; P < 0.05) and 1.27 (confidence interval: 1.06-1.51; P < 0.05) for DOA and DIP, respectively. The lower mortality risk ratios for DOA and DIP were recorded for January and March (P < 0.05). The aggregated data of the summer (June, July, and August) versus non-summer (January, March, September, and November) months showed a greater risk of pigs dying during the hot season when considering both transport and lairage (P < 0.05). The mortality risk ratio of DIP was lower at the slaughter house with the lowest stocking density (0.64 m(2)/100 kg live weight), large open windows on the roof and sidewalls, low brightness (40 lx) lights, and high-pressure sprinklers as cooling devices. The mortality risk ratio of DOA increased significantly for journeys longer than 2 h, whereas no relationship was found between length of transport and DIP. The piecewise analysis pointed out that 78.5 and 73.6 THI were the thresholds above which the mortality rate increased significantly for DOA and DIP, respectively. These results may help the pig industry to improve the welfare of heavy slaughter pigs during transport and lairage.

DNA replication is altered in Immunodeficiency Centromeric instability Facial anomalies (ICF) cells carrying DNMT3B mutations

ICF syndrome is a rare autosomal recessive disorder that is characterized by Immunodeficiency, Centromeric instability, and Facial anomalies. In all, 60% of ICF patients have mutations in the DNMT3B (DNA methyltransferase 3B) gene, encoding a de novo DNA methyltransferase. In ICF cells, constitutive heterochromatin is hypomethylated and decondensed, metaphase chromosomes undergo rearrangements (mainly involving juxtacentromeric regions), and more than 700 genes are aberrantly expressed. This work shows that DNA replication is also altered in ICF cells: (i) heterochromatic genes replicate earlier in the S-phase; (ii) global replication fork speed is higher; and (iii) S-phase is shorter. These replication defects may result from chromatin changes that modify DNA accessibility to the replication machinery and/or from changes in the expression level of genes involved in DNA replication. This work highlights the interest of using ICF cells as a model to investigate how DNA methylation regulates DNA replication in humans.

Lymph node dendritic cells harbor inducible replication-competent HIV despite years of suppressive ART

Although gut and lymph node (LN) memory CD4 T cells represent major HIV and simian immunodeficiency virus (SIV) tissue reservoirs, the study of the role of dendritic cells (DCs) in HIV persistence has long been limited to the blood due to difficulties to access lymphoid tissue samples. In this study, we show that LN migratory and resident DC subpopulations harbor distinct phenotypic and transcriptomic profiles. Interestingly, both LN DC subpopulations contain HIV intact provirus and inducible replication-competent HIV despite the expression of the antiviral restriction factor SAMHD1. Notably, LN DC subpopulations isolated from HIV-infected individuals treated for up to 14 years are transcriptionally silent but harbor replication-competent virus that can be induced upon TLR7/8 stimulation. Taken together, these results uncover a potential important contribution of LN DCs to HIV infection in the presence of ART.

Soluble Aβ42 Acts as Allosteric Activator of the Core Cholinergic Enzyme Choline Acetyltransferase

Two major questions in the field of Alzheimer-type dementia remain elusive. One is the native function of amyloid-β (Aβ) peptides and the other is an early deficit in the central cholinergic network. Nevertheless, recent evidence suggests that Aβ peptides are involved in the regulation of acetylcholine (ACh) homeostasis either by allosteric activation of ACh-degrading cholinesterases or by inhibiting the high-affinity choline uptake transporter. In the current study, we report that Aβ peptides, in particular Aβ42, allosterically enhances the catalytic rate of the core-cholinergic enzyme choline acetyltransferase (ChAT), responsible for biosynthesis of ACh. Detailed in vitro enzyme kinetic analysis indicated that both soluble Aβ40 and Aβ42 enhanced the catalytic efficiency of ChAT by ∼21% and 26% at physiological concentration ranges found in human cerebrospinal fluid (CSF). Further analyses indicated that activation of ChAT by Aβ was highly specific. Intriguingly, Aβ42 exhibited an EC₅₀ of activation potency at 10-fold lower concentrations compared to Aβ40. The activation was persistent even in the presence of a physiological Aβ 40/42 mixture ratio, expected in human CSF. In conclusion, we report for the first time that Aβ42 peptide acts as allosteric enhancers of ACh-biosynthesizing enzyme ChAT. Together with two previous observations, this points to a complex molecular cross-talk between Aβ and the enzymatic machinery involved in maintaining cellular, synaptic and extra-synaptic ACh homeostasis, warranting further investigation.

BAGE Hypomethylation Is an Early Event in Colon Transformation and Is Frequent in Histologically Advanced Adenomas

We showed earlier that BAGE (B melanoma antigen) loci are hypermethylated in normal tissues and hypomethylated in 98% of human cancers. More recently, we provided evidence that hypomethylation of BAGE loci represents an informative marker for colon cancer detection. In this study, we show that hypomethylation of BAGE loci was an early event that occurred in 43% of colorectal adenomas. Interestingly, hypomethylation of BAGE loci was frequent (50%) in tubulo-villous and villous adenomas, these adenomas having a high probability of being transformed into colorectal cancers.

Homomeric and Heteromeric Aβ Species Exist in Human Brain and CSF Regardless of Alzheimer's Disease Status and Risk Genotype

Background: A fundamental question in Alzheimer’s disease (AD) is whether amyloid-β (Aβ) peptides and their deposition in the brain signify a direct pathological role or they are mere outcome of the disease pathophysiological events affecting neuronal function. It is therefore important to decipher their physiological role in the brain. So far, the overwhelming focus has been on the potential toxicity of Aβ, often studied outside the crucial AD characteristics, i.e.: (i) the slow, decades-long disease progression that precedes clinical symptoms; (ii) the link to apolipoprotein-E ε4 allele as major risk factor; (iii) the selective early degeneration of cholinergic neurons. Previous studies, in vitro and cerebrospinal fluid (CSF) only, indicated one possible native function of Aβ peptides is the allosteric modulation of acetylcholine homeostasis, via molecular interactions between Aβ, apolipoprotein-E, and the acetylcholine-degrading enzymes, cholinesterases, resulting in the formation of acetylcholine-hydrolyzing complexes (BAβACs).

Methods: Here, by combining sucrose-density gradient fractionation of post-mortem brains and in-house developed sensitive ELISA assays on the obtained fractions, we investigated the presence, levels and molecular interactions between Aβ, apolipoprotein-E and cholinesterases for the first time in brain tissues. We examined three distinct brain regions of Alzheimer and non-demented subjects, plus a large number of Alzheimer CSF samples.

Results: We report that both monomeric and oligomeric (homomeric and heteromeric) forms of Aβ peptides are present in the brain of Alzheimer and non-demented individuals. Heteromeric Aβ was found in stable complexes with apolipoprotein-E and/or cholinesterases, irrespective of APOE genotype or disease status, arguing in favor of a physiological dynamic formation and function for these complexes in the brain. The patterns and molecular sizes of the detected soluble Aβ forms were closely matched between CSF and brain samples. This evinces that the detected Aβ-apolipoprotein-E complexes and BAβACs in CSF most likely originate from the interstitial fluids of the brain.

Conclusions: In conclusion, both light homomeric Aβ oligomers and heteromeric Aβ-ApoE and BAβACs are present and readily detectable in the brain, regardless of disease status and APOE4 genotype. Deeper knowledge of the physiological function of Aβ is crucial for better understanding the early pathological events that decades later lead to manifestation of AD.

T cell receptor precision editing of regulatory T cells for celiac disease

Celiac disease, a gluten-sensitive enteropathy, demonstrates a strong human leukocyte antigen (HLA) association, with more than 90% of patients carrying the HLA-DQ2.5 allotype. No therapy is available for the condition except for a lifelong gluten-free diet. To address this gap, we explored the therapeutic potential of regulatory T cells (Tregs). By orthotopic replacement of T cell receptors (TCRs) through homology-directed repair, we generated gluten-reactive HLA-DQ2.5-restricted CD4+ engineered (e) T effector cells (Teffs) and eTregs and performed in vivo experiments in HLA-DQ2.5 transgenic mice. Of five validated TCRs, TCRs specific for two immunodominant and deamidated gluten epitopes (DQ2.5-glia-α1a and DQ2.5-glia-α2) were selected for further evaluation. CD4+ eTeffs exposed to deamidated gluten through oral gavage colocalized with dendritic and B cells in the Peyer's patches and gut-draining lymph nodes and specifically migrated to the intestine. The suppressive function of human eTregs correlated with high TCR functional activity. eTregs specific for one epitope suppressed the proliferation and gut migration of CD4+ eTeffs specific for the same and the other gluten epitope, demonstrating bystander suppression. The suppression requires an antigen-specific activation of eTregs given that polyclonal Tregs failed to suppress CD4+ eTeffs. These findings highlight the potential of gluten-reactive eTregs as a therapeutic for celiac disease.