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SummaryMaintenance of pluripotency is a multifactorial process in which NF-κB is a negative regulator. Our previous work identified a chromatin role for IκBα, the master regulator of NF-κB signaling, that is critical for the proper regulation of various tissue stem cells. Here, we found that IκBα accumulates specifically in the chromatin fraction of pluripotent embryonic stem cells. IκBα depletion does not affect NF-kB-dependent transcription, but causes a profound epigenetic rewiring in pluripotent stem cells, including alterations in H3K27me3, a histone mark catalyzed by Polycomb repression complex 2. Chromatin changes induced by IκBα depletion affect a subset of pluripotency genes and are associated with altered gene transcription. At the cellular level, IκBα-deficient embryonic stem cells are arrested in a naive pluripotency state when cultured in serum/LIF conditions and fail to exit pluripotency under differentiation conditions. By constructing separation-of-function mutants, we show that the effects of IκBα in regulating stem cell pluripotency are NF-κB-independent, but mainly rely on its chromatin-related function. Taken together, our results reveal a novel mechanism by which IκBα participates in the regulation of the pluripotent state of embryonic stem cells and shed light on the interplay between inflammatory signals and the regulation of pluripotency.

Determining variants in the genome involves several bioinformatic procedures, such as eliminating low-quality sequences, aligning sequencing reads to the human reference genome, and establishing confidence in the presence of a variant based on a threshold. Once a variant is identified, it is annotated to predict its effect. The goal of this task is to establish a best practice protocol for data analysis of whole genome sequencing (WGS) for somatic variants. This protocol will include a recommended suite of software tools with settings that ensure results surpass a required quality threshold. As part of the 1+MG WG4 project, we are currently benchmarking quality metrics to assess the best standards in the practice of WGS for somatic variants. At the time of writing, we have completed the initial steps of the benchmark and evaluated the quality metrics corresponding to the library preparation and sequencing steps. We compared the performance of sequencing conducted by participating laboratories by examining the value and dispersion of relevant metrics, providing a first assessment of how different sequencing protocols impact the sequences produced. The sequencing laboratories got an overall performance score, and based on the protocols followed by the facilities producing the best results we suggest which are the best practices for library preparation and sequencing. A general conclusion is that all participants have achieved a good level of quality at the sequencing stage, and the metrics measuring it are largely consistent, as there is very little dispersion. Differences in library preparation and sequencing protocols do not appear to significantly impact the expected quality of results. In the following sections, we explain the performance of different participating laboratories for each one of the relevant sequencing metrics, and suggest general best practices to ensure the best quality. This deliverable has been significantly delayed due to an important backlog in the preparation, examination, and approval of all ethical requirements to protect sensitive patient data. We made considerable effort in drafting the material transfer agreement (MTA) to guarantee that patient data will be used with all precautions and strict anonymity because genomic data is identifiable.

The booklet is a compilation of inspiring stories that capture the "EUREKA moment" and highlight successes and learnings from activities conducted during the ORION Open Science project. The stories showcase a variety of different engagement and Open Science aspects: citizen science, co-creation, public dialogues, public engagement, science communication and training.

Abstract We assessed the duration and baseline determinants of antibody responses to SARS-CoV-2 spike antigens and the occurrence of reinfections in a prospective cohort of 173 Spanish primary health care worker patients followed up initially for nine months and subsequently up to 12.5 months after COVID-19 symptoms onset. Seropositivity to SARS-CoV-2 spike and receptor binding domain antigens up to 149-270 days was 92.49% (90.17% IgG, 76.3% IgA, 60.69% IgM). In a subset of 64 health care workers who had not yet been vaccinated by April 2021, seropositivity was 96.88% (95.31% IgG, 82.81% IgA) up to 322-379 days post symptoms onset. There were four suspected reinfections detected by passive case detection, two among seronegative individuals (five and seven months after the first episode), and one low antibody responder. Antibody levels significantly correlated with fever, hospitalization, anosmia/hypogeusia, allergies, smoking and occupation. Stable sustainment of IgG responses raises hope for long-lasting COVID-19 vaccine immunity.

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