Methodological considerations on how to identify human hematopoietic stem cells.

Recently, human CD34+ hematopoietic stem cells (HSCs) have been purified to a frequency of approximately 1 in 3 cells, a population denoted as CD34+CD38-CD45RA-CD90±EPCR+ HSCs. This work aimed to evaluate the methodology for CD34+ HSC isolation, exploring differences in antibody clones, conjugates, source of cells and additional cell surface antigens (integrin-α6, CLEC9A and GPRC5C) to enhance the purity of these EPCR+ HSCs. We are emphasizing here the importance of experimental planning and antibody panel selection concerning the isolation of these human HSCs from multiple sources and providing important notes on the pitfalls of the reagents used for such purposes. Our results should enable a better reproducibility of results between labs, as well as further pursue work towards improving the enrichment of human HSCs

Use of metabolic imaging to monitor heterogeneity of tumour response following therapeutic mTORC1/2 pathway inhibition.

The PI3K-mTOR-AKT pathway regulates tumour proliferation, gene expression and metabolism, but pathway inhibition induces heterogeneous feedback reactivation, limiting anti-tumour responses. Measuring heterogeneity of pathway inhibition in tissues using protein biomarker phosphorylation or location is challenging. An integrated multi-modal imaging workflow was developed to assess the heterogeneity of AZD2014 (mTORC1/2 inhibitor) response in a PTEN-null renal cancer model. Spatial responses of metabolite biomarkers were analysed by mass spectrometry imaging (MSI). Control and treated tumours were classified according to metabolite-defined regions enriched in control versus AZD2014-treated tumours, respectively. Noticeably, AZD2014-treated tumours retained regions similar to regions dominant in untreated tumours. Imaging mass cytometry analysis of protein biomarkers in 'control-like' regions following AZD2014 treatment showed reduced phospho-S6, indicating suppression, but retained high expression of the glucose transporter GLUT1. Increasing PI3K-AKT inhibition by combining with AZD8186 (PI3Kβ inhibitor) further decreased the control-like metabolic signature, showing PI3K-dependent resistance. This demonstrates that MSI-based workflows yield novel insights into the pharmacodynamic effects of mTORC1/2 inhibition in tumours, which classical biomarkers do not resolve. Coupling these workflows with spatial-omics approaches can deliver greater insights into heterogeneity of treatment response

Data from a framework analysis of RDM policies to determine openness

Data supporting a paper titled "Do data management policies become more open over time?"The data includes three matrices created as part of a framework analysis. The Reasons and Adjectives data show a binary coding of whether a policy contains the term or idea. The Policies matrix contains values from 0 - 4 with 0 representing a very closed policy type and 4 representing a very open policy type. The details of these policies can be found in ...[update when preprint is posted]Associated code can be found at: 10.25418/crick.28788704</p

Structural plasticity of Plasmodium falciparum plasmepsin X to accommodate binding of potent macrocyclic hydroxyethylamine inhibitors.

Plasmodium falciparum plasmepsin X (PMX) has become a target of choice for the development of new antimalarial drugs due to its essential role across the parasite life cycle. Here we describe the 1.7Å crystallographic structure of PMX noncovalently bound to a potent macrocyclic peptidomimetic inhibitor (7k) possessing a hydroxyethylamine (HEA) scaffold. Upon 7k binding, the enzyme adopts a novel conformation, with significant involvement of the S2'S2 loop (M526-H536) and the S2 flap (F311-G314). This results in partial closure of the active site with widespread interactions in both the prime (S') and the non-prime (S) sites of PMX. The catalytic aspartate residues D266 and D467 directly interact with the HEA pharmacophore. Docking of a 7k derivative, compound 7a, highlights a region in the S3 pocket near the S3 flexible loop (H242-F248) that may be key for ligand stabilisation. The dynamic nature of PMX and its propensity to undergo distinct types of induced fit upon inhibitor binding enables generation of potent inhibitors that target this essential malarial aspartic protease

Assessment of CRB1-associated retinopathies using the S-MAIA fast protocol and spectral-domain optical coherence tomography.

Background: A cross-sectional study was conducted at Moorfields Eye Hospital, UK, involving patients with CRB1-associated retinopathies: macular dystrophy (MD), cone-rod dystrophy (CORD), and early-onset severe retinal dystrophy/Leber congenital amaurosis (EOSRD/LCA). The study aimed to evaluate CRB1-associated retinopathies using microperimetry (macular integrity assessment (S-MAIA) fast protocol) and spectral domain optical coherence tomography (SD-OCT). Methods: Data quality and participant attrition were assessed in 18 patients (10 MD, 5 EOSRD/LCA, 3 CORD), aged 10-52 years, with a median best corrected visual acuity (BCVA) of 0.41 logMAR. Results: Microperimetry and SD-OCT data were obtained from 14 and 18 patients, respectively, but eccentric fixation hindered structure-function analysis. All participants showed overall abnormal sensitivity on the S-MAIA fast protocol. Parafoveal volume was significantly increased, while foveal thickness and volume were reduced compared to normative data (p < 0.01). Conclusions: This study highlights the challenges of participant attrition and the need for alternative functional metrics to complement traditional evaluations. It also reinforces previous findings of abnormal retinal architecture in CRB1-associated retinopathies, providing further insights into S-MAIA and SD-OCT assessments for this patient population

Structural and functional characterization of the extended-diKH domain from the antiviral endoribonuclease KHNYN.

Zinc finger antiviral protein (ZAP) binds CpG dinucleotides in viral RNA and targets them for decay. ZAP interacts with several cofactors to form the ZAP antiviral system, including KHNYN, a multidomain endoribonuclease required for ZAP-mediated RNA decay. However, it is unclear how the individual domains in KHNYN contribute to its activity. Here, we demonstrate that the KHNYN amino terminal extended-diKH (ex-diKH) domain is required for antiviral activity and present its crystal structure. The structure belongs to a rare group of KH-containing domains, characterized by a non-canonical arrangement between two type-1 KH modules, with an additional helical bundle. N4BP1 is a KHNYN paralog with an ex-diKH domain that functionally complements the KHNYN ex-diKH domain. Interestingly, the ex-diKH domain structure is present in N4BP1-like proteins in lancelets, which are basal chordates, indicating that it is evolutionarily ancient. While many KH domains demonstrate RNA binding activity, biolayer interferometry and electrophoretic mobility shift assays indicate that the KHNYN ex-diKH domain does not bind RNA. Furthermore, residues required for canonical KH domains to bind RNA are not required for KHNYN antiviral activity. By contrast, an inter-KH domain cleft in KHNYN is a potential protein-protein interaction site and mutations that eliminate arginine salt bridges at the edge of this cleft decrease KHNYN antiviral activity. This suggests that this domain could be a binding site for an unknown KHNYN cofactor

The bat influenza A virus subtype H18N11 induces nanoscale MHCII clustering upon host cell attachment.

Prior to the discovery of bat influenza A virus (IAV) subtypes H17N10 and H18N11, all IAVs were thought to bind sialic acid residues via hemagglutinin (HA) to mediate attachment and subsequent viral entry. However, H17 and H18 engage a proteinaceous receptor: the major histocompatibility complex class II (MHCII). The mechanistic details of this hitherto unknown protein-mediated entry are not understood. Given that conventional IAVs rely on multivalent binding to sialylated glycans, we hypothesized that bat HA similarly interacts with multiple MHCII molecules. Using photoactivated localization microscopy (PALM) on fixed and live cells, we demonstrate that bat IAV particles attach to pre-existing MHCII clusters and induce a further increase in cluster size upon binding. To measure the impact of viral attachment on the dynamics of MHCII, we employ an "inverse attachment" approach, immobilizing viral particles on coverslips before seeding live MHCII-expressing cells on top. Single-molecule tracking reveals that the mobility of MHCII is indeed slowed down in viral proximity leading to a local enrichment of MHCII molecules beneath the viral particle. These findings suggest that viral attachment induces MHCII clustering, a process similar to the MHCII dynamics observed during the formation of an immunological synapse

Time of day of vaccination does not influence antibody responses to pneumococcal and annual influenza vaccination in a cohort of healthy older adults.

Vaccines are less immunogenic in older adults, partly due to immunosenescence. Having previously shown that morning influenza vaccination may be more immunogenic in older adults (mean age 71), we assessed if this could be replicated in a younger cohort (mean age 57) and with a T-cell independent vaccine. This study examined whether diurnal timing of a single dose of Pneumovax® (PPV-23) and seasonal influenza vaccine influenced antibody responses in 140 healthy adults over the age of 50. Pneumococcal serotype-specific (PnPS) antibodies and Haemagglutination Inhibition Assays (HAI) were used to characterize antibody responses at Baseline, 1, 4, and 52 weeks post-vaccination. Protective thresholds were set at 0.35 μg/mL for two-thirds of PnPS tested (WHO≥8/12PnPS) and a titre of ≥40 HAI for H1N1, H3N2, and B/Victoria strains. Both AM and PM cohorts showed increased Pn-specific antibodies to one PPV-23 dose at weeks 1, 4, and 52; however, time of day did not significantly influence antibody responses. Baseline immunity for pneumococcus was high (57.1 % AM, 50.0 % PM had WHO≥8/12PnPS), and immunity was maintained with at least 7/12 serotypes elevated at 52 weeks. Time of day did not alter short- or long-term influenza antibody responses. H1N1 had the highest baseline immunity (67.6 % AM, 48.6 % PM had ≥40 HAI) and the most increased responses at week 4 post-vaccination (92.8 % AM, 94.1 % PM) that were maintained at 52 weeks post-vaccination (91.7 % AM, 89.3 % PM). The poorest serotype immunity was for the B/Victoria strain at all time points. Although time of day did not influence vaccine immunogenicity in AM and PM cohorts, sustained cohort-wide antibody responses were demonstrated in an older population. Identifying 18 % of the total cohort exhibited suboptimal responses to pneumococcal or influenza vaccines underscores the imperative for enhancing vaccine efficacy within this age group to reduce morbidity and mortality

Timed chromatin invasion during mitosis governs prototype foamy virus integration site selection and infectivity.

Selection of a suitable chromatin environment during retroviral integration is a tightly regulated process. Most retroviruses, including spumaretroviruses, require mitosis for nuclear entry. However, whether intrinsic chromatin dynamics during mitosis modulates retroviral genome invasion is unknown. Previous work uncovered critical interactions of prototype foamy virus (PFV) Gag with nucleosomes via a highly conserved arginine anchor residue. Yet, the regulation of Gag-chromatin interaction and its functional consequences for spumaretrovirus biology remain obscure. Here, we investigated the kinetics of chromatin binding by Gag during mitosis and proviral integration in synchronized cells. We showed that alteration of Gag affinity for nucleosome binding induced untimely chromatin tethering during mitosis, decreased infectivity, and redistributed viral integration sites to markers associated with late replication timing of chromosomes. Mutant Gag proteins were, moreover, defective in their ability to displace the histone H4 tail from the nucleosome acidic patch of highly condensed chromatin. These data indicate that the chromatin landscape during Gag-nucleosome interactions is important for PFV integration site selection and that spumaretroviruses evolved high-affinity chromatin binding to overcome early mitosis chromatin condensation

Sequential transcriptional programs underpin activation of hippocampal stem cells.

Adult neural stem cells exist on a continuum from deep to shallow quiescence that changes in response to injury or aging; however, the transcription factors controlling these stepwise transitions have not been identified. Single-cell transcriptomic analyses of mice with loss of function or increased levels of the essential activation factor Ascl1 reveal that Ascl1 promotes the activation of hippocampal neural stem cells by driving these cells out of deep quiescence, despite its low protein expression in this state. Subsequently, during the transition from deep to shallow quiescence, Ascl1 induces the expression of Mycn, which drives progression through shallow quiescent states toward a proliferating state. Together, these results define the required sequence of transcription factors during hippocampal neural stem cell activation and establish a combinatorial code for classifying these cells into deep and shallow quiescence