Relics of interspecific hybridization retained in the genome of a drought-adapted peanut cultivar.

Peanut (Arachis hypogaea L.) is a globally important oil and food crop frequently grown in arid, semi-arid, or dryland environments. Improving drought tolerance is a key goal for peanut crop improvement efforts. Here we present the genome assembly and gene model annotation for 'Line8', a peanut genotype bred from drought tolerant cultivars. Our assembly and annotation are the most contiguous and complete peanut genome resources currently available. The high contiguity of the Line8 assembly allowed us to explore structural variation both between peanut genotypes and subgenomes. We detect several large inversions between Line8 and other peanut genome assemblies, and there is a trend for the inversions between more genetically diverged genotypes to have higher gene content. We also relate patterns of subgenome exchange to structural variation between Line8 homeologous chromosomes. Unexpectedly, we discover that Line8 harbors an introgression from A.cardenasii, a diploid peanut relative and important donor of disease resistance alleles to peanut breeding populations. The fully resolved sequences of both haplotypes in this introgression provide the first in situ characterization of A.cardenasii candidate alleles that can be leveraged for future targeted improvement efforts. The completeness of our genome will support peanut biotechnology and broader research into the evolution of hybridization and polyploidy.

Pathophysiology of Prurigo Nodularis: Neuroimmune Dysregulation and the Role of Type 2 Inflammation.

Prurigo nodularis (PN) is a chronic, inflammatory skin condition characterized by multiple, intensely pruritic, distinctive nodular lesions. Subsequent scratching can further intensify the pruritus, culminating in a self-reinforcing itch-scratch cycle, which drives lesion development. The latest data indicate dysregulation of the neuroimmune axis in PN pathogenesis, including the involvement of sensory neurons, key effector immune cells, proinflammatory cytokines, dermal fibroblasts, and pruritogens. In this review, we highlight evidence supporting the role of type 2 immune axis dysregulation in driving the clinical presentation of PN and discuss how related signaling pathways may offer effective therapeutic targets to control PN signs and symptoms.

Closing the Loop on Concentric Tube Robot Design: A Case Study on Micro-Laryngeal Surgery.

Concentric tube robots (CTRs) are well-suited to address the unique challenges of minimally invasive surgical procedures due to their small size and ability to navigate highly constrained environments. However, uncertainties in the manufacturing process can lead to challenges in the transition from simulated designs to physical robots. In this work, we propose an end-to-end design workflow for CTRs that considers the oftenoverlooked impact of manufacturing uncertainty, focusing on two primary sources - tube curvature and diameter. This comprehensive approach incorporates a two-step design optimization and an uncertainty-based selection of manufacturing tolerances. Simulation results highlight the substantial influence of manufacturing uncertainties, particularly tube curvature, on the physical robot's performance. By integrating these uncertainties into the design process, we can effectively bridge the gap between simulation and real-world performance. Two hardware experiments validate the proposed CTR design workflow. The first experiment confirms that the performance of the physical robot lies within the simulated probability distribution from the optimization, while the second experiment demonstrates the feasibility of the overall system for use in micro-laryngeal surgical tasks. This work not only contributes to a more comprehensive understanding of CTR design by addressing manufacturing uncertainties, but also creates a new framework for robust design, as illustrated in the context of microlaryngeal surgery.

Interorgan, intraorgan and interplant communication mediated by nitric oxide and related species.

Plant survival to a potential plethora of diverse environmental insults is underpinned by coordinated communication amongst organs to help shape effective responses to these environmental challenges at the whole plant level. This interorgan communication is supported by a complex signal network that regulates growth, development and environmental responses. Nitric oxide (NO) has emerged as a key signalling molecule in plants. However, its potential role in interorgan communication has only recently started to come into view. Direct and indirect evidence has emerged supporting that NO and related species (S-nitrosoglutathione, nitro-linolenic acid) are mobile interorgan signals transmitting responses to stresses such as hypoxia and heat. Beyond their role as mobile signals, NO and related species are involved in mediating xylem development, thus contributing to efficient root-shoot communication. Moreover, NO and related species are regulators in intraorgan systemic defence responses aiming an effective, coordinated defence against pathogens. Beyond its in planta signalling role, NO and related species may act as ex planta signals coordinating external leaf-to-leaf, root-to-leaf but also plant-to-plant communication. Here, we discuss these exciting developments and emphasise how their manipulation may provide novel strategies for crop improvement.

The SAInT study: a protocol for a randomized controlled trial of steroid injection for subacromial pain syndrome using the anterolateral versus posterior approach.

Aims: Steroid injections are used for subacromial pain syndrome and can be administered via the anterolateral or posterior approach to the subacromial space. It is not currently known which approach is superior in terms of improving clinical symptoms and function. This is the protocol for a randomized controlled trial (RCT) to compare the clinical effectiveness of a steroid injection given via the anterolateral or the posterior approach to the subacromial space. Methods: The Subacromial Approach Injection Trial (SAInT) study is a single-centre, parallel, two-arm RCT. Participants will be allocated on a 1:1 basis to a subacromial steroid injection via either the anterolateral or the posterior approach to the subacromial space. Participants in both trial arms will then receive physiotherapy as standard of care for subacromial pain syndrome. The primary analysis will compare the change in Oxford Shoulder Score (OSS) at three months after injection. Secondary outcomes include the change in OSS at six and 12 months, as well as the Pain Numeric Rating Scale (0 = no pain, 10 = worst pain), Disabilities of Arm, Shoulder and Hand questionnaire (DASH), and 36-Item Short-Form Health Survey (SF-36) (RAND) at three months, six months, and one year after injection. Assessment of pain experienced during the injection will also be determined. A minimum of 86 patients will be recruited to obtain an 80% power to detect a minimally important difference of six points on the OSS change between the groups at three months after injection. Conclusion: The results of this trial will demonstrate if there is a difference in shoulder pain and function after a subacromial space steroid injection between the anterolateral versus posterior approach in patients with subacromial pain syndrome. This will help to guide treatment for patients with subacromial pain syndrome.

Recruitment of CXCR4+ type 1 innate lymphoid cells distinguishes sarcoidosis from other skin granulomatous diseases.

Sarcoidosis is a multiorgan granulomatous disease that lacks diagnostic biomarkers and targeted treatments. Using blood and skin from patients with sarcoid and non-sarcoid skin granulomas, we discovered that skin granulomas from different diseases exhibit unique immune cell recruitment and molecular signatures. Sarcoid skin granulomas were specifically enriched for type 1 innate lymphoid cells (ILC1s) and B cells and exhibited molecular programs associated with formation of mature tertiary lymphoid structures (TLSs), including increased CXCL12/CXCR4 signaling. Lung sarcoidosis granulomas also displayed similar immune cell recruitment. Thus, granuloma formation was not a generic molecular response. In addition to tissue-specific effects, patients with sarcoidosis exhibited an 8-fold increase in circulating ILC1s, which correlated with treatment status. Multiple immune cell types induced CXCL12/CXCR4 signaling in sarcoidosis, including Th1 T cells, macrophages, and ILCs. Mechanistically, CXCR4 inhibition reduced sarcoidosis-activated immune cell migration, and targeting CXCR4 or total ILCs attenuated granuloma formation in a noninfectious mouse model. Taken together, our results show that ILC1s are a tissue and circulating biomarker that distinguishes sarcoidosis from other skin granulomatous diseases. Repurposing existing CXCR4 inhibitors may offer a new targeted treatment for this devastating disease.

Incidence of Parental Requests to Discontinue Growth-Friendly Surgical Lengthening for Early Onset Scoliosis.

BACKGROUND: The STOP questionnaire was developed to document reasons for discontinuation of growth-friendly (GF) treatment in early onset scoliosis (EOS). This study investigated the incidence of parental request (PR) on the STOP questionnaire and compared clinical information and Early Onset Scoliosis 24-Item Questionnaire (EOSQ-24) scores of PR patients with those whose parents did not request discontinuation (non-parent request [NPR]). MATERIALS AND METHODS: An international pediatric spine registry was queried for EOS patients with STOP questionnaires completed by their surgeon. Age at discontinuation, sex, and EOS etiology were recorded. GF device, number of surgical procedures, complications, STOP questionnaire reasons for discontinuation, and definitive treatment were recorded. EOSQ-24 scores and clinical information in the PR cohort were compared with the NPR cohort. RESULTS: Data for 1326 patients were analyzed. PR was listed on the STOP questionnaires of 46 (3.5%) patients, completed at a mean age of 12 years (SD, 3.2 years). There were no statistical differences in number of procedures or complications when comparing the PR cohort with the NPR cohort. PR patients more frequently had neuromuscular EOS (P=.002), more frequently were treated with magnetically controlled growing rods (33% vs 14%, P=.036), and more frequently were observed after GF discontinuation (P=.628). EOSQ-24 scores for the PR cohort were significantly lower in most domains except pain/discomfort. CONCLUSION: For 3.5% of the EOS patients, PR was listed on the STOP questionnaire. They frequently had neuromuscular EOS and frequently were treated with magnetically controlled growing rods. Additionally, these patients had statistically lower EOSQ-24 scores across most domains. [Orthopedics. 20XX;4X(X):XXX-XXX.].

Assessing performance of simplified bioassays for soil-borne pathogens in smallholder systems of western Kenya.

Introduction: Soil-borne pathogens cause considerable crop losses and food insecurity in smallholder systems of sub-Saharan Africa. Soil and crop testing is critical for estimating pathogen inoculum levels and potential for disease development, understanding pathogen interactions with soil nutrient and water limitations, as well as for developing informed soil health and disease management decisions. However, formal laboratory analyses and diagnostic services for pathogens are often out of reach for smallholder farmers due to the high cost of testing and a lack of local laboratories. Methods: To address this challenge, we assessed the performance of a suite of simplified soil bioassays to screen for plant parasitic nematodes (e.g., Meloidogyne, Pratylenchus) and other key soil-borne pathogens (Pythium and Fusarium). We sampled soils from on-farm trials in western Kenya examining the impact of distinct nutrient inputs (organic vs. synthetic) on bean production. Key soil health parameters and common soil-borne pathogens were evaluated using both simple bioassays and formal laboratory methods across eleven farms, each with three nutrient input treatments (66 samples in total). Results and Discussion: The soil bioassays, which involved counting galls on lettuce roots and lesions on soybean were well correlated with the abundance of gall forming (Meloidogyne) and root lesion nematodes (e.g., Pratylenchus) recovered in standard laboratory-based extractions. Effectiveness of a Fusarium bioassay, involving the counting of lesions on buried bean stems, was verified via sequencing and a pathogenicity test of cultured Fusarium strains. Finally, a Pythium soil bioassay using selective media clearly distinguished pathogen infestation of soils and infected seeds. When examining management impact on nematode communities, soils amended with manure had fewer plant parasites and considerably more bacterivore and fungivore nematodes compared to soils amended with synthetic N and P. Similarly, Pythium presence was 35% lower in soils amended with manure, while the Fusarium assays indicated 23% higher Fusarium infection in plots with amended manure. Our findings suggest that relatively simple bioassays can be used to help farmers assess soil-borne pathogens in a timely manner, with minimal costs, thus enabling them to make informed decisions on soil health and pathogen management.

Identification of Meibomian gland stem cell populations and mechanisms of aging.

Meibomian glands secrete lipid-rich meibum, which prevents tear evaporation. Aging-related Meibomian gland shrinkage may result in part from stem cell exhaustion and is associated with evaporative dry eye disease, a common condition lacking effective treatment. The identities and niche of Meibomian gland stem cells and the signals controlling their activity are poorly defined. Using snRNA-seq, in vivo lineage tracing, ex vivo live imaging, and genetic studies in mice, we identified markers for stem cell populations that maintain distinct regions of the gland and uncovered Hh signaling as a key regulator of stem cell proliferation. Consistent with this, human Meibomian gland carcinoma exhibited increased Hh signaling. Aged glands displayed decreased Hh and EGF signaling, deficient innervation, and loss of collagen I in niche fibroblasts, indicating that alterations in both glandular epithelial cells and their surrounding microenvironment contribute to age-related degeneration. These findings suggest new approaches to treat aging-associated Meibomian gland loss.

Blood inflammation relates to neuroinflammation and survival in frontotemporal lobar degeneration.

Neuroinflammation is an important pathogenic mechanism in many neurodegenerative diseases, including those caused by frontotemporal lobar degeneration (FTLD). Postmortem and in vivo imaging studies have shown brain inflammation early in these conditions, proportionate to symptom severity and rate of progression. However, evidence for corresponding blood markers of inflammation and their relationship with central inflammation and clinical outcome are limited. There is a pressing need for such scalable, accessible and mechanistically relevant blood markers as these will reduce the time, risk, and costs of experimental medicine trials. We therefore assessed inflammatory patterns of serum cytokines from 214 patients with clinical syndromes associated with FTLD as compared to healthy controls, including their correlation with brain regional microglial activation and disease progression. Serum assays used the MesoScale Discovery V-Plex-Human Cytokine 36 plex panel plus five additional cytokine assays. A sub-group of patients underwent 11C-PK11195 TSPO PET imaging, as an index of microglial activation. A Principal Component Analysis (PCA) was used to reduce the dimensionality of cytokine data, excluding cytokines that were undetectable in >50% of participants. Frequentist and Bayesian analyses were performed on the principal components, to compare each patient cohort to controls, and test for associations with central inflammation, neurodegeneration-related plasma markers and survival. The first component identified by the PCA (explaining 21.5% variance) was strongly loaded by pro-inflammatory cytokines, including TNF-α, TNF-R1, M-CSF, IL-17A, IL-12, IP-10 and IL-6. Individual scores of the component showed significant differences between each patient cohort and controls. The degree to which a patient expressed this peripheral inflammatory profile at baseline correlated negatively with survival (higher inflammation, shorter survival), even when correcting for baseline clinical severity. Higher pro-inflammatory profile scores were associated with higher microglial activation in frontal and brainstem regions, as quantified with 11C-PK11195 TSPO PET. A permutation-based Canonical Correlation Analysis confirmed the association between the same cytokine-derived pattern and central inflammation across brain regions in a fully data-based manner. This data-driven approach identified a pro-inflammatory profile across the FTLD clinical spectrum, which is associated with central neuroinflammation and worse clinical outcome. Blood-based markers of inflammation could increase the scalability and access to neuroinflammatory assessment of people with dementia, to facilitate clinical trials and experimental medicine studies.

Upgrading of Grade Group 1 Prostate Cancer at Prostatectomy: Germline Risk Factors in a Prospective Cohort.

BACKGROUND: Localized prostate tumors show significant spatial heterogeneity, with regions of high-grade disease adjacent to lower-grade disease. Consequently, prostate cancer biopsies are prone to sampling bias, potentially leading to underestimation of tumor grade. To study the clinical, epidemiologic and molecular hallmarks of this phenomenon, we conducted a prospective study of grade upgrading: differences in detected prostate cancer grade between biopsy and surgery. METHODS: We established a prospective, multi-institutional cohort of men with Grade Group 1 (GG1) prostate cancer on biopsy who underwent radical prostatectomy. Upgrading was defined as detection of GG2+ in the resected tumor. Germline DNA from 192 subjects was subjected to whole-genome sequencing to quantify ancestry, pathogenic variants in DNA damage response genes and polygenic risk. RESULTS: Of 285 men, 67% upgraded at surgery. PSA density and percent of cancer in pre-prostatectomy positive biopsy cores were significantly associated with upgrading. No assessed genetic risk factor was predictive of upgrading, including polygenic risk scores for prostate cancer diagnosis. CONCLUSIONS: In a cohort of low-grade prostate cancer patients, a majority upgraded at radical prostatectomy. PSA density and percent of cancer in pre-prostatectomy positive biopsy cores portended the presence of higher-grade disease, while germline genetics was not informative in this setting. Patients with low-risk prostate cancer, but elevated PSA density or percent cancer in positive biopsy cores, may benefit from repeat biopsy, additional imaging or other approaches to complement active surveillance. IMPACT: Further risk stratification of patients with low-risk prostate cancer may provide useful context for active surveillance decision-making.

Assessing sociodemographic and regional disparities in Oncotype DX Genomic Prostate Score uptake.

BACKGROUND: The Oncotype DX Genomic Prostate Score (ODX-GPS) is a gene expression assay that predicts disease aggressiveness. The objective of this study was to identify sociodemographic and regional factors associated with ODX-GPS uptake. METHODS: Data from Surveillance Epidemiology and End Results registries on men with localized prostate cancer with a Gleason score of 3 + 3 or 3 + 4, PSA ≤20 ng/mL, and stage T1c to T2c disease from 2013 through 2017 were linked with ODX-GPS data. Census-tract level neighborhood socioeconomic status (nSES) quintiles were constructed using a composite socioeconomic score. Multivariable logistic regression was used to estimate the associations of ODX-GPS uptake with age at diagnosis, race and ethnicity, nSES, geographic region, insurance type, and marital status, accounting for National Comprehensive Cancer Network risk group, year of diagnosis, and clustering by census tract. RESULTS: Among 111,434 eligible men, 5.5% had ODX-GPS test uptake. Of these, 78.3% were non-Hispanic White, 9.6% were Black, 6.7% were Hispanic, and 3.6% were Asian American. Black men had the lowest odds of ODX-GPS uptake (odds ratio, 0.70; 95% confidence interval [CI], 0.63-0.76). Those in the highest versus lowest quintile of nSES were 1.64 times more likely (95% CI, 1.38-2.94) to have ODX-GPS uptake. The odds of ODX-GPS uptake were statistically significantly higher among men residing in the Northeast, West, and Midwest compared to the South. CONCLUSIONS: Disparities in ODX-GPS uptake by race, ethnicity, nSES, and geographical region were identified. Concerted efforts should be made to ensure that this clinical test is equitably available.

Live-cell imaging of RNA Pol II and elongation factors distinguishes competing mechanisms of transcription regulation.

RNA polymerase II (RNA Pol II)-mediated transcription is a critical, highly regulated process aided by protein complexes at distinct steps. Here, to investigate RNA Pol II and transcription-factor-binding and dissociation dynamics, we generated endogenous photoactivatable-GFP (PA-GFP) and HaloTag knockins using CRISPR-Cas9, allowing us to track a population of molecules at the induced Hsp70 loci in Drosophila melanogaster polytene chromosomes. We found that early in the heat-shock response, little RNA Pol II and DRB sensitivity-inducing factor (DSIF) are reused for iterative rounds of transcription. Surprisingly, although PAF1 and Spt6 are found throughout the gene body by chromatin immunoprecipitation (ChIP) assays, they show markedly different binding behaviors. Additionally, we found that PAF1 and Spt6 are only recruited after positive transcription elongation factor (P-TEFb)-mediated phosphorylation and RNA Pol II promoter-proximal pause escape. Finally, we observed that PAF1 may be expendable for transcription of highly expressed genes where nucleosome density is low. Thus, our live-cell imaging data provide key constraints to mechanistic models of transcription regulation.

Mixing and mingling in visual working memory: Inter-item competition is feature-specific during encoding and feature-general during maintenance.

Visual working memory (WM) is a central cognitive ability but is capacity-limited due to competition between remembered items. Understanding whether inter-item competition depends on the similarity of the features being remembered has important implications for determining if competition occurs in sensory or post-sensory stages of processing. Experiment 1 compared the precision of WM across homogeneous displays, where items belonged to the same feature type (e.g., colorful circles), and heterogeneous displays (e.g., colorful circles and oriented bars). Performance was better for heterogeneous displays, suggesting a feature-specific component of interference. However, Experiment 2 used a retro-cueing task to isolate encoding from online maintenance and revealed that inter-item competition during storage was not feature-specific. The data support recent models of WM in which inter-item interference - and hence capacity limits in WM - occurs in higher-order structures that receive convergent input from a diverse array of feature-specific representations.

Sensitivity analysis and quality indicators for an in vitro oral irritation assay.

Biocompatibility testing using in vivo tests is often one of the final evaluations of new dental materials. To reduce the likelihood of failure at this late stage, predictive biocompatibility testing using in vitro methods is needed. In this study, we describe a sensitivity analysis of an oral irritation test by evaluating changes in the viability, using the MTT assay, of 3-D models with EpiOral constructs as a case study. Experiments that tested sources of variability in the assay led to recommendations regarding the storage of the constructs after arrival, pipetting procedure, use of MTT reagents from different vendors, use of transepithelial electrical resistance measurements, and statistical analyses. A statistical model was proposed to evaluate whether test substances yield a positive or negative result and the associated statistical confidence. Testing several test compounds such as the Y-4 polymer, that contains a known irritant, and dentally relevant substances such as sodium dodecyl sulfate (SDS) at varying concentrations revealed statistically significant results as expected. Lastly, a software app was designed to support a multiwell culture plate layout design. Overall, the findings and suggestions documented here will support the further development and potential standardization of this assay system and may be useful for the development of other assays using 3-D constructs.

New in vitro methods can support the development of novel dental materials by yielding information about their biocompatibility. In this study, an in vitro oral irritation assay was investigated to better understand what aspects of the method contribute to its variability. There is a potential that such a method could yield similar information to in vivo experiments and reduce animal testing.

Neuroimaging and Clinical Findings in Healthy Middle-Aged Adults With Mild Traumatic Brain Injury in the PREVENT Dementia Study.

Importance: Traumatic brain injuries (TBI) represent an important, potentially modifiable risk factor for dementia. Despite frequently observed vascular imaging changes in individuals with TBI, the relationships between TBI-associated changes in brain imaging and clinical outcomes have largely been overlooked in community cases of TBI. Objective: To assess whether TBI are associated with and interact with midlife changes in neuroimaging and clinical features in otherwise healthy individuals. Design, Setting, and Participants: This cross-sectional analysis used baseline data from the PREVENT Dementia program collected across 5 sites in the UK and Ireland between 2014 and 2020. Eligible participants were cognitively healthy midlife adults aged between 40 and 59 years. Data were analyzed between January 2023 and April 2024. Exposure: Lifetime TBI history was assessed using the Brain Injury Screening Questionnaire. Main Outcomes and Measures: Cerebral microbleeds and other markers of cerebral small vessel disease (white matter hyperintensities [WMH], lacunes, perivascular spaces) were assessed on 3T magnetic resonance imaging. Clinical measures were cognition, sleep, depression, gait, and cardiovascular disease (CVD) risk, assessed using Computerized Assessment of Information Processing (COGNITO), Pittsburgh Sleep Quality Index, Center for Epidemiologic Studies Depression Scale, clinical interviews, and the Framingham Risk Score, respectively. Results: Of 617 participants (median [IQR] age, 52 [47-56] years; 380 female [61.6%]), 223 (36.1%) had a history of TBI. TBI was associated with higher microbleed count (ß = 0.10; 95% CI, 0.01-0.18; P = .03), with a dose-response association observed with increasing number of TBI events (ß = 0.05; 95% CI, 0.01-0.09; P = .03). Conversely, TBI was not associated with other measures of small vessel disease, including WMH. Furthermore, TBI moderated microbleed associations with vascular risk factors and clinical outcomes, such that associations were present only in the absence of TBI. Importantly, observations held when analyses were restricted to individuals reporting only mild TBI. Conclusions and Relevance: In this cross-sectional study of healthy middle-aged adults, detectable changes in brain imaging and clinical features were associated with remote, even mild, TBI in the general population. The potential contribution of vascular injury to TBI-related neurodegeneration presents promising avenues to identify potential targets, with findings highlighting the need to reduce TBI through early intervention and prevention in both clinical care and policymaking.

The respiratory route of transmission of virulent polioviruses.

AIMS: The route of transmission of wild and circulating vaccine-derived polioviruses remains controversial, between respiratory and faecal-oral, and we aim to identify the most plausible one to settle the controversy. METHODS: We explored available epidemiological clues and evidence in support of either route in order to arrive at an evidence-based conclusion. RESULTS: Historically the original concept was respiratory transmission based on epidemiological features of age distribution, which was later revised to faecal-oral as the rationale for popularising the live attenuated oral polio vaccine in preference to the inactivated poliovirus vaccine. Through epidemiological logic, we find no evidence for the faecal-oral route from available studies and observations, but all available information supports the respiratory route. CONCLUSIONS: The route is respiratory, not faecal-oral. The global polio eradication initiative assumed it was faecal-oral - and its gargantuan efforts based on this assumption have failed in two ways: eradication remains pending and circulating vaccine-derived polioviruses have seeded widely. With clarity on the route of transmission the choice of vaccine is also clear - it can only be the inactivated poliovirus vaccine.

Automated spatial omics landscape analysis approach reveals novel tissue architectures in ulcerative colitis.

The utility of spatial omics in leveraging cellular interactions in normal and diseased states for precision medicine is hampered by a lack of strategies for matching disease states with spatial heterogeneity-guided cellular annotations. Here we use a spatial context-dependent approach that matches spatial pattern detection to cell annotation. Using this approach in existing datasets from ulcerative colitis patient colonic biopsies, we identified architectural complexities and associated difficult-to-detect rare cell types in ulcerative colitis germinal-center B cell follicles. Our approach deepens our understanding of health and disease pathogenesis, illustrates a strategy for automating nested architecture detection for highly multiplexed spatial biology data, and informs precision diagnosis and therapeutic strategies.

Characterization of the SARS-CoV-2 antibody landscape in Norway in the late summer of 2022: high seroprevalence in all age groups with patterns of primary Omicron infection in children and hybrid immunity in adults.

BACKGROUND: According to Norwegian registries, 91% of individuals ≥ 16 years had received ≥ 1 dose of COVID-19 vaccine by mid-July 2022, whereas less than 2% of children < 12 years were vaccinated. Confirmed COVID-19 was reported for 27% of the population, but relaxation of testing lead to substantial underreporting. We have characterized the humoral immunity to SARS-CoV-2 in Norway in the late summer of 2022 by estimating the seroprevalence and identifying antibody profiles based on reactivity to Wuhan or Omicron-like viruses in a nationwide cross-sectional collection of residual sera, and validated our findings using cohort sera. METHODS: 1,914 anonymized convenience sera and 243 NorFlu-cohort sera previously collected from the Oslo-area with reported infection and vaccination status were analyzed for antibodies against spike, the receptor-binding domain (RBD) of the ancestral Wuhan strain and Omicron BA.2 RBD, and nucleocapsid (N). Samples were also tested for antibodies inhibiting RBD-ACE2 interaction. Neutralization assays were performed on subsets of residual sera against B.1, BA.2, XBB.1.5 and BQ.1.1. RESULTS: The national seroprevalence estimate from vaccination and/or infection was 99.1% (95% CrI 97.0-100.0%) based on Wuhan (spike_W and RBD_W) and RBD_BA2 antibodies. Sera from children < 12 years had 2.2 times higher levels of antibodies against RBD_BA2 than RBD_W and their seroprevalence estimate showed a 14.4 percentage points increase when also including anti-RBD_BA2 antibodies compared to Wuhan-antibodies alone. 50.3% (95% CI 45.0-55.5%) of residual sera from children and 38.1% (95% CI 36.0-40.4%) of all residual sera were positive for anti-N-antibodies. By combining measurements of binding- and ACE2-RBD-interaction-inhibiting antibodies, reactivity profiles indicative of infection and vaccination history were identified and validated using cohort sera. Residual sera with a profile indicative of hybrid immunity were able to neutralize newer Omicron variants XBB.1.5 and BQ.1.1. CONCLUSIONS: By late summer of 2022, most of the Norwegian population had antibodies to SARS-CoV-2, and almost all children had been infected. Antibody profiles indicated that children mostly had experienced a primary Omicron infection, while hybrid immunity was common among adults. The finding that sera displaying hybrid immunity could neutralize newer Omicron variants indicates that Wuhan-like priming of the immune response did not have a harmful imprinting effect and that infections induce cross-reacting antibodies against future variants.

Immunopeptidomics mapping of Listeria monocytogenes T cell epitopes in mice.

Listeria monocytogenes is a foodborne intracellular bacterial model pathogen. Protective immunity against Listeria depends on an effective CD8+ T cell response, but very few T cell epitopes are known in mice as a common animal infection model for listeriosis. To identify epitopes we screened for Listeria immunopeptides presented in the spleen of infected mice by mass spectrometry-based immunopeptidomics. We mapped more than 6,000 mouse self-peptides presented on MHC Class I molecules, including 12 high confident Listeria peptides from 12 different bacterial proteins. Bacterial immunopeptides with confirmed fragmentation spectra were further tested for their potential to activate CD8+ T cells, revealing VTYNYINI from the putative cell wall surface anchor family protein LMON_0576 as a novel bona fide peptide epitope. The epitope showed high biological potency in a prime boost model and can be used as a research tool to probe CD8+ T cell responses in mouse models of Listeria infection. Together, our results demonstrate the power of immunopeptidomics for bacterial antigen identification.