TLR9-dependent dendritic cell maturation promotes IL-6-mediated upregulation of cathepsin X.

Cysteine cathepsins are lysosomal proteases subject to dynamic regulation within antigen-presenting cells during the immune response and associated diseases. To investigate the regulation of cathepsin X, a carboxy-mono-exopeptidase, during maturation of dendritic cells (DCs), we exposed immortalized mouse DCs to various Toll-like receptor agonists. Using a cathepsin X-selective activity-based probe, sCy5-Nle-SY, we observed a significant increase in cathepsin X activation upon TLR-9 agonism with CpG, and to a lesser extent with Pam3 (TLR1/2), FSL-1 (TLR2/6) and LPS (TLR4). Despite clear maturation of DCs in response to Poly I:C (TLR3), cathepsin X activity was only slightly increased by this agonist, suggesting differential regulation of cathepsin X downstream of TLR activation. We demonstrated that cathepsin X was upregulated at the transcriptional level in response to CpG. This occurred at late time points and was not dampened by NF-κB inhibition. Factors secreted from CpG-treated cells were able to provoke cathepsin X upregulation when applied to naïve cells. Among these factors was IL-6, which on its own was sufficient to induce transcriptional upregulation and activation of cathepsin X. IL-6 is highly secreted by DCs in response to CpG but much less so in response to poly I:C, and inhibition of the IL-6 receptor subunit glycoprotein 130 prevented CpG-mediated cathepsin X upregulation. Collectively, these results demonstrate that cathepsin X is differentially transcribed during DC maturation in response to diverse stimuli, and that secreted IL-6 is critical for its dynamic regulation.

Classification of isolated versus multiple birth defects: An automated process for population-based registries.

Epidemiologic studies of birth defects often conduct separate analyses for cases that have isolated defects (e.g., spina bifida only) and cases that have multiple defects (e.g., spina bifida and a congenital heart defect). However, in some instances, cases with additional defects (e.g., spina bifida and clubfoot) may be more appropriately considered as isolated because the co-occurring defect (clubfoot) is believed to be developmentally related to the defect of interest. Determining which combinations should be considered isolated can be challenging and potentially resource intensive for registries. Thus, we developed automated classification procedures for differentiating between isolated versus multiple defects, while accounting for developmentally related defects, and applied the approach to data from the Texas Birth Defects Registry (1999-2018 deliveries). Among 235,544 nonsyndromic cases in Texas, 89% of cases were classified as having isolated defects, with proportions ranging from 25% to 92% across 43 specific defects analyzed. A large proportion of isolated cases with spina bifida (44%), lower limb reduction defects (44%), and holoprosencephaly (32%) had developmentally related defects. Overall, our findings strongly support the need to account for isolated versus multiple defects in risk factor association analyses and to account for developmentally related defects when doing so, which has implications for interpreting prior studies.

X-linked genetic associations in sporadic thoracic aortic dissection.

The male predominance in sporadic thoracic aortic aneurysm and dissection (TAD) suggests that the X chromosome contributes to TAD, but this has not been tested. We investigated whether X-linked variation-common (minor allele frequency [MAF] ≥0.01) and rare (MAF <0.01)-was associated with sporadic TAD in three cohorts of European descent (Discovery: 364 cases, 874 controls; Replication: 516 cases, 440,131 controls, and ARIC [Atherosclerosis Risk in Communities study]: 753 cases, 2247 controls). For analysis of common variants, we applied a sex-stratified logistic regression model followed by a meta-analysis of sex-specific odds ratios. Furthermore, we conducted a meta-analysis of overlapping common variants between the Discovery and Replication cohorts. For analysis of rare variants, we used a sex-stratified optimized sequence kernel association test model. Common variants results showed no statistically significant findings in the Discovery cohort. An intergenic common variant near SPANXN1 was statistically significant in the Replication cohort (p = 1.81 × 10-8). The highest signal from the meta-analysis of the Discovery and Replication cohorts was a ZNF182 intronic common variant (p = 3.5 × 10-6). In rare variants results, RTL9 reached statistical significance (p = 5.15 × 10-5). Although most of our results were statistically insignificant, our analysis is the most comprehensive X-chromosome association analysis of sporadic TAD to date.

Prevalence and descriptive epidemiology of choanal atresia and stenosis in Texas, 1999-2018.

Choanal atresia and stenosis are common causes of congenital nasal obstruction, but their epidemiology is poorly understood. Compared to bilateral choanal atresia/stenosis, unilateral choanal atresia/stenosis is generally diagnosed later and might be under-ascertained in birth defect registries. Data from the population-based Texas Birth Defects Registry and Texas vital records, 1999-2018, were used to assess the prevalence of choanal atresia/stenosis. Poisson regression models were used to evaluate associations with infant and maternal characteristics in two analytic groups: isolated choanal atresia/stenosis (n = 286) and isolated, bilateral choanal atresia/stenosis (n = 105). The overall prevalence of choanal atresia/stenosis was 0.92/10,000, and the prevalence of isolated choanal atresia/stenosis was 0.37/10,000 livebirths. Variables associated with choanal atresia/stenosis in one or both analytic groups included infant sex, pregnancy plurality, maternal race/ethnicity, maternal age, and maternal residence on the Texas-Mexico border. In general, adjusted prevalence ratios estimated from the two analytic groups were in the same direction but tended to be stronger in the analyses restricted to isolated, bilateral defects. Epidemiologic studies of isolated choanal atresia/stenosis should consider focusing on cases with bilateral defects, and prioritizing analyses of environmental, social, and structural factors that could account for the association with maternal residence on the Texas-Mexico border.

Cathepsin X deficiency alters the processing and localisation of cathepsin L and impairs cleavage of a nuclear cathepsin L substrate.

Proteases function within sophisticated networks. Altering the activity of one protease can have sweeping effects on other proteases, leading to changes in their activity, structure, specificity, localisation, stability, and expression. Using a suite of chemical tools, we investigated the impact of cathepsin X, a lysosomal cysteine protease, on the activity and expression of other cysteine proteases and their inhibitors in dendritic cells. Among all proteases examined, cathepsin X gene deletion specifically altered cathepsin L levels; pro-cathepsin L and its single chain accumulated while the two-chain form was unchanged. This effect was recapitulated by chemical inhibition of cathepsin X, suggesting a dependence on its catalytic activity. We demonstrated that accumulation of pro- and single chain cathepsin L was not due to a lack of direct cleavage by cathepsin X or altered glycosylation, secretion, or mRNA expression but may result from changes in lysosomal oxidative stress or pH. In the absence of active cathepsin X, nuclear cathepsin L and cleavage of the known nuclear cathepsin L substrate, Lamin B1, were diminished. Thus, cathepsin X activity selectively regulates cathepsin L, which has the potential to impact the degree of cathepsin L proteolysis, the nature of substrates that it cleaves, and the location of cleavage.

Ion Mobility-Based Enrichment-Free N-Terminomics Analysis Reveals Novel Legumain Substrates in Murine Spleen.

Aberrant levels of the asparaginyl endopeptidase legumain have been linked to inflammation, neurodegeneration, and cancer, yet our understanding of this protease is incomplete. Systematic attempts to identify legumain substrates have been previously confined to in vitro studies, which fail to mirror physiological conditions and obscure biologically relevant cleavage events. Using high-field asymmetric waveform ion mobility spectrometry (FAIMS), we developed a streamlined approach for proteome and N-terminome analyses without the need for N-termini enrichment. Compared to unfractionated proteomic analysis, we demonstrate FAIMS fractionation improves N-termini identification by >2.5 fold, resulting in the identification of >2882 unique N-termini from limited sample amounts. In murine spleens, this approach identifies 6366 proteins and 2528 unique N-termini, with 235 cleavage events enriched in WT compared to legumain-deficient spleens. Among these, 119 neo-N-termini arose from asparaginyl endopeptidase activities, representing novel putative physiological legumain substrates. The direct cleavage of selected substrates by legumain was confirmed using in vitro assays, providing support for the existence of physiologically relevant extra-lysosomal legumain activity. Combined, these data shed critical light on the functions of legumain and demonstrate the utility of FAIMS as an accessible method to improve depth and quality of N-terminomics studies.

Cleaning Tasks and Products and Asthma Among Health Care Professionals.

OBJECTIVE: Health care workers are at risk for work-related asthma, which may be affected by changes in cleaning practices. We examined associations of cleaning tasks and products with work-related asthma in health care workers in 2016, comparing them with prior results from 2003. METHODS: We estimated asthma prevalence by professional group and explored associations of self-reported asthma with job-exposure matrix-based cleaning tasks/products in a representative Texas sample of 9914 physicians, nurses, respiratory/occupational therapists, and nurse aides. RESULTS: Response rate was 34.8% (n = 2421). The weighted prevalence rates of physician-diagnosed (15.3%), work-exacerbated (4.1%), and new-onset asthma (6.7%) and bronchial hyperresponsiveness symptoms (31.1%) were similar to 2003. New-onset asthma was associated with building surface cleaning (odds ratio [OR], 1.91; 95% confidence interval [CI], 1.10-3.33), use of ortho-phthalaldehyde (OR, 1.77; 95% CI, 1.15-2.72), bleach/quaternary compounds (OR, 1.91; 95% CI, 1.10-3.33), and sprays (OR, 1.97; 95% CI, 1.12-3.47). CONCLUSION: Prevalence of asthma/bronchial hyperresponsiveness seems unchanged, whereas associations of new-onset asthma with exposures to surface cleaning remained, and decreased for instrument cleaning.

Murine norovirus infection of macrophages induces intrinsic apoptosis as the major form of programmed cell death.

Human norovirus is the leading cause of acute gastroenteritis worldwide, however despite the significance of this pathogen, we have a limited understanding of how noroviruses cause disease, and modulate the innate immune response. Programmed cell death (PCD) is an important part of the innate response to invading pathogens, but little is known about how specific PCD pathways contribute to norovirus replication. Here, we reveal that murine norovirus (MNV) virus-induced PCD in macrophages correlates with the release of infectious virus. We subsequently show, genetically and chemically, that MNV-induced cell death and viral replication occurs independent of the activity of inflammatory mediators. Further analysis revealed that MNV infection promotes the cleavage of apoptotic caspase-3 and PARP. Correspondingly, pan-caspase inhibition, or BAX and BAK deficiency, perturbed viral replication rates and delayed virus release and cell death. These results provide new insights into how MNV harnesses cell death to increase viral burden.

Exercise therapy for tendinopathy: a mixed-methods evidence synthesis exploring feasibility, acceptability and effectiveness.

Background: Tendinopathy is a common, painful and functionally limiting condition, primarily managed conservatively using exercise therapy. Review questions: (i) What exercise interventions have been reported in the literature for which tendinopathies? (ii) What outcomes have been reported in studies investigating exercise interventions for tendinopathy? (iii) Which exercise interventions are most effective across all tendinopathies? (iv) Does type/location of tendinopathy or other specific covariates affect which are the most effective exercise therapies? (v) How feasible and acceptable are exercise interventions for tendinopathies? Methods: A scoping review mapped exercise interventions for tendinopathies and outcomes reported to date (questions i and ii). Thereafter, two contingent systematic review workstreams were conducted. The first investigated a large number of studies and was split into three efficacy reviews that quantified and compared efficacy across different interventions (question iii), and investigated the influence of a range of potential moderators (question iv). The second was a convergent segregated mixed-method review (question v). Searches for studies published from 1998 were conducted in library databases (n = 9), trial registries (n = 6), grey literature databases (n = 5) and Google Scholar. Scoping review searches were completed on 28 April 2020 with efficacy and mixed-method search updates conducted on 19 January 2021 and 29 March 2021. Results: Scoping review - 555 included studies identified a range of exercise interventions and outcomes across a range of tendinopathies, most commonly Achilles, patellar, lateral elbow and rotator cuff-related shoulder pain. Strengthening exercise was most common, with flexibility exercise used primarily in the upper limb. Disability was the most common outcome measured in Achilles, patellar and rotator cuff-related shoulder pain; physical function capacity was most common in lateral elbow tendinopathy. Efficacy reviews - 204 studies provided evidence that exercise therapy is safe and beneficial, and that patients are generally satisfied with treatment outcome and perceive the improvement to be substantial. In the context of generally low and very low-quality evidence, results identified that: (1) the shoulder may benefit more from flexibility (effect sizeResistance:Flexibility = 0.18 [95% CrI 0.07 to 0.29]) and proprioception (effect sizeResistance:Proprioception = 0.16 [95% CrI -1.8 to 0.32]); (2) when performing strengthening exercise it may be most beneficial to combine concentric and eccentric modes (effect sizeEccentricOnly:Concentric+Eccentric = 0.48 [95% CrI -0.13 to 1.1]; and (3) exercise may be most beneficial when combined with another conservative modality (e.g. injection or electro-therapy increasing effect size by ≈0.1 to 0.3). Mixed-method review - 94 studies (11 qualitative) provided evidence that exercise interventions for tendinopathy can largely be considered feasible and acceptable, and that several important factors should be considered when prescribing exercise for tendinopathy, including an awareness of potential barriers to and facilitators of engaging with exercise, patients' and providers' prior experience and beliefs, and the importance of patient education, self-management and the patient-healthcare professional relationship. Limitations: Despite a large body of literature on exercise for tendinopathy, there are methodological and reporting limitations that influenced the recommendations that could be made. Conclusion: The findings provide some support for the use of exercise combined with another conservative modality; flexibility and proprioception exercise for the shoulder; and a combination of eccentric and concentric strengthening exercise across tendinopathies. However, the findings must be interpreted within the context of the quality of the available evidence. Future work: There is an urgent need for high-quality efficacy, effectiveness, cost-effectiveness and qualitative research that is adequately reported, using common terminology, definitions and outcomes. Study registration: This project is registered as DOI: 10.11124/JBIES-20-00175 (scoping review); PROSPERO CRD 42020168187 (efficacy reviews); https://osf.io/preprints/sportrxiv/y7sk6/ (efficacy review 1); https://osf.io/preprints/sportrxiv/eyxgk/ (efficacy review 2); https://osf.io/preprints/sportrxiv/mx5pv/ (efficacy review 3); PROSPERO CRD42020164641 (mixed-method review). Funding: This project was funded by the National Institute for Health and Care Research (NIHR) HTA programme and will be published in full in HTA Journal; Vol. 27, No. 24. See the NIHR Journals Library website for further project information.

Tendons are cords of strong, flexible tissue that attach muscles to bones, allowing joints to move. Tendinopathy is a common condition that can affect any tendon in the body, causing pain and limiting function. Exercise is often used to treat tendinopathy. We examined over 500 research papers on exercise for tendinopathy. The most common tendons to be studied were the calf (Achilles), knee (patellar), elbow and shoulder. Strengthening exercise was studied most often, especially in lower-limb tendinopathy. Other types of exercise such as stretching, balance and aerobic activity were less common, but were used to some extent in the upper and lower limbs. We found that exercise therapy is safe and beneficial for the tendinopathies that have been studied to date. Exercise may be most beneficial when combined with another intervention such as injection or electro-therapy. Strengthening exercise may be most beneficial for lower-limb tendinopathies. However, more research is needed on the type of strengthening and the dosage, such as how many exercises and how much resistance to use. Shoulder tendinopathies may benefit from exercise that targets joint flexibility and position more than strengthening. We also found that people who receive exercise therapy for tendinopathy are generally satisfied with the effect it has on their symptoms. Finally, we found that an individualised, person-centred approach to delivering exercise therapy is valued by people with tendinopathy. They also believe that the patient-healthcare provider relationship is important for promoting the confidence and motivation people need to continue with exercise programmes, especially when they complete them independently. Although we examined a lot of papers, many of the studies were low quality. This means there is still a need for high-quality studies to tell us how effective specific types of exercise are for specific tendinopathies. There is also a need for more studies on patients' and professionals' experiences of receiving or providing exercise for tendinopathy.

Chemical Tools to Image the Activity of PAR-Cleaving Proteases.

Protease-activated receptors (PARs) comprise a family of four G protein-coupled receptors (GPCRs) that have broad functions in health and disease. Unlike most GPCRs, PARs are uniquely activated by proteolytic cleavage of their extracellular N termini. To fully understand PAR activation and function in vivo, it is critical to also study the proteases that activate them. As proteases are heavily regulated at the post-translational level, measures of total protease abundance have limited utility. Measures of protease activity are instead required to inform their function. This review will introduce several classes of chemical probes that have been developed to measure the activation of PAR-cleaving proteases. Their strengths, weaknesses, and applications will be discussed, especially as applied to image protease activity at the whole organism, tissue, and cellular level.

Archaeal Hel308 suppresses recombination through a catalytic switch that controls DNA annealing.

Hel308 helicases promote genome stability in archaea and are conserved in metazoans, where they are known as HELQ. Their helicase mechanism is well characterised, but it is unclear how they specifically contribute to genome stability in archaea. We show here that a highly conserved motif of Hel308/HELQ helicases (motif IVa, F/YHHAGL) modulates both DNA unwinding and a newly identified strand annealing function of archaeal Hel308. A single amino acid substitution in motif IVa results in hyper-active DNA helicase and annealase activities of purified Hel308 in vitro. All-atom molecular dynamics simulations using Hel308 crystal structures provided a molecular basis for these differences between mutant and wild type Hel308. In archaeal cells, the same mutation results in 160000-fold increased recombination, exclusively as gene conversion (non-crossover) events. However, crossover recombination is unaffected by the motif IVa mutation, as is cell viability or DNA damage sensitivity. By contrast, cells lacking Hel308 show impaired growth, increased sensitivity to DNA cross-linking agents, and only moderately increased recombination. Our data reveal that archaeal Hel308 suppresses recombination and promotes DNA repair, and that motif IVa in the RecA2 domain acts as a catalytic switch to modulate the separable recombination and repair activities of Hel308.

Effect of resistance exercise dose components for tendinopathy management: a systematic review with meta-analysis.

OBJECTIVE: To investigate potential moderating effects of resistance exercise dose components including intensity, volume and frequency, for the management of common tendinopathies. DESIGN: Systematic review with meta-analysis and meta-regressions. DATA SOURCES: Including but not limited to: MEDLINE, CINAHL, SPORTDiscus, ClinicalTrials.gov and ISRCTN Registry. ELIGIBILITY CRITERIA FOR SELECTING STUDIES: Randomised and non-randomised controlled trials investigating resistance exercise as the dominant treatment class, reporting sufficient information regarding ≥2 components of exercise dose. RESULTS: A total of 110 studies were included in meta-analyses (148 treatment arms (TAs), 3953 participants), reporting on five tendinopathy locations (rotator cuff: 48 TAs; Achilles: 43 TAs; lateral elbow: 29 TAs; patellar: 24 TAs; gluteal: 4 TAs). Meta-regressions provided consistent evidence of greater pooled mean effect sizes for higher intensity therapies comprising additional external resistance compared with body mass only (large effect size domains: ß BodyMass: External = 0.50 (95% credible interval (CrI): 0.15 to 0.84; p=0.998); small effect size domains (ß BodyMass: External = 0.04 (95% CrI: -0.21 to 0.31; p=0.619)) when combined across tendinopathy locations or analysed separately. Greater pooled mean effect sizes were also identified for the lowest frequency (less than daily) compared with mid (daily) and high frequencies (more than once per day) for both effect size domains when combined or analysed separately (p≥0.976). Evidence for associations between training volume and pooled mean effect sizes was minimal and inconsistent. SUMMARY/CONCLUSION: Resistance exercise dose is poorly reported within tendinopathy management literature. However, this large meta-analysis identified some consistent patterns indicating greater efficacy on average with therapies prescribing higher intensities (through inclusion of additional loads) and lower frequencies, potentially creating stronger stimuli and facilitating adequate recovery.

Eat, prey, love: Pathogen-mediated subversion of lysosomal biology.

The mammalian lysosome is classically considered the 'garbage can' of the cell, contributing to clearance of infection through its primary function as a degradative organelle. Intracellular pathogens have evolved several strategies to evade contact with this harsh environment through subversion of endolysosomal trafficking or escape into the cytosol. Pathogens can also manipulate pathways that lead to lysosomal biogenesis or alter the abundance or activity of lysosomal content. This pathogen-driven subversion of lysosomal biology is highly dynamic and depends on a range of factors, including cell type, stage of infection, intracellular niche and pathogen load. The growing body of literature in this field highlights the nuanced and complex relationship between intracellular pathogens and the host lysosome, which is critical for our understanding of infection biology.

What are small, medium and large effect sizes for exercise treatments of tendinopathy? A systematic review and meta-analysis.

Objective: To quantify and describe effect size distributions from exercise therapies across a range of tendinopathies and outcome domains to inform future research and clinical practice through conducting a systematic review with meta-analysis. Design: Systematic review with meta-analysis exploring moderating effects and context-specific small, medium and large thresholds. Eligibility criteria: Randomised and quasi-randomised controlled trials involving any persons with a diagnosis of rotator cuff, lateral elbow, patellar, Achilles or gluteal tendinopathy of any severity or duration. Methods: Common databases, six trial registries and six grey literature databases were searched on 18 January 2021 (PROSPERO: CRD42020168187). Standardised mean difference (SMDpre) effect sizes were used with Bayesian hierarchical meta-analysis models to calculate the 0.25 (small), 0.5 (medium) and 0.75 quantiles (large) and compare pooled means across potential moderators. Risk of bias was assessed with Cochrane's Risk of Bias tool. Results: Data were obtained from 114 studies comprising 171 treatment arms 4104 participants. SMDpre effect sizes were similar across tendinopathies but varied across outcome domains. Greater threshold values were obtained for self-reported measures of pain (small=0.5, medium=0.9 and large=1.4), disability (small=0.6, medium=1.0 and large=1.5) and function (small=0.6, medium=1.1 and large=1.8) and lower threshold values obtained for quality of life (small=-0.2, medium=0.3 and large=0.7) and objective measures of physical function (small=0.2, medium=0.4 and large=0.7). Potential moderating effects of assessment duration, exercise supervision and symptom duration were also identified, with greater pooled mean effect sizes estimated for longer assessment durations, supervised therapies and studies comprising patients with shorter symptom durations. Conclusion: The effect size of exercise on tendinopathy is dependent on the type of outcome measure assessed. Threshold values presented here can be used to guide interpretation and assist with further research better establishing minimal important change.

Identifying syndromes in studies of structural birth defects: Guidance on classification and evaluation of potential impact.

Structural birth defects that occur in infants with syndromes may be etiologically distinct from those that occur in infants in whom there is not a recognized pattern of malformations; however, population-based registries often lack the resources to classify syndromic status via case reviews. We developed criteria to systematically identify infants with suspected syndromes, grouped by syndrome type and level of effort required for syndrome classification (e.g., text search). We applied this algorithm to the Texas Birth Defects Registry (TBDR) to describe the proportion of infants with syndromes delivered during 1999-2014. We also developed a bias analysis tool to estimate the potential percent bias resulting from including infants with syndromes in studies of risk factors. Among 207,880 cases with birth defects in the TBDR, 15% had suspected syndromes and 85% were assumed to be nonsyndromic, with a range across defect types from 28.5% (atrioventricular septal defects) to 98.9% (pyloric stenosis). Across hypothetical scenarios varying expected parameters (e.g., nonsyndromic proportion), the inclusion of syndromic cases in analyses resulted in up to 50.0% bias in prevalence ratios. In summary, we present a framework for identifying infants with syndromic conditions; implementation might harmonize syndromic classification across registries and reduce bias in association estimates.

Protease-activated receptors in health and disease.

Proteases are signaling molecules that specifically control cellular functions by cleaving protease-activated receptors (PARs). The four known PARs are members of the large family of G protein-coupled receptors. These transmembrane receptors control most physiological and pathological processes and are the target of a large proportion of therapeutic drugs. Signaling proteases include enzymes from the circulation; from immune, inflammatory epithelial, and cancer cells; as well as from commensal and pathogenic bacteria. Advances in our understanding of the structure and function of PARs provide insights into how diverse proteases activate these receptors to regulate physiological and pathological processes in most tissues and organ systems. The realization that proteases and PARs are key mediators of disease, coupled with advances in understanding the atomic level structure of PARs and their mechanisms of signaling in subcellular microdomains, has spurred the development of antagonists, some of which have advanced to the clinic. Herein we review the discovery, structure, and function of this receptor system, highlight the contribution of PARs to homeostatic control, and discuss the potential of PAR antagonists for the treatment of major diseases.

Maternal genetic factors in the development of congenital heart defects.

Congenital heart defects (CHDs) are among the most common, serious birth defects. However, the cause of CHDs is unknown for approximately half of affected individuals and there are few prevention strategies. Although not extensively investigated, maternal genes may contribute to CHD etiology by modifying the effects of maternal exposures (e.g. medications, nutrients), contributing to maternal phenotypes that are associated with an increased risk of CHDs in offspring (e.g. diabetes), or acting as maternal effect genes. Since maternal genes could serve as a target for the primary prevention of CHDs, efforts to further define the contribution of the maternal genome to CHD etiology are warranted.

Deciphering the language of antibodies using self-supervised learning.

An individual's B cell receptor (BCR) repertoire encodes information about past immune responses and potential for future disease protection. Deciphering the information stored in BCR sequence datasets will transform our understanding of disease and enable discovery of novel diagnostics and antibody therapeutics. A key challenge of BCR sequence analysis is the prediction of BCR properties from their amino acid sequence alone. Here, we present an antibody-specific language model, Antibody-specific Bidirectional Encoder Representation from Transformers (AntiBERTa), which provides a contextualized representation of BCR sequences. Following pre-training, we show that AntiBERTa embeddings capture biologically relevant information, generalizable to a range of applications. As a case study, we fine-tune AntiBERTa to predict paratope positions from an antibody sequence, outperforming public tools across multiple metrics. To our knowledge, AntiBERTa is the deepest protein-family-specific language model, providing a rich representation of BCRs. AntiBERTa embeddings are primed for multiple downstream tasks and can improve our understanding of the language of antibodies.