RAIN: machine learning-based identification for HIV-1 bNAbs.

Broadly neutralizing antibodies (bNAbs) are promising candidates for the treatment and prevention of HIV-1 infections. Despite their critical importance, automatic detection of HIV-1 bNAbs from immune repertoires is still lacking. Here, we develop a straightforward computational method for the Rapid Automatic Identification of bNAbs (RAIN) based on machine learning methods. In contrast to other approaches, which use one-hot encoding amino acid sequences or structural alignment for prediction, RAIN uses a combination of selected sequence-based features for the accurate prediction of HIV-1 bNAbs. We demonstrate the performance of our approach on non-biased, experimentally obtained and sequenced BCR repertoires from HIV-1 immune donors. RAIN processing leads to the successful identification of distinct HIV-1 bNAbs targeting the CD4-binding site of the envelope glycoprotein. In addition, we validate the identified bNAbs using an in vitro neutralization assay and we solve the structure of one of them in complex with the soluble native-like heterotrimeric envelope glycoprotein by single-particle cryo-electron microscopy (cryo-EM). Overall, we propose a method to facilitate and accelerate HIV-1 bNAbs discovery from non-selected immune repertoires.

Residual Partial Least Squares Learning: Brain Cortical Thickness Simultaneously Predicts Eight Non-pairwise-correlated Behavioural and Disease Outcomes in Alzheimer's Disease.

Alzheimer's Disease (AD) is the leading cause of dementia. It results in cortical thickness changes and is associated with a decline in cognition and behaviour. Such decline affects multiple important day-to-day functions, including memory, language, orientation, judgment and problem-solving. Recent research has made important progress in identifying brain regions associated with single outcomes, such as individual AD status and general cognitive decline. The complex projection from multiple brain areas to multiple AD outcomes, however, remains poorly understood. This makes the assessment and especially the prediction of multiple AD outcomes - each of which may unveil an integral yet different aspect of the disease - challenging, particularly when some are not strongly correlated. Here, uniting residual learning, partial least squares (PLS), and predictive modelling, we develop an explainable, generalisable, and reproducible method called the Residual Partial Least Squares Learning (the re-PLS Learning) to (1) chart the pathways between large-scale multivariate brain cortical thickness data (inputs) and multivariate disease and behaviour data (outcomes); (2) simultaneously predict multiple, non-pairwise-correlated outcomes; (3) control for confounding variables (e.g., age and gender) affecting both inputs and outcomes and the pathways in-between; (4) perform longitudinal AD disease status classification and disease severity prediction. We evaluate the performance of the proposed method against a variety of alternatives on data from AD patients, subjects with mild cognitive impairment (MCI), and cognitively normal individuals (n=1,196) from the Alzheimer's Disease Neuroimaging Initiative (ADNI). Our results unveil pockets of brain areas in the temporal, frontal, sensorimotor, and cingulate areas whose cortical thickness may be respectively associated with declines in different cognitive and behavioural subdomains in AD. Finally, we characterise re-PLS' geometric interpretation and mathematical support for delivering meaningful neurobiological insights and provide an open software package (re-PLS) available at https://github.com/thanhvd18/rePLS.

[CAR-T therapy for autoimmune diseases]. / Thérapie cellulaire CAR-T dans le traitement des maladies auto-immunes.

Cellular therapy using genetically modified T lymphocytes expressing synthetic receptors, known as CAR (Chimeric Antigen Receptor), has revolutionized the treatment of certain hematologic malignancies. This success has led to exploring the same approach in the treatment of severe autoimmune diseases refractory to conventional therapies. Initial results in systemic lupus erythematosus have shown complete remissions that appear to persist over time. Consequently, there is a growing number of ongoing clinical trials. In this review, we discuss the rationale behind the use of CAR-T therapies, the targeted autoimmune diseases, and the associated risks.

La thérapie cellulaire à base de lymphocytes T génétiquement modifiés exprimant des récepteurs synthétiques ou CAR (récepteur antigénique chimérique) a révolutionné le traitement de certaines maladies hémato-oncologiques. Ce succès a conduit à l'exploration de la même approche dans le traitement de maladies auto-immunes sévères et réfractaires aux thérapies conventionnelles. Les premiers résultats obtenus dans le lupus érythémateux systémique ont montré des rémissions complètes semblant persister dans le temps. Nous assistons donc actuellement à une prolifération importante d'essais cliniques. Dans cet article, nous abordons le rationnel derrière l'utilisation des thérapies CAR-T, les maladies auto-immunes ciblées, mais aussi les risques associés.

[Understanding hypersensitivity reactions to monoclonal antibodies]. / Comprendre les réactions d'hypersensibilité aux anticorps monoclonaux.

Biologic drugs are complex molecules synthesized by a living organism. Their use is increasingly prevalent across all medical specialties, exposing a growing number of patients to potential adverse reactions. In this review, we discuss the new classification of hypersensitivity reactions, along with the specific characteristics of monoclonal antibodies. We also address the available diagnostic tools and discuss the management of those reactions, including for patients requiring the continuation of these biologic drugs.

Les médicaments biologiques sont des molécules complexes synthétisées par un organisme vivant. Ils sont de plus en plus utilisés dans toutes les spécialités médicales, exposant ainsi les patients à des réactions indésirables. Dans cet article, nous abordons la nouvelle classification des réactions d'hypersensibilité ainsi que les caractéristiques spécifiques des anticorps monoclonaux. Nous évoquons également les outils diagnostiques disponibles et discutons de la prise en charge, y compris pour les patients nécessitant la poursuite de l'administration des médicaments biologiques.

Risk factors for allergy documentation in electronic health record: A retrospective study in a tertiary health center in Switzerland.

BACKGROUND: Most hospitals use electronic health records (EHR) to warn health care professionals of drug hypersensitivity (DH) and other allergies. Indiscriminate recording of patient self-reported allergies may bloat the alert system, leading to unjustified avoidances and increases in health costs. The aim of our study was to analyze hypersensitivities documented in EHR of patients at Lausanne University Hospital (CHUV). METHODS: We conducted a retrospective study on patients admitted at least 24 h to CHUV between 2011 and 2021. After ethical clearance, we obtained anonymized data. Because culprit allergen could be either manually recorded or selected through a list, data was harmonized using a reference allergy database before undergoing statistical analysis. RESULTS: Of 192,444 patients, 16% had at least one allergy referenced. DH constituted 60% of all allergy alerts, mainly beta-lactam antibiotics (BLA) (30%), NSAID (11%) and iodinated contrast media (ICM) (7%). Median age at first hospitalization and hospitalization length were higher in the allergy group. Female to male ratio was 2:1 in the allergic group. Reactions were limited to the skin in half of patients, and consistent with anaphylaxis in 6%. In those deemed allergic to BLA, culprit drug was specified in 19%, 'allergy to penicillin' otherwise. It was impossible to distinguish DH based on history alone or resulting from specialized work-up. CONCLUSIONS: Older age, longer hospital stays, and female sex increase the odds of in-patient allergy documentation. Regarding DH, BLA were referenced in 4% of inpatient records. Specific delabeling programs should be implemented to increase data reliability and patient safety.

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.

Intradermal skin test with mRNA vaccines as a surrogate marker of T cell immunity in immunocompromised patients.

OBJECTIVES: Intradermal skin test (IDT) with mRNA vaccines may represent a simple, reliable, and affordable tool to measure T cell response in immunocompromised patients who failed to mount serological responses following vaccination with mRNA covid-19 vaccines. METHODS: We compared anti-SARS-CoV-2 antibodies and cellular responses in vaccinated immunocompromised patients (n = 58), healthy seronegative naive controls (NC, n = 8), and healthy seropositive vaccinated controls (VC, n = 32) by Luminex, spike-induced IFN-γ Elispot and an IDT. A skin biopsy 24 h after IDT and single-cell RNAseq was performed in three vaccinated volunteers. RESULTS: Twenty-five percent of seronegative NC had a positive Elispot (2/8) and IDT (1/4), compared to 95% (20/21) and 93% (28/30) in seropositive VC, respectively. Single-cell RNAseq data in the skin of VC showed a predominant mixed population of effector helper and cytotoxic T cells. The TCR repertoire revealed 18/1064 clonotypes with known specificities against SARS-CoV-2, among which six were spike-specific. Seronegative immunocompromised patients with positive Elispot and IDT were in 83% (5/6) treated with B cell-depleting reagents, while those with negative IDT were all transplant recipients. CONCLUSIONS: Our results indicate that delayed local reaction to IDT reflects vaccine-induced T-cell immunity opening new perspectives to monitor seronegative patients and elderly populations with waning immunity.

Matching for HLA-DR excluding diabetogenic HLA-DR3 and HLA-DR4 predicts insulin independence after pancreatic islet transplantation.

Introduction: In pancreatic islet transplantation, the exact contribution of human leukocyte antigen (HLA) matching to graft survival remains unclear. Islets may be exposed to allogenic rejection but also the recurrence of type 1 diabetes (T1D). We evaluated the HLA-DR matching, including the impact of diabetogenic HLA-DR3 or HLA-DR4 matches. Methods: We retrospectively examined the HLA profile in 965 transplant recipients and 2327 islet donors. The study population was obtained from patients enrolled in the Collaborative Islet Transplant Registry. We then identified 87 recipients who received a single-islet infusion. Islet-kidney recipients, 2nd islet infusion, and patients with missing data were excluded from the analysis (n=878). Results: HLA-DR3 and HLA-DR4 were present in 29.7% and 32.6% of T1D recipients and 11.6% and 15.8% of the donors, respectively. We identified 52 T1D islet recipients mismatched for HLA-DR (group A), 11 with 1 or 2 HLA-DR-matches but excluding HLA-DR3 and HLA- DR4 (group B), and 24 matched for HLA-DR3 or HLA-DR4 (group C). Insulin-independence was maintained in a significantly higher percentage of group B recipients from year one through five post-transplantation (p<0.01). At five-year post-transplantation, 78% of group B was insulin-independent compared to 24% (group A) and 35% (group C). Insulin-independence correlated with significantly better glycemic control (HbA1c <7%), fasting blood glucose, and reduced severe hypoglycemic events. Matching HLA-A-B-DR (≥3) independently of HLA- DR3 or HLA-DR4 matching did not improve graft survival. Conclusion: This study suggests that matching HLA-DR but excluding the diabetogenic HLA-DR3 and/or 4 is a significant predictor for long-term islet survival.

[Hymenoptera venom allergy: what's new in 2023]. / Hypersensibilité aux venins d'hyménoptères : le point en 2023.

Hymenoptera venom allergy is a central thematic in allergology. The recent limitation in the obtention of certain venom products has forced Swiss centers to adapt their diagnostic and therapeutical approaches. In this review, we will discuss diagnostics tools using recombinants serologies, recent recommendations for the screening of indolent systemic mastocytosis and the different immunotherapy protocols available for venom desensitization using aqueous and aluminum hydroxide-adsorbed purified venoms.

L'hypersensibilité aux venins d'hyménoptères est une thématique importante en allergologie. La disponibilité limitée des produits de désensibilisation a forcé les centres universitaires suisses à adapter leurs pratiques médicales diagnostique et thérapeutique. Dans cet article, nous discutons des différentes sérologies recombinantes disponibles, comment aborder le dépistage de la mastocytose systémique indolente et, finalement, les différents schémas de désensibilisation à base d'une formulation aqueuse ou dépôt adsorbé sur de l'hydroxyde d'aluminium.

Incidence of Chronic Spontaneous Urticaria Following Receipt of the COVID-19 Vaccine Booster in Switzerland.

This cohort study examines the association of the COVID-19 vaccine booster with chronic spontaneous urticaria in Swiss patients.

Regulatory T cell homeostasis: Requisite signals and implications for clinical development of biologics.

Novel biologics are currently being tested in clinical trials for the treatment of autoimmune diseases and the prevention of transplant allograft rejection. Their premise is to deliver highly efficient immunosuppression while minimizing side-effects, as they specifically target inflammatory mediators involved in the dysregulation of the immune system. However, the pleiotropism of soluble mediators and cell-to-cell interactions with potential to exert both proinflammatory and regulatory influences on the outcome of the immune response can lead to unpredictable results. Predicting responses to biologic drugs requires mechanistic understanding of the cell type-specific effect of immune mediators. Elucidation of the central role of regulatory T cells (Treg), a small subset of T cells dedicated to immune homeostasis, in preventing the development of auto- and allo-immunity has provided a deeper understanding of the signaling pathways that govern immune tolerance. This review focuses on the requisite signals that promote Treg homeostasis and discusses the anticipated outcomes of biologics targeting these signals. Our goal is to inform and facilitate the design of cell-specific biologics that thwart T effector cells (Teff) while promoting Treg function for the treatment of autoimmune diseases and the prevention of transplant rejection.

Intradermal Testing With COVID-19 mRNA Vaccines Predicts Tolerance.

Background: The newly developed mRNA-based COVID-19 vaccines can provoke anaphylaxis, possibly induced by polyethylene glycol (PEG) contained in the vaccine. The management of persons with a history of PEG allergy or with a suspected allergic reaction after the first dose remains to be defined. Methods: In this real-life study, we defined two cohorts of individuals: one pre-vaccination including 187 individuals with high-risk profiles for developing anaphylaxis and a second post-vaccination including 87 individuals with suspected allergic reactions after the COVID-19 mRNA vaccine. Upon negative skin test with an mRNA vaccine, a two-step (10-90%) vaccination protocol was performed. Positive skin tests were confirmed with the basophil activation test (BAT). Results: Among 604,267 doses of vaccine, 87 suspected allergic reactions (5 after the booster) were reported to our division for further investigations: 18/87 (21%) were consistent with anaphylaxis, 78/87 (90%) were female, and 47/87 (54%) received the BNT162b2 mRNA vaccine. Vaccine skin tests were negative in 96% and 76% of the pre- and post-vaccination cohorts, respectively. A two-step vaccination was tolerated in 232/236 (98%) of individuals with negative tests. Four individuals experienced isolated asthmatic reactions during the two-step challenge. Vaccine-positive skin tests were consistently confirmed by BAT; CD63 and CD203c expression was selectively inhibited with ibrutinib, suggesting an IgE-dependent mechanism. Conclusion: Sensitization to SARS-CoV-2 mRNA vaccines can be detected with intradermal testing. Significantly more individuals were sensitized to mRNA vaccines in the post-vaccination cohort. A two-step 10-90%-vaccination protocol can be safely administered upon negative skin testing.

Atopy as an independent predictor for long-term patient and graft survival after kidney transplantation.

Background: Atopy is a genetic condition predisposing individuals to develop immunoglobulin E (IgE) against common allergens through T-helper 2 (Th2) polarization mechanisms. The impact of atopy on graft survival in solid organ transplantation is unknown. Methodology: We analyzed 268 renal allograft recipients from the Swiss Transplant Cohort Study, a prospective multicenter cohort studying patients after solid organ transplantation, with a 9-year median follow-up (IQR 3.0). We used the Phadiatop assay to measure IgE antibodies against a mixture of common inhaled allergens (grass, tree, herbs, spores, animals, and mites) to identify pre-transplantation atopic patients (>0.35 KU/L). Results: Of 268 kidney transplant recipients, 66 individuals were atopic (24.6%). Atopic patients were significantly younger than non-atopic patients (49.6 vs 58.0 years old, P = 0.002). No significant difference was found for gender, cold/warm ischemia time, preformed donor-specific antibodies (DSA), HLA mismatches, induction and maintenance immunosuppressive therapy, CMV serostatus, or cause of kidney failure. Patient and graft survival at ten years of follow-up were significantly better in the atopic group, 95.2% versus 69.2% patient survival (P < 0.001), and 87.9% versus 60.8% graft survival (P < 0.001), respectively. A multivariate Cox analysis revealed that atopy predicted recipient and graft survival independently of age and living donor donation. Finally, we found similar rates of biopsy-proven acute cellular and antibody-mediated rejections between atopic and non-atopic recipients. Conclusion: Atopy was associated with better long-term patient and graft survival, independently of age and living donor donation after kidney transplantation. Yet, atopy should not be used as a predictor for acute rejection.

Xenotransplantation: A New Era.

Organ allotransplantation has now reached an impassable ceiling inherent to the limited supply of human donor organs. In the United States, there are currently over 100,000 individuals on the national transplant waiting list awaiting a kidney, heart, and/or liver transplant. This is in contrast with only a fraction of them receiving a living or deceased donor allograft. Given the morbidity, mortality, costs, or absence of supportive treatments, xenotransplant has the potential to address the critical shortage in organ grafts. Last decade research efforts focused on creation of donor organs from pigs with various genes edited out using CRISPR technologies and utilizing non-human primates for trial. Three groups in the United States have recently moved forward with trials in human subjects and obtained initial successful results with pig-to-human heart and kidney xenotransplantation. This review serves as a brief discussion of the recent progress in xenotransplantation research, particularly as it concerns utilization of porcine heart, renal, and liver xenografts in clinical practice.

Management of Beta-Lactam Antibiotics Allergy: A Real-Life Study.

Beta-lactam allergy is a common problem in everyday medical practice and is recognized as a major public health issue. Carrying this label frequently leads to the avoidance of all beta-lactam antibiotics, favoring the use of other less preferred classes of antibiotics, that are more expensive and associated with more side effects and increased antimicrobial resistance. Therefore, delabeling a beta-lactam allergy is part of antimicrobial stewardship programs. Herein, we retrospectively examined the clinical records of 576 patients who were referred to our center for a label of allergy to beta-lactam antibiotics and were systematically investigated following a standardized algorithm. Our main aim was to evaluate the frequency of confirmed immediate- and delayed-type allergy to commonly prescribed subclasses of beta-lactam antibiotics (penicillin and cephalosporin), as well as the negative predictive value (NPV) and the sensitivity of skin tests. Our secondary aims were to examine the safety of beta-lactam skin testing and drug challenge. We identified that 260 patients reported a history of immediate reactions, 131 of delayed reactions, and 114 of unknown timing or mechanism of reactions. Following assessment and testing, 86 (18.3%) patients had a confirmed allergy to any beta-lactam antibiotics; 63 (13.4%) with an immediate- and 23 (4.9%) with a delayed-type reaction. Most frequently identified confirmed allergy was to penicillins (65 patients), followed by cephalosporins (21 patients). When immediate-type reactions were examined, NPV of skin tests were 96.3% and 100% for penicillins and cephalosporins, respectively. When delayed reactions were considered, NPV were 91.9 and 87.5% for penicillins and cephalosporins, respectively. Evaluation of the safety of skin tests according to the standardized procedure showed that systemic allergic reactions occurred in only 0.7% of skin tests and in 3.1% of drug challenges. Overall, our data indicate that only 18.3% of patients with a beta-lactam allergy label have a confirmed allergy and non-allergic patients can be safely delabeled through allergic workup based on skin tests and drug challenge. This approach supports the policy of saving second-line antibiotics through a standardized allergy workup.

[Human diseases caused by Anisakis simplex]. / Maladies causées par Anisakis simplex chez l'humain.

Anisakis simplex is a parasitic worm. It infects marine mammals that feed on fish and cephalopods, its intermediary hosts. Human disease is caused by accidental ingestion of Anisakis larvae. Upon consumption of contaminated fish, cuttlefish or squid, human may develop two distinct clinical pictures: Anisakiasis is provoked by living larvae penetrating the digestive mucosa. Allergy is caused by IgE-mediate hypersensitivity to living or dead larvae in a previously sensitized individual. Anisakiasis may manifests with violent epi gastric pain, acute abdomen or eosinophilic gastroenteritis. The larvae may be visualized by endoscopy or histology. The main Anisakis allergens are not denaturated by heat or cold and resist to digestion. Allergy diagnosis relies on careful history and detection of specific IgE.

Anisakis simplex est un ver parasite (helminthe) du groupe des nématodes. Il infeste les mammifères marins se nourrissant de poissons et de céphalopodes, ses hôtes intermédiaires. Chez l'homme, l'ingestion de poissons, de calamars ou de seiches contaminés est responsable de 2 tableaux cliniques. L'anisakiase est provoquée par la pénétration de la muqueuse digestive par des larves vivantes. L'allergie est une réaction IgE (immunoglobuline E) médiée aux parasites morts ou vivants chez une personne préalablement sensibilisée. L'anisakiase occasionne des épigastralgies, un abdomen aigu ou de manière plus sournoise une gastroentérite à éosinophiles. Les larves sont visualisables par endoscopie ou à l'histologie. Les principaux allergènes d'Anisakis résistent à la cuisson et à la digestion. Le diagnostic d'allergie se base sur l'anamnèse et la détection d'IgE spécifiques.

[Hypersensitivity reactions to intravenous iron: an allergist' perspective]. / Réactions d'hypersensibilité au fer intraveineux : le point de vue de l'allergologue.

Intravenous iron infusions rarely result in severe hypersensitivity reactions. The primary suspected hypersensitivity mechanism is an abnormal complement activation by non-IgE antibodies to the carbohydrate moieties stabilizing iron formulations. A major risk factor for hypersensitivity reactions is related to the infusion speed. Fishbane-like reactions usually resolve after pausing the infusion, which can be resumed under medical surveillance and at a lower infusion rate. Yet, anaphylactic reactions require emergency first aid and subsequent strict avoidance of intravenous iron. Desensitization protocols can be implemented in selected cases and under strict medical surveillance to reduce the risks of severe reactions upon re-exposure.

L'administration de fer intraveineux (IV) peut rarement se compliquer de réactions d'hypersensibilités sévères, parfois fatales. Le mécanisme supposé est celui d'une activation anormale du complément, possiblement liée à des anticorps non-IgE (immunoglobuline E) dirigés contre les groupements carbohydrates qui stabilisent la formulation de fer. Un débit de perfusion trop rapide est un facteur important de réaction d'hypersensibilité. En effet, les réactions légères se résolvent généralement après mise en pause de la perfusion, qui peut ensuite être reprise à un débit réduit. Les réactions anaphylactiques nécessitent en revanche un traitement d'urgence et une éviction stricte. Le recours à un protocole de désensibilisation sous surveillance médicale étroite permet, dans certaines situations, de limiter le risque de réaction lors d'une réadministration de fer IV.