Innate-like T cell subset commitment in the murine thymus is independent of TCR characteristics and occurs during proliferation.

How T-cell receptor (TCR) characteristics determine subset commitment during T-cell development is still unclear. Here, we addressed this question for innate-like T cells, mucosal-associated invariant T (MAIT) cells, and invariant natural killer T (iNKT) cells. MAIT and iNKT cells have similar developmental paths, leading in mice to two effector subsets, cytotoxic (MAIT1/iNKT1) and IL17-secreting (MAIT17/iNKT17). For iNKT1 vs iNKT17 fate choice, an instructive role for TCR affinity was proposed but recent data argue against this model. Herein, we examined TCR role in MAIT and iNKT subset commitment through scRNAseq and TCR repertoire analysis. In our dataset of thymic MAIT cells, we found pairs of T-cell clones with identical amino acid TCR sequences originating from distinct precursors, one of which committed to MAIT1 and the other to MAIT17 fates. Quantitative in silico simulations indicated that the number of such cases is best explained by lineage choice being independent of TCR characteristics. Comparison of TCR features of MAIT1 and MAIT17 clonotypes demonstrated that the subsets cannot be distinguished based on TCR sequence. To pinpoint the developmental stage associated with MAIT sublineage choice, we demonstrated that proliferation takes place both before and after MAIT fate commitment. Altogether, we propose a model of MAIT cell development in which noncommitted, intermediate-stage MAIT cells undergo a first round of proliferation, followed by TCR characteristics-independent commitment to MAIT1 or MAIT17 lineage, followed by an additional round of proliferation. Reanalyzing a published iNKT TCR dataset, we showed that this model is also relevant for iNKT cell development.

A conserved transcriptional program for MAIT cells across mammalian evolution.

Mucosal-associated invariant T (MAIT) cells harbor evolutionarily conserved TCRs, suggesting important functions. As human and mouse MAIT functional programs appear distinct, the evolutionarily conserved MAIT functional features remain unidentified. Using species-specific tetramers coupled to single-cell RNA sequencing, we characterized MAIT cell development in six species spanning 110 million years of evolution. Cross-species analyses revealed conserved transcriptional events underlying MAIT cell maturation, marked by ZBTB16 induction in all species. MAIT cells in human, sheep, cattle, and opossum acquired a shared type-1/17 transcriptional program, reflecting ancestral features. This program was also acquired by human iNKT cells, indicating common differentiation for innate-like T cells. Distinct type-1 and type-17 MAIT subsets developed in rodents, including pet mice and genetically diverse mouse strains. However, MAIT cells further matured in mouse intestines to acquire a remarkably conserved program characterized by concomitant expression of type-1, type-17, cytotoxicity, and tissue-repair genes. Altogether, the study provides a unifying view of the transcriptional features of innate-like T cells across evolution.

Combining crop-exposure matrices and land use data to estimate indices of environmental and occupational exposure to pesticides.

BACKGROUND: Exposure assessment represents a major challenge for studies on the relation between pesticides and health. OBJECTIVE: We developed a method combining information from crop-exposure matrices (CEMs) and land use data, in order to compute indices of environmental and occupational pesticide exposure. We illustrate our approach using French data (1979-2010). METHODS: We used CEMs for five crops (straw cereals, grain corn, corn fodder, potatoes, vineyards) that describe use (annual probability, frequency, intensity) of pesticide subgroups, chemical families, and active substances by region and time since 1960. We combined these data with land use data from agricultural censuses (1979, 1988, 2000, 2010) to compute indices of environmental and occupational pesticide exposure in cantons (small French administrative units). Indices of environmental exposure were calculated based on the area of each crop in the cantons, while indices of occupational exposure depended on combinations of crops in each farm from the cantons. To illustrate our approach, we selected a pesticide group (herbicides), chemical family of herbicides (phenoxyacetic acids), and active substance from the phenoxyacetic acids chemical family (2,4-D). RESULTS: The estimated proportion of the area of crops with CEMs and of farms sprayed with herbicides was close to 100% between 1979-2010, but the estimated average annual number of applications increased. There were decreasing time-trends for phenoxyacetic acids and 2,4-D over the same period for all indices of exposure. There was a high use of herbicides throughout France in 2010, except in the South coast. For phenoxyacetic acids and 2,4-D, the spatial distribution was heterogeneous for all indices of exposure, with the highest values in the Centre and North regions. IMPACT STATEMENT: Assessment of pesticide exposure is a key issue for epidemiological studies on their association with health outcomes. However, it presents some unique challenges, particularly for retrospective exposure and the investigation of chronic diseases. We present a method to compute indices of exposure by combining information from crop-exposure matrices for five crops and land use data. Specificities of environmental and occupational exposure are addressed using different methods. These methods are applied to pesticides used in agriculture in France for five crops (3 groups, 91 chemical families, 197 active substances) to produce indices at a small geographic scale from 1979 to 2010 for the whole metropolitan France. Besides using these indices in French epidemiological studies, our approach could be relevant for other countries.

Role of MR1-driven signals and amphiregulin on the recruitment and repair function of MAIT cells during skin wound healing.

Tissue repair processes maintain proper organ function following mechanical or infection-related damage. In addition to antibacterial properties, mucosal associated invariant T (MAIT) cells express a tissue repair transcriptomic program and promote skin wound healing when expanded. Herein, we use a human-like mouse model of full-thickness skin excision to assess the underlying mechanisms of MAIT cell tissue repair function. Single-cell RNA sequencing analysis suggested that skin MAIT cells already express a repair program at steady state. Following skin excision, MAIT cells promoted keratinocyte proliferation, thereby accelerating healing. Using skin grafts, parabiosis, and adoptive transfer experiments, we show that MAIT cells migrated into the wound in a T cell receptor (TCR)-independent but CXCR6 chemokine receptor-dependent manner. Amphiregulin secreted by MAIT cells following excision promoted wound healing. Expression of the repair function was probably independent of sustained TCR stimulation. Overall, our study provides mechanistic insights into MAIT cell wound healing function in the skin.

In vivo genome-wide CRISPR screens identify SOCS1 as intrinsic checkpoint of CD4+ TH1 cell response.

Although CD8+ T cells undergo autonomous clonal proliferation after antigen stimulation in vivo, the expansion of activated CD4+ T cells is limited by intrinsic factors that are poorly characterized. Using genome-wide CRISPR-Cas9 screens and an in vivo system modeling of antigen-experienced CD4+ T cell recruitment and proliferation during a localized immune response, we identified suppressor of cytokine signaling 1 (SOCS1) as a major nonredundant checkpoint imposing a brake on CD4+ T cell proliferation. Using anti­interleukin-2 receptor (IL-2R) blocking antibodies, interferon-γ receptor (IFN-γR) knockout mice, and transcriptomic analysis, we show that SOCS1 is a critical node integrating both IL-2 and IFN-γ signals to block multiple downstream signaling pathways abrogating CD4+ T helper 1 (TH1) cell response. Inactivation of SOCS1 in both murine and human CD4+ T cell antitumor adoptive therapies restored intratumor accumulation, proliferation/survival, persistence, and polyfunctionality and promoted rejection of established tumors. However, in CD8+ T cells, SOCS1 deletion did not affect the proliferation but rather improved survival and effector functions, which allowed for optimal therapeutic outcome when associated with SOCS1 inactivation in CD4+ T cells. Together, these findings identify SOCS1 as a major intracellular negative checkpoint of adoptive T cell response, opening new possibilities to optimize CAR-T cell therapy composition and efficacy.

Association between Self-Reported Gluten Avoidance and Irritable Bowel Syndrome: Findings of the NutriNet-Santé Study.

Self-management of irritable bowel syndrome (IBS) is increasingly focusing on exclusion diets. In particular; patients are showing a significant interest in the gluten-free diet for the treatment of IBS. However; the lack of scientific evidence prevents the establishment of clear dietary guidelines and attention is needed as dietary restriction can lead to potentially adverse effects. This cross-sectional study aims to explore the practice of gluten avoidance in participants identified with IBS in a large cohort of non-celiac French adults. The population included 15,103 participants of the NutriNet-Santé study who completed a functional gastrointestinal disorder questionnaire based on the Rome III criteria to identify IBS in 2013 and a food avoidance questionnaire in 2016. Data on diet and anthropometric and sociodemographic characteristics were collected. Multivariate logistic regression models were used to compare the avoidance of gluten between IBS and non-IBS participants. Participants were mainly women (73.4%) and the mean age in this population was 55.8 ± 13.2 years. Among these individuals, 804 (5.4%) participants were identified as IBS cases. Among them, the prevalence of gluten avoidance was estimated at 14.8%, of which 3.0% reported total avoidance; versus 8.8% and 1.6% in non-IBS participants. After adjustments; gluten avoidance was higher in IBS participants compared to their non-IBS counterparts: (OR = 1.86; 95%CI = 1.21, 2.85) for total and (OR = 1.71; 95%CI = 1.36, 2.14) for partial avoidance. Participants identified with IBS were more associated with gluten avoidance than non-IBS participants. Further studies are needed to explore the long-term consequences of dietary interventions and to provide consistent dietary guidance connected to patient perception.

Pesticides expenditures by farming type and incidence of Parkinson disease in farmers: A French nationwide study.

BACKGROUND: Professional pesticides exposure is associated with PD risk, but it remains unclear whether specific products, which strongly depend on farming type, are specifically involved. We performed a nationwide ecological study to examine the association of pesticides expenditures for the main farming types with PD incidence in French farmers. METHODS: We used the French National Health Insurance database to identify incident PD cases in farmers (2010-2015). We combined data on pesticides expenditures with the agricultural census to compute pesticides expenditures for nine farming types in 2000 in 3571 French cantons. The association between pesticides expenditures and PD age/sex standardized incidence was examined using multilevel Poisson regression, adjusted for smoking, neurologists' density, and deprivation index. RESULTS: 10,282 incident PD cases were identified. Cantons with the highest pesticides expenditures for vineyards without designation of origin were characterized by 16% (95% CI = 6-28%) higher PD incidence (p-trend corrected for multiple testing = 0.006). This association was significant in men and older farmers. There was no association with pesticides expenditures for other farming types, including vineyards with designation of origin. CONCLUSIONS: PD incidence increased significantly with pesticides expenditures in vineyards without designation of origin characterized by high fungicide use. This result suggests that agricultural practices and pesticides used in these vineyards may play a role in PD and that farmers in these farms should benefit from preventive measures aiming at reducing exposure. Our study highlights the importance of considering farming type in studies on pesticides and PD and the usefulness of pesticides expenditures for exposure assessment.

Organic food consumption and gluten-free diet, is there a link? Results in French adults without coeliac disease.

The rising popular belief that gluten is unhealthy has led to growth in gluten avoidance in people without coeliac disease. Little information is available on their dietary profiles and their dietary behaviours. Our aim was to compare the consumption of organic foods between gluten avoiders and non-avoiders, and their places of food purchase. We described their sociodemographic and dietary profiles. The study population included participants of the NutriNet-Santé cohort who completed both a food exclusion questionnaire and an organic semi-quantitative FFQ (n 23 468). Food intake and organic food consumption ratios were compared using multivariable adjusted ANCOVA models. Associations between gluten avoidance and organic food consumption as well as places of food purchase were investigated with multivariable logistic regression. Participants avoiding gluten were more likely to be women and had a healthier dietary profile. Organic food consumption was higher among gluten avoiders (48·50 % of total diet for total avoiders, 17·38 % for non-avoiders). After adjustments for confounders, organic food consumption and purchase in organic stores were positively associated with gluten avoidance: adjusted OR (aOR)Q5 v.Q1 organic food = 4·95; 95 % CI 3·70, 6·63 and aORorganic stores v.supermarkets = 1·82; 95 % CI 1·42, 2·33 for total avoiders. Our study highlights that individuals avoiding gluten are high organic consumers and frequently purchase their foods in organic stores which propose an extended offer of gluten-free food. Further research is needed to determine the underlying common motivations and the temporality of the dietary behaviours of healthy people avoiding gluten.

Gluten-free diet in French adults without coeliac disease: sociodemographic characteristics, motives and dietary profile.

The number of people avoiding gluten is growing in many Western countries. However, little information is available on their sociodemographic and dietary profiles. We aimed to describe sociodemographic, behavioural and dietary profiles of participants avoiding gluten in the NutriNet-Santé cohort. Participants of the NutriNet-Santé cohort - excluding coeliac patients - who completed a questionnaire about food exclusions, with complete data on sociodemographic characteristics and dietary intake were included (n 20 456). Food group consumptions and nutrient intakes according to self-reported avoidance of gluten were estimated using ANCOVA adjusted for age, sex and daily energy intake. Based on principal component analysis, three dietary patterns (DP) were identified. Association between DP and avoidance of gluten was investigated using multivariate logistic regression. All data were weighted on the French census. A total of 10·31 (95 % CI 9·90, 10·73) % of the participants declared avoiding gluten, of which 1·65 % totally. They were more likely to be women, older persons, non-smokers, to have a lower educational level and declared more food intolerances. They had higher consumption of fruit, vegetables and lower consumption of dairy products, salty/sweet and fatty foods and alcohol. After adjustments on confounders, a healthy dietary pattern was positively associated with total gluten avoidance (ORQuintile5vsQuintile1 = 14·44, 95 % CI 8·62, 24·19). Our study highlighted that, in this population, individuals who avoid gluten from their diet tend to have a diet more favourable to health. These results can serve as a basis for future studies investigating the potential consequences of a gluten-free diet in non-coeliac population.