Climate change, economic constraints and social concern for a sustainable agriculture will strongly influence animal production systems. Poultry production is a major source of proteins for human food all over the world. Improving the adaptation of chicken lines to variable conditions of climate and feed is a requirement to meet the challenge of a growing human population by 2050, particularly in Asian and African countries with a hot climate. Whereas heat tolerance in chickens has been studied for many years, a global understanding of the genetic control of adaptation is still absent and targeted selection criteria are also lacking. Variation in feed consumption is known to influence heat tolerance in chickens and genetic variation in feed intake must be taken into account in order to analyse mechanisms of heat tolerance. Furthermore, feed quality is likely to fluctuate, especially because of economic constraints. Thus, the possible connection between mechanisms of heat adaptation and mechanisms of adaptation to feed change needs to be thoroughly investigated. We propose to use up-to-date genomic methods to study mechanisms of adaptation to heat (heat waves in particular) or to feed change (use of co-products of grains and oilseeds for example) of a range of contrasted genotypes, in order to cover a wide range of genetic and epigenetic variation, within and between populations. The laying hen is targeted because it has a long production cycle and is particularly exposed to the risk of seasonal heat waves. The project takes advantage of the availability of different lines or breeds maintained at INRA in order to provide a body of fundamental knowledge on adaptive mechanisms regarding heat tolerance and adaptation to feed change in a domestic bird. Four experimental lines will be studied: brown egg layers selected for a low residual feed intake (R-) or a high residual feed intake (R+); a line of Fayoumi chickens, from the Egyptian Fayoumi breed known to be heat tolerant and disease resistant; a line of brown-egg layers carrying the "naked neck" and "dwarfism" genes which decrease the effects of heat on performance. These lines are moderately inbred and exhibit strong variation between them. A commercial line from Novogen (partner of the project) will be studied in connection with an on-going project on genomic selection (ANR UtOpIGe) where sires are genotyped and tested. Sire families differing in adaptation to a feed change will be produced to be tested for heat tolerance. The work program is organised in 6 tasks: coordination; challenging and phenotyping; transcriptomics; epigenetics; data integration; dissemination. All genotypes will be challenged with a heat stress at the time of high egg production, just after the peak of lay. The R- and R+ lines and Novogen line only will be tested independently on the sub-optimal diet already used to challenge the commercial line. A control, unstressed, group will be maintained for each genotype. Hypothalamus, liver and leukocytes (at 2 time points) will be collected for DNA and RNA extraction. Performance records and physiological indicators will be combined with transcriptomic and DNA methylation studies in order to identify regulatory pathways of adaptation. Heritability of methylation pattern of a subset of loci will be estimated in the commercial line. Analyses will benefit from data produced by two related, already funded projects that will provide genetic data (marker genotypes and genetic values for Novogen and resequencing of the whole genome for R-R+). These data obtained in a wide range of domains (genomics selection, functional genomics, physiology and production) in contrasted genotypes will give us a unique opportunity to build an integrative scheme for adaptation mechanisms and regulation, in chicken.

Spondyloarthritis (SpA) are chronic inflammatory rheumatic diseases affecting both axial and peripheral skeleton joints and leading to bone growth and fusion. The major histocompatibility complex class I antigen, HLA-B27 is the strongest genetic factor associated with disease predisposition. HLA B27 associates with human ß2-microglobulin (hß2m), to present antigenic peptides to T CD8+ cells. Despite 46 years of research, the mechanism by which HLA-B27 predisposes to SpA remains unsolved, although hypotheses have speculated either on the presentation of particular peptides to CD8+ T cells or on non-canonical functions. Partners 1 and 2 collaborated to produce Drosophila transgenic for HLA-B27 in combination with hß2m, speculating that this simplified animal model could facilitate deciphering of the non-canonical effects of the molecule in the absence of its role on adaptive immunity that may mask some of its pathogenic effects. Interestingly transgenic flies, carrying two SpA-associated HLA-B27 subtypes -but not SpA-non-associated HLA-B7 allele- developed abnormal phenotypes, only in the presence of hß2m that allows localization of well-folded HLA-B27 molecules at the cell surface. Partner 1 showed that this phenotype was due to a disturbance of the bone morphogenetic proteins (BMP) signaling pathway. BMPs are members of the TGF-ß superfamily. In Drosophila, HLAB27/hß2m repressed Sax BMPR1 function and increased BMP signaling. Consistently, Partner 1&2 showed that HLA-B27/hß2m well-folded conformers co-localized with Sax, and with the Sax mammalian ortholog ALK2 in immune cells from SpA patients. The hypothesis of an altered BMP pathway in SpA patients is also supported by Partner 2 and others showing dysregulation of BMP effectors or ligands in dendritic cells from HLA-B27 transgenic rat or in patients’ serum respectively. These results indicate that the pathogenic role of HLA-B27 in SpA may result from a TGFß/BMP signaling misregulation at the crossroad between inflammation and ossification. The TGFß superfamily also contains key regulators of intestinal homeostasis in both Drosophila and human. Intestinal in?ammatory diseases are frequently associated with SpA. The effect of HLA-B27 on these diseases remains unclear and could result from HLA-B27-mediated misregulation in either immune or intestinal cells. Upon infection, BMP signaling regulates hemocyte (Drosophila macrophage-like cells) proliferation and adhesion. BMPs are also an essential signal secreted by hemocytes to trigger intestinal regeneration. Additionally, Partner 1 showed that HLA-B*2705 in the hemocytes -unlike SpA non-associated alleles- decreases Drosophila lifespan, and we hypothesize that this reduced lifespan may result from intestinal dyshomeostasis through HLA-B27 action on BMP signaling in hemocytes. This project will be realized by a Consortium already engaged in collaboration. Our objective is to decipher misregulation of the TGFß/BMP pathway induced by HLA B27. Task 1 will be to further identify receptors of the TGFß superfamily that interact with and are misregulated by HLA-B27 and to characterize their effects on BMP signaling both in Drosophila and patients’ cells. Task 2 will characterize HLA-B27 peptidome in Drosophila and compare it to rat and human peptidomes to identify specific peptides that could modulate HLA-B27 processing in mammalian cells. Task 3 will address the role of HLA-B27 on hemocyte and intestinal cell homeostasis. The expression of HLA-B27 will be driven either in Drosophila hemocytes or in intestinal cells and its impact on intestine regeneration after infection will be studied. Drosophila is a novel model to study non-canonical effects of HLA-B27. It is complementary to the HLA-B27 transgenic rat model and patients’ cells also used by the consortium in this project. The results may have important translational impacts to patients with SpA in terms of novel therapeutic interventions.

The climate is changing and according to the recent estimates from the IPCC, the likelihood of heat wave events is expected to increase both in number and in intensity. Temperature is projected to increase from 1.8 to 4.0°C from 1980-1999 to 2090-2099. Hence, heat stress-related costs in pig production will be amplified in the future, both in temperate areas (summer heat waves) and tropical areas (hot and humid environment). Meanwhile, world pig production is moving rapidly to tropical and subtropical regions reaching now more than 50% of the total production. The world development of pig production has been achieved through improvement of animal genetics and management in temperate countries. However, selection performed in optimally controlled conditions has increased the sensitivity of animals to high ambient temperature. Heat stressed pigs reduce their feed intake which impair their growth or reproduction performances. Management solutions are available to attenuate the effect of heat stress on pigs, such as environmental solutions (water or feeding management). However, these solutions are technically and economically difficult to implement. The genetic selection for improving environmental adaptation in pig production is the most promising long term option. The PigHeaT project aims 1) at identifying QTLs for heat adaptation, by examining direct responses to find genes involved in metabolic ways, indirect responses to find genes affecting growth or robustness to environmental variations, 2) at better understanding the physiological mechanisms underlying heat adaptation. It will provide tools for improving breeding strategies to face the upcoming global warming, and knowledge to better comprehend the physiological reactions of animals submitted to short and long term heat stress. The PigHeaT project is based on original biological resources and original experimental facilities. The studied population will be a backcross between Large White pigs, productive but poorly thermotolerant breed, and Creole pigs, low productive but highly thermotolerant breed. The progeny issued from this backcross will express all possible levels of thermal tolerance and production performances when submitted to heat stress, depending on the alleles received from their parents. High throughput phenotyping, metabolomics on all the progeny, and transcriptomics on a subset of extreme pigs selected on thermal tolerance response, will be applied. It will allow to refine the phenotypes and to achieve a high level of accuracy in QTL detection in the frame of the PigHeaT project. Additionally, the design will benefit from the unique combination of experimental facilities available at INRA: the first part of the project will rely on the backcross population raised in the experimental facilities located in the West Indies (Guadeloupe, tropical environment). The concomitant production of the same population in the experimental facilities available in temperate France (Charente Maritime) will allow the detection of genetic by environment (GxE) effects for the QTL detected in Guadeloupe. Moreover, a heat wave phenomenon will be systematically simulated in the temperate environment at the end of the growing period. As a result, chromosomal regions robust or susceptible to GxE interactions will be identified, GxE being either tropical vs temperate, or tropical vs heat wave. Finally, an integrated analysis of the (fine) phenotypes and QTL will be proposed to better understand the metabolic pathways involved in heat stress responses. The respective use of the QTL and biological knowledge in further breeding strategies will finally be considered.

Mitochondrial dysfunction is a hallmark of numerous major human diseases including neurodegenerative diseases. Mitochondria is a key organelle for iron metabolism, being the place of heme and iron-sulfur (Fe-S) clusters biogenesis, two iron-containing cofactors involved in key cellular pathways. Iron, an essential but also highly reactive element, can participate to the generation of the harmful reactive oxygen species and ultimately cell death by ferroptosis. Ferroptosis has raised interest of the scientific community for its potential as a new therapeutic target in cancers and neurodegenerative diseases. The FeMiSid project aims at understanding the role of sideroflexins (SFXN) in iron metabolism. SFXN form a family of mitochondrial carriers that remain poorly characterized. Since SFXN exist in all eukaryotes, we hypothesize that they are essential for mitochondrial activities. Accordingly, loss-of-function mutations of human SFXN4 cause the COXPD18 syndrome, a rare mitochondrial disease. Recent studies provided evidence for a role of SFXN in iron metabolism but the molecular bases of this regulatory activity are not fully depicted. There are five family members in humans and their functions are still unclear, especially in brain physiology and pathology. Whereas SFXN1 and SFXN3 may be deregulated in Alzheimer’s (AD) and Parkinson’s (PD) diseases, their respective roles in neuronal physiopathology remain largely unknown. The FeMiSid project focuses more specifically on SFXN1, that was recently described as the mitochondrial serine transporter, thus playing a central role in the one-carbon metabolism (OCM). OCM is a universal metabolic pathway and its perturbation favors cancer cell hyperproliferation and neuronal defects. Given that mitochondrial activities are impaired during neurodegeneration and that an accumulation of brain iron as well as a neuronal death by ferroptosis were described in some neurodegenerative disease (such as AD and PD), our main objectives are to uncover the role of SFXN1: 1) in iron metabolism; 2) in heme and Fe-S clusters biogenesis; 3) in the cellular response to oxidative stress and ferroptosis; 4) in neuronal physiology and neurodegeneration. To address these main questions, a consortium of experts on mitochondrial physiology and neurodegenerative diseases has been formed allowing the generation of interesting preliminary results on human cells, but also on yeast and fruit fly, that display only one and two SFXN genes respectively. Additionally, Drosophila and rodent models will be used to study SFXN effect on neurodegeneration in whole organisms. The innovative FeMiSid project focuses on a relatively free niche and will certainly yield major progresses on the role of mitochondria in physiopathology. Data obtained may impact different scientific fields given the wide involvement of mitochondria in human disease (including neurodegenerative diseases, cancer, diabetes, cardiovascular pathologies). Especially, our project could give valuable information on the role of mitochondria and SFXN in AD and PD etiology, the most common neurodegenerative diseases. In the long term, we hope that the knowledge of SFXN functions may permit the design of new therapeutic avenues for neurodegenerative diseases or other diseases involving mitochondrial impairment.