The EC-Earth3 Earth system model for the Coupled Model Intercomparison Project 6

The Earth system model EC-Earth3 for contributions to CMIP6 is documented here, with its flexible coupling framework, major model configurations, a methodology for ensuring the simulations are comparable across different high-performance computing (HPC) systems, and with the physical performance of base configurations over the historical period. The variety of possible configurations and sub-models reflects the broad interests in the EC-Earth community. EC-Earth3 key performance metrics demonstrate physical behavior and biases well within the frame known from recent CMIP models. With improved physical and dynamic features, new Earth system model (ESM) components, community tools, and largely improved physical performance compared to the CMIP5 version, EC-Earth3 represents a clear step forward for the only European community ESM. We demonstrate here that EC-Earth3 is suited for a range of tasks in CMIP6 and beyond.Peer reviewe

The Expanding Role of APRIL in Cancer and Immunity

Proteins of the tumour necrosis factor (TNF) family are implicated in the regulation of essential cell processes such as proliferation, differentiation, survival and cell death. Altered expression of TNF family members is often associated with pathological conditions such as autoimmune disease and cancer. The TNF-like ligand APRIL (A PRoliferation Inducing Ligand), first described in 1998, was named for its capacity to stimulate tumour cell proliferation in vitro. APRIL expression was initially reported in haematopoietic cells in physiological conditions, and it is overexpressed in certain tumour tissues. APRIL is now known to be involved in activation and immune responses of B cells, as well as in B cell malignancies. This review focuses on recent advances in understanding APRIL and its receptors in physiology and tumour pathology, including the accumulating evidence that specific Toll-like receptor ligands can trigger APRIL-mediated responses, and the identification of new sources of APRIL such as epithelial cells and tumour-infiltrating neutrophil

Thymus-independent class switch recombination is affected by APRIL

The tumour necrosis factor (TNF) family member a proliferation-inducing ligand (APRIL) is implicated in various B-cell processes, such as class switch recombination, plasma cell differentiation and plasma cell survival. This was suggested from initial studies analysing B-cell responses in APRIL-deficient and transgenic mice, and mice deficient for the TNF receptors of APRIL, transmembrane activator and CAML interactor (TACI) and B-cell maturation antigen. Here, we present additional evidence for the importance of APRIL in thymus-independent (TI) B-cell responses, using APRIL-deficient and transgenic mice. APRIL-deficient mice show an impaired immunoglobulin A (IgA) response towards TI B-cell antigens, whereas APRIL transgenic mice show exaggerated TI B-cell responses. Moreover, antibody titres to TI antigens were sustained in APRIL transgenic mice for a long time and even increased up to 75 days in the case of IgA against 4-hydroxy-nitrophenacetyl-lipopolysaccharid

APRIL affects antibody responses and early leukocyte infiltration, but not influenza A viral control

A proliferation inducing ligand (APRIL) is implicated in the regulation of class switch recombination to IgA in T-independent B cell responses. Since B cells play an important role in the immunity to influenza A virus and resistance against the virus is partly controlled by T-independent IgA B cell responses, we studied the role of APRIL during an influenza A infection in vivo. APRIL transgenic, wild-type and APRIL deficient mice were intranasally infected with a non-lethal dose of a mouse adapted strain of influenza A. Compared to wild-type mice, APRIL deficient mice showed a twofold reduction in the amount of macrophages in the lungs and a tendency towards decreased granulocyte influx in the early leukocyte recruitment phase. Although the T cell immune response against influenza was unaffected, APRIL Tg mice showed prolonged influenza-specific IgM production and differential class switching. Unexpectedly, the IgA B cell response was completely T helper cell dependent and also not affected by the absence or presence of APRIL. In addition, viral clearance and recovery from the infection was not influenced by APRIL. Combined these results indicate that APRIL affects specific aspects of the anti-influenza response, but plays a limited role in disease recover

The proteoglycan (heparan sulfate proteoglycan) binding domain of APRIL serves as a platform for ligand multimerization and cross-linking

A proliferation-inducing ligand (APRIL) (also known as TALL-2 and TRDL-1) is a member of the tumor necrosis factor (TNF) superfamily that has tumorigenic properties but is also important for the induction of humoral immune responses. APRIL binds two TNF receptors: transmembrane activator and calcium modulator and cyclophilin ligand interactor (TACI) and B-cell maturation antigen (BCMA) as well as heparan sulfate proteoglycans (HSPGs). The aim of this study was to clarify the role of the HSPG interaction in canonical APRIL signaling, because it has been proposed to act as a docking site and also to play a role in direct signaling. In this study, we generated point mutants of soluble APRIL that lack either the capacity to bind HSPGs or TACI and BCMA and then tested the function of these mutants in mouse B-cell assays. In contrast to previous reports, we found that APRIL alone is sufficient to costimulate B-cell proliferation and drive IgA production and does not require artificial antibody cross-linking. We found no evidence that APRIL requires signaling through HSPGs but, notably, were able to show that binding of APRIL to HSPGs is crucial for mediating natural APRIL cross-linking to allow for optimal activation of murine B cells.-Kimberley, F. C., van Bostelen, L., Cameron, K., Hardenberg, G., Marquart, J. A., Hahne, M., Medema, J. P. The proteoglycan (heparan sulfate proteoglycan) binding domain of APRIL serves as a platform for ligand multimerization and cross-linking. FASEB J. 23, 1584-1595 (2009

APRIL promotes B-1 cell-associated neoplasm

A tumor-supporting role for the TNF-like ligand APRIL has been suggested. Here we describe that 9- to 12-month-old APRIL transgenic mice develop lymphoid tumors that originate from expansion of the peritoneal B-1 B cell population. Aging APRIL transgenic mice develop progressive hyperplasia in mesenteric lymph nodes and Peyer's patches, disorganization of affected lymphoid tissues, mucosal and capsular infiltration, and eventual tumor cell infiltration into nonlymphoid tissues such as kidney and liver. We detected significantly increased APRIL levels in sera of B cell chronic lymphoid leukemia (B-CLL) patients, indicating that APRIL promotes onset of B-1-associated neoplasms and that APRIL antagonism may provide a therapeutic strategy to treat B-CLL patient

Prevention of murine autoimmune diabetes by CCL22-mediated Treg recruitment to the pancreatic islets

Type 1 diabetes is characterized by destruction of insulin-producing β cells in the pancreatic islets by effector T cells. Tregs, defined by the markers CD4 and FoxP3, regulate immune responses by suppressing effector T cells and are recruited to sites of action by the chemokine CCL22. Here, we demonstrate that production of CCL22 in islets after intrapancreatic duct injection of double-stranded adeno-associated virus encoding CCL22 recruits endogenous Tregs to the islets and confers long-term protection from autoimmune diabetes in NOD mice. In addition, adenoviral expression of CCL22 in syngeneic islet transplants in diabetic NOD recipients prevented β cell destruction by autoreactive T cells and thereby delayed recurrence of diabetes. CCL22 expression increased the frequency of Tregs, produced higher levels of TGF-β in the CD4+ T cell population near islets, and decreased the frequency of circulating autoreactive CD8+ T cells and CD8+ IFN-γ–producing T cells. The protective effect of CCL22 was abrogated by depletion of Tregs with a CD25-specific antibody. Our results indicate that islet expression of CCL22 recruits Tregs and attenuates autoimmune destruction of β cells. CCL22-mediated recruitment of Tregs to islets may be a novel therapeutic strategy for type 1 diabetes

HighResMIP versions of EC-Earth : EC-Earth3P and EC-Earth3P-HR - description, model computational performance and basic validation

A new global high-resolution coupled climate model, EC-Earth3P-HR has been developed by the EC-Earth consortium, with a resolution of approximately 40 km for the atmosphere and 0.25∘ for the ocean, alongside with a standard-resolution version of the model, EC-Earth3P (80 km atmosphere, 1.0∘ ocean). The model forcing and simulations follow the High Resolution Model Intercomparison Project (HighResMIP) protocol. According to this protocol, all simulations are made with both high and standard resolutions. The model has been optimized with respect to scalability, performance, data storage and post-processing. In accordance with the HighResMIP protocol, no specific tuning for the high-resolution version has been applied. Increasing horizontal resolution does not result in a general reduction of biases and overall improvement of the variability, and deteriorating impacts can be detected for specific regions and phenomena such as some Euro-Atlantic weather regimes, whereas others such as the El Niño–Southern Oscillation show a clear improvement in their spatial structure. The omission of specific tuning might be responsible for this. The shortness of the spin-up, as prescribed by the HighResMIP protocol, prevented the model from reaching equilibrium. The trend in the control and historical simulations, however, appeared to be similar, resulting in a warming trend, obtained by subtracting the control from the historical simulation, close to the observational one.The EC-Earth simulations from SMHI were performed on resources provided by the Swedish National Infrastructure for Computing (SNIC). The EC-EARTH simulations from BSC were performed on resources provided by ECMWF and the Partnership for Advanced Computing in Europe (PRACE; MareNostrum, Spain). Froila M. Palmeiro and Javier García-Serrano were partially supported by the Spanish GRAVITOCAST project (ERC2018-092835) and the “Ramón y Cajal” program (RYC-2016-21181), respectively, and MR was supported by “Beca de collaboració amb la Universitat de Barcelona” (2019.4.FFIS.1). The EC-Earth simulations from CNR were performed on resources provided by CINECA and ECMWF (special projects SPITDAVI and SPITMAVI). The EC-Earth simulations from KNMI were partly performed on resources provided by ECMWF (special project SPNLHAAR).Peer ReviewedPostprint (published version