Probing of a human proteome microarray with a recombinant pathogen protein reveals a novel mechanism by which hookworms suppress B-cell receptor signaling.

Na-ASP-2 is an efficacious hookworm vaccine antigen. However, despite elucidation of its crystal structure and studies addressing its immunobiology, the function of Na-ASP-2 has remained elusive. We probed a 9000-protein human proteome microarray with Na-ASP-2 and showed binding to CD79A, a component of the B-cell antigen receptor complex. Na-ASP-2 bound to human B lymphocytes ex vivo and downregulated the transcription of approximately 1000 B-cell messenger RNAs (mRNAs), while only approximately 100 mRNAs were upregulated, compared with control-treated cells. The expression of a range of molecules was affected by Na-ASP-2, including factors involved in leukocyte transendothelial migration pathways and the B-cell signaling receptor pathway. Of note was the downregulated transcription of lyn and pi3k, molecules that are known to interact with CD79A and control B-cell receptor signaling processes. Together, these results highlight a previously unknown interaction between a hookworm-secreted protein and B cells, which has implications for helminth-driven immunomodulation and vaccine development. Further, the novel use of human protein microarrays to identify host-pathogen interactions, coupled with ex vivo binding studies and subsequent analyses of global gene expression in human host cells, demonstrates a new pipeline by which to explore the molecular basis of infectious diseases.This is the author accepted version. The final version is available at http://dx.doi.org/10.1093/infdis/jiu451

Visual and biochemical evidence of glycocalyx disruption in human dengue infection, and association with plasma leakage severity

Background: Dengue is the most common arboviral infection globally; a minority of patients develop shock due to profound plasma leak through a disrupted endothelial barrier. Understanding of the pathophysiology underlying plasma leak is incomplete, but emerging evidence indicates a key role for degradation of the endothelial glycocalyx. Methods: We conducted an observational study in Vietnam to evaluate the sublingual microcirculation using sidestream darkfield imaging in (1) outpatients with confirmed dengue (2) patients hospitalized with dengue and (3) outpatients with other febrile illness (OFI). We estimated the glycocalyx degradation by measuring the perfused boundary region (PBR hf) and an overall microvascular health score (MVHS) with the software application GlycoCheckTM at enrolment, 48 h later and hospital discharge/defervescence. We measured plasma syndecan1 and endocan at the same time-points. We compared PBR hf, MVHS, syndecan1 and endocan, between (1) outpatients with confirmed dengue vs. OFI and (2) patients with dengue subdivided by clinical severity of plasma leak. Results: We included 75 patients with dengue (41 outpatients, 15 inpatients, 19 in intensive care) and 12 outpatients with OFI. Images from 45 patients were analyzed using GlycoCheckTM. There was no significant difference in PBR hf or MVHS between outpatients with dengue and OFI. Median plasma syndecan1 was not significantly different in outpatients with dengue vs. OFI, while median plasma endocan was significantly lower among patients with dengue vs. OFI during the critical phase. In patients with dengue, PBR hf was higher in patients with Grade 2 vs. Grade 0 plasma leakage during the critical phase (PBR hf 1.96 vs. 1.36 μm for Grade 2 vs. Grade 0 plasma leakage on days 4–6, respectively, p < 0.001). Median levels of plasma syndecan1 and endocan were higher in Grade 2 vs. Grade 0 plasma leakage, especially during the critical phase (Syndecan1 2,613.8 vs. 125.9 ng/ml for Grade 2 vs. Grade 0 plasma leakage on days 4–6, respectively, p < 0.001, and endocan 3.21 vs. 0.16 ng/ml for Grade 2 vs. Grade 0 plasma leakage on days 4–6, respectively). Conclusions: We present the first human in vivo evidence of glycocalyx disruption in dengue, with worse visual glycocalyx damage and higher plasma degradation products associated with more severe plasma leak

Immunization with lytic polysaccharide monooxygenase CbpD induces protective immunity against Pseudomonas aeruginosa pneumonia

publishedVersio

Immunization with apical membrane antigen 1 confers sterile infection-blocking immunity against Plasmodium sporozoite challenge in a rodent model

Apical membrane antigen 1 (AMA-1) is a leading blood-stage malaria vaccine candidate. Consistent with a key role in erythrocytic invasion, AMA-1-specific antibodies have been implicated in AMA-1-induced protective immunity. AMA-1 is also expressed in sporozoites and in mature liver schizonts where it may be a target of protective cell-mediated immunity. Here, we demonstrate for the first time that immunization with AMA-1 can induce sterile infection-blocking immunity against Plasmodium sporozoite challenge in 80% of immunized mice. Significantly higher levels of gamma interferon (IFN-γ)/interleukin-2 (IL-2)/tumor necrosis factor (TNF) multifunctional T cells were noted in immunized mice than in control mice. We also report the first identification of minimal CD8 and CD4 T cell epitopes on Plasmodium yoelii AMA-1. These data establish AMA-1 as a target of both preerythrocytic- and erythrocytic-stage protective immune responses and validate vaccine approaches designed to induce both cellular and humoral immunity

A modified Sequential Organ Failure Assessment score for dengue: development, evaluation and proposal for use in clinical trials

Background Dengue is a neglected tropical disease, for which no therapeutic agents have shown clinical efficacy to date. Clinical trials have used strikingly variable clinical endpoints, which hampers reproducibility and comparability of findings. We investigated a delta modified Sequential Organ Failure Assessment (delta mSOFA) score as a uniform composite clinical endpoint for use in clinical trials investigating therapeutics for moderate and severe dengue. Methods We developed a modified SOFA score for dengue, measured and evaluated its performance at baseline and 48 h after enrolment in a prospective observational cohort of 124 adults admitted to a tertiary referral hospital in Vietnam with dengue shock. The modified SOFA score included pulse pressure in the cardiovascular component. Binary logistic regression, cox proportional hazard and linear regression models were used to estimate association between mSOFA, delta mSOFA and clinical outcomes. Results The analysis included 124 adults with dengue shock. 29 (23.4%) patients required ICU admission for organ support or due to persistent haemodynamic instability: 9/124 (7.3%) required mechanical ventilation, 8/124 (6.5%) required vasopressors, 6/124 (4.8%) required haemofiltration and 5/124 (4.0%) patients died. In univariate analyses, higher baseline and delta (48 h) mSOFA score for dengue were associated with admission to ICU, requirement for organ support and mortality, duration of ICU and hospital admission and IV fluid use. Conclusions The baseline and delta mSOFA scores for dengue performed well to discriminate patients with dengue shock by clinical outcomes, including duration of ICU and hospital admission, requirement for organ support and death. We plan to use delta mSOFA as the primary endpoint in an upcoming host-directed therapeutic trial and investigate the performance of this score in other phenotypes of severe dengue in adults and children

BLOOM: A 176B-Parameter Open-Access Multilingual Language Model

Large language models (LLMs) have been shown to be able to perform new tasks based on a few demonstrations or natural language instructions. While these capabilities have led to widespread adoption, most LLMs are developed by resource-rich organizations and are frequently kept from the public. As a step towards democratizing this powerful technology, we present BLOOM, a 176B-parameter open-access language model designed and built thanks to a collaboration of hundreds of researchers. BLOOM is a decoder-only Transformer language model that was trained on the ROOTS corpus, a dataset comprising hundreds of sources in 46 natural and 13 programming languages (59 in total). We find that BLOOM achieves competitive performance on a wide variety of benchmarks, with stronger results after undergoing multitask prompted finetuning. To facilitate future research and applications using LLMs, we publicly release our models and code under the Responsible AI License

Function and regulation of TLR9

Macrophages, dendritic cells and B cells detect bacterial DNA containing unmethylated CpG motifs via Toll-like receptor 9 (TLR9) and respond by producing proinflammatory mediators such as IL-6, IL-12 and TNF, and upregulating cell surface expression of co-stimulatory molecules. These properties can be mimicked by synthetic oligonucleotides (ODNs) that contain an unmethylated CG dinucleotide that is flanked by appropriate 5’ and 3’ sequences, but other motifs in DNA can actually inhibit cellular responses to stimulatory CpG DNA. Chapter 3 aimed to characterize the inhibitory effects of different classes of inhibitory ODNs by investigating their mode of action and their specificity for TLR9 versus other TLR family members. G-rich inhibitory ODNs had the greatest specificity as TLR9 inhibitors, but these ODN also partially antagonized responses to the TLR1/2 ligand, Pam3Cys. Whilst it is well documented that TLR9 is required for anti-viral responses and is the receptor for bacterial DNA, at the commencement of this thesis no studies had assessed the function of TLR9 in bacterial infection models. Chapter 4 investigated the function of TLR9 in the macrophage response to S. typhimurium. Whilst Salmonella-induced cytokine production did not depend on TLR9, intracellular S. typhimurium bacterial loads were enhanced in TLR9-deficient bone marrow-derived macrophages (BMMs), implying a role in the anti-microbial response. G-rich inhibitory ODN, which suppressed TLR9 signalling, also greatly enhanced intracellular bacterial loads, but intriguingly this effect was TLR9-independent. Thus, inhibitory ODNs, which have been proposed as therapeutic agents for the treatment of chronic inflammatory disease, have TLR9-independent effects that may compromise the host response to bacterial pathogens. Due to their ability to potently activate the innate immune system and direct development of the acquired response, bacterial products have therapeutic potential as vaccine adjuvants. CpG DNA has been widely pursued as a vaccine adjuvant because it activates innate immune cells, primes Th1 responses and is relatively non-toxic in vivo. The major macrophage growth factor, macrophage colony stimulating factor (MCSF/ CSF-1) is a potent inhibitor of TLR9 expression and CpG DNA responsiveness in mouse macrophages. Chapter 5 therefore explored the hypothesis that antagonism of CSF-1 action would enhance CpG DNA efficacy. AFS98, a monoclonal antibody against the CSF-1R, amplified TLR9 expression in CSF-1-replete BMM and amplified expression of CSF-1-repressed genes in vivo. AFS98 also amplified CpG DNA responses in vivo, although this effect was highly variable between experiments. To examine if antagonizing CSF-1 action in human cells mimics the effects that were apparent in the mouse, the regulation of TLR9 expression by CSF-1 in human monocytes and macrophages was also assessed. The effects were variable, but at least in some donors, TLR9 mRNA expression was inhibited by CSF-1 in human monocytes and during monocyte to macrophage differentiation. In summary, this thesis explored the hypotheses that TLR9 function could be manipulated for therapeutic applications and that TLR9 plays a role in the host response to bacterial pathogens. v

Les Travaux sur le champ littéraire. Enjeux, acquis, perspectives

Infectious diseases remain a leading global cause of morbidity and mortality and there is an urgent need for effective approaches to develop vaccines, especially against complex pathogens. The availability of comprehensive genomic, proteomic and transcriptomic datasets has shifted the paradigm of vaccine development from microbiological to sequence-based approaches. However, how to effectively translate raw data into candidate vaccines is not yet obvious. Herein, we review cutting-edge technologies and screening strategies to mine genomic sequence information for state-of-the-art rational vaccine design, and highlight recent trends. Interdisciplinary approaches which cross the traditional boundaries of genomics, molecular biology, cell biology, immunology and computer science, and which prioritise antigens according to clinically relevant criteria, offer potential solutions to the widespread threat that complex pathogens pose to public health

Novel Plasmodium antigens identified via genome-based antibody screen induce protection associated with polyfunctional T cell responses

The development of vaccines against complex intracellular pathogens, such as Plasmodium spp., where protection is likely mediated by cellular immune responses, has proven elusive. The availability of whole genome, proteome and transcriptome data has the potential to advance rational vaccine development but yet there are no licensed vaccines against malaria based on antigens identified from genomic data. Here, we show that the Plasmodium yoelii orthologs of four Plasmodium falciparum proteins identified by an antibody-based genome-wide screening strategy induce a high degree of sterile infection-blocking protection against sporozoite challenge in a stringent rodent malaria model. Protection increased in multi-antigen formulations. Importantly, protection was highly correlated with the induction of multifunctional triple-positive T cells expressing high amounts of IFN-γ, IL-2 and TNF. These data demonstrate that antigens identified by serological screening are targets of multifunctional cellular immune responses that correlate with protection. Our results provide experimental validation for the concept of rational vaccine design from genomic sequence data