Enterome (France)

BackgroundEOADR1–19/SPENCER study is a phase 1/2 trial of EO2401, evaluating the combination of EO2401 with nivolumab, for the treatment of patients with locally advanced or metastatic adrenocortical carcinoma (ACC) or malignant pheochromocytoma/paraganglioma (MPP). EO2401 is a novel immunotherapy designed to activate memory T cells specific to gut microbiota derived peptides crossreacting with tumor-associated antigens (TAAs). EO2401 comprises three HLA-A2 restricted peptides derived from commensal proteins (EO2316, EO2317 and EO2318), mimicking three TAAs overexpressed in adrenal tumors: IL13RA2, BIRC5 and FOXM1. The study (NCT04187404) was approved by all participating institution’s Ethics Boards.MethodsBlood samples were collected at baseline, every two weeks during the first 3 months, then every month until disease progression. Immune response in cryopreserved PBMCs was investigated using tetramer staining and IFNγ ELISpot ex vivo and after in vitro stimulation (IVS). The functionality of specific CD8+T cells was also studied through cytotoxic T-cell based killing assays using T2 cells and intracellular cytokine staining (ICS) after IVS.ResultsThe efficacy of EO2401 in generating immune responses against TAAs was studied ex vivo or after IVS. Commensal-specific T cells were detected through tetramer staining against at least one peptide in 92% of tested patients (35/38) while TAA specific T cells were observed in 88% of tested patients (32/36). Positivity could be detected as early as two weeks after the treatment initiation (with 1 injection) and maintained for at least 20 months (longer follow up). The most immunogenic peptides were EO2317 and EO2318 with 80% and 72% of responding patients respectively. Lower immunogenicity was observed for EO2316. Moreover, when investigated using IFNγ ELISpot, 87% and 80% of patients showed functional T cells against the pool of commensal-derived peptides or of TAAs. Notably, generated antigen specific CD8+ T cells observed ex vivo displayed a memory phenotype (TEM and TEMRA). Finally, cytotoxic killing assays using T2 cells loaded with commensal-derived peptides, showed that to date, 3 out of 4 patients tested presented a specific killing of T2 cells correlated with a strong capacity of cytokine production (ICS) after IVS.ConclusionsEO2401, in combination with nivolumab induces fast, strong and long-lasting immune response, with detection of bacterial peptide- and TAA- specific functional CD8+ T cells in almost all patients. These results highlight the potential of this innovative approach to overcome the limitations of current cancer vaccine strategies.Ethics ApprovalThe study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Ethics Committee of CPP Ouest II Angers – France (ref 19.10.18.72055 – 2020/25); the Ethics Committee of Hospital Universitari Vall d’Hebron - Spain; the Ethics Committee of Universität Würzburg - Germany (ref 264/19_m); the Ethics Committee of Di Brescia – Italy; the Ethics Committee from the Center for Regional Udvikling – Denmark (ref: H-20003010); the CCMO – Netherlands (ref: CCMO20.021/JvG/rm/71766); the Överklagandenämnden för etikprövning – Sweden (Dnr 34–2020/3.1) and the Institutional Review Board from the Office of Human subject Protection of MD Anderson Center (IRB ID: 2020–0054).ConsentAll subjects gave their informed consent for inclusion before participating in the study

2020 Background: EO2401 was designed to activate/expand existing memory T cells recognizing specific protein sequences from gut bacteria, which cross-react with tumor associated antigens (TAAs). E contains 3 CD8 HLA-A2 epitopes with mimicry to GB-TAAs (IL13Rα2, BIRC5, and FOXM1) and the CD4 epitope UCP2. Methods: Patients (pt) at 1st progression GB received E (300 µg/peptide, q2w x4 then q4w) with N (3 mg/kg q2w) in cohorts: 1a E x2 → EN; 2a/1, 2a/2 and 2b EN from start; 2c EN x2 → surgery → EN; 3/1 and 3/2 EN + B (10mg/kg q2w) (Table). Results: Among 100 treated pt EN+/-B was well tolerated, with E associated events limited to local skin reactions (45% of pt; 96% Grades 1/2, and 4% Grade 3) and N-/B-tox consistent with historical data. EN induced immune response against all 3 mimics in 94% of 35 tested pt (all pt responded against at least 2 mimics), detectable as early as 2 weeks after first EN, and with durations beyond 10 months. Cross-reactivity against human peptides found in 89%. Conclusions: EN +/- B was well tolerated and generated fast and durable immune responses. EN survival like current standards. Delayed N was not advantageous for outcome. sLDB increased trt duration of EN, and improved efficacy. Continuous B plus EN further improved efficacy. Neo-/adjuvant EN was clinically feasible. Updated data, including C3/2 to confirm C3/1, to be presented. Clinical trial information: NCT04116658 . [Table: see text]

Non-alcoholic fatty liver disease (NAFLD) affects about 20–40% of the adult population in high-income countries and is now a leading indication for liver transplantation and can drive to hepatocellular carcinoma. The link between gut microbiota dysbiosis and NAFLD is now clearly established. Through analyses of the gut microbiota with shotgun metagenomics, we observed that compared to healthy controls, Adlercreutzia equolifaciens is depleted in patients with liver diseases such as NAFLD. Its abundance also decreases as the disease progresses and eventually disappears in the last stages indicating a strong association with disease severity. Moreover, we show that A. equolifaciens possesses anti-inflammatory properties, both in vitro and in vivo in a humanized mouse model of NAFLD. Therefore, our results demonstrate a link between NAFLD and the severity of liver disease and the presence of A. equolifaciens and its anti-inflammatory actions. Counterbalancing dysbiosis with this bacterium may be a promising live biotherapeutic strategy of liver diseases..

We consider the problem of incorporating evolutionary information (e.g., taxonomic or phylogenic trees) in the context of metagenomics differential analysis. Recent results published in the literature propose different ways to leverage the tree structure to increase the detection rate of differentially abundant taxa. Here, we propose instead to use a different hierarchical structure, in the form of a correlation-based tree, as it may capture the structure of the data better than the phylogeny. We first show that the correlation tree and the phylogeny are significantly different before turning to the impact of tree choice on detection rates. Using synthetic data, we show that the tree does have an impact: smoothing p-values according to the phylogeny leads to equal or inferior rates as smoothing according to the correlation tree. However, both trees are outperformed by the classical, non-hierarchical, Benjamini–Hochberg (BH) procedure in terms of detection rates. Other procedures may use the hierarchical structure with profit but do not control the False Discovery Rate (FDR) a priori and remain inferior to a classical Benjamini–Hochberg procedure with the same nominal FDR. On real datasets, no hierarchical procedure had significantly higher detection rate that BH. Intuition advocates that the use of hierarchical structures should increase the detection rate of differentially abundant taxa in microbiome studies. However, our results suggest that current hierarchical procedures are still inferior to standard methods and more effective procedures remain to be invented.

Abstract Background Tumour necrosis factor α-like ligand 1A (TL1A) acts as a synergistic cytokine that amplifies pro-inflammatory signals to increase T-cell, natural killer (NK) cell, and innate lymphoid cell production of cytokines, which are thought to be key drivers of inflammatory bowel disease (IBD) and intestinal fibrosis. The recent Phase 2a TUSCANY study demonstrated the efficacy of PF-06480605, a fully human immunoglobulin G1 monoclonal antibody targeting TL1A, in the treatment of participants with moderate to severe active Ulcerative Colitis (UC). Here, we present transcriptomic analysis of intestinal tissue biopsies and metagenomic analysis of the faecal microbiome to further evaluate the treatment effect of PF-06480605. Methods The Phase 2a, open-label, multicentre, single-arm TUSCANY study (NCT02840721) evaluated the safety, tolerability and efficacy of PF-06480605 in participants with moderate to severe UC. Participants received 500 mg intravenous (IV) PF-06480605 every 2 weeks (Q2W) for a total of 7 doses, with a 14-week follow-up period. We performed RNA sequencing of colonic biopsies and metagenomic sequencing (>40 million reads per sample) of faecal samples taken prior to and after 12 weeks of therapy. Differential expression and cell subset deconvolution by CytoReason were used to identify genes and immune cells involved in response to therapy. Differential abundance analyses based on taxonomic profiling was performed using the GOTTCHA metagenome mapping algorithm to discover whether microbial taxa changed in response to treatment. Results Tissue transcriptomic analysis identified a robust inhibition of adaptive (Th1, Th2 and Th17) and innate (macrophage) inflammatory pathways known to be associated with UC pathogenesis and a significant reduction in fibrosis-associated pathways (MMP3, MMP7 and MMP10). Transcriptomic responses were most pronounced in participants achieving endoscopic improvement (Mayo endoscopic subscore of ≤1). A candidate baseline gene signature was predictive of endoscopic improvement (area under the curve [AUC] 0.75; p-value = 0.03). Metagenomic analysis revealed a significant reduction in inflammatory pathobiont species (S. salivarius, S. parasanguinis, and H. parainfluenzae) following treatment. Conclusion These results provide insight into the molecular and microbial mechanisms underlying the efficacy of anti-TL1A therapy for UC. We defined a baseline transcriptomic signature to predict response and a pathobiont treatment signature. These findings may enable the development of precision medicine strategies for anti-TL1A therapy in the treatment of intestinal inflammation.

MotivationAnalysis toolkits for shotgun metagenomic data achieve strain-level characterization of complex microbial communities by capturing intra-species gene content variation. Yet, these tools are hampered by the extent of reference genomes that are far from covering all microbial variability, as many species are still not sequenced or have only few strains available. Binning co-abundant genes obtained from de novo assembly is a powerful reference-free technique to discover and reconstitute gene repertoire of microbial species. While current methods accurately identify species core parts, they miss many accessory genes or split them into small gene groups that remain unassociated to core clusters.ResultsWe introduce MSPminer, a computationally efficient software tool that reconstitutes Metagenomic Species Pan-genomes (MSPs) by binning co-abundant genes across metagenomic samples. MSPminer relies on a new robust measure of proportionality coupled with an empirical classifier to group and distinguish not only species core genes but accessory genes also. Applied to a large scale metagenomic dataset, MSPminer successfully delineates in a few hours the gene repertoires of 1661 microbial species with similar specificity and higher sensitivity than existing tools. The taxonomic annotation of MSPs reveals microorganisms hitherto unknown and brings coherence in the nomenclature of the species of the human gut microbiota. The provided MSPs can be readily used for taxonomic profiling and biomarkers discovery in human gut metagenomic samples. In addition, MSPminer can be applied on gene count tables from other ecosystems to perform similar analyses.Availability and implementationThe binary is freely available for non-commercial users at www.enterome.com/downloads.Supplementary informationSupplementary data are available at Bioinformatics online.

Added support for interleaved paired-end FASTQ inputs (--interleaved) Now reports MREVERSE SAM flag for unaligned end when only one end of a pair aligns Fixed issue where first character of some read names was omitted from SAM output when using tabbed input formats Added --sam-no-qname-trunc option, which causes entire read name, including spaces, to be written to SAM output. This violates SAM specification, but can be useful in applications that immediately postprocess the SAM. Fixed compilation error caused by pointer comparison issue in aligner_result.cpp Removed termcap and readline dependencies introduced in v2.3.1 Fixed compilation issues caused by gzbuffer function when compiling with zlib v1.2.3.5 and earlier. Users compiling against these libraries will use the zlib default buffer size of 8Kb when decompressing read files. Fixed issue that would cause Bowtie 2 hang when aligning FASTA inputs with more than one thread

Smoking has a negative impact on Crohn's disease (CD), but the mechanisms underlying this association are unclear. We compared the gut microbiota composition of smoking with nonsmoking patients with CD using a metagenomic approach. Stool samples and clinical data were collected from current smokers and nonsmokers with CD from France and the Netherlands, matched for country, gender, age, disease activity, and body mass index. Fecal DNA was sequenced on an Illumina HiSeq 2500. On average, 40 million paired-end reads were generated per sample. Gene richness and the Shannon index were computed to assess microbial diversity. Wilcoxon's signed-rank tests for paired samples were performed to detect differences between the 2 groups. In total, 21 smoking and 21 nonsmoking patients with CD were included. Compared with nonsmoking patients, gut microbial gene richness (P = 0.01), genus diversity (P < 0.01), and species diversity (P = 0.01) were decreased in smoking patients. This was accompanied by a reduced relative abundance of the genera Collinsella (P = 0.02), Enterorhabdus (P = 0.02), and Gordonibacter (P = 0.02) in smokers. No statistically significant differences at the species level were observed, although smokers had lower proportions of Faecalibacterium prausnitzii (P = 0.10). Gut microbial diversity is reduced in smokers with CD compared with nonsmokers with CD. The microbial profile differs between these groups at the genus level. Future studies should evaluate whether intestinal microbes mediate the adverse effects of smoking in CD.