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Despite the availability of batch effect correcting algorithms (BECA), no comprehensive tool that combines batch correction and evaluation of the results exists for microbiome datasets. This work outlines the Microbiome Batch Effects Correction Suite development that integrates several BECAs and evaluation metrics into a software package for the statistical computation framework R.

Supplementary Data from Therapy-Related Transcriptional Subtypes in Matched Primary and Recurrent Head and Neck Cancer

Supplementary Table from Therapy-Related Transcriptional Subtypes in Matched Primary and Recurrent Head and Neck Cancer

Purpose:The genetic relatedness between primary and recurrent head and neck squamous cell carcinomas (HNSCC) reflects the extent of heterogeneity and therapy-driven selection of tumor subpopulations. Yet, current treatment of recurrent HNSCC ignores the molecular characteristics of therapy-resistant tumor populations.Experimental Design:From 150 tumors, 74 primary HNSCCs were RNA sequenced and 38 matched primary/recurrent tumor pairs were both whole-exome and RNA sequenced. Transcriptome analysis determined the predominant classical (CL), basal (BA), and inflamed-mesenchymal (IMS) transcriptional subtypes according to an established classification. Genomic alterations and clonal compositions of tumors were evaluated from whole-exome data.Results:Although CL and IMS subtypes were more common in primary HNSCC with low recurrence rates, the BA subtype was more prevalent and stable in recurrent tumors. The BA subtype was associated with a transcriptional signature of partial epithelial-to-mesenchymal transition (p-EMT) and early recurrence. In 44% of matched cases, the dominant subtype changed from primary to recurrent tumors, preferably from IMS to BA or CL. Expression analysis of prognostic gene sets identified upregulation of hypoxia, p-emt, and radiotherapy resistance signatures and downregulation of tumor inflammation in recurrences compared with index tumors. A relevant subset of primary/recurrent tumor pairs presented no evidence for a common clonal origin.Conclusions:Our study showed a high degree of genetic and transcriptional heterogeneity between primary/recurrent tumors, suggesting therapy-related selection of a transcriptional subtype with characteristics unfavorable for therapy. We conclude that therapy decisions should be based on genetic and transcriptional characteristics of recurrences rather than primary tumors to enable optimally tailored treatment strategies.

Supplementary Figure from Therapy-Related Transcriptional Subtypes in Matched Primary and Recurrent Head and Neck Cancer

IntroductionHematologic malignancies are currently underrepresented in multidisciplinary molecular-tumor-boards (MTB). This study assesses the potential of precision-oncology in primary-refractory plasmablastic-lymphoma (prPBL), a highly lethal blood cancer.MethodsWe evaluated clinicopathological and molecular-genetic data of 14 clinically annotated prPBL-patients from initial diagnosis. For this proof-of-concept study, we employed our certified institutional MTB-pipeline (University-Cancer-Center-Schleswig-Holstein, UCCSH) to annotate a comprehensive dataset within the scope of a virtual MTB-setting, ultimately recommending molecularly stratified therapies. Evidence-levels for MTB-recommendations were defined in accordance with the NCT/DKTK and ESCAT criteria.ResultsMedian age in the cohort was 76.5 years (range 56-91), 78.6% of patients were male, 50% were HIV-positive and clinical outcome was dismal. Comprehensive genomic/transcriptomic analysis revealed potential recommendations of a molecularly stratified treatment option with evidence-levels according to NCT/DKTK of at least m2B/ESCAT of at least IIIA were detected for all 14 prPBL-cases. In addition, immunohistochemical-assessment (CD19/CD30/CD38/CD79B) revealed targeted treatment-recommendations in all 14 cases. Genetic alterations were classified by treatment-baskets proposed by Horak et al. Hereby, we identified tyrosine-kinases (TK; n=4), PI3K-MTOR-AKT-pathway (PAM; n=3), cell-cycle-alterations (CC; n=2), RAF-MEK-ERK-cascade (RME; n=2), immune-evasion (IE; n=2), B-cell-targets (BCT; n=25) and others (OTH; n=4) for targeted treatment-recommendations. The minimum requirement for consideration of a drug within the scope of the study was FDA-fast-track development.DiscussionThe presented proof-of-concept study demonstrates the clinical potential of precision-oncology, even in prPBL-patients. Due to the aggressive course of the disease, there is an urgent medical-need for personalized treatment approaches, and this population should be considered for MTB inclusion at the earliest time.

Background Colorectal cancer (CRC) is one of the most prevalent cancers, with over one million new cases per year. Overall, prognosis of CRC largely depends on the disease stage and metastatic status. As precision oncology for patients with CRC continues to improve, this study aimed to integrate genomic, transcriptomic, and proteomic analyses to identify significant differences in expression during CRC progression using a unique set of paired patient samples while considering tumour heterogeneity. Methods We analysed fresh-frozen tissue samples prepared under strict cryogenic conditions of matched healthy colon mucosa, colorectal carcinoma, and liver metastasis from the same patients. Somatic mutations of known cancer-related genes were analysed using Illumina's TruSeq Amplicon Cancer Panel; the transcriptome was assessed comprehensively using Clariom D microarrays. The global proteome was evaluated by liquid chromatography-coupled mass spectrometry (LC‒MS/MS) and validated by two-dimensional difference in-gel electrophoresis. Subsequent unsupervised principal component clustering, statistical comparisons, and gene set enrichment analyses were calculated based on differential expression results. Results Although panomics revealed low RNA and protein expression of CA1, CLCA1, MATN2, AHCYL2, and FCGBP in malignant tissues compared to healthy colon mucosa, no differentially expressed RNA or protein targets were detected between tumour and metastatic tissues. Subsequent intra-patient comparisons revealed highly specific expression differences (e.g., SRSF3, OLFM4, and CEACAM5) associated with patient-specific transcriptomes and proteomes. Conclusion Our research results highlight the importance of inter- and intra-tumour heterogeneity as well as individual, patient-paired evaluations for clinical studies. In addition to changes among groups reflecting CRC progression, we identified significant expression differences between normal colon mucosa, primary tumour, and liver metastasis samples from individuals, which might accelerate implementation of precision oncology in the future.

High-grade B-cell lymphoma accompanied with double/triple-hit MYC and BCL2 and/or BCL6 rearrangements (HGBLDH/ TH) poses a cytogenetically-defined provisional entity among aggressive B-cell lymphomas that is traditionally associated with unfavorable prognosis. In order to better understand the mutational and molecular landscape of HGBLDH/ TH we here performed whole-exome sequencing and deep panel next-generation sequencing of 47 clinically annotated cases. Oncogenic drivers, mutational signatures and perturbed pathways were compared with data from follicular lymphoma (FL), diffuse large B-cell lymphoma (DLBCL) and Burkitt lymphoma (BL). We find an accumulation of oncogenic mutations in NOTCH, IL6/JAK/STAT and NFκB signaling pathways and delineate the mutational relationship within the continuum between FL/DLBCL, HGBL-DH/TH and BL. Further, we provide evidence of a molecular divergence between BCL2 and BCL6 rearranged HGBL-DH. Beyond a significant congruency with the C3/EZB DLBCL cluster in BCL2 rearranged cases on an exome-wide level, we observe an enrichment of the SBS6 mutation signature in BCL6 rearranged cases. Differential gene set enrichment and subsequent network propagation analysis according to cytogenetically defined subgroups revealed an impairment of TP53 and MYC pathway signaling in BCL2 rearranged cases, whereas BCL6 rearranged cases lacked this enrichment, but instead showed impairment of E2F targets. Intriguingly, HGBL-TH displayed intermediate mutational features considering all three aspects. This study elucidates a recurrent pattern of mutational events driving FL into MYC-driven BCL2-rearranged HGBL, unveiling the mutational pathogenesis of this provisional entity. Through this refinement of the molecular taxonomy for aggressive, germinal center-derived B-cell lymphomas, this calls into question the current World Health Organization classification system, especially regarding the status of MYC/BCL6- rearranged HGBL.

GEP-NETs are heterogeneous tumors originating from the pancreas (panNET) or the intestinal tract. Only a few patients with NETs are amenable to curative tumor resection, and for most patients, only palliative treatments to successfully control the disease or manage symptoms remain, such as with synthetic somatostatin (SST) analogs (SSAs), such as octreotide (OCT) or lanreotide (LAN). However, even cells expressing low levels of SST receptors (SSTRs) may exhibit significant responses to OCT, which suggests the possibility that SSAs signal through alternative mechanisms, e.g., transforming growth factor (TGF)-β. This signaling mode has been demonstrated in the established panNET line BON but not yet in other permanent (i.e., QGP) or primary (i.e., NT-3) panNET-derived cells. Here, we performed qPCR, immunoblot analyses, and cell counting assays to assess the effects of SST, OCT, LAN, and TGF-β1 on neuroendocrine marker expression and cell proliferation in NT-3, QGP, and BON cells. SST and SSAs were found to regulate a set of neuroendocrine genes in all three cell lines, with the effects of SST, mainly LAN, often differing from those of OCT. However, unlike NT-3 cells, BON cells failed to respond to OCT with growth arrest but paradoxically exhibited a growth-stimulatory effect after treatment with LAN. As previously shown for BON, NT-3 cells responded to TGF-β1 treatment with induction of expression of SST and SSTR2/5. Of note, the ability of NT-3 cells to respond to TGF-β1 with upregulation of the established TGF-β target gene SERPINE1 depended on cellular adherence to a collagen-coated matrix. Moreover, when applied to NT-3 cells for an extended period, i.e., 14 days, TGF-β1 induced growth suppression as shown earlier for BON cells. Finally, next-generation sequencing-based identification of microRNAs (miRNAs) in BON and NT-3 revealed that SST and OCT impact positively or negatively on the regulation of specific miRNAs. Our results suggest that primary panNET cells, such as NT-3, respond similarly as BON cells to SST, SSA, and TGF-β treatment and thus provide circumstantial evidence that crosstalk of SST and TGF-β signaling is not confined to BON cells but is a general feature of panNETs.

Colorectal cancer (CRC) is one of the most prevalent cancers, with over one million new cases. The prognosis of CRC considerably depends on the disease stage and metastatic status. As precision oncology for patients with CRC continues to improve, this study aims to integrate genomic, transcriptomic, and proteomic analyses to identify significant expression differences during colorectal progression using a unique set of paired patient samples concerning tumor heterogeneity.We analyzed fresh-frozen tissue samples of matched healthy colon mucosa, colorectal carcinoma, and liver metastasis from same patients prepared under strict cryogenic conditions. While somatic mutations of known cancer-related genes were analyzed using Illumina’s TruSeq Amplicon Cancer Panel, the transcriptome was assessed comprehensively using Clariom D microarrays. The global proteome was evaluated by liquid chromatography-coupled mass spectrometry (LC-MS/MS) and validated by two-dimensional difference in-gel electrophoresis. Subsequent unsupervised principal component clustering, statistical comparisons, and gene set enrichment analyses were calculated using differential expression results.While panomics revealed low RNA and protein expression of CA1, CLCA1, MATN2, AHCYL2, and FCGBP in malignant tissues compared to healthy colon mucosa, no differentially expressed RNA or protein targets were detected between tumor and metastatic tissues. Subsequent intra-patient comparisons revealed highly specific expression differences (e.g., SRSF3, OLFM4, and CEACAM5) associated with a patient-individual transcriptome and proteome.In conclusion, the results highlight the importance of inter- and intra-tumor heterogeneity alongside the individual, patient-paired evaluation for clinical studies. Next to changes among groups reflecting colorectal cancer progression, we identified significant expression differences between patient-individual normal colon mucosa, primary tumor, and liver metastasis, which could speed up the implementation of precision oncology in the future.

Impaired glucose homeostasis is a significant risk factor for cardiometabolic diseases, whereas the efficacy of available standard therapies is limited, mainly because of poor adherence. This post-marketing study assessed the glucose-lowering potential of a synbiotic-based formulation.One hundred ninety-two participants were enrolled in a digital nutrition program with continuous glucose monitoring (CGM) and received a study product comprisingSupplementation with the study product resulted in significant improvements in glucose parameters (delta values: fasting glucose -2,13% ± 8.86; iAUCThis study indicates that the synbiotic composition is an effective and convenient approach to counteract hyperglycemia. Further placebo-controlled studies are warranted to test its efficacy in the treatment of cardiometabolic diseases.

Alterations in the oral microbiota composition may influence mental health. However, linkages between compositional changes in the oral microbiota and their role in mental health among cigarette smokers remain largely unknown. In this study, we used shotgun metagenomics data for the oral microbiome of 105 participants. The data showed Bacteroidota, Fusobacteriota, Firmicutes, Proteobacteria, and Actinobacteria to be the most abundant phyla; Streptococcus, Haemophilus D, and Veillonella are the most abundant genera. Then, we clustered our subjects into avoidance and activation groups based on the behavioral activation for depression scale (BADS). Interestingly, the avoidance group exhibited a higher oral microbiome richness and diversity (alpha diversity). Differential abundance testing between BADS avoidance and activation groups showed the phyla Bacteroidota (effect size 0.5047, q = 0.0037), Campylobacterota (effect size 0.4012, q = 0.0276), Firmicutes A (effect size 0.3646, q = 0.0128), Firmicutes I (effect size 0.3581, q = 0.0268), and Fusobacteriota (effect size 0.6055, q = 0.0018) to be significantly increased in the avoidance group, but Verrucomicrobiota (effect size−0.6544, q = 0.0401), was found to be significantly decreased in the avoidance risk group. Network analysis of the 50 genera displaying the highest variation between both groups identified Campylobacter B, Centipeda, and Veillonella as hub nodes in the avoidance group. In contrast, Haemophilus and Streptococcus were identified as hub nodes in the activation group. Next, we investigated functional profiles of the oral microbiota based on BADS avoidance and activation groups and found Lysine degradations pathway was significantly enriched between both groups (ANCOM-BC, q = 0.0692). Altogether, we provide evidence for the presence of depression-related changes in the oral microbiota of smokers and possible functional contribution. The identified differences provide new information to enrich our understanding of oral microbiota-brain axis interplay and their potential impact on mental health.

BackgroundLike its human counterpart, canine atopic dermatitis (cAD) is a chronic relapsing condition; thus, most cAD-affected dogs will require lifelong treatment to maintain an acceptable quality of life. A potential intervention is modulation of the composition of gut microbiota, and in fact, probiotic treatment has been proposed and tried in human atopic dermatitis (AD) patients. Since dogs are currently receiving intensive medical care, this will be the same option for dogs, while evidence of gut dysbiosis in cAD is still missing, although skin microbial profiling in cAD has been conducted in several studies. Therefore, we conducted a comprehensive analysis of both gut and skin microbiota in cAD in one specific cAD-predisposed breed, Shiba Inu. Additionally, we evaluated the impact of commonly used medical management on cAD (Janus kinase; JAK inhibitor, oclacitinib) on the gut and skin microbiota. Furthermore, we genotyped the Shiba Inu dogs according to the mitochondrial DNA haplogroup and assessed its association with the composition of the gut microbiota.ResultsStaphylococcus was the most predominant bacterial genus observed in the skin; Escherichia/Shigella and Clostridium sensu stricto were highly abundant in the gut of cAD-affected dogs. In the gut microbiota, Fusobacteria and Megamonas were highly abundant in healthy dogs but significantly reduced in cAD-affected dogs. The abundance of these bacterial taxa was positively correlated with the effect of the treatment and state of the disease. Oclacitinib treatment on cAD-affected dogs shifted the composition of microbiota towards that in healthy dogs, and the latter brought it much closer to healthy microbiota, particularly in the gut. Additionally, even within the same dog breed, the mtDNA haplogroup varied, and there was an association between the mtDNA haplogroup and gut microbial composition.ConclusionsDysbiosis of both the skin and the gut was observed in cAD in Shiba Inu dogs. Our findings provide a basis for the potential treatment of cAD by manipulating the gut microbiota as well as the skin microbiota.

De novo variants in the myelin regulatory factor (MYRF), a transcription factor involved in the differentiation of oligodendrocytes, have been linked recently to the cardiac and urogenital syndrome, while familiar variants are associated with nanophthalmos. Here, we report for the first time on a patient with a de novo stop-gain variant in MYRF (p.Q838*) associated with Scimitar syndrome, 46,XY partial gonadal dysgenesis (GD) and severe hyperopia. Since variants in MYRF have been described in both 46,XX and 46,XY GD, we assumed a role of MYRF in the early development of the bipotential gonad. We used publicly available single cell sequencing data of human testis and ovary from different developmental stages and analysed them for MYRF expression. We identified MYRF expression in the subset of coelomic epithelial cells at stages of gonadal ridge development in 46,XX and 46,XY individuals. Differential gene expression analysis revealed significantly upregulated genes. Within these, we identified CITED2 as a gene containing a MYRF binding site. It has been shown that Cited2−/− mice have gonadal defects in both testis and ovary differentiation, as well as defects in heart development and establishment of the left–right axis. This makes MYRF a potential candidate as an early regulator of gonadal and heart development via upregulation of the transcriptional cofactor CITED2.

Squats are rather complex failure mechanisms in rails and challenge railway operators all over the world, thus calling for a detailed investigation of squats by means of finite element analysis to locate the initiation and propagating mechanisms. In this work, a cyclic three-dimensional (3D) finite element model of a wheel-rail contact including an initial penny-shaped defect is used. This work presents the implementation of the starting penny-shaped crack in the rail for a wheel-rail simulation by utilising a submodel strategy. Moreover, viable evaluation options are shown. In the future, this set-up will help to assess multiple crack positions and possible squat growth mechanisms.

Onychomycosis (OM) is a common fungal nail infection. Based on the rich mycobial diversity in healthy toenails, we speculated that this is lost in OM due to the predominance of a single pathogen. We used next generation sequencing to obtain insights into the biodiversity of fungal communities in both healthy individuals and OM patients. By sequencing, a total of 338 operational-taxonomic units were found in OM patients and healthy controls. Interestingly, a classifier distinguished three distinct subsets: healthy controls and two groups within OM patients with either a low or high abundance of Trichophyton. Diversity per sample was decreased in controls compared to cases with low Trichophyton abundance (LTA), while cases with a high Trichophyton abundance (HTA) showed a lower diversity. Variation of mycobial communities between the samples showed shifts in the community structure between cases and controls—mainly driven by HTA cases. Indeed, LTA cases had a fungal β-diversity undistinguishable from that of healthy controls. Collectively, our data provides an in-depth characterization of fungal diversity in health and OM. Our findings also suggest that onychomycosis develops either through pathogen-driven mechanisms, i.e., in HTA cases, or through host and/or environmental factors, i.e., in cases with a low Trichophyton abundance.

Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is an aggressive malignancy assumed to originate from plasmacytoid dendritic cells (pDCs), which mostly affects the skin, bone marrow, lymph nodes and sequentially other organ systems. RNA-, targeted- and exome sequencing studies have identified molecular characteristics, associated with BPDCN-pathogenesis, yet an integrative molecular assessment of BPDCN remains pending. Here, we combined paired WES/RNA-Seq with genome-wide copy-number analysis to characterize 47 BPDCN patients for mutational drivers, cytogenetic aberrations and gene-expression profiles. We identified alterations in epigenetic regulators (TET2, EP300, DNMT3A, SF3B1, EZH2) and a mutational disruption of RTK-RAS signaling (NF1, NRAS, EGFR) as drivers of BPDCN alongside deletions of tumor suppressors (CDKN2A, RB1, TP53), amplifications of oncogenes (IDH2, MET, EZH2) and recurrent fusions (MYB, ALK). The mutational landscape further provides evidence for frequent induction of PDGF signaling and extracellular matrix interactions as well as a gender specificity and a subset of MSIhigh patients. Many genes affected in BPDCN are shared with chronic myelomonocytic leukemia (CMML), emphasizing a close relationship between these entities and to a lesser extent with acute myeloid leukemia (AML). Ontological assessment of RNA-Seq data revealed two BPDCN subtypes, a typical pDC-derived subtype (C1) and a (common) cDC-enriched subtype (C2), which were then shown to exhibit distinct mutational (EP300, ARID2, NF1 mutations in typical pDC vs. DNMT3A, SRSF2 mutations in the cDC-enriched subtype) and clinical features.In summary, our hitherto most comprehensive characterization of BPDCN reveals molecular hallmarks alongside actionable vulnerabilities and highlights two novel subtypes that are molecularly and clinically distinct.Key Points-Paired WES/RNA-Seq and copy number analysis of a large BPDCN cohort reveals two molecularly and clinically distinct subtypes.-Multi-omics identify recurrent therapeutic targets and vulnerabilities including MSIhigh and mutations within epigenetic regulation of gene expression and RTK-RAS signaling.

It is well-appreciated that the diet is a crucial tool to counteract cardiometabolic disturbances due to its impact on blood glucose concentration and gut microbiome. This retrospective analysis aimed to examine whether the inclusion of isomaltulose and prebiotic inulin-type fructans (ITF) into the habitual diet has an impact on glycemic control and gut microbiota. Furthermore, we examined interindividual differences in glycemic response to sugar replacement with isomaltulose. We retrospectively analyzed data of 117 individuals who participated in a digital nutrition program including a 14-day continuous glucose measurement. Participants underwent six test days with sweetened drinks (isomaltulose vs. sucrose) consumed with their usual breakfasts and lunches. Dinner was supplemented with ITF for 11 days. Postprandial glycemia and 24 h-glycemic variability were determined following test meals and days, respectively. Fecal microbiota was analyzed by 16S rRNA sequencing before and after test phase. Meals with isomaltulose-sweetened drinks compared to meals with sucrose-sweetened drinks induced lower postprandial glycemia. Moreover, glucose oscillations over 24 h were lower on isomaltulose when compared to sucrose test days and improved further during ITF supplementation. Furthermore, ITF modulated gut microbiota composition beneficially. Responder analysis revealed that 72% of participants benefited from the sugar replacement with isomaltulose and that their gut microbiota differed from the low responders. Taken together, the incorporation of isomaltulose and ITF into the habitual diet was shown to be an effective strategy to improve glucose control and beneficially modulate gut microbiota, and thereby aid to maintain metabolic health. Data indicate interindividual differences in glycemic response to ingredients and suggest that gut microbiota might be somehow related to it.

We present genomes and pupal transcriptomes of the Mediterranean flour moth

Atopic dermatitis (AD) is a multifactorial inflammatory skin disease and an altered skin microbiota with an increase of Staphylococcus aureus has been reported. However, the role of fungi remains poorly investigated.We aimed to improve the understanding of the fungal skin microbiota, the mycobiota, in AD in relation to the bacterial colonization.Skin swabs of 16 AD patients and 16 healthy controls (HC) from four different skin sites, that is antecubital crease, dorsal neck, glabella and vertex from multiple time points were analysed by DNA sequencing of the internal transcribed spacer region 1 (ITS1) and 16S rRNA gene for fungi and bacteria, respectively.Malassezia spp. were the predominant fungi in all subjects but with a decreased dominance in severe AD patients in favour of non-Malassezia fungi, for example Candida spp. For bacteria, a decrease of Cutibacterium spp. in AD patients in favour of Staphylococcus spp., particularly S. aureus, was observed. Further, both bacterial and fungal community compositions of severe AD patients significantly differed from mild-to-moderate AD patients and HC with the latter two having overall similar microbiota showing some distinctions in bacterial communities.We conclude that severe AD is associated with a pronounced dysbiosis of the microbiota with increased fungal diversity. Potentially infectious agents, for example Staphylococcus and Candida, were increased in severe AD.

The prognosis of pancreatic ductal adenocarcinoma (PDAC) is exceedingly poor. Although surgical resection is the only curative treatment option, multimodal treatment is of the utmost importance, as only about 20% of tumors are primarily resectable at the time of diagnosis. The choice of chemotherapeutic treatment regimens involving gemcitabine and FOLFIRINOX is currently solely based on the patient’s performance status, but, ideally, it should be based on the tumors’ individual biology. We established two novel patient-derived primary cell lines from surgical PDAC specimens. LuPanc-1 and LuPanc-2 were derived from a pT3, pN1, G2 and a pT3, pN2, G3 tumor, respectively, and the clinical follow-up was fully annotated. STR-genotyping revealed a unique profile for both cell lines. The population doubling time of LuPanc-2 was substantially longer than that of LuPanc-1 (84 vs. 44 h). Both cell lines exhibited a typical epithelial morphology and expressed moderate levels of CK7 and E-cadherin. LuPanc-1, but not LuPanc-2, co-expressed E-cadherin and vimentin at the single-cell level, suggesting a mixed epithelial-mesenchymal differentiation. LuPanc-1 had a missense mutation (p.R282W) and LuPanc-2 had a frameshift deletion (p.P89X) in TP53. BRCA2 was nonsense-mutated (p.Q780*) and CREBBP was missense-mutated (p.P279R) in LuPanc-1. CDKN2A was missense-mutated (p.H83Y) in LuPanc-2. Notably, only LuPanc-2 harbored a partial or complete deletion of DPC4. LuPanc-1 cells exhibited high basal and transforming growth factor (TGF)-β1-induced migratory activity in real-time cell migration assays, while LuPanc-2 was refractory. Both LuPanc-1 and LuPanc-2 cells responded to treatment with TGF-β1 with the activation of SMAD2; however, only LuPanc-1 cells were able to induce TGF-β1 target genes, which is consistent with the absence of DPC4 in LuPanc-2 cells. Both cell lines were able to form spheres in a semi-solid medium and in cell viability assays, LuPanc-1 cells were more sensitive than LuPanc-2 cells to treatment with gemcitabine and FOLFIRINOX. In summary, both patient-derived cell lines show distinct molecular phenotypes reflecting their individual tumor biology, with a unique clinical annotation of the respective patients. These preclinical ex vivo models can be further explored for potential new treatment strategies and might help in developing personalized (targeted) therapy regimens.

Approximately 5% of the world-wide population is affected by autoimmune diseases. Overall, autoimmune diseases are still difficult to treat, impose a high burden on patients, and have a significant economic impact. Like other complex diseases, e.g., cancer, autoimmune diseases develop over several years. Decisive steps in the development of autoimmune diseases are (i) the development of autoantigen-specific lymphocytes and (often) autoantibodies and (ii) potentially clinical disease manifestation at a later stage. However, not all healthy individuals with autoantibodies develop disease manifestations. Identifying autoantibody-positive healthy individuals and monitoring and inhibiting their switch to inflammatory autoimmune disease conditions are currently in their infancy. The switch from harmless to inflammatory autoantigen-specific T and B-cell and autoantibody responses seems to be the hallmark for the decisive factor in inflammatory autoimmune disease conditions. Accordingly, biomarkers allowing us to predict this progression would have a significant impact. Several factors, such as genetics and the environment, especially diet, smoking, exposure to pollutants, infections, stress, and shift work, might influence the progression from harmless to inflammatory autoimmune conditions. To inspire research directed at defining and ultimately targeting autoimmune predisease, here, we review published evidence underlying the progression from health to autoimmune predisease and ultimately to clinically manifest inflammatory autoimmune disease, addressing the following 3 questions: (i) what is the current status, (ii) what is missing, (iii) and what are the future perspectives for defining and modulating autoimmune predisease.

In this study, T-Gamma and Wedge models have been compared with each other for the prediction of surface-initiated rolling contact fatigue cracks on rail surfaces. Both models are able to account for different observed rolling contact fatigue-wear regimes in tracks, but with very different physical backgrounds. The T-Gamma model uses empirically determined damage functions by introducing a relationship between the wear number (T-Gamma) and the rolling contact fatigue damage increment. Different rolling contact fatigue-wear regimes are considered in this empirical approach based on the idea that initiated cracks get partially or fully removed by the wear mechanism, not accounting for the full complexity of the occurring tribological phenomena. The Wedge model represents a physical approach, where contact stresses and its impact on plastic deformations and related material anisotropy are considered. Thus, the prediction of different rolling contact fatigue-wear regimes is based on these physical relationships, where plastic shear deformations in the near-surface layer play a key role. For comparison, the wheel–rail contact data from stochastic multibody dynamics simulations of a metro vehicle with conventional bogie technology running in three curve radii have been used. While the T-Gamma model always predicts the same rolling contact fatigue damage increment for a given T-Gamma value, the Wedge model shows a scattering of the predicted rolling contact fatigue damage increments when plotting them over T-Gamma because of the explicit consideration of contact stresses. Thus, each scenario consisting, for example, of certain vehicles, curve radius, wheel–rail profile combination, friction conditions, rail material, etc. needs its own damage function in the T-Gamma world. This should be kept in mind when applying the standard T-Gamma model to scenarios which differ significantly from the scenario it has been parameterised for.

It is well-appreciated that the diet is a crucial tool to counteract cardiometabolic disturbances due to its impact on blood glucose concentration and gut microbiome. This retrospective analysis aimed to examine whether the inclusion of isomaltulose and prebiotic inulin-type fructans (ITF) into the habitual diet has an impact on glycemic control and gut microbiota. Furthermore, we examined interindividual differences in glycemic response to sugar replacement with isomaltulose. We retrospectively analyzed data of 117 individuals who participated in a digital nutrition program including a 14-day continuous glucose measurement. Participants underwent six test days with sweetened drinks (isomaltulose vs. sucrose) consumed with their usual breakfasts and lunches. Dinner was supplemented with ITF for 11 days. Postprandial glycemia and 24 h-glycemic variability were determined following test meals and days, respectively. Fecal microbiota was analyzed by 16S rRNA sequencing before and after test phase. Meals with isomaltulose-sweetened drinks compared to meals with sucrose-sweetened drinks induced lower postprandial glycemia. Moreover, glucose oscillations over 24 h were lower on isomaltulose when compared to sucrose test days and improved further during ITF supplementation. Furthermore, ITF modulated gut microbiota composition beneficially. Responder analysis revealed that 72% of participants benefited from the sugar replacement with isomaltulose and that their gut microbiota differed from the low responders. Taken together, the incorporation of isomaltulose and ITF into the habitual diet was shown to be an effective strategy to improve glucose control and beneficially modulate gut microbiota, and thereby aid to maintain metabolic health. Data indicate interindividual differences in glycemic response to ingredients and suggest that gut microbiota might be somehow related to it.

High-grade B-cell lymphoma accompanied with double/triple-hit MYC and BCL2 and/or BCL6 rearrangements (HGBLDH/ TH) poses a cytogenetically-defined provisional entity among aggressive B-cell lymphomas that is traditionally associated with unfavorable prognosis. In order to better understand the mutational and molecular landscape of HGBLDH/ TH we here performed whole-exome sequencing and deep panel next-generation sequencing of 47 clinically annotated cases. Oncogenic drivers, mutational signatures and perturbed pathways were compared with data from follicular lymphoma (FL), diffuse large B-cell lymphoma (DLBCL) and Burkitt lymphoma (BL). We find an accumulation of oncogenic mutations in NOTCH, IL6/JAK/STAT and NFκB signaling pathways and delineate the mutational relationship within the continuum between FL/DLBCL, HGBL-DH/TH and BL. Further, we provide evidence of a molecular divergence between BCL2 and BCL6 rearranged HGBL-DH. Beyond a significant congruency with the C3/EZB DLBCL cluster in BCL2 rearranged cases on an exome-wide level, we observe an enrichment of the SBS6 mutation signature in BCL6 rearranged cases. Differential gene set enrichment and subsequent network propagation analysis according to cytogenetically defined subgroups revealed an impairment of TP53 and MYC pathway signaling in BCL2 rearranged cases, whereas BCL6 rearranged cases lacked this enrichment, but instead showed impairment of E2F targets. Intriguingly, HGBL-TH displayed intermediate mutational features considering all three aspects. This study elucidates a recurrent pattern of mutational events driving FL into MYC-driven BCL2-rearranged HGBL, unveiling the mutational pathogenesis of this provisional entity. Through this refinement of the molecular taxonomy for aggressive, germinal center-derived B-cell lymphomas, this calls into question the current World Health Organization classification system, especially regarding the status of MYC/BCL6- rearranged HGBL.

Key Points WES coupled with RNA-sequencing of a large PBL cohort reveals genetic drivers of oncogenesis in RTK-RAS, NF-kB, and JAK/STAT signaling.The mutational landscape and SCNV data emphasize the distinctness of EBV+/EBV– PBL from both DLBCL and multiple myeloma., Visual Abstract, Plasmablastic lymphoma (PBL) represents a clinically heterogeneous subtype of aggressive B-cell non-Hodgkin lymphoma. Targeted-sequencing studies and a single-center whole-exome sequencing (WES) study in HIV-positive patients recently revealed several genes associated with PBL pathogenesis; however, the global mutational landscape and transcriptional profile of PBL remain elusive. To inform on disease-associated mutational drivers, mutational patterns, and perturbed pathways in HIV-positive and HIV-negative PBL, we performed WES and transcriptome sequencing (RNA-sequencing) of 33 PBL tumors. Integrative analysis of somatic mutations and gene expression profiles was performed to acquire insights into the divergent genotype–phenotype correlation in Epstein-Barr virus–positive (EBV+) and EBV– PBL. We describe a significant accumulation of mutations in the JAK signal transducer and transcription activator (OSMR, STAT3, PIM1, and SOCS1), as well as receptor tyrosine-kinase RAS (ERBB3, NRAS, PDGFRB, and NTRK) pathways. We provide further evidence of frequent perturbances of NF-κB signaling (NFKB2 and BTK). Induced pathways, identified by RNA-sequencing, closely resemble the mutational profile regarding alterations accentuated in interleukin-6/JAK/STAT signaling, NF-κB activity, and MYC signaling. Moreover, class I major histocompatibility complex–mediated antigen processing and cell cycle regulation were significantly affected by EBV status. An almost exclusive upregulation of phosphatidylinositol 3-kinase/AKT/mTOR signaling in EBV+ PBL and a significantly induced expression of NTRK3 in concert with recurrent oncogenic mutations in EBV– PBL hint at a specific therapeutically targetable mechanism in PBL subgroups. Our characterization of a mutational and transcriptomic landscape in PBL, distinct from that of diffuse large B-cell lymphoma and multiple myeloma, substantiates the pathobiological independence of PBL in the spectrum of B-cell malignancies and thereby refines the taxonomy for aggressive lymphomas.

Background The treatment of psoriasis has been revolutionized by the development of biologic therapies. However, the pathogenesis of psoriasis, in particular the role of the cutaneous microbiome, remains incompletely understood. Moreover, skin microbiome studies have relied heavily on 16S rRNA sequencing data in the absence of bacterial culture. Objectives To characterize and compare the cutaneous microbiome in 20 healthy controls and 23 patients with psoriasis using metagenomic analyses and to determine changes in the microbiome during treatment. Methods Swabs from lesional and nonlesional skin from patients with psoriasis, and from controls matched for site and skin microenvironment, were analysed using both 16S rRNA sequencing and traditional culture combined with mass spectrometry (MALDI-TOF) in a prospective study. Results Psoriasis was associated with an increased abundance of Firmicutes and a corresponding reduction in Actinobacteria, most marked in lesional skin, and at least partially reversed during systemic treatment. Shifts in bacterial community composition in lesional sites were reflected in similar changes in culturable bacteria, although changes in the microbiota over repeated swabbing were detectable only with sequencing. The composition of the microbial communities varied by skin site and microenvironment. Prevotella and Staphylococcus were significantly associated with lesional skin, and Anaerococcus and Propionibacterium with nonlesional skin. There were no significant differences in the amount of bacteria cultured from the skin of healthy controls and patients with psoriasis. Conclusions Shifts in the cutaneous microbiome in psoriasis, particularly during treatment, may shed new light on the pathogenesis of the disease and may be clinically exploited to predict treatment response. What's already known about this topic? Alterations in the composition of the cutaneous microbiome have been described in psoriasis, although methodological differences in study design prevent direct comparison of results. To date, most cutaneous microbiome studies have focused on 16S rRNA sequencing data, including both living and dead bacteria. What does this study add? This prospective observational study confirms that changes in the composition of the cutaneous microbiome, detected by 16S rRNA sequencing, are consistent with those identified by bacterial culture and mass spectrometry. The changes in the microbiome during antipsoriasis therapy should be further investigated to determine whether these represent potential novel biomarkers of treatment response. What is the translational message? Characterization of cutaneous microbiota may ultimately move into the clinic to help facilitate treatment selection, not only by optimizing currently available treatments, but also by identifying new therapeutic targets.

Recessive dystrophic epidermolysis bullosa is characterized by skin blistering and wounds. To uncover the changes in the skin and mucosal microbiome related to age and disease progression and microbiome impact on clinical and inflammatory laboratory parameters, swabs from wounded and unwounded skin, oral mucosa, and stool samples of 28 children with recessive dystrophic epidermolysis bullosa and 28 healthy controls were subjected to 16S-ribosomal RNA gene sequencing. Skin microbiome of patients with recessive dystrophic epidermolysis bullosa showed significantly reduced alpha diversity compared with that of healthy controls and showed significantly early, age-dependent predominance of Staphylococcus aureus, first in wounded skin and then in unwounded skin. These findings were more pronounced in the severe disease with higher abundances of S. aureus than in intermediate disease. S. aureus abundance correlated significantly with both acute and chronic wound burden. Changes in oral mucosal and gut microbiome were discrete, with no significant differences in alpha diversity. Our findings show that children with recessive dystrophic epidermolysis bullosa experience skin microbiome changes early in life. Longitudinal studies should confirm that dysbiosis starts in wounds and later extends to unwounded skin. The predominance of S. aureus significantly correlates with wound burden and disease activity and, to some extent, with systemic inflammation.

The present work investigates the technical feasibility of a condition monitoring setup aiming at the detection of gauge corner cracks (aka head checks) in pearlitic railway rails, using a wayside (i.e., stationary) setup with surface acoustic waves (SAW) as its detection principle. The experimental SAW setup consists of a pitch-catch setup using piezo transducers equipped with comb adaptors to excite and measure narrowband Rayleigh waves with a center frequency of 1 MHz. SAW experiments were performed on a rail subjected to cyclic loading in a 1:1 wheel–rail test rig yielding the specific rolling contact fatigue, i.e., head checks. Elastodynamic finite integration technique (EFIT) simulations were performed to analyze the surface and bulk wave propagation in the rail and to predict the signals at specific receiver positions. SAW transmission and reflection scenarios at cracks were analyzed numerically via modelled variations of gauge corner crack configurations according to number of cracks (0–3) and depth (0, 0.5 mm and 1 mm). The numerical and the experimental results each show a clear correlation between the appearance and intensity of head check damage and the wave attenuation in transmission mode.

Purpose Plasmablastic lymphoma (PBL) is a rare and aggressive B-cell malignancy with a heterogenous clinical and prognostic spectrum, determined by multiple factors, including age, HIV- and MYC-status. While there exist several validated scoring systems for diffuse large B-cell lymphoma, which incorporate basic clinical features (age, lactate dehydrogenase, sites of (extranodal) involvement, stage and performance), none of these have been systematically assessed in PBL. Methods We determined the (age-adjusted; aa)-International Prognostic Index (IPI), revised IPI (R-IPI), and National Comprehensive Cancer Network IPI (NCCN-IPI) in a comprehensive multi-center cohort (n = 78) of PBL patients. Further, all indices were comparatively investigated for model quality and concordance. Results Univariate analysis revealed significant prognostic capabilities for all indices, all of which identified a subgroup with favorable outcome. Discriminatory power between patients with less benign prognosis and especially refractory disease exhibited significant variability. Subsequently, stratified models for each risk score were compared employing corrected Akaike’s information criterion (cAIC) and Harrel’s concordance index (c-index). Here, the NCCN-IPI outperformed both IPI and R-IPI regarding c-index with ambiguous cAIC results, underlining its clinical utility and suggesting it for preferential use in clinical practice. Conclusion Our current observations support the use of the IPI and its enhanced derivatives in PBL patients. There is, however, a distinct requirement for novel prognostic tools to better delineate subgroups at risk for early relapse or refractory disease as well as late relapse. A comprehensive molecular characterization of a clinically annotated cohort of PBL patients is therefore urgently warranted.

As one of the current global health conundrums, COVID-19 pandemic caused a dramatic increase of cases exceeding 79 million and 1.7 million deaths worldwide. Severe presentation of COVID-19 is characterized by cytokine storm and chronic inflammation resulting in multi-organ dysfunction. Currently, it is unclear whether extrapulmonary tissues contribute to the cytokine storm mediated-disease exacerbation. In this study, we applied systems immunology analysis to investigate the immunomodulatory effects of SARS-CoV-2 infection in lung, liver, kidney, and heart tissues and the potential contribution of these tissues to cytokines production. Notably, genes associated with neutrophil-mediated immune response (e.g. CXCL1) were particularly upregulated in lung, whereas genes associated with eosinophil-mediated immune response (e.g. CCL11) were particularly upregulated in heart tissue. In contrast, immune responses mediated by monocytes, dendritic cells, T-cells and B-cells were almost similarly dysregulated in all tissue types. Focused analysis of 14 cytokines classically upregulated in COVID-19 patients revealed that only some of these cytokines are dysregulated in lung tissue, whereas the other cytokines are upregulated in extrapulmonary tissues (e.g. IL6 and IL2RA). Investigations of potential mechanisms by which SARS-CoV-2 modulates the immune response and cytokine production revealed a marked dysregulation of NF-κB signaling particularly CBM complex and the NF-κB inhibitor BCL3. Moreover, overexpression of mucin family genes (e.g. MUC3A, MUC4, MUC5B, MUC16, and MUC17) and HSP90AB1 suggest that the exacerbated inflammation activated pulmonary and extrapulmonary tissues remodeling. In addition, we identified multiple sets of immune response associated genes upregulated in a tissue-specific manner (DCLRE1C, CHI3L1, and PARP14 in lung; APOA4, NFASC, WIPF3, and CD34 in liver; LILRA5, ISG20, S100A12, and HLX in kidney; and ASS1 and PTPN1 in heart). Altogether, these findings suggest that the cytokines storm triggered by SARS-CoV-2 infection is potentially the result of dysregulated cytokine production by inflamed pulmonary and extrapulmonary (e.g. liver, kidney, and heart) tissues.

We recently reported on two mouse strains carrying different single nucleotide variations in the mitochondrial complex I gene, i.e., B6-mtBPL mice carrying m.11902T>C and B6-mtALR carrying m.4738C>A. B6-mtBPL mice exhibited a longer lifespan and a lower metabolic disease susceptibility despite mild mitochondrial functional differences in steady-state. As natural polymorphisms in the mitochondrial DNA (mtDNA) are known to be associated with distinct patterns of gut microbial composition, we further investigated the gut microbiota composition in these mice strains. In line with mouse phenotypes, we found a significantly lower abundance of Proteobacteria, which is positively associated with pathological conditions, in B6-mtBPL compared to B6-mtALR mice. A prediction of functional profile of significantly differential bacterial genera between these strains revealed an involvement of glucose metabolism pathways. Whole transcriptome analysis of liver samples from B6-mtBPL and B6-mtALR mice confirmed these findings. Thus, both host gene expression and gut microbial changes caused by the mtDNA variant differences may contribute to the ageing and metabolic phenotypes observed in these mice strains. Since gut microbiota are easier to modulate, compared with mtDNA variants, identification of such mtDNA variants, specific gut bacterial species and bacterial metabolites may be a potential intervention to modulate common diseases, which are differentially susceptible to individuals with different mtDNA variants.

The formation and detailed spectroscopic characterization of the first biuret-containing monoanionic superoxido-NiII intermediate [LNiO2 ]- as the Li salt [2; L=MeN[C(=O)NAr)2 ; Ar=2,6-iPr2 C6 H3 )] is reported. It results from oxidation of the corresponding [Li(thf)3 ]2 [LNiII Br2 ] complex M with excess H2 O2 in the presence of Et3 N. The [LNiO2 ]- core of 2 shows an unprecedented nucleophilic reactivity in the oxidative deformylation of aldehydes, in stark contrast to the electrophilic character of the previously reported neutral Nacnac-containing superoxido-NiII complex 1, [L'NiO2 ] (L'=CH(CMeNAr)2 ). According to density-functional theory (DFT) calculations, the remarkably different behaviour of 1 versus 2 can be attributed to their different charges and a two-state reactivity, in which a doublet ground state and a nearby spin-polarized doublet excited-state both contribute in 1 but not in 2. The unexpected nucleophilicity of the superoxido-NiII core of 2 suggests that such a reactivity may also play a role in catalytic cycles of Ni-containing oxygenases and oxidases.

Telmisartan prevents diet-induced obesity (DIO) in rodents. Given that the precise underlying mechanism is not known, we examined whether a gut-related mechanism might be involved. Sprague-Dawley rats received cafeteria diet (CD) for 3 months to develop DIO and were administered either telmisartan (8 mg/kgbw) or vehicle. In addition, pair-fed (PF) rats received CD adjusted to TEL and control rats (CON) only received chow. Stool samples were analysed by 16 S rRNA gene amplicon sequencing. CD-fed rats became obese while TEL, PF and CON rats remained lean. Alpha diversity analyses indicated that bacterial diversity was similar before the study but changed over time. Beta diversity revealed a time-, CD- and telmisartan-dependent effect. The Firmicutes/Bacteroidetes ratio and the abundance of Blautia, Allobaculum and Parasutterella were higher in DIO and PF than in CON, but not in TEL. Enterotype (ET)-like clustering analyses, Kleinberg’s hub network scoring and random forest analyses also indicated that telmisartan induced a specific signature of gut microbiota. In response to stool transfer from telmisartan-pre-treated donor to high-fat fed acceptor mice, body weight gain was slightly attenuated. We attribute the anti-obesity action of telmisartan treatment to diet-independent alterations in gut microbiota as the microbiota from telmisartan-treated, CD-fed rats clearly differed from those of DIO and PF rats. ET-like clustering network, random forest classification and the higher stability in bacterial co-occurrence network analyses indicate that there is more than one indicator species for telmisartan’s specific signature, which is further strengthened by the fact that we cannot identify a single indicator species.

Bullous pemphigoid (BP) is the most common autoimmune blistering disease in Europe. As both the incidence of the disease and the relative proportion of the elderly population continue to rise, it represents a significant medical burden. Whereas some progress has been achieved in defining genetic risk factors for autoimmune blistering diseases, no environmental agent has been conclusively identified. Emerging evidence suggests that host immunity may influence the skin microbiota, while the latter modulates cutaneous immunity. Nevertheless, the relationship between skin microbial communities and autoimmune bullous disease has yet to be studied in humans. Here, we aim to characterise and compare the skin microbiome of patients with BP and healthy, age-matched controls at numerous body sites. Similar to what has been shown in healthy controls, the composition of skin microbiota in patients with BP appears to be very divergent and site specific. Microbial phylum abundances differ between perilesional sites of patients with BP and the same anatomic locations of control patients. A distinct cutaneous microbiota profile, which correlates with BP, further strengthens the significance of commensal-host interaction on our immune system. Moreover, these results raise the possibility that the cutaneous microbiome may contribute to the pathogenesis of BP, with important implications for the treatment of this disease. © 2017 John Wiley Sons Ltd.

Background:The morbidity and mortality of systemic sclerosis (SSc) are largely determined by vascular and fibrotic pathologies. Levels of autoantibodies (ab) against G protein-coupled receptors (GPCR), growth factors (GF) and growth factor receptors (GFR) are altered in SSc compared to healthy controls (HC) 1. Thus, higher angiotensin II receptor type 1 - (AT1R) and endothelin receptor type A - (ETAR) ab levels are associated with severe disease and SSc-related mortality 2. CXC motiv chemokine receptor 3 - (CXCR3) and 4 - (CXCR4) ab have predictive value for deterioration of pulmonary fibrosis (PF) 3.Objectives:We used statistical methods to identify associations between disease manifestations and 28 new ab directed against GPCR, GF and GFR in SSc.Methods:Ab against the following targets were measured in sera from SSc patients (n = 177) and HC (n = 88): Adrenoceptors alpha-1 (ADRA1), alpha-2 (ADRA2), beta-1 (ADRB1), beta-2 (ADRB2); muscarinoceptors 1-5 (M1R - M5R); AT1R, ETAR, endothelin B receptor (ETBR); CXCR3, CXCR4; complement receptors 3a (C3aR) and 5a (C5aR); protease-activated receptors 1 (PAR1) and 2 (PAR2); vascular endothelial growth factor A (VEGFA) and its receptors 1 (VEGFR1) and 2 (VEGFR2), epithelial growth factor (EGF)/ - receptor (EGFR); hepatocyte growth factor (HGF)/ - receptor (HGFR), platelet-derived growth factor-AA (PDGFAA), placental growth factor (PlGF).The organ involvement (PF, cardiac involvement, PAH, gastrointestinal tract) and quantitative markers (modified Rodnan skin score, SSc activity score, pulmonary function, cardiac enzymes and echocardiography, routine laboratory, autoimmune diagnostics) as well as demographic data were recorded retrospectively at the time of sample collection. Statistical analysis was performed using the Mann-Whitney U test (MWU), Pearson correlations, ROC analysis, and age-adjusted logistic regression models.Results:In SSc 20 of 28 measured ab levels are significantly altered compared to HC. According to the Pearson correlation matrix, the ab-levels are highly correlated and build a network that differs between HC and SSc. Furthermore, altered network signatures are formed in the differentiated analysis of several disease manifestations of SSc such as SSc-subtype or PF. Based on ROC analysis, FGF-ab, ADRB1-ab and PlGF-ab are well suited to predict SSc (Figure 1).In addition, limited cutaneous SSc (lSSc) patients displayed lower levels of most ab than diffuse cutaneous SSc patients, whereas cardiac and pulmonary involvement are associated with higher ab levels. In the logistic regression lSSc is associated with lower levels of ab against M1R, M2R, C5aR, ETAR, AT1R, PAR1, EGFR. Higher levels for ab against M1R, M2R, ETBR, C5aR are associated with PF, higher levels of ab against complement receptors, adrenoreceptors and EGF with NT-proBNP elevation.Conclusion:The newly described antibodies against GPCR, GF and GFR are highly correlated. Associations with morbidity- and mortality-determining organ involvement indicate their possible functional relevance and novel pathophysiological mechanisms. As new biomarkers, some of the ab have prognostic value for SSc; for other manifestations, their value should be evaluated in further studies.References:[1]Cabral-Marques, O., Marques, A., Giil, L.M. et al. GPCR-specific autoantibody signatures are associated with physiological and pathological immune homeostasis. Nat Commun9, 5224 (2018). https://doi.org/10.1038/s41467-018-07598-9[2]Riemekasten G, Philippe A, Näther M, et al. Involvement of functional autoantibodies against vascular receptors in systemic sclerosis Annals of the Rheumatic Diseases 2011;70:530-536.[3]Weigold, F., Günther, J., Pfeiffenberger, M. et al. Antibodies against chemokine receptors CXCR3 and CXCR4 predict progressive deterioration of lung function in patients with systemic sclerosis. Arthritis Res Ther 20, 52 (2018). https://doi.org/10.1186/s13075-018-1545-8Disclosure of Interests:Kristina Sterner: None declared, Césaire J. K. Fouodo: None declared, Inke König: None declared, Axel Künstner: None declared, Hauke Busch: None declared, Harald Heidecke Shareholder of: Owner of CellTrend, Anja Schumann: None declared, Antje Müller: None declared, Gabriela Riemekasten: None declared, Susanne Schinke Grant/research support from: UCB sponsors EULAR registration fees

Gut commensal bacteria exert profound effects on the immune system of the mammalian host. In particular, Lactobacillus species have a long-standing history as putative probiotics, generally being characterized as safe and/or beneficial for the mammalian host. Despite this fact, current literature points to both pro- and anti-inflammatory roles for this genus, with little consensus as to the mechanisms governing these divergent outcomes. Using mouse models, we and others have previously shown that, unexpectedly, stable commensal colonization with Lactobacillus reuteri (L. reuteri) is correlated with, and sufficient to enhance host susceptibility to experimental autoimmune encephalomyelitis (EAE), in association with alterations in tryptophan derived metabolites in host circulation. To identify the underlying mechanisms, we characterized the genomes of commensal L. reuteri isolates, along with two other representative Lactobacillus species, L. murinus and L. johnsonii. Whole genome sequencing revealed an enrichment in the enzymatic machinery necessary to catabolize dietary tryptophan into immunomodulatory indole derivatives in L. reuteri. Mechanistically, supplementation with high dietary tryptophan sustained an L. reuteri-dependent exacerbation of EAE and augmented inflammatory T cell populations, while depletion of dietary tryptophan profoundly suppressed EAE in a microbiome-specific manner. Taken together, our data reveal considerable variation in the genetic landscape of commensal Lactobacilli, and demonstrate mechanisms responsible for differential modulation of autoimmunity by gut microbiota, including an unexpected disease-promoting role for catabolism of host dietary tryptophan.

In pemphigoid diseases, direct immunofluorescence can be used to differentiate 2 patterns of antibody deposition at the dermal–epidermal junction; u- and n-serrated pattern. The u-serrated pattern is found in epidermolysis bullosa acquisita, and n-serrated pattern in all other pemphigoid diseases. To determine the detection frequency of these serrated patterns and the optimal thickness of biopsy cryosections, 2 patient cohorts obtained form our routine autoimmune laboratory were analysed; a retrospective cohort (n = 226) and a prospective cohort (n = 156). [AQ1] In 76% (291/382) of biopsies, a pattern was recog­nized, of which 96% (278/291) and 4% (13/291) had an n- or u-serrated pattern, respectively. A u-serrated pattern was seen in all epidermolysis bullosa acquisita biopsies confirmed by serology. No antibodies against type VII collagen were detected in any of the sera from biopsies with n-serrated pattern. No differences between the detection frequencies of serrated pattern were seen with respect to age, sex, biopsy site, or section thickness, while the detection frequency was higher in patients with serum anti-BP180 reactivity compared with those without. In conclusion, serrated pattern analysis using direct immunofluorescence has a high detection frequency and specificity for epidermolysis bullosa acquisita and will further facilitate the diagnosis of latter disorder.