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Insulin resistance is among the key risk factors for the development of non-alcoholic fatty liver disease (NAFLD). Recently, it has been reported that GW9662, shown to be a potent peroxisome proliferator-activated receptor gamma (PPARγ) antagonist, may improve insulin sensitivity in settings of type 2 diabetes. Here, we determined the effects of GW9662 on the development of NAFLD and molecular mechanisms involved.Female C57BL/6J mice were pair-fed either a liquid control diet (C) or a fat-, fructose- and cholesterol-rich diet (FFC) for 8 weeks while either being treated with GW9662 (1 mg/kg body weight; C+GW9662 and FFC+GW9662) or vehicle (C and FFC) i.p. three times weekly. Indices of liver damage and inflammation, parameters of glucose metabolism and portal endotoxin levels were determined. Lipopolysaccharide (LPS)-challenged J774A.1 cells were treated with 10 μM GW9662.Despite similar caloric intake the development of NAFLD and insulin resistance were significantly attenuated in FFC+GW9662-treated mice when compared to FFC-fed animals. Bacterial endotoxin levels in portal plasma were almost similarly increased in both FFC-fed groups while expressions of toll-like receptor 4 (Tlr4), myeloid differentiation primary response 88 (Myd88) and interleukin 1 beta (Il1b) as well as nitrite (NOIn summary, our data suggest that the PPARγ antagonist GW9662 attenuates the development of a diet-induced NAFLD and that this is associated with a protection against the activation of the TLR4 signaling cascade.

Background Relapsed/refractory multiple myeloma (RRMM) is characterized by a high inter- and intratumor heterogeneity and a complex interplay of myeloma cells with the bone marrow microenvironment (BME). Accordingly, there is an urgent need to dissect subclone structure, transcriptional heterogeneity and cellular interactions to unravel the molecular mechanisms underlying drug resistance in RRMM. Methods Single cell RNA sequencing (scRNA-seq) of ~210,000 cells from bone marrow aspirates sorted into CD138+ and CD138– fractions was conducted for 20 heavily pretreated RRMM patients. RRMM subclones were called from the scRNA-seq data based on a copy number aberration (CNA) analysis that was confirmed by interphase fluorescence in situ hybridization and whole genome sequencing. From the scRNA-seq data the composition and abundance of immune cell types in the BME was determined. Interactions of myeloma cells with the BME were characterized by an analysis of the correlated expression of ligand-receptor pairs. Selected findings from the scRNA-seq analysis were validated by flow cytometry. Results Subclones with distinct chromosomal aberrations were reliably identified at the single cell level based on CNAs inferred from scRNA-seq data. The analysis revealed a subclonal 1q-gain (+1q) in 10/20 samples, for which a gene expression signature of recurrently upregulated genes was derived. These +1q subclones frequently expanded during treatment. Furthermore, RRMM cells shaped an immune suppressive BME by upregulation of inflammatory cytokines and close interplay with the myeloid compartment. RRMM cells appear to reprogram the BME by upregulation of inflammatory cytokines and ligands of inhibitory receptors expressed on T and NK-cells. Specifically, the immune cell compartment of RRMM patients displayed an accumulation of PD1+ γδ T-cells and myeloid populations compared to healthy donors or early disease. In addition, we observed a depletion of hematopoietic progenitors in patients with high expression of genes associated with inflammatory signaling in the BME. Upon treatment with immunomodulatory drugs, reprogrammed plasmacytoid dendritic cells expanded. Focusing on patients with +1q, we found an enrichment of a rare M2-like tumor associated macrophage population while GZMB+ NK effector cells were depleted in these patients, indicating that +1q has a distinct effect on the BME in RRMM. Conclusions Our study resolves transcriptional features of subclones in RRMM and mechanisms of microenvironmental reprogramming. The insight gained in our study on the evolution of RRMM heterogeneity and its bone marrow milieu will support the development of novel treatment approaches and potentially guide clinical decision making.

Introduction Despite new treatment approaches, in most patients with multiple myeloma (MM) resistant subclones expand, finally resulting in the development of relapsed/refractory disease (RRMM). Recent single-cell transcriptomic (scRNA-seq) studies have improved our understanding of tumor heterogeneity in MM, but our knowledge about the regulatory processes and gene expression signatures in resistant subclones is still limited. Thus, we performed single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) as well as scRNA-seq from the same MM patient samples and developed a new approach for the analysis of the transcriptome and epigenome of competing subclones. Methods CD138+ bone marrow cells of 11 RRMM patients were longitudinally collected and profiled using 10X Genomics scRNA- and scATAC-seq platform. Pre-processing was performed with CellRanger and downstream analysis using Seurat and ArchR. To determine clones based on copy number variations (CNVs), we leveraged inferCNV for scRNA-seq and developed a sliding window approach adapted from a previously published method by Satpathy et al. for scATAC-seq data. Whole genome sequencing was available to confirm the identified CNV clones. Results We obtained chromatin accessibility profiles of >43000 cells after quality control, establishing the first epigenetic map of RRMM with clearly separated clusters for each patient. Samples from distinct MM subgroups, particularly t(4;14) and t(11;14), clustered together in a pseudo-bulk analysis based on transcription factor activity scores from scATAC. To investigate treatment-induced clonal dynamics we aligned sc chromatin accessibility profiles to clones inferred in scRNA-seq based on CNVs enabling us to track individual tumor subclones over time. An example for clonal adaptation is a patient with two subclones that both responded differently to pomalidomide plus anti-CD38 treatment: while clone 1 showed a higher activity for members of IRF family, ZEB1 and KLF family members were more active in clone 2. Branching evolution was e.g. observed in a patient treated with a MEK/BRAF inhibitor. This patient showed two subclones before treatment, achieved a complete remission and relapsed with one dominant clone. One of the initial subclones could be identified as the precursor of this dominant clone with both showing high activity of NFKB family members, while higher activity of SOX10/15 was only observed upon MEK/BRAF inhibition. An example for combined clonal adaptation and selection was observed in a patient with bi-allelic inactivation of TP53 in one of the two subclones before MCL1 inhibition. Interestingly, this clone was depleted at relapse. Conclusions In summary, our new approach to track individual tumor subclones over time indicates clonal adaptation or selection in virtually all RRMM patients and reveals new insights into regulatory mechanisms underlying treatment-resistance, opening potential avenues for new therapies.

Introduciton Tumor heterogeneity plays a significant role in the development of therapy resistance in multiple myeloma (MM). Focal accumulations of myeloma cells called focal lesions (FLs) have been shown to be the hotspots of spatial tumor heterogeneity, which is characterized by unique tumor sub-clones at different sites in the bone marrow (BM). However, little is known about the sub-clonal architecture in FLs, the mechanisms leading to site-unique mutations, and the link between sub-clones in FLs and treatment-resistance. Methods To fill this gap in knowledge, we used a comprehensive approach to characterize CD138-sorted tumor cells from FLs and random BM aspirates (RBMA) in 12 newly diagnosed MM patients, applying whole genome sequencing (WGS), single-cell(sc)-RNA-sequencing and sc assay for transposase-accessible chromatin (ATAC)-sequencing. Sc data was generated using the 10X Genomics platform. Pre-processing of the sc data was performed with CellRanger and the R-packages Seurat, ArchR and inferCNV were used for downstream analysis. WGS data was analyzed using inhouse pipelines. Mutations, copy-number-variations and mutational signatures were called using mpileup, ACESeq and mmsig. Neoantigen epitopes were predicted using NeoPredPipe. Results In the majority of patients (n=10/12) we found significant differences in the chromosomal and mutational profiles between FLs and paired RBMAs from the iliac crest. To identify the mechanisms underlying heterogenous mutations, we performed mutational signature analysis and found COSMIC signature SBS18 to be enriched in these mutations, suggesting that they were caused by reactive oxygen species. Interestingly several site-unique mutations were predicted as potential neoantigens. Driver gene mutations associated with relapse such as KRAS, CYLD, CDKN2C and TP53, were more often seen in FL sub-clones. Using a combination of WGS, sc-RNA and sc-ATAC-sequencing to characterize these sub-clones in more detail, we found increased regulatory accessibility and expression of genes associated with disease aggressiveness and drug resistance such as CXCR4 and members of the NFKB- and interferon pathways. The latter implies that FLs could play a significant role in the development of treatment resistance. Indeed, comparing sub-clones at baseline and after high-dose melphalan and autologous stem cell transplantation in one patient, we demonstrate expansion of a single tumor cell, which was closely related to the main sub-clone from the baseline FL. Conclusion In conclusion, our data provides novel insights into the mechanisms underlying site-unique mutations and the sub-clonal architecture at different sites in the BM. The combination of bulk and sc-techniques showed that FLs are enriched for sub-clones with genetic, transcriptional and regulatory markers characteristic for aggressive disease and can be the source of relapse in MM-patients. This implies that targeting FLs is essential for achieving a cure of MM.

Background: Universally accepted therapeutic strategies for the treatment of nonalcoholic steatohepatitis (NASH) are still lacking. Studies suggest a preventive effect of oral Gln supplementation on the development of NASH; however, whether Gln also has therapeutic potential for pre-existing NASH has not yet been clarified.Objective: The aim of the present study was to determine whether Gln prevents the progression of diet-induced NASH in mice.Methods: For 8 wk, female C57BL/6J mice (6-8 wk old) were pair-fed a liquid Western-style diet [WSD, 25% of energy from fat, 50% wt:wt fructose, 0.16% wt:wt cholesterol] or control diet (C diet) to induce liver damage. From week 8 to 13, they were pair-fed the C diet or WSD alone or supplemented with l-Gln to provide 2.1 g/kg body weight (C diet + Gln or WSD + Gln). Energy intake was adjusted to the group with the lowest energy intake. Indexes of liver damage and inflammation, intestinal barrier function, and toll-like receptor 4 (Tlr4) signaling in the liver were determined.Results: The liver histology scores significantly increased from 8 to 13 wk (+31%) in WSD-fed mice and were significantly higher than in controls (P ≤ 0.05 for both time comparisons), whereas scores did not differ between C diet-fed and WSD + Gln-fed mice after 13 wk of feeding. The occludin protein concentrations in the small intestinal tissue were similarly reduced in both WSD-fed groups when compared with controls [WSD compared with C diet (-53%) and C diet + Gln (-42%), P ≤ 0.05; WSD + Gln compared with C diet + Gln (-34%), P ≤ 0.05] after 13 wk, whereas the expression of myeloid differentiation primary response gene 88 mRNA and concentration of inducible nitric oxide synthase and 4-hydroxynonenal protein adducts were significantly higher only in livers of WSD-fed mice (P ≤ 0.05 for the WSD group compared with all other groups; WSD + Gln group compared with the C diet groups: NS).Conclusion: Taken together, our data suggest that oral Gln supplementation protects mice from the progression of pre-existing, WSD-induced NASH.

Background Non-alcoholic fatty liver disease (NAFLD) is one of the most common liver diseases worldwide lacking universally accepted therapies. Studies suggest that coffee consumption is associated with a reduced risk of NAFLD; however, molecular mechanisms and ingredients involved remain to be fully understood. Here, we determined the effects of regular intake of decaffeinated coffee on the development of NAFLD in mice, and molecular mechanisms involved. Methods Female C57BL/6J mice (n = 6–7/ group) were pair-fed either a liquid control diet (C) or fat-, fructose- and cholesterol-rich diet (FFC) +/- decaffeinated coffee (DeCaf, 6 g/kg BW) for 4 days or 6 weeks. Indices of liver damage, hepatic inflammation and parameters of insulin resistance and intestinal permeability as well as nitric oxide system were determined. Results Early signs of insulin resistance and non-alcoholic steatohepatitis (NASH) found after 6 weeks of FFC feeding were significantly lower in FFC+DeCaf-fed mice when compared to FFC-fed animals. Moreover, elevation of portal endotoxin levels and loss of tight junction proteins in proximal small intestine found in FFC-fed mice were significantly attenuated in FFC+DeCaf-fed animals. These beneficial effects of DeCaf were associated with a protection against the significant induction of inducible NO-synthase protein levels and 3-nitrotyrosine protein adducts found in proximal small intestine of FFC-fed mice. Similar protective effects of DeCaf were also found in mice fed the FFC diet short-term. Conclusion Our results suggest that protective effects of DeCaf on the development of NAFLD are at least in part related to maintaining intestinal barrier function., Graphical abstract fx1, Highlights • decaffeinated coffee protects mice from the development of NAFLD. • decaffeinated coffee attenuated increased translocation of bacterial endotoxins. • decaffeinated coffee prevents diet-induced induction of iNOS in small intestine.

Non-alcoholic fatty liver disease (NAFLD) is by now the most prevalent liver disease worldwide. The non-proteogenic amino acid l-citrulline (L-Cit) has been shown to protect mice from the development of NAFLD. Here, we aimed to further assess if L-Cit also attenuates the progression of a pre-existing diet-induced NAFLD and to determine molecular mechanisms involved. Female C57BL/6J mice were either fed a liquid fat-, fructose- and cholesterol-rich diet (FFC) or control diet (C) for 8 weeks to induce early stages of NASH followed by 5 more weeks with either FFC-feeding +/- 2.5 g L-Cit/kg bw or C-feeding. In addition, female C57BL/6J mice were either pair-fed a FFC +/- 2.5 g L-Cit/kg bw +/- 0.01 g/kg bw i.p. N(ω)-hydroxy-nor-l-arginine (NOHA) or C diet for 8 weeks. The protective effects of supplementing L-Cit on the progression of a pre-existing NAFLD were associated with an attenuation of 1) the increased translocation of bacterial endotoxin and 2) the loss of tight junction proteins as well as 3) arginase activity in small intestinal tissue, while no marked changes in intestinal microbiota composition were prevalent in small intestine. Treatment of mice with the arginase inhibitor NOHA abolished the protective effects of L-Cit on diet-induced NAFLD. Our results suggest that the protective effects of L-Cit on the development and progression of NAFLD are related to alterations of intestinal arginase activity and intestinal permeability., Graphical abstract Image 1, Highlights • l-citrulline diminished progression of non-alcoholic fatty liver disease (NAFLD). • l-citrulline protects from fructose-induced small intestinal barrier dysfunction. • NASH development is associated with a loss of arginase activity in small intestine. • l-citrulline improves intestinal arginase activity in diet-induced NAFLD. • Arginase inhibitor attenuates effects of l-citrulline on NAFLD development.

Background Absolute dietary fat intake but even more so fatty acid pattern is discussed to be critical in the development of non-alcoholic fatty liver disease (NAFLD). Here, we determined if switching a butterfat enriched diet to a rapeseed oil (RO) enriched diet affects progression of an existing NAFLD and glucose intolerance in mice. Methods For eight weeks, female C57Bl/6J mice were either fed a liquid control (C) or a butterfat-, fructose- and cholesterol-rich diet (BFC, 25E% butterfat) to induce early signs of steatohepatitis and glucose intolerance in mice. For additional five weeks mice received either BFC or C or a fat-, fructose- and cholesterol-rich and control diet, in which butterfat was replaced with RO (ROFC and CRO). Markers of glucose metabolism, liver damage and intestinal barrier were assessed. Results Exchanging butterfat with RO attenuated the progression of BFC diet-induced NAFLD and glucose intolerance. Beneficial effects of RO were associated with lower portal endotoxin levels and an attenuation of the induction of the toll-like receptor-4-dependent signaling cascades in liver. Peroxisome proliferator-activated receptor γ activity was induced in small intestine of ROFC-fed mice. Conclusion Taken together, exchanging butterfat with RO attenuated the progression of diet-induced steatohepatitis and glucose intolerance in mice.

Symptoms of allergic attacks frequently exhibit diurnal variations. Accordingly, we could recently demonstrate that mast cells and eosinophils – known as major effector cells of allergic diseases – showed an intact circadian clock. Here, we analyzed the role of the circadian clock in the functionality of mast cells and eosinophils. Human intestinal mast cells (hiMC) were isolated from intestinal mucosa; human eosinophils were isolated from peripheral blood. HiMC and eosinophils were synchronized by dexamethasone before stimulation every 4 h around the circadian cycle by FcɛRI crosslinking or fMLP, respectively. Signaling molecule activation was examined using Western blot, mRNA expression by real-time RT-PCR, and mediator release by multiplex analysis. CXCL8 and CCL2 were expressed and released in a circadian manner by both hiMC and eosinophils in response to activation. Moreover, phosphorylation of ERK1/2, known to be involved in activation of hiMC and eosinophils, showed circadian rhythms in both cell types. Interestingly, all clock genes hPer1 , hPer2 , hCry1 , hBmal1 , and hClock were expressed in a similar circadian pattern in activated and unstimulated cells indicating that the local clock controls hiMC and eosinophils and subsequently allergic reactions but not vice versa .