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Haller, D.

Publications and source records attributed to Haller, D..

At least 19 recordsLinked to original sources

The Human Rectus Femoris Muscle Receives an Independent Common Synaptic Input During Isometric Leg Extensions

The distribution of common synaptic inputs across spinal motor neuron pools within and across synergist muscles reveals direct insight in the neural control of movement. We previously documented two dominant common inputs in the human vastus lateralis (VL) and medialis (VM) muscle during isometric leg extensions. Whether these inputs are also shared with rectus femoris (RF), a synergist muscle that contributes substantially to leg extension but is biarticular, remains unknown. We simultaneously recorded motor unit activity from VM, RF, and VL using multiple targeted intramuscular electromyographic sensors during isometric knee extension. Decomposed motor unit spike trains were analyzed using discharge characteristics, pairwise correlation, spectral coherence, explained variance, and factor analysis to characterize the structure of common synaptic input within and across muscles. Despite their shared mechanical output via a common patellar tendon, the three muscles exhibited distinct patterns of neural organization. RF consistently received a strong, low-dimensional common input that was largely independent of the drive to VM and VL, as evidenced by elevated within-muscle correlation and coherence, low between-muscle coupling, and an invariant dedicated latent factor across all participants. VM and VL shared a substantial proportion of common synaptic input, but the degree of coupling and the underlying factor structure varied across individuals, ranging from a single shared factor to largely independent muscle-specific inputs. These findings indicate that the quadriceps are organized in a muscle- and subject-specific manner, with RF receiving a dedicated independent input.

neuroscience↗

Microbial Invasion and Immunosuppression Drives Adenoma Progression in Early Colorectal Cancer Development

Several inherited predispositions to colorectal cancer exist, most notably familial adenomatous polyposis (FAP), which typically involves a germline loss-of-function mutation in one APC allele. A second hit in APC or related loci leads to aberrant Wnt signalling, triggering adenoma formation with near-complete penetrance. Yet, substantial variability in disease onset and severity, even among siblings with identical APC germline mutations, implicates environmental modifiers. Emerging evidence points to the gut microbiome as a critical regulator of adenoma initiation and progression, particularly in early-onset CRC. Here, we show that bacterial invasion is associated with neutrophil immunosuppression, T-cell exclusion and adenoma progression in a porcine model of FAP. Longitudinal mapping of progressing and regressing polyps using single-cell RNA sequencing, spatial transcriptomics and integrated microbiome profiling resolved the cellular and microbial architecture underlying these divergent lesion states. Single-cell RNA-seq identified 35 cell subpopulations and showed that regressing polyps are enriched for central-memory CD4+ T cells, cytotoxic CD8+ T cells and inflammatory neutrophils, whereas progressing polyps contain immunosuppressive/PD-L1-associated neutrophils, regulatory and dysfunctional T cells. Spatial transcriptomics with a custom host panel and targeted bacterial probes linked bacterial-high adenomatous regions to immunosuppressive neutrophil niches and T cell exclusion, while regressing lesions showed predominantly lumen-adjacent bacterial localization and spatially organized immune surveillance. These results provide a spatially resolved map of cellular and microbial organisation in early colorectal polyp progression and regression and reveal a microbiome-driven, neutrophil-mediated mechanism of early tumour progression with implications for CRC interception. Grant support: This study was funded by the German Research Foundation (DFG) through SFB1371 "Microbiome signature" (Project no. 395357507; TF, DS, FE, DH) and by the German Ministry for Research and Education (BMBF) through Mi-EOCRC consortium project (Project no. 01KD2102D; KF and DH).

cancer biology↗

Distinct colorectal cancer genotypes shape microbial ecosystems and reveal stage-specific microbiota dependencies

The gut microbiota has emerged as an important modifier of colorectal cancer (CRC), yet how tumor genotype influences host-microbiota interactions and whether microbial signals are required throughout tumor progression remain unclear. Here, we combined genetically engineered mouse models, microbial multi-omics and a germ-free-compatible orthotopic transplantation system to define the functional contribution of the microbiota across distinct stages of CRC evolution. Across multiple CRC genotypes, we identified tumor-associated microbial ecosystem states characterized by distinct taxonomic, functional and metabolic configurations. To directly test their contribution to tumor progression, we established the first orthotopic CRC transplantation platform compatible with long-term experimentation in germ-free mice, enabling side-by-side comparison of genetically identical tumors in the presence or absence of microbiota. Using organoids spanning low-grade adenoma, high-grade adenoma and adenocarcinoma states, we found that the dependence on the presence of microbiota progressively decreases during malignant evolution. Whereas adenoma-derived organoids exhibited profound dependence on microbial exposure and failed or were markedly impaired in establishing tumors under germ-free conditions, adenocarcinoma organoids engrafted and metastasized in both germ-free and specific pathogen-free (SPF) hosts. Unexpectedly, comprehensive histological, immunological and transcriptomic analyses revealed highly similar tumor ecosystem states in advanced tumors arising under both microbial conditions, arguing against broad immune or epithelial defects as a primary explanation for the observed phenotype. Together, our findings demonstrate that distinct oncogenic drivers establish specific microbial ecosystem states and reveal a stage-dependent role of the microbiota during colorectal tumorigenesis. Whereas microbial signals are critical during early stages of tumor progression and may promote malignant transformation, advanced tumors progressively acquire microbiota-independent growth programs and increasingly impose genotype-specific ecological signatures on the surrounding microbial ecosystem. More broadly, we establish a versatile framework for the causal dissection of tumor-microbiota interactions in cancer.

cancer biology↗

A transient CD87-centred axis enhances the Th17 potential of cDC2 in neonates

Type 2 conventional dendritic cells (cDC2) orchestrate T cell immunity, yet the signals that regulate their tissue-specific functions across development remain poorly defined. We demonstrate that splenic cDC2/DC3 subset heterogeneity is established perinatally and that splenic ESAMhi cDC2A undergo a transcriptional and functional transition around the time of weaning, which occurs independently of microbiota. Comparative transcriptomics identified neonatal-specific regulatory programs, including elevated expression of Plaur, encoding CD87/uPAR. CD87 sensitizes neonatal ESAMhi cDC2A to coagulation factor XII (FXII), thereby enhancing their capacity to promote Th17 differentiation. In human infants, CD87 expression was high on cDC2, its expression declined with age and in plasma of preterm infants CD87 positively correlated with Th17-associated cytokines. Together, we identify a conserved link between coagulation pathways and cDC2 developmental programming that may offer new opportunities to modulate Th17 responses in infancy. SummarySplenic cDC2 undergo a transcriptional and functional remodeling around weaning. Elevated CD87 expression on neonatal cDC2 enhances their FXII-driven Th17 potential. Conserved in human infants, elevated CD87 expression reveals a coagulation-linked pathway shaping early-life dendritic cell function and suggests targets to improve vaccination.

immunology↗

Probiotic formula intervention in infants leads to colonization and competitive strain displacement independent of IgA binding

Early-life microbiota assembly is affected by environmental exposure, diet, and immunity. We performed shotgun metagenomics sequencing of fecal samples (N=401) from a controlled infant intervention trial to evaluate how pre- and probiotic exposure affects bacterial strain dynamics, maternal-to-offspring strain transmissibility, strain persistence, and host immune responses. Species- and strain-level analyses revealed that the early-life intervention with Bifidobacterium longum subsp. infantis (BL subsp. infantis), Bifidobacterium breve, and galacto-oligosaccharides (GOS) replaced main resident strains of these species unlike breast-feeding and exclusive infant formula. BL subsp. infantis low-diversity clusters were representative of several populations and were enriched for genes linked to recombination, mobilization, and antimicrobial activity. lnterestingly, Bifidobacterium bifidum but not Bifidobacterium longum or B. breve was heavily targeted by mucosal lgA, regardless of feeding type. These findings suggest that early-life pro- and prebiotic interventions promote colonization of specific dominant strains, potentially by outcompeting and displacing existing strains, independently of host immune responses.

microbiology↗

Periweaning diet-induced activation of an IFNγ-mediated regulatory circuit promotes the homeostasis of cytotoxic CD8+ T Cells

Balancing pathogen defence with maintaining tolerance to environmental antigens, such as food or commensals, in neonates is essential for survival and the establishment of life-long immune homeostasis. Instructed by environmental signals type 1 conventional dendritic cells (cDC1) drive either T cell tolerance or immunity. Here, we uncover an interferon (IFN)-{gamma}-driven regulatory circuit in early life that relays dietary cues to spleen cDC1. Loss-of-function demonstrates that IFN{gamma}-mediated STAT1-signaling induces an immunogenic maturation program in spleen cDC1 that instructs cDC1 to expand effector memory CD8 T cells. This program emerges during weaning, when IFN{gamma} production from lymphocytes rises, it occurs in germ-free mice and remains responsive to dietary intervention in adult mice. During the transition from breastfeeding to solid food at weaning, this circuit relays dietary information to spleen cDC1 to shape the effector phenotype of food-antigen specific CD8+ T cells in a feed-forward manner, allowing cDC1 to recalibrate the T cell pool at the moment of nutritional independence.

immunology↗

Gut microbiota within-host evolution enforces colonization resistance against enteric infection

Limited resource availability in the gut promotes competitive interactions between bacteria, which drive adaptive within-host evolution (1-3). While adaptive evolution of bacterial communities has been increasingly studied in the recent years (4-7), its functional implications for host physiology remain unknown. Here, we show that within-host evolution of the human commensal Enterococcus faecalis boosts colonization resistance to enteric Salmonella enterica serovar Typhimurium (S. Typhimurium) infection. During gut colonization, E. faecalis evolves the ability to metabolize fructoselysine, an abundant Amadori rearrangement product generated by thermal food processing. The depletion of this diet-derived nutrient prevents S. Typhimurium colonization by restricting an essential resource. This protective mechanism was conserved across independent mouse colonies and arises via diverse evolutionary trajectories, including nucleotide polymorphisms, gene amplifications, and a horizontal gene transfer event. Additionally, analysis of E. faecalis isolates from human infants revealed that adaptation to fructoselysine availability occurs in a diet-dependent manner. Isolates from infants fed with fructoselysine-rich formula were able to utilize fructoselysine, whereas those from infants fed with fructoselysine-poor breast milk were not. Conclusively, our results identify an inherent microbiome-driven self-healing mechanism, wherein bacterial evolution restores colonization resistance against enteric pathogens through evolved nutrient depletion. Understanding these evolutionary dynamics will inform microbiome-targeted approaches to prevent and treat infectious diseases by harnessing adaptive bacterial metabolism.

microbiology↗

Extensive genomic diversity in Desulfovibrio species reveals species-specific functional traits associated with disease

Desulfovibrio spp. are associated with inflammatory diseases and human health, yet limited representative genomes and isolates hinder our understanding of their role in disease. Here, we assembled a comprehensive database of 2,658 Desulfovibrio genomes across 90 diseases and 32 countries, including 24 human isolates. Genomic analyses showed extensive species diversity and revealed disease-associated functional traits, including flagellin and virulence genes (i.e. ureases). Flagellin-mediated Toll-like receptor 5 activation was species-specific and D. desulfuricans flagellin downregulated TGF-beta signalling in murine small intestinal organoids, suggesting impaired immune tolerance. Additionally, we investigated genomic capacity for hydrogen sulfide (H2S) production, a main Desulfovibrio metabolite. While health- and disease-associated Desulfovibrio spp. mainly encoded dissimilatory sulfate reduction, tetrathionate metabolism-encoding bacteria were exclusively detected in inflammatory bowel diseases, including Proteus mirabilis and Morganella morganii. Overall, our study provides a comprehensive genomic Desulfovibrio resource and identifies new links associating strain variation, functional traits and H2S-production with inflammatory diseases.

genomics↗

Voluntary Dissociation of Motor Unit Activity in the Vastii Muscles

The CNS coordinates movement through consistent activation patterns across muscles and motor units, suggesting the presence of a relatively fixed and high-dimensional number of neural constraints on voluntary actions. In the human quadriceps, the vastus medialis (VM) and vastus lateralis (VL) control the knee extensor torque and are considered a synergistic pair largely activated by shared neural inputs. However, some evidence suggests that these muscles, or even subregions within them, can be controlled independently. In this study, we investigated whether humans can dissociate neural input to VM and VL during isometric contractions. Ten participants received real-time feedback from multiple intramuscular EMG electrodes that targeted different regions of the VM and VL while attempting to activate each muscle or sub-regions selectively. We found that nine out of ten subjects were able to clearly separate VM and VL activity based on the intramuscular EMG feedback. However, motor unit decomposition from the intramuscular EMGs revealed that selective recruitment of a unique set of motor units was possible only within the proximal region of VM. In contrast, VL and distal VM showed highly correlated activation, indicating tight functional coupling. Correlation analyses confirmed that the proximal VM exhibited distinct activation profiles compared with both distal VM and VL, supporting the existence of compartmentalized control within VM. These findings demonstrate that it is possible to dissociate the activation of motor units within this synergistic muscle group during low-force isometric contractions.

neuroscience↗

A microbial metabolite protects against graft-versus-host disease via mTORC1 and STING-dependent intestinal regeneration

Changes in the intestinal microbiome and microbiota-derived metabolites predict clinical outcomes after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Here, we report that desaminotyrosine (DAT), a product of bacterial flavonoid metabolism, correlates with improved overall survival and reduced relapse rates in allo-HSCT patients. In preclinical mouse models, treatment with synthetic DAT prevents graft-versus-host disease by protecting the intestinal barrier and promoting intestinal regeneration and contributes to graft-vs.-leukemia responses. DATs beneficial effects on intestinal regeneration remain effective despite broad-spectrum antibiotics-induced dysbiosis, also when administered by fecal microbiota transfer with flavonoid-degrading F. plautii. Mechanistically, DAT promotes mTORC1-dependent activation and proliferation of intestinal stem cells, with concomitant engagement of the innate immune receptor STING required to mitigate metabolic stress and maintain an undifferentiated stem cell state independently of type-I interferon responses. Additionally, DAT can skew T cells towards an effector phenotype to modulate graft-versus-leukemia responses. Our data uncover DATs dual, tissue- and immune-modulating properties and underscore its potential in precision microbiome-based therapies to improve tissue regeneration and minimize immune-mediated side effects.

immunology↗

Reduced intestinal GLP-1+ cell numbers are associated with an inflammation-related epithelial metabolic signature

Background & AimsEnteroendocrine cells (EECs) are known for their role in digestion and metabolism, yet their role in intestinal inflammation remains unclear. In inflammatory bowel diseases (IBD), a contribution of EECs to pathogenesis is indicated by autoantibodies affecting EEC function and general disease symptoms like insulin resistance and altered intestinal motility. Particularly, the L cell-derived hormone glucagon-like peptide 1 (GLP-1), suggested to orchestrate metabolic-inflammatory responses may influence inflammatory pathways in the intestine. MethodsWe quantified numbers of GLP-1+ cells in 4 different mouse models of intestinal inflammation and performed transcriptional analyses of colonic epithelial cells from inflamed interleukin (IL)10-deficient mice. Using a publicly available single-cell RNA sequencing dataset including mucosal biopsies from Crohns disease (CD) patients, we confirmed findings from the murine models. A model of mitochondrial dysfunction (ClpP{Delta}IEC mice) as well as murine and human intestinal organoids were used to study molecular mechanisms. ResultsNumbers of GLP-1 expressing cells are consistently reduced at the site of active disease in mouse models and CD patients. Despite this reduction, L cells from inflamed IL-10-deficient mice remained functional regarding GLP-1 secretion. Transcriptional analyses of intestinal epithelial cells indicate altered differentiation correlating with an inflammatory metabolic fingerprint. Reduced GLP-1+ cells in ClpP{Delta}IEC mice and inhibition of respiration in organoid cultures supports a causative role for metabolism in steering differentiation. ConclusionReduction of GLP-1+ cells represents a general feature of ileal and colonic inflammation in mice and human. Given the numerous properties of GLP-1, this reduction likely affects inflammatory processes in the mucosa and disease-related symptoms on multiple levels, and therefore, should be considered a therapeutic target in IBD. Data TransparencyAll data generated or analyzed during this study are included in this published article. Additional datasets, including raw data, are available from the corresponding author upon reasonable request. SynopsisThis study examines GLP-1+ cells in intestinal inflammation, showing consistent reductions in inflamed areas. Findings from mouse models and human data reveal an inflammatory metabolic profile linked to altered epithelial differentiation. GLP-1, involved in endocrine-immune crosstalk, may impact mucosal inflammation and symptoms, making it a therapeutic target. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/641577v2_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@136158borg.highwire.dtl.DTLVardef@1c08461org.highwire.dtl.DTLVardef@332635org.highwire.dtl.DTLVardef@117d5f_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

Susceptibility to inflammatory bowel diseases promotes invasive carcinomas in a murine model of ATF6-driven colon cancer

Chronic inflammation in inflammatory bowel disease (IBD) patients represents a risk factor for developing colitis-associated cancer (CAC). We previously linked the endoplasmic reticulum unfolded protein response (UPRER) signal transducer activating transcription factor 6 (ATF6) with spontaneous microbiota-dependent colonic adenoma development in mice expressing epithelial-specific activated ATF6 (nATF6IEC). To investigate IBD-related risk factors in ATF6-mediated tumorigenesis, we crossed tumor-free monoallelic (tg/wt) nATF6IEC mice with Interleukin-10 deficient mice (Il10-/-). IL10 deficiency initiated tumor susceptibility, with 77% of 12-week tg/wt;Il10-/- mice developing colonic adenomas and invasive carcinomas in this novel CAC mouse model. Tumor formation correlated with mucosal immune cell infiltration, characterized by CD11b+ granulocytes and monocytes, and mucosa-associated dysbiosis. Colonization of germ-free nATF6IEC;Il10-/- mice with minimal biosynthetic consortia and IBD stool re-established CAC, confirming microbiota-dependent ATF6-driven tumorigenesis. Increased ATF6 expression in IBD patients during active disease highlights its human relevance. Our findings show that IBD susceptibility heightens the risk for ATF6-driven tumorigenesis. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=103 SRC="FIGDIR/small/624835v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@17e280eorg.highwire.dtl.DTLVardef@177ceacorg.highwire.dtl.DTLVardef@a1916borg.highwire.dtl.DTLVardef@152374f_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

Microbiota metabolized Bile Acids accelerate Gastroesophageal Adenocarcinoma via FXR inhibition

BackgroundThe incidence of Barrett esophagus (BE) and Gastroesophageal Adenocarcinoma (GEAC) correlates with obesity and a diet rich in fat. Bile acids (BA) support fat digestion and undergo microbial metabolization in the gut. The farnesoid X receptor (FXR) is an important modulator of the BA homeostasis. The capacity of inhibiting cancer-related processes when activated, make FXR an appealing therapeutic target. In this work, we assess the role of diet on the microbiota-BA axis and evaluate the role of FXR in disease progression. ResultsHere we show that high fat diet (HFD) accelerated tumorigenesis in L2-IL1B mice (BE- and GEAC- mouse model) while increasing BA levels and enriching gut microbiota that convert primary to secondary BA. While upregulated in BE, expression of FXR was downregulated in GEAC in mice and humans. In L2-IL1B mice, FXR knockout enhanced the dysplastic phenotype and increased Lgr5 progenitor cell numbers. Treatment of murine organoids and L2-IL1B mice with the FXR agonist obeticholic acid (OCA) deacelerated GEAC progression. ConclusionWe provide a novel concept of GEAC carcinogenesis being accelerated via the diet-microbiome-metabolome axis and FXR inhibition on progenitor cells. Further, FXR activation protected with OCA ameliorated the phenotype in vitro and in vivo, suggesting that FXR agonists have potential as differentiation therapy in GEAC prevention. Statement of significanceIf its inhibition is linked to disease progression and its activation to cancer prevention, exploring the potential of FXR as a therapeutic target has great clinical relevance in GEAC context.

cancer biology↗

Endoplasmic reticulum stress signaling actively contributes to therapy resistance in colorectal cancer

PurposeWe investigated the involvement of endoplasmic reticulum (ER) stress signaling in cancer cell responses to chemo- and radiotherapy, focusing on three main ER stress mediators, the transcription factors ATF4, XBP1 and ATF6. MethodsPublic cancer genome datasets were assessed for alterations in ER stress mediators. Surgically resected colorectal cancer tissues were tested by flow cytometry and used to generate patient-derived organoids. Human cell lines and organoids were characterized under oxaliplatin treatment, alone or combined with pharmacological inhibitors of the three ER stress branches, or X-ray irradiation, for cytotoxicity, activation of ER stress and proteome changes. To monitor ER stress in real time, stable HEK293 kidney epithelial cell lines were established expressing ATF4, XBP1, or ATF6, fused with a fluorophore. ResultsGenomic amplification of ATF6, but not ATF4 or XBP1, was frequent in solid tumor entities like breast, lung and colorectal cancer and significantly associated with reduced disease-free survival. In colorectal cancer, increased ATF6 was associated with genetic instability. Basal ER stress mediator expression was correlated to chemoresistance in colorectal cancer cell lines, and generally high in cancer cells compared to HEK293 cells. With proteomics and live HEK293-based reporter lines, we noted that oxaliplatin treatment induced ER stress in a remarkably different way from the canonical ER stress inducer thapsigargin. Moreover, modulation of ER stress signaling by exogenous expression of the stress mediators positively affects chemoresistance, and pharmacological inhibition of ATF6 sensitizes ER-stressed HCT116 colorectal cancer cells to chemotherapy. Of note, cellular stress responses was strongly dependent on the individual transcription factor: XBP1-driven response appeared multi-functional, involved in ribosome biogenesis stress and associated with oxaliplatin resistance. ATF6-dependent stress signaling was involved in DNA damage repair, and was essential for radioresistance. Moreover, chemoresistance in HCT116 cancer cells was impaired by pharmacological ATF6 inhibition. ConclusionActivation of the ER stress signaling may be critically involved in acquired chemo- and radioresistance. Due to their apparent cytoprotective roles, ATF6 and XBP1 could be attractive predictive biomarkers and putative therapeutic targets. SUMMARYTo address their roles in the clinical context, genomic alterations of ATF4, XBP1 and/or ATF6 in human solid tumors were assessed with respect to prognosis and genomic instability. Moreover, surgically resected CRC patient tissues were tested for expression of ER stress markers by flow cytometry and associated with clinical characteristics. In addition, a panel of human cell lines and patient-derived colon organoids were characterized under therapeutic conditions for expression and activation of ER stress proteins, and resulting cytotoxicity was determined. To monitor and modulate ER stress activation in live cells with subcellular resolution, stable reporter cell lines expressing ATF4, sXBP1 or ATF6 proteins fused with a fluorophore were established. These lines were tested for gene or protein expression and cytotoxicity assays to analyze how activation or inhibition of ER stress proteins affects the cellular responses to oxaliplatin treatment or X-ray irradiation. Finally, mass spectrometric proteome analysis was performed to obtain an unbiased readout on the cellular responses to chemotherapy driven by the activation of the ER stress proteins.

cancer biology↗

On the limits of 16S rRNA gene-based metagenome prediction and functional profiling

Molecular profiling techniques such as metagenomics, metatranscriptomics or metabolomics offer important insights into the functional diversity of the microbiome. In contrast, 16S rRNA gene sequencing, a widespread and cost-effective technique to measure microbial diversity, only allows for indirect estimation of microbial function. To mitigate this, tools such as PICRUSt2, Tax4Fun2, PanFP and MetGEM infer functional profiles from 16S rRNA gene sequencing data using different algorithms. Prior studies have cast doubts on the quality of these predictions, motivating us to systematically evaluate these tools using matched 16S rRNA gene sequencing, metagenomic datasets, and simulated data. Our contribution is threefold: (i) using simulated data, we investigate if technical biases could explain the discordance between inferred and expected results; (ii) considering human cohorts for type 2 diabetes, colorectal cancer and obesity, we test if health-related differential abundance measures of functional categories are concordant between 16S rRNA gene-inferred and metagenome-derived profiles and; (iii) since 16S rRNA gene copy number is an important confounder in functional profiles inference, we investigate if a customised copy number normalisation with the rrnDB database could improve the results. Our results show that 16S rRNA gene-based functional inference tools generally do not have the necessary sensitivity to delineate health-related functional changes in the microbiome and should thus be used with care. Furthermore, we outline important differences in the individual tools tested and offer recommendations for tool selection.

bioinformatics↗

ATF6 activation alters colonic lipid metabolism causing tumor-associated microbial adaptation

Endoplasmic reticulum unfolded protein responses (UPRER) contribute to cancer development and the activating transcription factor 6 (ATF6) is involved in microbiota-dependent tumorigenesis. Here, we substantiate the clinical relevance of ATF6 in early-onset and late colorectal cancer patient cohorts. Transcriptional analysis in intestinal epithelial cells (IEC) of ATF6 transgenic mice (nATF6IEC) identified bacteria-specific changes in cellular metabolism enriched for fatty acid biosynthesis. Untargeted metabolomics and isotype-labeling confirmed ATF6-related enrichment of long chain fatty acids in colonic tissue of patients, mice and organoid cultures. FASN inhibition and microbiota transfer in germ-free nATF6IEC mice confirmed the causal involvement of ATF6-induced lipid alterations in tumorigenesis. The selective expansion of tumor-relevant microbial taxa was mechanistically linked to long chain fatty acid exposure, using bioorthogonal non-canonical amino acid tagging (BONCAT) and growth analysis of Desulfovibrio isolates. We postulate chronic ATF6 signaling in the epithelium to select for tumor-promoting microbiota by altering lipid metabolism. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=126 SRC="FIGDIR/small/565267v2_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@be3756org.highwire.dtl.DTLVardef@231da4org.highwire.dtl.DTLVardef@16f3aaeorg.highwire.dtl.DTLVardef@1758fe3_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract:C_FLOATNO Chronic ATF6 signaling in the colonic epithelium alters lipid metabolism to select a tumor-promoting microbiota C_FIG O_LIBiallelic expression of activated ATF6 (p50 nuclear fragment) in intestinal epithelial cells (nATF6IEC) induces spontaneous colon tumors in SPF but not GF mice C_LIO_LIMechanistically, biallelic SPF nATF6IEC mice alter colonic lipid metabolism, including the upregulation of LCFAs and Fasn C_LIO_LIInhibition of FASN prevents colon tumor formation in mice, and reduces the tumor-promoting potential of the intestinal microbiota (FMT) C_LIO_LIExposure of fl/fl control mouse microbiota to LCFAs ex vivo translationally activates tumor-associated bacteria, including Desulfovibrio fairfieldensis C_LIO_LIHuman CRC patients show ATF6 upregulation, FASN co-occurrence and increased LCFAs in T tissue C_LIO_LIATF6 activity links with CRC-associated microbiota in patients, including Desulfovibrio C_LI Created with BioRender.com nATF6: activated activating transcription factor 6; LCFA: long-chain fatty acids; SAFA: saturated fatty acids; Fasn: fatty acid synthase; C75 i.p.: intraperitoneal injection of the Fasn inhibitor C75.

cancer biology↗

Diurnal rhythmicity of fecal microbiota and metabolite profiles in the first year of life: a randomized controlled interventional trial with infant formula

Microbiota assembly in the infant gut is influenced by time and duration of dietary exposure to breast-milk, infant formula and solid foods. In this randomized controlled intervention study, longitudinal sampling of infant stool (n=998) showed similar development of fecal bacterial communities (16S rRNA/shallow metagenomics sequencing) between formula- and breast-fed infants during the first year of life (N=210). Infant formula supplemented with galacto-oligosaccharides (GOS) was most efficient to sustain high levels of bifidobacteria compared to formula containing B. longum and B. breve or placebo. In addition to primary endpoints, metabolite and bacterial profiling revealed 24-hour oscillations and data integration identified circadian networks. Rhythmicity in bacterial diversity, specific taxa and functional pathways increased with age and was strongest following breast-feeding and GOS-supplementation. Circadian rhythms in dominant taxa were discovered ex-vivo in a chemostat model. Hence, microbiota rhythmicity develops early in life, likely via bacterial intrinsic clock mechanism and is affected by diet.

microbiology↗

Mitochondrial perturbation of the epithelium causes microbial dysbiosis and unresolved tissue injury in intestinal inflammation

Mitochondrial dysfunction is associated with inflammatory bowel diseases (IBD). To understand how microbial-metabolic circuits contribute to intestinal tissue injury, we disrupt mitochondrial function in the epithelium by deleting heat shock protein 60 (Hsp60{Delta}/{Delta}IEC). While metabolic perturbation causes self-resolving tissue injury, regeneration is disrupted in the absence of aryl hydrocarbon receptor (Hsp60{Delta}/{Delta}IEC;AhR-/-) or IL-10 (Hsp60{Delta}/{Delta}IEC;Il10-/-) leading to IBD-like pathology. Injury is absent in the distal colon of germ-free (GF) Hsp60{Delta}/{Delta}IEC mice, highlighting bacterial control of metabolic injury. Selective colonization of GF Hsp60{Delta}/{Delta}IEC mice with the synthetic community OMM12 confirms consistent expansion of metabolically-flexible Bacteroides spp. across all models and mono-colonization with B. caecimuris recapitulates injury. Transcriptional profiling of metabolically-impaired epithelium identifies gene signatures, including Ido1, Nos2, and Duox2, distinguishing active from inactive tissue inflammation in 343 resected samples from Crohns disease patients. In conclusion, mitochondrial perturbation of the epithelium causes microbiota-dependent tissue injury and discriminative inflammatory gene profiles relevant for IBD. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=171 SRC="FIGDIR/small/549844v6_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@240c5forg.highwire.dtl.DTLVardef@a84382org.highwire.dtl.DTLVardef@e829e3org.highwire.dtl.DTLVardef@163625_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract:C_FLOATNO Control of metabolic injury by microbial signals. C_FIG O_LIMitochondrial perturbation of the intestinal epithelium induces tissue injury C_LIO_LILoss of IL-10 and AhR-related host mechanisms accelerate injury and inflammation C_LIO_LIMitochondrial dysfunction induces dysbiosis and expansion of Bacteroides spp. C_LIO_LIMetabolic injury gene signature discriminates inflamed vs. non-inflamed IBD samples C_LI

microbiology↗