BIBBOX, a FAIR toolbox and App Store for life science research

Data quality has recently become a critical topic for the research community. European guidelines recommend that scientific data should be made FAIR: findable, accessible, interoperable and reusable. However, as FAIR guidelines do not specify how the stated principles should be implemented, it might not be straightforward for researchers to know how actually to make their data FAIR. This can prevent life-science researchers from sharing their datasets and pipelines, ultimately hindering the progress of research. To address this difficulty, we developed the BIBBOX, which is a platform that supports researchers publishing their datasets and the associated software in a FAIR manner.

Hepatic farnesoid X receptor is necessary to facilitate ductular reaction and expression of heme biosynthetic genes

BACKGROUND

Bile, which contains bile acids, the natural ligands for farnesoid x receptor (FXR), moves from the liver to the intestine through bile ducts. Ductular reaction often occurs during biliary obstruction. A subset of patients with erythropoietic protoporphyria, an inherited genetic mutation in heme biosynthetic enzyme ferrochelatase, accumulate porphyrin-containing bile plugs, leading to cholestasis. Here, we examined the link between FXR, bile plug formation, and how heme biosynthesis relates to this connection.

METHODS

We treated female and male wild-type and global and tissue-specific Fxr knockout mice with a diet containing 3,5-diethoxycarbonyl-1,4-dihydrocollidine, an inhibitor of ferrochelatase, and examined the expression of heme biosynthetic genes. We mined FXR mouse ChIP-Seq data, performed biochemical and histological analysis, and tested HepG2 and primary human hepatocytes after treatment with obeticholic acid, an FXR agonist.

RESULTS

We observed that hepatic but not intestinal Fxr loss resulted in reduced bile plugs and ductular reaction in the liver. Then, we examined if FXR plays a regulatory role in heme biosynthesis and found significantly lower porphyrin accumulation in 3,5-diethoxycarbonyl-1, 4-dihydrocollidine-fed Fxr knockout mice. Gene expression and FXR mouse ChIP-Seq atlas analysis revealed that FXR orchestrates the expression of multiple heme biosynthetic enzymes. Finally, human HepG2 cells and primary human hepatocytes treated with obeticholic acid, showed increased expression of several heme biosynthetic genes.

CONCLUSIONS

Overall, our data show that hepatic Fxr is necessary to maintain ductular reaction and accumulation of bile plugs. FXR can direct the expression of multiple heme biosynthetic genes. Thus, modulating FXR activity in EPP patients may help alleviate its associated liver disease.

Colorectal cancer risk stratification on histological slides based on survival curves predicted by deep learning

Studies have shown that colorectal cancer prognosis can be predicted by deep learning-based analysis of histological tissue sections of the primary tumor. So far, this has been achieved using a binary prediction. Survival curves might contain more detailed information and thus enable a more fine-grained risk prediction. Therefore, we established survival curve-based CRC survival predictors and benchmarked them against standard binary survival predictors, comparing their performance extensively on the clinical high and low risk subsets of one internal and three external cohorts. Survival curve-based risk prediction achieved a very similar risk stratification to binary risk prediction for this task. Exchanging other components of the pipeline, namely input tissue and feature extractor, had largely identical effects on model performance independently of the type of risk prediction. An ensemble of all survival curve-based models exhibited a more robust performance, as did a similar ensemble based on binary risk prediction. Patients could be further stratified within clinical risk groups. However, performance still varied across cohorts, indicating limited generalization of all investigated image analysis pipelines, whereas models using clinical data performed robustly on all cohorts.

Understanding and Explaining Diagnostic Paths: Toward Augmented Decision Making

The process of finding a diagnosis in the medical domain relies on implicit knowledge and the experience of a human expert. In this article, we report on the observation of human decision making, shown by the example of pathology. By tracking the diagnostic steps, individual building blocks are identified, which not only contribute to a diagnostic finding, but can also be used in the future to train and develop artificial intelligence (AI) algorithms. This work also provides insights into the interaction of human experts regarding the observation time of so-called "hot spots," the magnification used for specific findings, and the overall observation and decision path followed. The documentation scheme yields a standardized examination procedure that shows the concept the pathologist is actually looking for as well as the possible features of findings that can be identified. This contribution indicates how important visualization is for human-centered AI, and specifically for enabling human oversight with respect to AI implementation in high-stake areas, such as medicine.

RF03 | PMON288 Determining Mechanisms of Farnesoid×Receptor Regulation of Heme Biosynthesis and Ductular Reaction

Bile acids are increasingly becoming recognized as hormones, and their main endogenous receptor is the farnesoid X receptor (FXR). In order to investigate whether FXR is necessary to maintain proliferation of the bile ducts in response to injury, we challenged male and female wild-type (WT) and Fxr knockout (FxrKO) mice with 0.1% 1,4 dihydro 2,4,6 trimethyl 3,5 pyridinediacarboxylic acid diethyl ester (DDC) in the diet for two weeks. DDC is an inhibitor of ferrochelatase, the final enzyme of heme biosynthesis, resulting in a buildup of bile plugs in the liver causing an inflammatory response called ductular reaction. We found that deletion of Fxr led to a dramatic reduction in the ductular reaction independent of the sex. Then we tested if the inhibition of ferrochelatase was compensated for in FxrKO mice by analyzing the expression of genes in the heme biosynthesis pathway. Although we find a decrease in basal Alad gene expression in FxrKO mice in both sexes, upon DDC treatment, expression does not decrease as much as seen in the WT mice. Intriguingly, we also noted sex-specific changes. Cpox expression was increased in male FxrKO mice, but FxrKO mice showed reduced suppression of Cpox expression when treated with DDC. Conversely, Ppox expression was reduced in male FxrKO mice compared to WT mice, and both male WT and FxrKO mice had a comparable reduction in Ppox expression upon DDC treatment. Female FxrKO mice showed a significant decrease in Fech expression basally that did not change with DDC treatment. These results suggest that FXR may contribute towards regulating expression of genes in the heme biosynthesis pathway. However, these observations do not explain the lack of ductular reaction. Since PGC1α was previously shown to control heme biosynthesis through its downstream targets, FOXO1 and NRF1, we examined their transcript expression in our study to determine if the pathway is playing a role in our observations. We examined this pathway and observed a significant decrease in Foxo1 expression in both sexes of WT and FxrKO mice basally but only a reduction in Nrf1 expression upon DDC treatment. We are currently investigating other potential regulators of heme biosynthesis and ductular reaction, such as Klf1 which regulates erythropoiesis and plays a role in ductular reaction and the nuclear receptors Rev-Erbα/β that use heme as a ligand, to determine how FXR is regulating heme biosynthesis.

Presentation: Saturday, June 11, 2022 1:24 p.m. - 1:29 p.m., Monday, June 13, 2022 12:30 p.m. - 2:30 p.m.

Meta-analysis and Consolidation of Farnesoid X Receptor Chromatin Immunoprecipitation Sequencing Data Across Different Species and Conditions

Farnesoid X receptor (FXR) is a nuclear receptor that controls gene regulation of different metabolic pathways and represents an upcoming drug target for various liver diseases. Several data sets on genome-wide FXR binding in different species and conditions exist. We have previously reported that these data sets are heterogeneous and do not cover the full spectrum of potential FXR binding sites. Here, we report the first meta-analysis of all publicly available FXR chromatin immunoprecipitation sequencing (ChIP-seq) data sets from mouse, rat, and human across different conditions using a newly generated analysis pipeline. All publicly available single data sets were biocurated in a standardized manner and compared on every relevant level from raw reads to affected functional pathways. Individual murine data sets were then virtually merged into a single unique "FXR binding atlas" spanning all potential binding sites across various conditions. Comparison of the single biocurated data sets showed that the overlap of FXR binding sites between different species is modest and ranges from 48% (mouse-human) to 55% (mouse-rat). Moreover, in vivo data among different species are more similar than human in vivo data compared to human in vitro data. The consolidated murine global FXR binding atlas virtually increases sequencing depth and allows recovering more and novel potential binding sites and signaling pathways that were missed in the individual data sets. The FXR binding atlas is publicly searchable (https://fxratlas.tugraz.at). Conclusion: Published single FXR ChIP-seq data sets and large-scale integrated omics data sets do not cover the full spectrum of FXR binding. Combining different individual data sets and creating an "FXR super-binding atlas" enhances understanding of FXR signaling capacities across different conditions. This is important when considering the potential wide spectrum for drugs targeting FXR in liver diseases.

Investigating the Role of Farnesoid X Receptor in Heme Biosynthesis and Ductular Reaction

Bile acids (BAs) have gained traction not just as emulsifiers of fat, but also as hormones. Nuclear receptor Farnesoid X receptor (FXR) is the master regulator of BAs and can also control glucose and lipid metabolism. We examined if FXR contributed towards heme biosynthesis and induction of a ductular reaction. Male and female whole body Fxr knockout (FxrKO) mice, as well as liver- and intestine-specific knockouts (LFxrKO and IFxrKO, respectively) were treated with 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC, a ferrochelatase inhibitor) for two weeks. At the end of the two weeks, mice were fasted for four hours and euthanized. All groups of mice had lost a similar percentage of body weight when fed the DDC diet. However, female FxrKO mice had significantly increased liver to body weight ratio, while male FxrKO mice had significantly decreased liver to body weight ratio when fed the DDC diet compared with their wild type counterparts. Serum liver injury markers were analyzed and liver histology and changes in genes involved in the heme biosynthesis pathway were examined. Both male and female whole body FxrKO livers had decreased ductular reaction with minimal bile plugs (porphyrin accumulation) compared with their wild type counterparts. LFxrKO mice mimicked diminished ductular reaction, while IFxrKO mice exhibited severe ductular reaction similar to that of wild type mice, indicating that the ductular reaction is dependent on hepatic FXR. ChIP-Seq for FXR revealed binding peaks in the heme biosynthesis genes, Alas1, Alad, Uros, and Fech, suggesting that FXR may act as a transcription factor for these genes. Further investigation revealed that Pbgd gene expression was increased, while Fech gene expression was decreased in female FxrKO mice compared to wild type mice. In male mice, Pbgd, Uros, Urod, and Cpox gene expression was increased in the absence of Fxr. In conclusion, Fxr is necessary to mount a ductular reaction and plays a key role in heme biosynthesis in the liver.

A Comprehensive FXR Signaling Atlas Derived from Pooled ChIP-seq Data

BACKGROUND

ChIP-seq is a method to identify genome-wide transcription factor (TF) binding sites. The TF FXR is a nuclear receptor that controls gene regulation of different metabolic pathways in the liver.

OBJECTIVES

To re-analyze, standardize and combine all publicly available FXR ChIP-seq data sets to create a global FXR signaling atlas.

METHODS

All data sets were (re-)analyzed in a standardized manner and compared on every relevant level from raw reads to affected functional pathways.

RESULTS

Public FXR data sets were available for mouse, rat and primary human hepatocytes in different treatment conditions. Standardized re-analysis shows that the data sets are surprisingly heterogeneous concerning baseline quality criteria. Combining different data sets increased the depth of analysis and allowed to recover more peaks and functional pathways.

CONCLUSION

Published single FXR ChIP-seq data sets do not cover the full spectrum of FXR signaling. Combining different data sets and creating a "FXR super-signaling atlas" enhances understanding of FXR signaling capacities.