PSC study

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Authors and affiliations

Lukas Bajer^1,*, Petra Polakovičova^2,11*, Marie Heczkova², Kristian Holm^4,5,6 Mikal J. Hole^4,5,6, Mojmir Hlavaty¹, Alena Bohdanecka², Pavel Drastich¹, Filip Tichanek³, Malin H. Meyer-Myklestad⁷, Asle W. Medhus^5,8, Dag Henrik Reikvam^5,7, Kristin K. Jørgensen^4,5,9, Jan Brezina¹, Peter Macinga¹, Pavel Wohl¹, Johannes R. Hov^4,5,6,10,#, Monika Cahova^2,#

^* These authors have contributed equally to this work and share first authorship
^# These authors have contributed equally to this work and share last authorship

¹ Institute for Clinical and Experimental Medicine, Department of Hepatogastroenterology, Prague ² Institute for Clinical and Experimental Medicine, Center for Experimental Medicine, Prague ³ Institute for Clinical and Experimental Medicine, Department of Data Science, Prague ⁴ Norwegian PSC Research Center, Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway ⁵ Institute of Clinical Medicine, University of Oslo, Oslo, Norway ⁶ Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway ⁷ Department of Infectious Diseases, Division of Medicine, Oslo University Hospital, Oslo, Norway ⁸ Department of Gastroenterology, Division of Medicine, Oslo University Hospital, Oslo, Norway ⁹ Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway ¹⁰ Section of Gastroenterology, Depatrment of Transplantation Medicine, Oslo University Hospital, Oslo, Norway ¹¹ Faculty of Science, Charles University, Prague, Czech Republic

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General information

This repository provides a comprehensive report of the study Geography-independent mucosal microbiota alterations in primary sclerosing cholangitis persist after liver transplantation

All reported results can be reproduced using the code in this repository. Feel free to contact Petra Polakovicova by petra.polakovicova@ikem.cz if you have any questions about the computational part of the study.

📚 Citation

If you find this code and report helpful, cite the original publication:

TO BE ADDED

💾 Data Availability

• Czech cohort:

SRA PRJNA1250244

• Norwegian cohort:

10.1002/hep.32773

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Report info

This project analyses biopsy samples from two cohorts (Czech and Norwegian), namely data from amplicon sequencing of the 16S rRNA gene (region V3-V4) and related clinical parameters relevant to PSC disease. 370 subjects are included, from whom a total of 1083 samples were collected.

📁 Project Structure

Below is an overview of the folder structure:

• scripts/ - Source code for bioinformatics processing of raw sequencing data to ASV taxonomic tables (mainly bash scripts)

• analysis/

  • scripts/

    • merged_sites/ – scripts for analyzing the data of terminal ileum and colon sites
      • main_analysis/ – main part of analysis, whose results are directly reported in the publication
      • supplementary_analysis/ – additional part of the analysis, where different methods or metrics were used
    • split_sites/ – scripts for analyzing the data of terminal ileum, left_colon and right_colon sites

  • results/ – results generated directly via provided scripts

Methodology

🧬🖥️ Bioinformatics processing

TO BE ADDED

📊📈 Statistical analysis

TO BE ADDED

📑✔️ ## Results

The code with reported results can be found:

• Q1_analysis: reports the comparison of pre-LTx, post-LTx, and HC
• Q2_analysis: reports the comparison of rPSC vs. non-rPSC
• Q3_analysis: reports the comparison of IBD vs. non-IBD
• Q5_analysis: reports the comparison between patients with low and high fecal calprotectin values
• MDI_analysis: calculation and exploration of the microbiome dysbiosis index
• ALD_analysis: reports the comparison between Czech ALD and PSC samples
• clinical_analysis: explores associations between the microbiome and clinical features
• ML_overfitting_check: reports all models used in this study and shows the results with reshuffled labels, confirming that the original datasets perform well

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Acknowledgment

This study was supported by grant MH CR no. NU21J-06-00027, by the project National Institute for Research of Metabolic and Cardiovascular Diseases (Programme EXCELES, Project No. LX22NPO5104) - Funded by the European Union - Next Generation EU and by MH CR –DRO (Institute for Clinical and Experimental medicine –IKEM, IN 00023001”). JRH was funded by the European Research Council (StopAutoimmunity, no. 802544).