Front matter

Preface

This work is based on three published manuscripts, each forming a separate chapter. I am the sole lead author of all of them as I have performed the vast majority of all computational analyses and have written every manuscript myself.

The following manuscripts are included as part of this thesis

  1. Holland CH, Szalai B, Saez-Rodriguez J. “Transfer of regulatory knowledge from human to mouse for functional genomics analysis.” Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms. (2020). DOI: 10.1016/j.bbagrm.2019.194431.

  2. Holland CH, Tanevski J, Perales-Patón J, Gleixner J, Kumar MP, Mereu E, Joughin BA, Stegle O, Lauffenburger DA, Heyn H, Szalai B, Saez-Rodriguez, J. “Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data.” Genome Biology. (2020). DOI: 10.1186/s13059-020-1949-z.

  3. Holland CH, Ramirez Flores RO, Myllys M, Hassan R, Edlund K, Hofmann U, Marchan R, Cadenas C, Reinders J, Hoehme S, Seddek A, Dooley S, Keitel V, Godoy P, Begher-Tibbe B, Trautwein C, Rupp C, Mueller S, Longerich T, Hengstler JG#, Saez-Rodriguez J#, Ghallab A#. “Transcriptomic cross-species analysis of chronic liver disease reveals consistent regulation between humans and mice.” Hepatology Communications. (2021). DOI: 10.1002/hep4.1797.

Other publications that I have contributed to but are not presented in this thesis

Next to these three main projects, I contributed during my candidature also to several other projects that are not directly related to the topic of this thesis, but still made up an essential part of my Ph.D.

  1. Garcia-Alonso L, Holland CH, Ibrahim MM, Turei D, Saez-Rodriguez J. “Benchmark and integration of resources for the estimation of human transcription factor activities.” Genome Research. (2019). DOI: 10.1101/gr.240663.118.

  2. Szalai B, Subramanian V, Holland CH, Alföldi R, Puskás LG, Saez-Rodriguez J. “Signatures of cell death and proliferation in perturbation transcriptomics data - from confounding factor to effective prediction.” Nucleic Acids Research. (2019). DOI: 10.1093/nar/gkz805.

  3. Ghallab A, Myllys M, Holland CH, Zaza A, Murad W, Hassan R, Ahmed YA, Abbas T, Abdelrahim EA, Schneider KM, Matz-Soja M, Reinders J, Gebhardt R, Berres ML, Hatting M, Drasdo D, Saez-Rodriguez J, Trautwein C, Hengstler JG. “Influence of Liver Fibrosis on Lobular Zonation.” Cells. (2019). DOI: 10.3390/cells8121556.

  4. Tajti F*, Kuppe C*, Antoranz A, Ibrahim MM, Kim H, Ceccarelli F, Holland CH, Olauson H, Floege J, Alexopoulos LG, Kramann R, Saez-Rodriguez J. “A functional landscape of chronic kidney disease entities from public transcriptomic data.” Kidney International Reports. (2020). DOI: 10.1016/j.ekir.2019.11.005.

  5. Mohs A, Otto T, Schneider KM, Peltzer M, Boekschoten M, Holland CH, Hudert CA, Kalveram L, Wiegand S, Saez-Rodriguez J, Longerich T, Hengstler JG, Trautwein C. “Hepatocyte-specific NRF2 activation controls fibrogenesis and carcinogenesis in steatohepatitis.” Journal of Hepatology. (2020). DOI: 10.1016/j.jhep.2020.09.037.

  6. Ramirez Flores RO*, Lanzer JD*, Holland CH, Leuschner F, Most P, Schultz J-H, Levinson RT#, Saez-Rodriguez J#. “Consensus Transcriptional Landscape of Human End-Stage Heart Failure.” Journal of the American Heart Association. (2021). DOI: 10.1161/JAHA.120.019667.

  7. Lopez-Dominguez R, Toro-Dominguez D, Martorell-Marugan J, Garcia-Moreno A, Holland CH, Saez-Rodriguez J, Goldman D, Petri M, Alarcón-Riquelme ME#, Carmona-Sáez P#.Transcription Factor Activity Inference in Systemic Lupus Erythematosus.” Life. (2021). DOI: 10.3390/life11040299.

  8. Robrahn L, Dupont A, Jumpertz S, Zhang K, Holland CH, Guillaume J, Rappold S, Roth J, Cerovic V, Saez-Rodriguez J, Hornef MW, Cramer T. “Stabilization but no functional influence of HIF-1a expression in the intestinal epithelium during Salmonella Typhimurium infection.” Infection and Immunity. (2022). DOI: 10.1128/iai.00222-21.

  9. Hernansaiz-Ballesteros R, Holland CH, Dugourd A, Saez-Rodriguez J. “FUNKI: Interactive functional footprint-based analysis of omics data.” Bioinformatics. (2022). DOI: 10.1093/bioinformatics/btac055.

  10. Badia-i-Mompel P, Vélez J, Braunger J, Geiss C, Dimitrov D, Müller-Dott S, Taus P, Dugourd A, Holland CH, RO Ramirez Flores, Saez-Rodriguez J. “decoupleR: Ensemble of computational methods to infer biological activities from omics data.” Bioinformatics Advances. (2022). DOI: 10.1093/bioadv/vbac016.

  11. Schneider KM*, Mohs A*, Gui W, Gálvez EJC, Candels LS, Hoenicke L, Muthukumarasamy U, Holland CH, Elfers C, Kilic K, Schneider CV, Schierwagen R, Strnad P, Wirtz TH, Marschall HU, Latz E, Lelouvier B, Saez-Rodriguez J, de Vos W, Strowig T, Trebicka J and Trautwein C. “Imbalanced gut microbiota fuels hepatocellular carcinoma development by shaping the hepatic inflammatory microenvironment.” Nature Communications. (2022). DOI: 10.1038/s41467-022-31312-5.

*Shared first authorship #Shared senior authorship

All of these fruitful and successful collaborations, which I have either led or contributed to, have made it possible for me to meet many fantastic scientists around the world, as illustrated in my collaboration network (Figure 0.1). This list of people is by no means exhaustive but just highlights the personal known collaborators with whom I have published joint scientific articles.

My Ph.D. collaboration network. Edge width corresponds to the number of joined publications. As my supervisor Julio Saez-Rodriguez was involved in all my collaborations we are represented in the network by a single node.

Figure 0.1: My Ph.D. collaboration network. Edge width corresponds to the number of joined publications. As my supervisor Julio Saez-Rodriguez was involved in all my collaborations we are represented in the network by a single node.

Acknowledgements

When I started my Ph.D. back in May 2017 in Aachen I would have never expected to finally submit my thesis four years later at Heidelberg University. Looking back, I am thankful for every experience and memory I was able to collect that allowed me to grow as an early career researcher but also as a human being. However, I would never have achieved anything presented in this thesis just on my own. Professionally and privately I was always fortunate to be accompanied by many patient, supportive, and friendly persons, I would like to thank here:

First of all, I wish to express my deepest gratitude to my doctoral supervisor Prof. Dr. Julio Saez-Rodriguez who gave me the chance to perform my studies in his lab. Throughout this entire time, I felt welcomed and respected. His liberal way of leading the lab promoted a great working atmosphere I have never experienced before to this extent. I truly enjoyed the freedom and always felt safe if things went badly or ended up in a dead-end. Moreover, through the open-door sessions, Julio was reachable on a daily basis which I definitely don’t take for granted. In summary, Julio was the best supervisor I could have imagined and I deeply cherished the time I was allowed to spend in his lab.

Also, I am indebted to my faculty supervisor Prof. Dr. Ursula Klingmüller. Though it was not possible to share my entire Ph.D. process from the beginning with you due to the movement from Aachen to Heidelberg, I am nevertheless thankful for the lively discussions and feedback I received in the remaining time. Also, I would like to thank Prof. Dr. Robert Russell who kindly agreed to act as the chair of my thesis advisory committee. Lastly, I thank Prof. Dr. Karsten Rippe who completes my thesis advisory committee.

Next, I am thankful for every past and current “saezlab” member who made this time very special and makes me now also kind of sad that this time has come to an end.

In particular, I wish to show my gratitude to the former postdoc Dr. Bence Szalai who especially during the first two years took care of me from my very first day. Just like Julio Bence has the talent to generate a psychologically safe and motivating environment. In the end, Bence’s unwavering support and supervision were an existential decisive factor for my scientific and personal development. I am more than happy that our joyful collaboration was successfully crowned by several joint publications.

Also, I would like to thank other lab members who always felt much more like friends than colleagues: Alberto, Attila, Aurélien, Hyojin, Javier, Jovan, Luis, Nico, Mi, Olga, Rico, Rosa. All of you contributed in your own way to my Ph.D. Either with scientific discussions, valuable and highly appreciated contributions to my projects, or with fun activities outside of the office. Although I am no longer in contact with all of you, I am more than happy to have met you and will keep our time in the lab in memory.

I also wish to acknowledge the significant contributions of my many collaborators, without them the completion of my thesis would not have been possible. In particular, I would like to mention Prof. Dr. Jan Hengstler from Dortmund University who especially supported me in my liver disease-related project. With his outstanding knowledge of liver physiology, he complemented my bioinformatics analyses so we formed a successful and fruitful interdisciplinary collaboration.

Furthermore, I would like to thank the open-source software community who partially on a voluntary basis develop and maintain software. Without this community, my work would not have been possible.

Also I am especially grateful to my family who has supported me ever since.

Last but not least I wish to express my deepest gratitude to my girlfriend Laura: Laura, ich danke Dir von ganzem Herzen, dafür, dass du mir tagtäglich zur Seite standest und mir über all die Jahre den Rücken freigehalten hat, sodass ich mich, wenn es drauf ankam, voll und ganz auf meine Promotion fokussieren konnte. Auch hast du mich stets in all meinen, teils sehr weitreichenden, Entscheidungen unterstützt, wie z.B. der Entschluss, dass ich mit der Arbeitsgruppe nach Heidelberg umziehe und insgesamt für knapp 2 Jahre jede zweite Woche in Heidelberg verbracht habe, oder die Entscheidung für ein halbes Jahr in die Schweiz zu ziehen um Industrieerfahrung zu sammeln. Und selbst wenn ich dann zuhause war habe ich abends dann doch noch regelmäßig vor dem Laptop gesessen und “noch schnell eine Mail geschrieben” oder “nur kurz eine Idee ausprobiert”. Zum jetzigen Zeitpunkt steht es noch nicht fest wo unsere nächste gemeinsame Station sein wird, aber wo auch immer es ist, wir werden dort zusammen sein. Ich liebe dich.

Abstract

High-throughput techniques such as microarrays and RNA-sequencing enable the relatively easy and inexpensive collection of bulk gene expression profiles from any biological condition. Recently, also the transcriptome of single cells can be efficiently captured via novel single-cell RNA-sequencing technologies. Functional analysis of bulk or single-cell gene expression data has been proven to be a powerful approach as they summarize the large and noisy gene expression space into a smaller number of biologically meaningful features such as pathway and transcription factor activities. In the first part of this thesis, I expanded the scope of the pathway analysis tool PROGENy and the transcription factor analysis tool DoRothEA through thorough benchmarking pipelines. First I transferred their regulatory knowledge from human to mouse to enable the functional characterization of gene expression profiles from mice. Moreover, I demonstrated the robustness and applicability of both tools on human single-cell RNA-sequencing data. In the second part of this thesis, I focussed on the analysis of gene expression profiles from mice and humans in the context of acute and chronic liver diseases. Finally, I identified and functionally characterized exclusively and commonly regulated genes of chronic and acute liver damage in mice and a set of genes that were consistently altered in a novel chronic mouse model and patients of chronic liver disease. Especially the latter demonstrates that, although major interspecies differences remain, there is a common and consistent transcriptomic response to chronic liver damage in mice and humans. This set of genes could be further investigated to study the pathophysiology of the liver in in-vitro and in-vivo studies.