PROGRAM &

ABSTRACT BOOK
ISBN 978-615-5270-80-2

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Organizers

Sponsors

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Timetable

Scientific program
Monday - 17 July 2023
14:00 Arrival and registration
16:00 Opening ceremony
Chair: Tamás Korcsmáros
16:15 Opening Keynote lecture:
Jasmin Fisher (University College London, UK):
Executable signalling networks: From mechanisms to therapeutic applications

17:00 Opening Keynote lecture:

Nick Powell (Imperial College London, UK):
Harnessing cytokine-responsive transcriptomics to predict patient trajectories in
inflammatory bowel disease

18:00 Welcome coctail and dinner

20:00 Informal evening program (bowling, table soccer, swimming, etc)

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Tuesday - 18 July 2023
Disease models and organoids
Chair: Diána Papp
9:00 Keynote lecture:
Eduardo Villablanca (Karolinska Institutet, SE):
Spatial cell profiling of the whole gastrointestinal tract during intestinal
inflammation
9:45 Expert talk 1:
Joana F. Neves (King's College London, UK):
Mucosal organoids reveal innate lymphoid cells' functions
10:15 Expert talk 2:
Kristine Schauer (Gustave Roussy Institut, FR):
Towards a high resolution map of the cancer cell: focus on lysosome
dysfunction
10:45 Tea/Coffee
Disease models and organoids
Chair: Jasmin Fisher
11:15 Expert talk 3:
Julio Saez-Rodriguez (University of Heidelberg, DE):
Knowledge-based machine learning to extract disease mechanisms from multi-
omics data
11:45 Amisha Modasia (Quadram Institute, UK):
Assessing the effects of dietary fibre fermentation in an in vitro model of the
intestinal epithelium
12:00 Andrea Checcoli (INSERM, FR):
The immunogenic cell death (ICD) is a type of cell death that elicits an
anticancer immune response
12:15 Nadezhda Doncheva (University of Copenhagen, DK):
Cytoscape stringApp 2.0: Analysis and visualization of heterogeneous biological
networks
12:30 Lunch
14:00 Teamwork – part 1
Getting know each other
14:30 Teamwork – part 1
Presenting the problem to be solved
16:00 Teamwork – part 1
Medieval team building competition, informal discussions in the meantime
17:30 Special renaissance dinner
19:15 Double Sunset Cruise
21:30 Poster session 1
22:30 Informal evening program

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Wednesday - 19 July 2023
Microbiome and host-microbe analyses
Chair: Isabelle Hautefort
9:00 Keynote lecture:
Jost Enninga (Institut Pasteur, FR):
Imaging the modulation of host trafficking and signaling by bacterial effector
proteins
9:45 Expert talk 1:
Paul Wilmes (University of Luxembourg, LU):
Systems ecology of human-microbiome interactions
10:15 Expert talk 2:
Cynthia Whitchurch (Quadram Institute, UK):
Challenges in imaging microbiomes and biofilms on host tissues
10:45 Tea/Coffee
Microbiome and host-microbe analyses
Chair: Laura Nolan
11:15 Expert talk 3:
Falk Hildebrand (Quadram Institute, UK):
Gut metagenomics: finding good descriptors of bacterial communities and
their members
11:45 Federica Ungaro (Università Vita-Salute San Raffaele, IT):
Not just a bystander: may the microbiota be the leading actor in gut diseases?
12:00 Douglas Brubaker (Case Western Reserve University School of Medicine, US):
Pharmacobiome: realizing the therapeutic potential of microbes and microbial
products
12:15 László Mérő(Turbine.Ai, HU):
Can we overcome bias in machine learning models predicting drug sensitivity
and gene essentiality?
12:30 Lunch
14:00 Teamwork – part 2
Discussing the problem to be solved
16:00 Tea/Coffee
16:30 Catamaran race on the Danube, informal discussion in the meantime
19:00 BBQ Picnic Dinner in the Garden of the Hotel Visegrád
21:30 Poster session 2
22:30 Informal evening program

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Thursday - 20 July 2023
Modeling and Precision Medicine
Chair: Dezső Módos
9:00 Keynote lecture:
Chris Tape (University College London, UK):
Single-cell signalling analysis of tumour microenvironment organoidsproteins
9:45 Expert talk 1:
Fabian Fröhlich (Crick Institute, UK):
Anti-cancer drug sensitivity prediction using mathematical models of signalling
10:15 Pathways
Expert talk 2:
Laurence Calzone (Institute Curie, FR):
Simulating dynamic populations of cell types in cancer: from data to predictive
10:45 models.
Tea/Coffee
Modeling and Precision Medicine
Chair: Fabian Fröhlich
11:15 Livia Perfetto (University of Rome La Sapienza, IT):
A computational strategy to produce actionable and patient-specific networks
of intracellular signaling in Pancreatic Ductal Adenocarcinoma
11:30 Avlant Nilsson (Massachusetts Institute of Technology, US):
A deep learning model of intracellular networks
11:45 Orsolya Kapuy (Semmelweis University, HU):
A systems biological study of ATF4-controlled autophagy induction in
inflammatory bowel disease
12:00 Closing Talk:
Tamás Korcsmáros (Imperial College London, UK):
Patient- and cell-type specific networks to explain heterogeneity in IBD
12:30 Lunch
14:00 Presentations of teams (15 min / team + discussion)
16:00 Tee/Coffee
16:30 Moderated panel discussion on: team presentations, novel ideas, and concrete
actions (e.g. collaborations)
17:00 Moderated panel discussion on: Women / Family in Science
17:45 Award presentation for teams and poster presenters and Closing remarks
18:15 Walk and free time in the Court of Crafts
19:00 Workshop Closing Feast in the Court of Foods
22:00 Informal evening program with music

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Poster session 1 - 18 July 2023
IBD - Chairs: Federica Ungaro, Julio Saez-Rodriguez
Balázs Bohár P-01 Systems genomics analysis on gene regulatory networks in inflammatory
bowel disease

Margita Ágnes P-02 A systems biological study of the role of endoplasmic stress upon
Márton inflammatory bowel disease

Dezső Módos P-03 Systems Genomics and Network Approaches Uncover How Single
Nucleotide Polymorphisms in Crohn’s Disease and Ulcerative Colitis Affect
Common Processes Through Different Mechanisms

Francisca Castillo P-04 Characterization of a novel molecular stratification of Ulcerative Colitis

patients

Polina Kornilova P-05 Paralog proteins play a crucial role in rewiring cell-type specific signalling
processes in Ulcerative Colitis and Crohn’s disease

Viera Kovacova P-06 Unveiling the Hidden Potential of Unmapped Reads in Transcriptomic
Analyses: Implications for IBD

John Thomas P-07 Conserved sex differences in intestinal adaptive immunity are present in the
healthy and Crohn’s disease ileum which are underpinned by sexually
dimorphic transcriptional regulation

Disease modelling and networks - Chairs: Nadezhda Doncheva, Joana F. Neves

Veronica P-08 Signaling profiler, a computational strategy to produce actionable and
Venafra context-specific networks of intracellular signaling

Matthieu Najm P-09 A systems biology approach for Cystic Fibrosis

Isabelle Hautefort P-10 Why do we need in vitro co-culture systems?

Gustavo P-11 Spatially resolved proteogenomic atlas of the upper gastrointestinal tract
Monasterio

Marton Olbei P-12 Cytokine Networks in Immune Mediated Inflammatory Diseases

Dénes Türei P-13 OmniPath: database knowledge for mechanistic modeling, cell-cell
communication and more

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Poster session 2 - 19 July 2023
Microbiome - Chairs: Paul Wilmes, Jost Enninga
Carmela Errico P-14 The Caudovirales Class of Viruses is Associated with Dendritic Cell
Impairment in CD Patients

Joachim Fritscher P-15 (in) no time to strain: strain-resolved metagenomic profiling with protal

Laura Nolan P-16 Towards a comprehensive understanding of polymicrobial biofilm

development and community interactions

Lejla Potari-Gul P-17 Development of a host-microbe interaction pipeline to reveal the cell- and
condition-specific effects of bacteria using single-cell transcriptomics data

Cancer - Chairs: Kristine Schauer, Chris Tape

Stefania Cagliani P-18 The role of mfsd2a in the resolution of colorectal cancer-promoting
inflammation: implications for innovative therapies

Norbert Deutsch P-19 DisCanVis: Visualizing integrated structural and functional annotations to
better understand the effect of cancer mutations located within disordered
proteins

Dávid Keresztes P-20 Investigation of the role of COP9 signalosome in the epithelial-mesenchymal
transition

Marco Ruscone P-21 Multiscale Model of the Different Modes of Cancer Cell Invasion

Amanda P-22 Investigating the role of gut eukaryotic virome in contributing to colorectal
Facoetti cancer carcinogenesis

Autophagy and modelling - Chairs: Livia Perfetto, Bence Szalai

Valentina Madár P-23 How yeast go multicellular

Yuseok Moon P-24 Integrated stress response facilitates mucoprotective reprogramming

against acute renointestinal distress

Luca Csabai P-25 AutophagyNet: High-resolution data source for the analysis of autophagy
and its regulation

Bence Hajdú P-26 A systems biological study of oscillatory characteristic of autophagy

induction under cellular stress

Márk Kerestély P-27 Reversal of epithelial-msenchymal transition in a compartmentalized in silico

boolean model

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 ABSTRACTS OF
SELECTED ORAL
PRESENTATIONS

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Assessing the effects of dietary fibre fermentation in
an in vitro model of the intestinal epithelium
Amisha A Modasia1,†, Fred J Warren1, Hannah C Harris1, Alaa Alhasani2,3,
Luca Marciani2,3, Gleb Yakubov2,3, Robin C Spiller2,3

1 Food, Innovation and Health, Quadram Institute Bioscience, Norwich, UK

2 NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals, NHS Trust and the University
of Nottingham, Nottingham, UK
3 Nottingham Digestive Diseases Centre, University of Nottingham, Nottingham, UK
† Corresponding Author.
Correspondence to Dr Amisha A Modasia, Food, Innovation and Health, Quadram Institute Bioscience,
Norwich, UK; [email protected]

Background
Irritable bowel syndrome (IBS) is a chronic and debilitating functional gastrointestinal
disorder. Inulin-type fructans are associated with increased severity of symptoms, however,
despite the clinical short-term benefit of exclusion diets, are associated with negative
alterations in microbial composition. Microbial fermentation products, short-chain fatty acids
(SCFAs), possess multiple beneficial physiological effects on host intestinal barrier function
and is therefore unsurprising that altered epithelial barrier integrity and permeability are also
reported in IBS patients.
Alternative approaches to regulating colonic fermentation of dietary fibres include
supplementation with the viscous fibre psyllium which has been shown to reduce IBS
symptoms without inhibiting overall fermentation.

Objectives
To determine the effects on intestinal barrier permeability and integrity from fermentation of
inulin and psyllium and identify which products of microbial fermentation may be
responsible.

Methods
A single-vessel batch fermentation model with human stool donors was used to assess the
fermentation of inulin and psyllium, with samples collected over a 5-day period. SCFAs, that
serve as a surrogate marker for intraluminal intestinal fermentation, were assessed by nuclear
magnetic resonance (NMR) to determine the magnitude of intestinal fermentation to the
different substrates. To determine the impact of fibre fermentation on intestinal barrier
function, an in vitro cell culture-based approach with Caco-2 cells modelling the intestinal
epithelium was used to assess barrier permeability and integrity.

Impact
Supplementation with the resistant fibre psyllium, provides a promising method of alleviating
IBS symptoms without restricting prebiotic intake, therefore promoting proper epithelial
barrier function.

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The immunogenic cell death (ICD) is a type of cell
death that elicits an anticancer immune response
Andrea Checcoli

Centre de Recherche des Cordeliers - INSERM UMRS 1138, Paris, France

ICD-inducing agents (Oxaliplatin, Mitoxantrone) induce cancer cells to release some

stress/danger signals that attract and activate dendritic cells (DCs) and initiate the cancer-
immunity cycle.

Tumor antigens are engulfed and cross-presented by DCs to T lymphocytes, creating a

positive feedback loop in which the antitumor immunity further improves the therapeutic
efficacy against cancer cells spared by the cytotoxic agent.

Importantly, not all chemotherapeutic drugs currently approved for cancer treatments are
able to induce ICD; some commonly used agents (e.g Cisplatin) fail to activate some
processes of ICD.

Yet, beside a robust characterization of the ICD hallmarks, we still lack of knowledge of the
underlying mechanisms of ICD.

Our work approach is a combination of literature-based and experimental data, including

longitudinal transcriptomic and proteomic datasets.

In order to assess the dynamics of both the cancer cell and the immune microenvironment
under the regimen of ICD, we combined in vitro and in vivo approaches to build a
mathematical model of ICD.

The model is based on discrete Boolean formalism and simulated with a software based on
MaBoSS framework.

We simulate the model behavior by running stochastic simulations with continuous time,
considering the dynamics of a multicellular system with appropriate timing of events and
population dynamics for each cell type.

We will apply this model to predict the effect of perturbations on the simulated biological
system.

These predictions will be experimentally validated.

Altogether, our in silico model should facilitate the identification of novel druggable targets
and the development of optimized combination regimens including ICD inducers for the
care of cancers.

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Cytoscape stringApp 2.0: analysis and visualization of
heterogeneous biological networks
Nadezhda T. Doncheva1, John “Scooter” Morris2, Henrietta Holze1, Rebecca Kirsch1,
Katerina Nastou1, Yesid Cuesta-Astroz3, Thomas Rattei4, Damian Szklarczyk5,6,
Christian von Mering5,6, Lars Juhl Jensen1

1 Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark
2 Resource on Biocomputing, Visualization, and Informatics, University of California, San Francisco, USA
3 Instituto Colombiano de Medicina Tropical, Universidad CES, Colombia
4 Centre for Microbiology and Environmental Systems Science, University of Vienna, Austria
5 Department of Molecular Life Sciences, University of Zurich, Switzerland
6 SIB Swiss Institute of Bioinformatics, Switzerland

Complex biological systems are often represented as biological networks containing several
types of molecular entities. Analyzing and visualizing such networks can advance our
knowledge of the underlying cellular mechanisms. This can be accomplished with online
databases and software tools like STRING, Cytoscape, and its many apps. Specifically,
Cytoscape stringApp has focused on providing intra-species protein–protein interactions
from STRING to facilitate the interpretation of data from omics studies, such as proteomics
and transcriptomics.

Results: Here, we highlight the latest stringApp and STRING functionality that opens new
avenues for exploring results from high-throughput experiments. Version 2.0 of stringApp
greatly improves the support for heterogeneous networks, thus making it possible to create
networks that contain both proteins and interactions from STRING as well as other molecular
entities or associations from external sources. We exemplify this on a published SARS-CoV-2
interactome in Cytoscape using stringApp. Thereby, we also showcase the new group-wise
enrichment analysis, which can be performed automatically on several subnetworks, as well
as the retrieval of both functional associations and physical interactions from STRING. In
another example, we demonstrate how the new cross-species query can be used to retrieve
protein–protein interactions between the eukaryotic parasite malaria, its hosts human, and
its mosquito vector.

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Not just a bystander: may the microbiota be the
leading actor in gut diseases?
Ungaro Federica1, Amanda Facoetti1, Luca Massimino2, Carmela Errico1,
Omar Almolla1, Stefania Cagliani1, Tommaso Lorenzo Parigi1, Silvio Danese2

1 Università Vita-Salute San Raffaelem Milan, Italy

2 IRCCS Ospedale San Raffaele, Milan, Italy

The human microbiota is a densely populated community colonizing all mucosal surfaces of
our body, especially those lining the gastrointestinal tract, namely the gut microbiota(1). The
gut microbiota is a key component of our wellness and a refined equilibrium between the
different components of the gut microbiota and between the gut microbiota and the host
has to be preserved, to ensure the correct immune and physiological responses and mucosal
homeostasis(2).

It is now well-accepted that any unbalance that can discontinue this delicate equilibrium
shifts the healthy mucosa to an altered state, activating a series of mucosal responses that
may lead to uncontrolled immune and non-immune reactions at the basis of the
pathogenesis of chronic inflammatory disorders, such as ulcerative colitis (UC)(1).

UC is a chronic inflammatory disorder of the colonic tract characterized by mucosal

ulcerations and complex biological and immune pathways orchestrating its pathogenesis.
Despite the availability of several lines of intervention, many patients still do not respond to
anti-inflammatory treatment or experience disease relapse. In this multifaceted scenario,
microbiota dysbiosis has been already described as a participant in the UC pathogenesis,
but if specific microbial entities may be direct triggers of UC is far from being fully
defined(3,4).

Our group has been showing during the last years great interest in elucidating further the
roles of the microbiota in directing intestinal inflammation and how it can directly impact
mucosal physiology and functions. We recently demonstrated the virome-derived protein
hepatitis B protein X (HBx) to induce epithelial barrier damage independently of the other
components of the microbiota, altering immune functions and provoking mucosal
ulcerations that in turn alter the gut bacteriome composition in mice. This viral factor was also
associated with UC pathogenesis in a specific cohort of patients, indicating that it could
become a targettable molecule for some individuals carrying this protein in their gut
microbiota(5).

Therefore, starting from these pieces of evidence, we believe we are on the correct path
toward the full understanding of how the microbiota is involved in chronic intestinal disorders,
although much more studies are needed and mechanistic insights should be provided to
implement the current lines of intervention for the management of chronic inflammatory
disorders and ameliorate the overall patients’ quality of life.

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Bibliography

1. Nishida A, Inoue R, Inatomi O, Bamba S, Naito Y, Andoh A. Gut microbiota in the pathogenesis of
inflammatory bowel disease. Clin J Gastroenterol. 2018 Feb;11(1):1–10.
2. Popkes M, Valenzano DR. Microbiota-host interactions shape ageing dynamics. Philos Trans R Soc
Lond B Biol Sci. 2020 Sep 28;375(1808):20190596.
3. Ungaro R, Mehandru S, Allen PB, Peyrin-Biroulet L, Colombel J-F. Ulcerative colitis. Lancet. 2017 Apr
29;389(10080):1756–70.
4. Ungaro F, Massimino L, D’Alessio S, Danese S. The gut virome in inflammatory bowel disease
pathogenesis: From metagenomics to novel therapeutic approaches. United European
Gastroenterol J. 2019 Oct;7(8):999–1007.
5. Massimino L, Palmieri O, Facoetti A, Fuggetta D, Spanò S, Lamparelli LA, et al. Gut virome-colonising
Orthohepadnavirus genus is associated with ulcerative colitis pathogenesis and induces intestinal
inflammation in vivo. Gut. 2023 Feb 14;

14
The pharmacobiome: Realizing the therapeutic
potential of microbes and microbial products
The Brubaker Lab1,2,3, Douglas K. Brubaker1,2,3

1 Weldon School of Biomedical Engineering, Purdue University, West Lafayette, USA

2 Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University School of
Medicine, Cleveland, USA
3 Blood Heart Lung Immunology Research Center, University Hospitals, Cleveland, USA

Several studies have shown interactions between the human microbiome and health, but
precise understanding of the functions of microbiomes and their products are not fully
elucidated. This lack of knowledge comes in part because systematic methods to
functionally characterize microbiomes are lacking. Here, we propose a systems biology
concept to characterize microbes and their products termed the Pharmacobiome. The
Pharmacobiome is the characterization of a microbe and its products in terms of known
drugs and pathways by studying associations between the microbiome and disease states,
phenotypes, pathways, networks, known drug functions and how the human clinical
demographic characteristics impact the above associations. The Pharmacobiome
perspective emphasizes deriving insights from the application of novel computational
frameworks to primarily human-context multi-omics data spanning disease states and
microbiome sites.

Here, I will share our lab’s efforts to (1) understand the regulatory relationships of microbiomes
on host signaling pathways, (2) characterize the anti-cancer potential of microbiomes, and
(3) identify microbes and microbial products with the potential to mimic the effects of known
pharmacologic compounds. The techniques we employ combine existing correlational and
data-driven modeling techniques into novel workflows, linking latent variable approaches to
interpretable statistical models more powerful than the component methods individually.
Examples of our work span both the gut and vaginal microbiomes to include microbiome
regulation of mTOR, estrogen, and progesterone signaling and the identification of
microbiome mimics of drugs including paclitaxel, cisplatin, and mifepristone.

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Can we overcome bias in machine learning models
predicting drug sensitivity and gene essentiality?
Bence Szalai, László Mérő

Turbine.Ai, Budapest, Hungary

Machine learning models help cancer research by predicting how cancer cells respond to
different drugs and gene knock-outs with the aim to help identify new therapies and
personalised treatment options for cancer patients. However, we realised that most currently
used performance metrics to evaluate ML models are very sensitive to biases in the data.
Even without adversarial construction, most of the performance of sensitivity predictions
come from fitting hidden biases in the data. We developed a statistical framework to
highlight how much model predictions surpass bias, capturing the biologically interesting,
bias independent component of drug sensitivity and gene essentiality. We show how
standard machine learning models perform predicting drug sensitivity and gene essentiality
in this new framework. We used multimodal models with different complexity (linear
regression, Random Forest, Multi Layer Perceptron) with different cell line (gene expression,
mutation) and perturbation (chemical structure, target network topology etc.) specific
features to predict drug sensitivity from the GDSC and gene essentiality from the DepMap
databases. We found that there is indeed interesting additional information above bias in
most models, but it’s hidden from standard global metrics. We suggest that focusing on the
bias independent performance of ML models can boost their usability in drug discovery and
precision medicine applications.

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A computational strategy to produce actionable and
patient-specific networks of intracellular signaling in
Pancreatic Ductal Adenocarcinoma
Lorentz Nicolaeasa1#, Veronica Venafra1#, Francesca Sacco1, Livia Perfetto1, 2, 3

1 Department of Biology, University of Tor Vergata, Roma, Italy

2 Department of Biology and Biotechnology “Charles Darwin”, University of La Sapienza, Roma, Italy
3 Computational Biology Research Centre, Human Technopole, Milan, Italy
# these authors contributed equally to the project

With a 11% 5-yr survival rate, PDAC is one of the deadliest cancer types. No effective
treatment can be offered to patients diagnosed with PDAC as most patients remain
refractory to current regimens. A major factor that contributes to PDAC resistance to
treatment is its dense fibrotic stroma intertwined with the extracellular matrix, which,
together, provide a physical barrier that protects the tumor and promotes its growth and
invasiveness. Uncovering these mechanisms at the patient- resolution level will be crucial to
underpin mechanisms of PDAC tumorigenesis and progression and to develop efficient
therapies.

We recently implemented SignalingProfiler, a generally applicable modelling strategy that

combines transcriptomics and phosphoproteomics datasets with prior knowledge
annotated in our in-house resource, SIGNOR, to produce context-specific ‘mechanistic
models’ representing the remodeling of the signal transduction cascade at the PTM-
resolution level. We recently applied SignalingProfiler to genomics, transcriptomics,
proteomics and phosphoproteomics data from 105 treatment-naïve Pancreatic Ductal
Adenocarcinoma (PDAC) biopsies, extracted from the CPTAC portal. By this approach we
were able to generate patient-specific mechanistic models of PDAC tumorigenesis and
progression. These ‘mechanistic models’ can recapitulate, in a genotype-specific context,
the activation status of key signal transduction proteins basing on the regulatory interactions
that affect their activities. Integration of these models with clinical data made it possible to
stratify patients according to the key activity of signal transduction effectors, revealing the
translational impact of the approach.

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A deep learning model of intracellular networks
Avlant Nilsson1, Joshua M. Peters2, Nikolaos Meimetis2, Daniel Schafer2, Bryan Bryson2,
and Douglas A. Lauffenburger2

1 Massachusetts Institute of Technology, Cambridge, USA

2 Department of Cell and Molecular Biology, Karolinska Institutet, Sweden

Human cells are signal-processors; ligands bind receptors on the cell-surface and the signals
are integrated through a molecular network to activate transcription factors (TFs) that
govern cell fate. Disruptions to this network are common in disease, e.g. in cancer it can
cause unrestricted growth. Simulations of these processes could help predict disease
mechanisms and identify suitable drug targets. However, the human signaling network
consists of thousands of molecules with tens of thousands of interactions, and it has been
challenging to parametrize systems-wide models using traditional approaches.

Aims: To address this, we developed LEMBAS (Large-scale knowledge EMBedded Artificial

Signaling networks). It represents the processes as a recurrent neural network with signaling
molecules as hidden nodes with interactions constrained to prior knowledge of their
connections (Figure 1A). We aimed to evaluate LEMBAS’ ability to predict unseen test-data
from living cells after fitting it to training data. To this end we measured gene expression in
macrophages in response to combinations of 19 different ligands (Figure 1B), including
growth factors, interferons, and both inflammatory and anti-inflammatory interleukins.

Results: LEMBAS generalizes to unseen test data (Figure 1C). Through a combination of
sensitivity analysis and perturbations on the trained models we inferred causative signaling
cascades that could explain signaling under the tested conditions. We are currently
expanding the framework to integrate signaling, metabolism, and gene regulation for a
more complete mechanistic description of cellular activities.

Figure 1. – Deep learning model of macrophage signaling. A) model structure. B) transcriptomic response to
ligand combinations. C) 10-fold fold cross validation.

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A systems biological study of ATF4-controlled
autophagy induction in inflammatory bowel disease
Orsolya Kapuy, Bence Hajdú, Marianna Holczer, Margita Márton

Semmelweis University, Department of Molecular Biology at the Institute of Biochemistry and Molecular Biology,
Budapest, Hungary

Inflammatory bowel disease (IBD) is a chronic disease in the gastrointestinal tract. It has
shown that disturbance in autophagy-dependent survival might cause IBD, however, the
proper dynamical characteristic of IBD regulatory network remains largely unknown. It is well-
known that autophagy is essential for the cell to respond various stress events, where the
main element of autophagy activator complex, called ULK1, is tightly regulated by the two
sensor molecules of nutrient conditions and energy status, called mTOR and AMPK kinases,
respectively.

By using various systems biological method, we introduce AMPK-induced activating

transcription factor 4, ATF4, as an essential regulatory element of autophagy induction by
upregulating ULK1 and down-regulating mTOR in IBD. We propose that ATF4 plays a key role
in fine-tuning the induction of autophagy-dependent survival in IBD.

Since ATF4 deficiency can cause severe ulcerative colitis, this study will bring us closer to
understand the dynamical features of fatal IBD. Corresponding to experimental data our
theoretical analysis has also demonstrated that inhibition of mTOR (e.g. with rapamycin) or
activation of AMPK (e.g. with AICAR) can restore dysfunctional autophagy in ATF4-
deficiency induced ulcerative colitis, thereby the symptoms of IBD might be postponed.

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POSTER ABSTRACTS

20
P-01 - Systems genomics analysis reveals different
upstream biological processes impacting gene
regulatory networks in Crohn’s disease and ulcerative
colitis patients
Balázs Bohár1*, John P. Thomas2,3*, Dezso Modos3,4, Simon Carding4,
Severine Vermeire5, Bram Verstockt6, Johanne Brooks-Warburton4,7,8,9,
Tamás Korcsmáros3,4

1 Department of Genetics, Eötvös Loránd University, Budapest, Hungary

2 Gut signalling and metabolism group, MRC London Institute of Medical Sciences, London, UK
3 Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
4 Quadram Institute, Norwich Research Park, Norwich, NR4 7UQ, UK
5 Translational Research in GastroIntestinal Disorders, KU Leuven, Belgium
6 Department of Gastroenterology and Hepatology at the University Hospitals Leuven, Belgium
7 Earlham Institute, Norwich Research Park, Norwich, UK
8 Department of Clinical, Pharmaceutical and Biological Sciences, University of Hertfordshire, Hertford, UK
9 Gastroenterology Department, Lister Hospital, Stevenage, UK
* equal contribution

Inflammatory Bowel Diseases, including Crohn’s disease (CD) and ulcerative colitis (UC), are
thought to arise due to complex interactions between multiple single nucleotide
polymorphisms (SNPs) and environmental risk factors, which result in pathological immune
activation in the gut. Currently, there is still no cure for inflammatory bowel disease (IBD) and
the majority of patients fail to achieve long-lasting remission. These shortcomings are
reflective of our lack of understanding of IBD pathogenesis. In particular, we are yet to
appreciate how these pathomechanisms are likely to vary between individual patients due
to the complex gene-environment interactions underpinning IBD. To further understand the
genetic risk underpinning IBD, we previously modelled the impact of non-coding IBD-
associated SNPs on downstream cell signalling networks in IBD (Brooks-Warburton et al. 2022).
Specifically, we studied how IBD-associated non-coding SNPs can affect the binding of
transcription factors (TFs) to transcription factor binding sites (TFBS) in promoter and enhancer
regions of the genome, resulting in perturbed downstream cell signalling networks. However,
little is known about the upstream signals (including extrinsic and environmental signals)
which may influence TFs that bind to IBD-associated non-coding SNPs.

Aim: In this project, we aimed to develop a novel in-silico pipeline to infer the likely upstream
signals impacting gene regulatory networks using genotype data from a large cohort of UC
and CD patients. In other words, we sought to predict potential biological processes that
may impact TFs which bind to IBD-associated non-coding SNPs and in turn, their downstream
signalling pathways.

Results: We constructed a novel in-silco pipeline to map the likely upstream signals impacting
TFs that bind to IBD non-coding SNPs by building on the foundations of the iSNP pipeline and
also utilising other resources including the gene ontology resource and the IBD Transcriptome
and Metatranscriptome Meta-Analysis (IBD TaMMA) framework. Our novel in-silico workflow
identified different upstream processes impacting gene regulatory mechanisms in UC and
CD. In UC patients, we found that the most common upstream signals influencing gene

21
regulatory networks included B cell differentiation, epithelial cell proliferation, positive
regulation of epithelial-to-mesenchymal transition, cellular response to LPS, and cell matrix
adhesion. In CD patients, the most frequent upstream signals included positive regulation of
VEGF, response to oestradiol, response to virus, regulation of epithelial cell proliferation, and
cellular response to IL1. These findings suggest different environmental/extrinsic factors may
interact with gene regulatory mechanisms to drive UC (e.g. gram-negative bacteria) and
CD (e.g. viruses, oestradiol signalling) pathogenesis. This work could serve as a starting point
for future experimental approaches that aim to mechanistically characterise these upstream
biological pathways.

22
P-02 - A systems biological study of the role of
endoplasmic stress upon inflammatory bowel disease
Margita Márton1, Marianna Holczer1, Tamás Korcsmáros2,3,4,5, Orsolya Kapuy1

1. Semmelweis University, Department of Molecular Biology at the Institute of Biochemistry and Molecular
Biology, Budapest, Hungary
2. Earlham Institute, Norwich Research Park, Norwich, UK
3. Eötvös Loránd University, Department of Genetics, Budapest, Hungary
4. Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
5. Imperial College London, Department of Metabolism, Digestion and Reproduction, London, UK

Inflammatory bowel disease (IBD) is a chronic disease in the gastrointestinal tract. IBD is
characterised already onset at a young age, and the number of affected patients has risen
sharply. Therefore, there is a pressing need to understand the pathologies of IBD and create
effective treatments. Recent studies have shown that any disturbance in endoplasmic
reticulum (ER) is critical factor, therefore reestablishing intestinal homeostasis by correcting
ER-stress induced control mechanism is emerging as a potential therapeutic target for IBD.

Our goal is to explore the essential regulatory motifs of ER-stress induced life-anddeath
decision in IBD directly focusing on unfolded protein response (UPR). Our scientific questions
will be approached from a systems biological perspective by using various theoretical
biological tools (such as dynamical modelling and bioinformatic analysis) and molecular
biology techniques.

We develop a simple mathematical model which describes the decision making process
between autophagy-dependent survival and cell death upon ER stress. We explore the
systems-level feedback loops of the control network and confirm the key intra-, and
intermolecular-crosstalks of ER-stress induced unfolded protein response. By exploring the key
feedback loops we try to understand how autophagy-dependent cellular survival can be
extended and therefore the fatal effects of IBD might be postponed. We plan to identify
novel agents which might have therapeutical role in the future to expand lifespan of people
suffering from IBD.

23
P-03 - Systems genomics and network approaches
uncover how single nucleotide polymorphisms in
Crohn’s disease and ulcerative colitis affect common
processes through different mechanisms
Dezso Modos1,2,3, Martina Poletti2,3, John Thomas1,4, Johanne Brooks-Warburton5,6,
Balázs Bohár1,7, Matthew Madgwick3, Wen-Xin Kang1, Simon Carding2,8,
Bram Verstockt9,10, Séverine Vermeire9,10, Tamás Korcsmáros1,2,3

1 Department of Metabolism, Digestion and Reproduction, Imperial College, London, UK

2 Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
3 Earlham Institute, Norwich Research Park, Norwich, UK
4 Gut Signalling and Metabolism Group, MRC London Institute of Medical Sciences
5 Department of Gastroenterology, Lister Hospital, Stevenage, UK
6 Department of Clinical, Pharmaceutical and Biological Sciences, University of Hertfordshire, Hertford, UK
7 Department of Genetics, Eötvös Loránd University, Budapest, Hungary
8 Norwich Medical School, University of East Anglia, Norwich, UK
9 University Hospitals Leuven, Department of Gastroenterology and Hepatology, KU Leuven, Leuven, Belgium
10 KU Leuven, Department of Chronic diseases and Metabolism, Leuven, Belgium

Inflammatory bowel disease (IBD) has two main types Crohn’s disease (CD) and ulcerative
colitis (UC). The IBD related single nucleotide polymorphisms are predominantly in non-
coding regions of the genome making them challenging to understand. We developed the
iSNP pipeline to predict how SNPs in transcription factor (TF) binding sites and miRNA target
sites affect signaling networks and contribute to pathogenesis. Here, we further developed
iSNP to investigate the pathomechanism of UC and CD in downstream regulatory levels, and
to compare these mechanisms.

We analyzed IBD-associated SNP affected genes from 1695 CD and 941 UC patients. To
uncover downstream signaling pathways and regulatory processes affected by patient-
specific SNPs, we used a heat propagation model to connect SNP-affected proteins to other
proteins via a signaling network (using OmniPath), ultimately reaching affected TFs, and their
target genes through TF-target gene networks (using DoRothEA).

The iSNP pipeline predicted 83 SNP affected proteins in CD and 121 in UC. Network
propagation analysis further identified 518 and 330 proteins affected significantly in CD and
UC, respectively; with only 99 proteins overlapping. The functional analysis of the shared
proteins indicated the importance of T-cell mediated immunity and the WNT pathway, but
also identified disease specific pathways. The affected regulatory networks contain 2067 and
3352 genes in CD and UC, respectively. The patient clusters based on their regulatory
networks corresponded to cell specific differentially expressed genes in CD. Furthermore, the
regulatory network in UC corresponded to the inflammatory response based on other
transcriptomic studies.

Single cell analysis with regulatory network analysis uncovered cell and patient specific
manifestation of CD. We showed how different CD and UC associated SNPs use the same
biological mechanisms to influence similar immune and developmental pathways with
distinguishable outcomes.

24
P-04 - Characterization of a novel molecular
stratification of Ulcerative Colitis patients
Francisca A. Castillo1,2, Katja A. Selin1,2, Oscar E. Diaz1,2, Srustidhar Das1,2,
Charlotte Hedin3 & Eduardo J. Villablanca1,2

1 Division of immunology and Allergy, Department of Medicine, Solna, Karolinska Institutet and University
Hospital, 17176 Stockholm, Sweden
2 Center of Molecular Medicine, 17176 Stockholm, Sweden
3 Gastroenterology unit, Patient Area Gastroenterology, Dermatovenereology and Rheumatology, Karolinska
University Hospital, Stockholm, Sweden.

Ulcerative colitis (UC) is a highly heterogeneous chronic inflammatory bowel disease (IBD)
that primarily affects the colon. Although there are some available classifications, mostly
based on clinical parameters, the lack of a molecular stratification prevents full
comprehension of the diagnostic and prognostic heterogeneity of patients, and thus from
correctly predicting their response to available treatments. We have recently developed an
unbiased stratification of UC patients (UC1/UC2) based on their transcriptomic profiles
(Czarnewski P; et al. Nature Communications, 2019), which holds great potential for the design
of personalized medicine in IBD. However, further characterization is necessary to validate it
and consolidate its clinical application. To achieve this goal, we used bulk and single-cell
RNA sequencing (sc-RNAseq) datasets from a prospective cohort of Swedish IBD patients to
understand whether UC1 and UC2 are different diseases or states of the same disease, and
to deeply characterize the cellular composition of UC1 and UC2 patients. In addition, we
took advantage of murine spatial transcriptomics datasets of colonic tissues at steady state
or during mucosal healing, to get insights into2 the spatiotemporal dynamics of UC1/UC2
transcriptional profiles.

A longitudinal analysis of UC1/UC2 transcriptomic profiles as well as gene module analysis

revealed that UC1 and UC2 profiles are fluctuant during the course of disease, eventually
representing different stages of the same disease. scRNAseq analysis allowed us to identify
specific cell types characterizing UC2 patients. Finally, while genes defining UC2 patients
distributed homogenously within the murine mouse colon at steady state and during
mucosal healing, UC1 genes primarily mapped within damage/regeneration regions.

This study details the differences in immune cell composition and molecular pathways in UC1
and UC2 patients, contributing to a more comprehensive understanding of the new
molecular stratification system we have developed for ulcerative colitis patients.

25
P-05 - Paralog proteins play a crucial role in rewiring
cell-type specific signalling processes in Ulcerative
Colitis and Crohn’s disease
Polina Kornilova1,4, Lejla Gul2, Dezso Modos2, Matthew Madgwick1,3, Wilfried Haerty1,
Tamas Korcsmaros1,2,3

1 Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ UK

2 Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
3 Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
4 University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK

Cells communicate through signalling pathways which help to coordinate biological

processes within multicellular organisms. These processes are complex networks of cross-talks
of signalling pathways. Paralog proteins, which derive from homologue genes originating
from gene duplication, could be key signalling members and have different functions,
leading to a different signalling outcome. The aim of this study is to explore the diverse
expression and role of these paralog proteins in signalling pathways in inflammatory bowel
disease, including the two main subtype, ulcerative colitis (UC) and Crohn’s disease (CD)
from biopsies consisting of the three cell lineages (epithelial, immune and stromal cells). Using
network biology approaches combined with single-cell RNA-seq data, we identified paralog
groups that show cell and/or condition specificity. We were focusing on the JAK/STAT
signalling in different cell types. Based on the results, paralog genes show diverse expression
patterns in cells depending on the condition. Highlighting the role of JAK and STAT proteins
we found that their dimers show IBD condition specific expression. We built up regulatory
networks including the target genes of STAT dimers and showed that STAT3 and STAT1
mediate the activation of genes in a condition-specific manner in several immune and
epithelial cells. In conclusion, we have developed a pipeline that facilitates the identification
of potential key differences among- paralog proteins in cell signalling not only cell-
specifically but also in a condition-specific way.

26
P-06 - Unveiling the hidden potential of unmapped
reads in transcriptomic analyses: implications for IBD
Viera Kovacova, Michael Lässig

Institute for Biological Physics, University of Cologne, Zuelpicher Str. 77, 50937 Cologne, Germany

Transcriptomic studies routinely encounter a substantial fraction of unmapped reads, yet

these data hold significant potential for refining downstream analysis outcomes. The impact
of analytical variations, including alignment methods, mismatch tolerances, and indel
handling, on mapping results is considerable and influences the nature of mapped reads,
variant calls, and gene expression measurements.

Our work underscores the need to optimize mapping criteria and to perform de novo
assembly of unmapped reads. Notably, strict mapping criteria can increase the proportion
of unmapped reads. For instance, the genetic divergence at the bacterial sub-species level
(5%), equivalent to fifty point mutations in a 1000 bp locus, can reduce the proportion of
mapped reads by 10% under the default settings of the STAR aligner.

Further, our exploration of the 'NGS sequencing dark matter' (unmapped reads) from the
Inflammatory Bowel Disease Transcriptome and Metatranscriptome Meta-Analysis (IBD
TaMMA) illuminates an array of rare human transcripts and transcripts derived from the
microbiome. These rare human transcripts are disease-correlated and display significant
functional and protein-protein interaction enrichment.

The emerging potential from the often-overlooked fraction of transcriptomic data suggests
that revisiting the methodological strategies could be advantageous. Doing so can further
enhance our understanding and management of complex diseases like IBD.

27
P-07 - Conserved sex differences in intestinal
adaptive immunity are present in the healthy and
Crohn’s disease ileum which are underpinned by
sexually dimorphic transcriptional regulation
John P Thomas1,2, Dezso Modos2, Domenico Cozzetto2, Irene Miguel-Aliaga1,
Nicholas Powell2, Tamás Korcsmáros2

1 Gut Signalling and Metabolism Group, MRC London Institute of Medical Sciences, UK
2 Department of Metabolism, Digestion and Reproduction, Imperial College London, UK

Inflammatory bowel disease (IBD), including Crohn’s disease (CD) and ulcerative colitis (UC),
exhibits important sex differences in epidemiology, disease course, severity of disease, and
therapeutic response. However, the underlying pathomechanisms contributing to sex
differences in IBD have been largely understudied thus far. Recent landmark studies in model
organisms have revealed that intestinal tissues are highly sexually dimorphic with significant
sex differences in intestinal homeostasis including epithelial cell growth, nutrition, and
metabolism. Given these findings, we performed explorative in silico analyses of bulk and
single-cell transcriptomics data from murine and human intestinal mucosal samples to
evaluate whether sex differences are present in intestinal immunity in both health and IBD.

We identified that there are consistent sex-biased immune signatures primarily relating to
adaptive immunity in the healthy and CD ileum which are conserved across species –
specifically, a female sex-bias for B cell signalling, and lymphocyte proliferation and
differentiation. Granulocyte chemotaxis also appears to be sexually dimorphic although the
directionality of the sex bias was not consistent across species or disease states (healthy vs
CD). Using gene regulatory network analysis, we identified that differences in transcriptional
regulation may underlie these sex biases - in particular EGR1, which appears to be driving
the female sex bias in B cell signalling and lymphocyte proliferation & differentiation in both
healthy humans and mice. In the healthy murine ileum, other transcription factors also
regulate lymphocyte pathways in females including Esr1, Hnf4a, and Tfap2c. In the CD
human ileum, these pathways appear to be regulated in females by FOXP3.

The findings that B cell signalling, lymphocyte proliferation, and lymphocyte differentiation
are female sex-biased pathways, suggest that there could be sex differences in gut
associated lymphoid tissues (GALT) in both the healthy and CD ileum. This may contribute to
some of the sex differences observed in CD. Future work will aim to further characterise these
sex differences in intestinal humoral immunity in vivo using immunophenotyping and single-
cell sequencing approaches in both mouse models of ileitis and CD patients.

28
P-08 - Signaling profiler, a computational strategy to
produce actionable and context-specific networks of
intracellular signaling
Veronica Venafra, Francesca Sacco* and Livia Perfetto*

1 Department of Biology, University of Tor Vergata, Roma, Italy

2 Department of Biology and Biotechnology “Charles Darwin”, University of La Sapienza, Roma, Italy
3 Computational Biology Research Centre, Human Technopole, Milan, Italy
* Co-corresponding authors

Cell signaling is composed of an intricated architecture that is finely tuned to maintain

homeostasis. Signaling rewiring is the primary strategy for cells to evolve toward a malignant
phenotype or to acquire a drug-resistant phenotype1,2. Computational modeling strategies
have been exploited in the last 15 years to unravel the complex mechanisms regulating
biological systems or to identify promising intervention targets3.

We have recently implemented a generally applicable modeling strategy, dubbed

‘Signaling Profiler’ (SP)4 (https://github.com/SaccoPerfettoLab/SignalingProfiler), which
builds up mechanistic models recapitulating the key axes driving a disease or a resistant
phenotype.

SP is a flexible and modular pipeline composed of three customizable steps:

• Inference of protein activities: the context-specific activity modulation of key

signaling proteins (transcription factors, kinases, phosphatases, and phosphorylated
proteins) is computed from transcriptomic and (phosphor)proteomic data by
integrating widely used methods, such as VIPER5, with ad hoc developed
methodologies, such as PhosphoScore and ProteoScore.

• Naïve network generation and optimization: the signal propagation is

reconstructed in a two-steps process: (i) generation of a naïve network that connects
a user-defined set of receptors to the previously inferred proteins through directed and
signed interactions annotated in our in-house resource, SIGNOR6; (ii) optimization of
causal edges over the experimentally derived activities of proteins through the
CARNIVAL algorithm7.

• Model validation through hallmark phenotype activity inference: SP provides

an in-silico validation framework, called PhenoScore, to integrate the signal over
system-specific hallmarks phenotypes, which are connected to the model exploiting
our novel resource, ProxPath.

We successfully applied SP on FLT3-ITD driven AML multi-omics datasets to detect resistance

axes to both Tyrosine Kinase Inhibitors4 and cytarabine (in press). The SP-identified axes were
experimentally validated, and their inhibition could restore sensitivity to drugs in both AML
cellular models and ex vivo AML patients’ blasts.

29
 Figure 1. – Signaling Profiler workflow. Signaling Profiler requires as input: (i) multiomics data tables containing
the fold-change between two conditions and (ii) a prior knowledge network derived from literature. SP is
composed of three steps: 1) Inference of protein activities with three different techniques. The footprint-based
analysis (left panel) infers the activity of transcription factors (kinases/phosphatases) from the modulation in the
experimental data of their target genes (phosphosites); the PhosphoScore technique (right top panel) assigns
to phosphorylated proteins an activity score combining the regulatory role of its phosphosites with their fold-
change in the experimental data; the ProteoScore (right down panel) transforms the protein abundance
modulation in an activity score. 2) Network construction and optimization, in which a user-defined set of
receptors is connected to the previously inferred proteins in a highly customizable way. The user can create
three types of naïve networks: a one-layer network in which the receptor(s) is linked to all the inferred proteins; a
two-layer network where the receptor is connected to kinases and phosphoproteins and then kinases and
phosphoproteins are linked to transcription factors; a three-layer network where the receptor is connected to
kinases, then kinases are connected to phosphoproteins (second layer), and finally, the second layer is
connected to the transcription factors. Then, CARNIVAL reconstructs the signal propagation combining the
naïve network with the protein activities inferred in step one. The network represents the remodeling of the
signal due to treatment (if the user is comparing treated vs control) or driving a specific disease (if the user is
comparing disease vs healthy). 3) The hallmark phenotypes activity inference provides a model in-silico

30
 validation framework. It allows the user to check if the model recapitulates expected phenotypes. The
computation of phenotypes score (PhenoScore) is obtained by integrating the signal over system-specific
hallmarks phenotypes, which are connected to the model exploiting our novel resource, ProxPath.

References

1. Kolch, W., Halasz, M., Granovskaya, M. & Kholodenko, B. N. The dynamic control of signal
transduction networks in cancer cells. Nat. Rev. Cancer 15, 515–527 (2015).
2. Sacco, F. et al. Deep Proteomics of Breast Cancer Cells Reveals that Metformin Rewires Signaling
Networks Away from a Pro-growth State. Cell Syst. 2, 159–171 (2016).
3. Hughey, J. J., Lee, T. K. & Covert, M. W. Computational Modeling of Mammalian Signaling Networks.
Wiley Interdiscip. Rev. Syst. Biol. Med. 2, 194–209 (2010).
4. Massacci, G. et al. A key role of the WEE1-CDK1 axis in mediating TKI-therapy resistance in FLT3-ITD
positive acute myeloid leukemia patients.
http://biorxiv.org/lookup/doi/10.1101/2022.05.16.492070 (2022) doi:10.1101/2022.05.16.492070.
5. Dugourd, A. & Saez-Rodriguez, J. Footprint-based functional analysis of multiomic data. Curr. Opin.
Syst. Biol. 15, 82–90 (2019).
6. Lo Surdo, P. et al. SIGNOR 3.0, the SIGnaling network open resource 3.0: 2022 update. Nucleic Acids
Res. 51, D631–D637 (2023).
7. Liu, A. et al. From expression footprints to causal pathways: contextualizing large signaling networks
with CARNIVAL. Npj Syst. Biol. Appl. 5, 40 (2019).

31
P-09 - A systems biology approach to Cystic Fibrosis
Matthieu Najm1, Isabelle Sermet-Gaudelus2, Loredana Martignetti1,
Laurence Calzone1, Véronique Stoven1

1 Institut Curie/Mines Paris – PSL, Paris, France

2 Institut Necker Enfants Malades, Paris, France

Cystic Fibrosis (CF) is caused by mutations in the gene coding the Cystic Fibrosis
Transmembrane Regulator (CFTR) protein. However, the overall pathophysiology cannot be
solely linked to the loss of the CFTR function. Indeed, although CF is a monogenic disease,
CFTR belongs to a yet not fully deciphered network of proteins involved in various biological
pathways. Absence of a functional CFTR leads to perturbations of these pathways, leading
to deleterious CF phenotypes.

We used publicly available transcriptomic CF datasets to identify the most frequently

deregulated biological pathways. We adopted a systems biology approach to connect
these pathways and thereby define the CF biological network. CFTR was connected to this
network based on its known direct protein interactors (i.e. CFTR interactome) that were
present in the network or connected to it. The biological pathways present in the network
and their resulting phenotypes were found consistent with today’s CF knowledge. This
indicates that the approach employed in this study did capture relevant information about
the disease.

The topological analysis of the network highlighted a few proteins that may initiate or
propagate deregulations from CFTR into the network, and explain the observed CF
phenotypes. Importantly, modulators or drugs are known against these proteins, which allows
experimental validation, and further offers potential drug repositioning opportunities.

This initial network model can be refined with other types of omics data such as proteomic.
Although our research is focused on CF, we believe that our approach could be used to
study other monogenic diseases as well.

32
P-10 - Why do we need in vitro co-culture systems?
Isabelle Hautefort1,2, Diana Papp1, James Lazenby2, Cynthia Whitchurch2 and
Tamás Korcsmáros1,2

1 Imperial College London, The Commonwealth Building, The Hammersmith Hospital, Du Cane Road, London
W12 0NN, United Kingdom
2 Quadram Institute, Rosalind Franklin Road, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom

Mucosal surfaces, such as the ones found in the intestine or lungs of all mammals, are the
stage of many interactions between the different epithelial cell types lining the gut, the
underlying tissue on one side including diverse immune cells, enteric neurons and glial cells,
and the dynamic and highly complex microbial community residing on the other side.
Unfortunately, until recently, no simplified in vitro systems were reliably reproducing the in vivo
cell diversity to decipher cell-cell and cell-microbe interactions. In the last fifteen years, the
emergence of self-assembling stem cell-derived 3D structures, called organoids, has
revolutionised a wide range of research fields.

Organoids can recapitulate, in a dish, the diverse epithelial cell populations normally found
in vivo. Many organs can now be modelled using these organoid models. For the first time,
tissue development, regeneration and maintenance can be studied in patient-derived
organoids, showing great promise for the future of precision and regenerative medicine.
However, it is becoming apparent that we now need to bring back elements of the whole
tissue complexity in our investigations. Cell-cell interactions and the impact of gut-resident or
transiently passing microbes need recapitulating in vitro too. For that, access to reliable co-
culture systems is imperatively needed.

Many microfluidics systems are being developed to address this need, each one
complementing the others. Some are based on single chips that reproduce many of the
shear forces and luminal flux observed in vivo, improving the degree of differentiation of the
epithelial cells, but they do not allow live imaging of the dynamic responses cells may have
upon exposure to other cellular protagonists. They are also incompatible with high
throughput format assays. Others, more recently developed, have adopted a multiple-chip
high throughput format and provide thin observation windows permitting full-thickness
imaging of live or fixed samples. They can be applied to multiomic data outputs and enable
drug or health-promoting compounds to be screened on patient-derived organoids.

We are developing protocols allowing the culture of human colon organoid-derived cells in
the Organoplate microfluidic system from Mimetas (https://www.mimetas.com/en/our-
technology/). First, we validated the functionality of the system with the Caco-2 immortalised
human intestinal cell line. In that system, we succeeded in growing epithelial cell tubes
offering access to both the luminal and basal sides of the intestinal epithelial layer. We then
attempted to expose Caco-2 cell tubules to biofilm-forming microbes, such as the
opportunist pathogen Pseudomonas aeruginosa. In this model, we monitored the alteration
of tight junctions in the Caco-2 cell tubules by fluorescence immunolabelling and high-
content imaging. Currently, we are optimising numerous parameters for growing organoid-
derived human epithelial cell tubules. Next, we will infect these tubules with P. aeruginosa,
and possibly members of the gut microbiota or their metabolites. Successful optimisation will
open the door to many projects and lead to future translational applications.

33
P-11 - Spatially resolved proteogenomic atlas of the
upper gastrointestinal tract
Gustavo Monasterio1, Ludvig Larsson2, Srustidhar Das1, Xesus Abalo2,
Joakim Lundeberg2, Eduardo J Villablanca1

1 Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institute and University
Hospital, Stockholm, Sweden
2 Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm,
Sweden

INTRODUCTION: The oral mucosa has long been regarded as a particular barrier with
privileged healing properties. However, there is still a poor understanding of the site-specific
cellular and molecular circuitry that characterizes this barrier. Here we present the first spatial
proteogenomic atlas of the entire murine upper gastrointestinal tract (UGIT) combining
spatial transcriptomic (ST, 10x VISIUM) and spatial proteomic (CANOPY, ChipCytometry),
together with an innovative dissection/mounting technique (oro-esophagealstomach rolls –
ORES rolls). By spatially resolving gene expression and protein detection, we provide a
reference atlas for exploring cellular and genetic programs in the upper GI tract, either under
steady-state conditions or after challenges, with a special focus on the oral barrier (OB).

METHODS: Male wild type C57BL/6J mice between 8 and 10 weeks of age were used for
tissue obtention. Oral, oesophageal and stomach tissues from untreated mice were
harvested, rolled, and processed for ST or proteomic studies. To spatially resolve the
transcriptomic data, we used non-negative matrix factorization (NNMF) to deconvolved it
into 55 factors. Then, each factor was manually annotated based on colocalization with
histological features.

RESULTS: As previously shown for colon, using ST and NNMF we were able to identify a
previously unappreciated level of molecular regionalization of murine UGIT at steady state,
both at proximal-distal and basal-luminal axes. At steady state, we found that Krt76, Krt16,
Krt14, Krt6a, and Krt24 were highly expressed in the OB. While Crnn (Cornulin) and Hrnr
(Hornerin, involved in cornification of cornified epithelium) were enriched in proximal OB,
Iffo2, Gdpd2, and Krt16b were highly expressed in the distal OB. Our data aligns with previous
reports showing high Krt76 expression in the OB, and further reveal potential markers defining
proximal-to-distal OB molecular regionalization. Finally, using 18-plex SP, we identified a highly
compartmentalized regionalization of immune cells along the UGIT.

DISCUSSION & CONCLUSIONS: The current study uncovered spatial transcriptomic patterns
that are present at steady state conditions in the UGIT, characterized by unique
transcriptional signatures that coincided with different histological processes and immune
cells’ location. This reference atlas laid the foundation for further exploring the distinctive
proteogenomic signatures of the oral barrier, compared to the oesophageal and stomach
barriers, at steady state or upon local or distal challenges that can perturb the healing
process of the oral mucosa.

34
P-12 - Cytokine networks in immune mediated
inflammatory diseases
Márton Olbei1, Luca Csabai2, Domenico Cozzetto1, Matthew Madgwick1,3,
John Thomas1, Dezso Modos1,3,4, Nick Powell1, Tamás Korcsmáros1,3,4

1 Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Imperial College
London, United Kingdom
2 Department of Genetics, Eotvos Lorand University, Budapest, Hungary
3 Earlham Institute, Norwich, United Kingdom
4 Quadram Institute, Norwich, United Kingdom

Cytokines, small peptides that facilitate communication between various cell types, are
crucial components of the immune system. They form intricate networks of interactions where
different cytokines positively and negatively influence each other's production and activity.
These networks play a vital role in maintaining the balance and specificity of immune
responses during illness and infection. In drug development, targeting cytokine
communication is often crucial for managing overactive immune responses in immune-
mediated inflammatory diseases (IMIDs), a group of ostensibly unrelated disorders
characterised by chronic inflammation and tissue damage resulting from an overactive
immune system. Common IMIDs include inflammatory bowel disease (IBD), rheumatoid
arthritis (RA), and systemic lupus erythematosus (SLE).

In this study, we created and analysed cytokine-cytokine interaction (CCI) networks for
prevalent IMIDs using publicly accessible single-cell RNA-Seq datasets, aiming to uncover
shared and distinct immune signalling pathways impacting IMID patients. The generated
networks reveal potential intervention points where the exacerbated immune response
could be mediated. We established statistically significant CCIs by comparing our results with
experimental cytokine response data deposited to the CytoSig database, and determined
the likely intracellular pathways connecting upstream and target cytokines using the
OmniPath interaction resource and the NicheNet software.

Our research provides new insights into the role of cytokines in IMIDs, and has the potential
to aid development of novel treatments for these conditions that could be utilised when
patients do not respond to direct intervention of central cytokines.

35
P-13 - OmniPath: database knowledge for mechanistic
modeling, cell-cell communication and more
Dénes Türei1, Michal Klein2, Melih Darcan3, Ömer Kaan Vural3, Erva Ulusoy3,
Tennur Kiliç3, Nicolàs Palacio1, Alberto Valdeolivas1, Dezső Módos4, Olga Ivanova1,
Christina Schmidt1, Sophia Müller-Dott1, Marco Ruscone5, Lejla Gul4, Márton Ölbei4,
Daniel Dimitrov1, Atabey Ünlü3, Bünyamin Sen3, Elif Çevrim3, Sebastian Lobantanzer1,
Attila Gábor1, Ahmet Rifaioglu1, Åsmund Flobak6, Tunca Dogan3, Fabian Theis2,
Tamás Korcsmáros4, Julio Saez-Rodriguez1

1 University Hospital Heidelberg, Heidelberg, Germany

2 Helmholtz Center Munich, Munich, Germany
3 Hacettepe University, Ankara, Turkey
4 Imperial College London, London, UK
5 Institut Curie, France
6 Norwegian University of Science and Technology, Norway

OmniPath is a molecular biology database combining more than 170 original resources. It
covers a broad variety of data, including signalling, metabolic, gene regulatory and miRNA
networks, along with rich annotations of protein and gene function, structure, localization.
OmniPath is publicly available by a web API (omnipathdb.org), with convenient access from
R and Python by dedicated packages. Thanks to its integration with the DecoupleR and
AnnData packages, it seamlessly supports transcription factor and pathway activity
inference from bulk or single cell transcriptomics. Its literature curated network of activatory
and inhibitory molecular interactions is routinely applied for causal reasoning by the software
CARNIVAL and COSMOS, deriving mechanistic insights from transcriptomics or multi-omics
data. OmniPath also features comprehensive knowledge about intercellular signalling
which, connected to the LIANA module, enables easy inference of cell-cell communication
from single cell transcriptomics. These are only a few examples for the applications of
OmniPath's diverse data. The integration of OmniPath into the above mentioned workflows
is realised with the support of the HPC/Exascale Centre of Excellence for Personalised
Medicine in Europe (PerMedCoE) programme.

36
P-14 - The caudovirales class of viruses is associated
with dendritic cell impairment in CD patients
Carmela Errico1, Luca Massimino1, Amanda Facoetti1, Stefania Cagliani1,
Salvatore Spanò1, Tommaso Lorenzo Parigi2, Omar Almolla1, Silvio Danese1,2,
Federica Ungaro1

1 Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele, Milan, Italy
2 Department of Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milan, Italy

The gut virome has been established to hold a key role in the pathogenesis of Crohn’s disease
(CD), belonging to the Inflammatory Bowel Disease (IBD) class. Indeed, some years ago
Norman and colleagues described the expansion of Caudovirales as associated with CD
pathogenesis and coupled with decreased bacterial diversity1. To further explore this
aspect, we exploited the IBD TaMMA framework2, and we found the Autographiviridae,
belonging to the class of Caudovirales was highly abundant in the CD colon by comparison
with the healthy control (Fig. 1a), confirming the previous study. Therefore, to further
investigate the role of this family in the different mucosal cell compartments, CD- and
healthy-derived intestinal biopsies were digested to obtain a cell suspension undergoing flow
cytometry cell sorting (FACS) to isolate immune and non-immune cells according to cell
population-specific markers. Specifically, CD8 and CD4 T cells, B cells, macrophages,
dendritic cells, epithelium, endothelium, and fibroblasts were obtained and underwent
transcriptomics and metatranscriptomics. Interestingly, the gene ontology (GO) revealed
that the sole CD cell populations showing impaired biological response to viral insults by
comparison with the healthy were the dendritic cells, fibroblasts, and epithelial cells (Fig. 1b-
d) suggesting that in CD mucosa only specific cell compartments were impacted by viral
entities. Furthermore, by metatranscriptomics analysis we identified the CD dendritic cells to
retain a higher abundance of the Autographiviridae family by comparison with the healthy
(Fig. 1e), indicating that the virome dysbiosis in these cells may underlie CD pathogenesis by
altering their biological functions. Consistently, the heatmap of differentially regulated genes
in CD versus healthy dendritic cells displayed downregulation of the transcripts key for
dendritic cell-directed immune response (Fig. 1f).

Similar results have been recently proposed by our group to explain ulcerative colitis (UC)
pathogenesis, where we identified a virome-derived protein, belonging to the
Hepadnaviridae family, to directly disrupt the epithelial barrier and guide the development
of intestinal inflammation3. Therefore, given the growing evidence of the viral entities as
triggers for IBD, these data are promising and may pave the way to the discovery of viruses
directly involved in CD pathogenesis that can represent a target for the development of
novel strategies of intervention, ultimately ameliorating the CD management soon.

1 Norman, J.M. et al. “Disease-specific alterations in the enteric virome in inflammatory bowel
disease.” Cell vol. 160,3 (2015): 447-60.
2 Massimino, L. et al. The Inflammatory Bowel Disease Transcriptome and Metatranscriptome Meta-
Analysis (IBD TaMMA) framework. Nat Comput Sci 1, (2021):511–515.
3 Massimino, L. et al. Gut virome-colonising Orthohepadnavirus genus is associated with ulcerative
colitis pathogenesis and induces intestinal inflammation in vivo. Gut. 2023 Feb 14:gutjnl-2022-
328375.

37
Figure 1 - Autographiviridae viral family abundance in CD colon and the modulation of biological processes to
viral insult in CD-derived dendritic cell. a) MA-plot showing Autographiviridae viral familiy abundance in CD
colon compared to control colon. b-d) GO plots displaying gene set enrichments of the specific viral biological
processes in CD dendritic cells (b), CD fibroblasts (c) and CD epithelial cells (d) versus healthy counterparts. e)
Violin plot showing the differential abundances of Autographiviridae in dendritic cells compared to healthy-
derived cell population (*p= 0.031). f) Gene expression heatmap related to dendritic cell functions.

38
P-15 - (In) no time to strain: strain-resolved
metagenomic profiling with protal
Joachim Fritscher1,2, Ezgi Ozkurt1,2, Falk Hildebrand1,2

1 Quadram Institute Bioscience, Norwich, UK

2 Earlham Institute, Norwich, UK

Disclaimer: This data is preliminary and not intended for wider sharing.

Metagenomic profilers process metagenomic sequencing data to reveal the microbial

composition and functional potential of microbial communities in a multitude of different
environments. Current metagenomic profilers often lack in speed, accuracy and user-
friendliness, especially for strain-level. To keep up with the increasing amount of meta-analysis
studies encompassing many thousand metagenomic samples and facilitate novel
discoveries at reasonable computational cost, profilers need to provide accurate results and
fast speeds on species and on strain-level. Here, we present protal (profiling through
alignment), a metagenomic profiler operating on strain-level, offering accuracy on-par or
better and speed outperforming other state-of-the-art tools.

Aims: Strain-level analysis is still not a standard in metagenomics and tools are either slow or
focus on target taxa in a community to reduce computational demands. Protal offers fast
strain-resolved profiling for all species of a set of samples and thus allows more researchers
to reach strain-level.

Results: We tested protal against mOTUs3, MetaPhlAn3 and MetaPhlAn4 to assess the ability
to accurately detect taxa and reconstruct their abundances. Protal has a sensitivity and
precision similar or better than state-of-the-art tools for taxonomic classification (Figure 1A)
at speeds up to 8x faster than the other tools (Figure 1B). Early development strain-level results
on synthetic data with akkermansia muciniphila indicate that reads from the same genome
consistently cluster together in phylogenetic trees created from the multiple sequencing
alignments produced by protal (Figure 2). For protal, most of the strain-level computations
are already included in the speed benchmark on species level and it is thus to be expected
that the speed difference between protal and other strain-level tools will be even greater.

39
 Figure 1. – Protal was tested against mOTUs3, MetaPhlAn3 and MetaPhlAn4 on the synthetic dataset from the
CAMI-Challenge (Human data and Mouse gut). A Each boxplot with each datapoint within being a sample is
the comparison between the tools for a certain simulated environment while he leftmost column is the summary
of all environments. The top row contains F1 scores and the bottom row displays the Bray-Curtis dissimilarity. B, C
The tools were compared regarding the runtime and memory requirement, respectively, on a subset of the
data used in A.

Figure 2. – Reads were simulated from random Akkermansia muciniphila strains to assess protals ability to cluster
together samples containing the same strain. Tip color indicates the genome whereas the outer ring color
encodes for simulated vertical coverage.

40
P-16 - Towards a comprehensive understanding of
polymicrobial biofilm development and community
interactions
Micaela Mossop1, Cynthia B. Whitchurch2 and Laura M. Nolan1,2

1 National Heart and Lung Institute, Imperial College London, SW3 6LR, United Kingdom
2 Microbes and Food Safety, Quadram Institute Bioscience, NR4 7UQ, United Kingdom

Biofilms are the normal mode of growth for microbes. A biofilm is a complex 3D structure
where microbes are encased in an extracellular matrix. The matrix protects inhabitants from
exogenous stresses like antibiotics, disinfectants, and the immune system, which means that
biofilms are often challenging to remove. This recalcitrance can be either beneficial or
problematic for the host or local environment. Examples of beneficial biofilms include those
in the mammalian gut and oral cavity, in some fermented foods, and in wastewater
treatment plants. Conversely, examples of detrimental biofilms include those in the cystic
fibrosis (CF) lung, in chronic wounds, on ship hulls, and on spoiled food.

Our overall research aim is to understand microbial biofilm development in relevant settings
and how microbe-microbe interactions shape population profile dynamics in these
communities. We are working on two main biofilm areas: (1) those associated with the CF
lung and (2) with food spoilage. The goal is to use our knowledge to develop interventions
that (1) alter the CF lung microbial population profile to obtain the most beneficial outcome
for the patient, and (2) develop interventions that reduce food spoilage and extend food
shelf-life.

Biofilms are heterogenous at the physical and chemical level, and at the level of community
composition, gene expression, and protein and metabolite production, which makes them
challenging to study. We are currently using several global ‘omics and single-cell
approaches to study biofilms however, we are seeking collaborators to develop additional
global (metabolomics and proteomics) and single-cell (CLASIFISH and single-cell RNAseq)
approaches for our research. Given that all these approaches generate large amounts of
data in various formats we are also seeking collaborators to integrate and effectively analyse
the multi-omics and single-cell data we are obtaining to get the maximum value out of these
datasets and increase our understanding of these complex systems.

41
P-17 - Development of a host-microbe interaction
pipeline to reveal the cell- and condition-specific
effects of bacteria using single-cell transcriptomics
data
Lejla Potari-Gul1, Matthew Madgwick2,3, Dezso Modos2,3, Sonia Fonseca3,
John P. Thomas1,4, Padhmanand Sudhakar2,3,5, Catherine Booth6, Régis Stentz3,
Simon R Carding3,7, Tamas Korcsmaros1,2,3.

1 Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK

2 Earlham Institute, Norwich, UK
3 Gut Microbes and Health Research Programme, Quadram Institute Bioscience Norwich, UK
4 Department of Gastroenterology, Norfolk and Norwich University Hospital, Norwich, UK
5 KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for
Gastrointestinal Disorders (TARGID), Leuven, Belgium
6 Core Science Resources, Quadram Institute Bioscience, Norwich, UK
7 Norwich Medical School, University of East Anglia, Norwich, UK

The human microbiome regulates physiological processes through interactions with the host.
Disruptions to the microbiome composition can result in inflammation and the emergence
of diseases, such as inflammatory bowel disease (IBD) in the gut. Short linear motifs are short
sequences of amino acids that facilitate specific protein-protein interactions through
physical connections, usually via domains. These interactions are vital in host-microbe
interactions as they have the ability to regulate host immune responses and modify cellular
signalling pathways.

We have updated our MicrobioLink pipeline, an algorithm predicting microbe-host

interactions through domain-motif and domain-domain interactions using the ELM
database. It focuses on cell type-specific effects of bacteria in health and disease through
utilising functional analysis and network propagation tools to uncover direct microbe-
affected processes and downstream pathways affected by bacteria.

To demonstrate the usefulness of the pipeline, we analysed the impact of Bacteroides

thetaiotaomicron (Bt) on human immune cells focusing on Toll-like receptor signalling, and
found that proteins in extracellular vesicles secreted by Bt may modulate the pathway
intracellularly in a cell-type and condition-specific way.

The pipeline offers detailed mechanistic insight into the relationship between bacteria and
host cells that will improve our understanding of how microbial proteins may be of
therapeutic value in inflammatory diseases, such as IBD.

42
P-18 - The role of MFSD2A in the resolution of
colorectal cancer-promoting inflammation: implications
for innovative therapies
Stefania Cagliani1, Luca Massimino1,2, Gaia Colasante3, Salvatore Spanò1,2,
Amanda Facoetti1, Danial Behi1, Annalisa Maroli4, Matteo Sacchi4,
Antonino Spinelli4,5, Silvio Danese2,6 and Federica Ungaro1,2.

1. Laboratory of Experimental Gastroenterology, Division of Immunology, Transplantation and Infectious

Disease, San Raffaele Research Institute, Milan, Italy
2. Department of Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milan, Italy
3. Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132
Milan, Italy
4. Colorectal Surgery Unit, IRCCS Humanitas Clinical and Research, Hospital, Milan, Italy
5. Department of Biomedical Sciences, Hunimed, Milan Italy
6. Faculty of Medicine, Università Vita-Salute San Raffaele, Milan, Italy

Inflammation is a recognized hallmark of colorectal cancer (CRC), contributing to its

development and progression. CRC-associated inflammation may be contrasted by
specialized pro-resolving lipid mediators (SPMs) derived from omega-3 polyunsaturated fatty
acids as recently proposed. We previously demonstrated that the endothelial Major
Facilitator Superfamily Domain-containing 2A (MFSD2A) promotes the resolution of chronic
intestinal inflammation by overseeing the release of SPMs. Therefore, we hypothesized that
the endothelial MFSD2A might have also a role in hampering CRC-associated inflammation.

To test this hypothesis, we performed a transcriptomic analysis on Human Intestinal

Microvascular Endothelial Cells (HIMEC). Besides the increased levels of MFSD2A transcript in
CRC by comparison with the healthy, this analysis pointed out the activation of the resolution
phase-related biological processes in CRC as compared to the healthy, proposing the
endothelium as a player also in CRC pathogenesis. Furthermore, by lipidomics, CRC HIMEC
displayed increased release of SPMs and reduced levels of the pro-inflammatory lipids by
comparison with the healthy control cells. Interestingly, upon MFSD2A silencing, CRC HIMEC
switched to a proinflammatory phenotype, characterized by the activation of pro-
inflammatory biological processes and the increased release of pro-inflammatory lipids.
Notably, the enhancement of MFSD2A expression both in vitro and in vivo reduces cancer
cell growth and shapes tumor microenvironment. These data suggested that MFSD2A might
contrast the tumor-associated inflammation and ensure the correct balance between pro-
inflammatory and pro-resolving milieu, offering novel insights into the development of
innovative therapies suitable for CRC patient management.

43
 Figure 1. CRC displays an enrichment of inflammation-related pathways, including MFSD2A.
A. Gene ontology analysis performed by Gene Set Enrichment Analysis framework for comparison between
CRC GFP and healthy GFP cells.
B. MFSD2A abundance per conditions (CRC GFP Vs healthy GFP cells). Data are represented as mean ± s.e.m.
*P<0.05. C. AA and DHA lipid abundance per conditions (CRC shCTRL Vs healthy shCTRL cells). Data are
represented as mean ± s.e.m. *P<0.05; **P<0.01.

Figure 2. MFSD2A silencing in CRC increases inflammatory processes promoting AA metabolism.

A. Lipid ontology analysis performed by Lipid Set Enrichment analysis framework for comparison between CRC
shMFSD2A and CRC GFP.
B. DHA and AA lipid abundance per conditions (healthy shCTRL, CRC shCTRL and CRC shMFSD2A). Data are
represented as mean ± s.e.m. **P<0.01.

44
 Figure 3. Enhancement of MFSD2A expression reduces cancer cell growth.
A. Percentage of Ki67+ CACO cells co-coltured 24h with different HIMEC conditions (healthy GFP, healthy
MFSD2A, healthy shCTRL, healthy shMFSD2A). Data are represented as mean ± s.e.m. **P<0.01;
***0.0001<P<0.01; ****P<0.0001.
B. Generation of Mfsd2a-inducible mouse model: by crossing Mfsd2aloxSTOP mouse with the VE-Cad-CreERT2
mouse, the STOP cassette will be removed by Cre upon tamoxifen injections and gene expression will be
conditionally reactivated only in the intestinal endothelium, finally restoring Mfsd2a driven by its own regulative
region.
C. Exploitation of transgenic mouse model to induce experimental CRC: Mfsd2a expression will be maintained
OFF and reactivated at different time-points before and after CRC induction to evaluate the timely Mfsd2a
activation.

45
P-19 - DisCanVis: Visualizing integrated structural and
functional annotations to better understand the
effect of cancer mutations located within disordered
proteins
Norbert Deutsch, Mátyás Pajkos, Gábor Erdős, Zsuzsanna Dosztányi

MTA-ELTE Momentum Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University,
Budapest, Hungary

Keywords: Intrinsically disordered proteins (IDP) , cancer, visualization, functional and structural
annotation, web server, tool

Intrinsically disordered proteins (IDPs) play important roles in a wide range of biological
processes and have been associated with various diseases, including cancer. In the last few
years, cancer genome projects have systematically collected genetic variations underlying
multiple cancer types. In parallel, the number and different types of disordered proteins
characterized by experimental methods have also significantly increased. Nevertheless, the
role of IDPs in various types of cancer is still not well understood. In the presented work I
introduce DisCanVis, a novel visualization tool for cancer mutations with a special focus on
IDPs. In order to aid the interpretation of observed mutations, genome level information is
combined with information about the structural and functional properties of proteins. To ease
the access to the data presented in DisCanVis, we introduced multiple tables that group the
data based on certain properties, such as known driver genes, significantly mutated regions

or experimentally verified disordered proteins

Figure 1: Example of visualization with RAF proto-oncogene serine/threonine-protein kinase

The web server enables users to inspect individual proteins, collect examples with existing
annotations of protein disorder and associated function or to discover currently
uncharacterized examples with likely disease relevance. For large scale analysis we offer
processed data collection in the web server and programmatic access via REST API.

46
P-20 - Investigation of the role of COP9 signalosome
in the epithelial-mesenchymal transition
Dávid Keresztes1, Erik Seitz1, Nina Kunsic1, Tibor Szarvas2, Péter Csermely1

1. Semmelweis University, Department of Molecular Biology, Budapest, Hungary

2. Semmelweis University, Department of Urology, Budapest, Hungary

Epithelial-mesenchymal transition (EMT) promotes metastasis formation of primary tumors

which can develop in parallel with drug resistance. Since EMT is a gradually evolving process,
intermediate phenotypic states emerge (hybrid-E/M), showing both epithelial (E) and
mesenchymal (M) properties. Hybrid-E/M and M state cancer cells possess invasiveness and
chemotherapy resistance. Therefore, reversing EMT - known as mesenchymal-epithelial
transition (MET) - has a promising therapeutic potential. In our in silico intercellular EMT
network model, knock-out of COP9 signalosome complex (CSN) was able to induce MET of
the hybrid-E/M and M cells’ networks.

Aims: The aim of this project is the in vitro validation and further exploration of the CSN
complex in the process of EMT/MET, for which appropriate cell lines had to be chosen.

Results: Docetaxel (DOC)-sensitive (PC3, DU145) and -resistant (DU145-DR, PC3DR) prostate
cancer cell lines were selected for the experiments. The DR sublines went through EMT during
the development of DOC-resistance, which was confirmed by measuring the gene
expression of EMT markers (CDH, VIM, ZEB1, ZEB2) using qRT-PCR. The expression of the
functional subunits of the CSN (CSN5, CSN6) was determined (Western blot), and their
silencing was performed by RNA interference. Based on our measurements, DOC-sensitive
cells proved to have E, the PC3-DR cells hybrid-E/M, while the DU145-DR cells proved to have
M phenotype. The expression of both CSN5 and CSN6 was detectable in both pairs of cell
lines, and their RNA-silencing was also successful.

These results indicate that our cell lines can be considered as suitable in vitro systems for the
validation of our in silico results. In parallel with gene silencing, we will perform functional
experiments such as migration, invasion and viability assays, which may prove the role of CSN
in EMT, and will also possibly influence DOC resistance.

47
P-21 - Multiscale model of the different modes of
cancer cell invasion
Marco Ruscone1, Arnau Montagud2, Philippe Chavrier3, Olivier Destaing4,
Isabelle Bonnet1, Andrei Zinovyev1, Emmanuel Barillot1, Vincent Noël1,
Laurence Calzone1

1 Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris,
France
2 Barcelona Supercomputing Center (BSC), Barcelona, Spain
3 Institut Curie, PSL Research University, CNRS, UMR 144, Paris, France
4 Institute for Advanced Biosciences, Centre de Recherche Université Grenoble Alpes, Inserm U 1209, CNRS
UMR 5309, France

Motivation: Mathematical models of biological processes altered in cancer are built using
the knowledge of complex networks of signaling pathways, detailing the molecular
regulations inside different cell types, such as tumor cells, immune and other stromal cells. If
these models mainly focus on intracellular information, they often omit a description of the
spatial organization among cells and their interactions, and with the tumoral
microenvironment.

Methods: We present here a model of tumor cell invasion simulated with PhysiBoSS, a
multiscale framework which combines agent-based modeling and continuous time Markov
processes applied on Boolean network models. With this model, we aim to study the different
modes of cell migration, by considering both spatial information obtained from the agent-
based simulation and intracellular regulation obtained from the Boolean model.

Results: Our multiscale model integrates the impact of gene mutations with the perturbation
of the environmental conditions and allows the visualization of the results with 2D and 3D
representations (Fig. 1). The model successfully reproduces single and collective migration
processes and is validated on published experiments on cell invasion (Fig.2). In silico
experiments are suggested to search for possible targets that can block the more invasive
tumoral phenotypes.

Optional figures:

48
 Fig.1 3D
representation of
the model.

Fig.2 Comparison with In-vitro experiment (Moitrier et al. CommunPhys2, 98, 2019).

49
P-22 - Investigating the role of gut eukaryotic virome
in contributing to colorectal cancer carcinogenesis
Amanda Facoetti1, Luca Massimino1,2, Salvatore Spanò1,2, Stefania Cagliani1,
Carmela Errico1, Tommaso Lorenzo Parigi1,2, Silvio Danese1,2 and Federica ungaro1,2

1. Laboratory of Experimental Gastroenterology, Division of Immunology, Transplantation and Infectious

Disease, San Raffaele Research Institute, Milan, Italy
2. Department of Gastroenterology and Digestive Endoscopy, IRCCS San Raffaele Hospital, Milan, Italy

Colorectal cancer (CRC) is the third most commonly diagnosed malignancy and the fourth
leading cause of cancer death in the world. Besides the genetic aberrations, considered the
pillars of CRC etiopathogenesis, intestinal dysbiosis and inflammation are widely
documented to characterize its pathogenesis. Some of our recent findings pointed out a gut
viromeassociated Orthohepadnaviridae protein, namely Hepatitis B protein X (HBx), to
correlate with Ulcerative Colitis pathogenesis and promote intestinal inflammation in mice.
Moreover, we showed that HBx is able to induce DNA damage-related biological processes
and active biological processes related to the Wnt pathway, known to be involved in
colorectal carcinogenesis.

Based on this evidence we hypothesize that HBx may fill the gap existing between intestinal
inflammation and CRC onset by stimulating pro-inflammatory and/or pro-carcinogenic
effects. Metatranscriptomic analysis revealed that HBx is abundantly present in CRC-derived
mucosal samples (Figure 1A) compared with healthy individuals, strengthening the link
between a virome protein-induced inflammation and tumor development in patients.

Moreover, HBx overexpression in intestinal epithelial cells directly provokes DNA damage
(Figure 1B), suggesting the direct HBx impact on intestinal epithelium genomic stability.

Interestingly, HBx administration in mice led to the development of polypoid structures in the
colonic mucosa (Figure 1C) characterized by decreased abundance of T cells, including
effector T cells and NK T cells (Figure 1G). Of note, in vivo HBx modulated the expression of
genes involved in the regulation of transcription and activation of the proto-oncogene PIM3
(Figures 1D-F) further supporting the role of a viral protein on CRC onset.

This study introduces unconventional and innovative insights for giving CRC studies a new
direction for the scientific and clinical investigations, looking at the gut virome as an active
component and not as a mere bystander entity of the microbiota, ultimately promoting a
new standpoint in the CRC studies and management in the short-term future.

50
 Figure 1. HBx induces carcinogenic properties
(A) Violin plot showing the Log2 abundance of HBx transcript in CRC-derived mucosal samples.
(B) FACS analysis panels showing γH2AX positivity in HBx-overexpressing Caco-2 by comparison with the control.
(C) Representative images of endoscopies performed on HBx- and GFP-treated mice. White arrows indicate
polypoid structure in HBx-treated mice.
(D-F) MA-plot (D) and heatmap (E) show differentially expressed genes in HBxtreated mouse colons by
comparison with the GFP. Red and blue dots indicate upregulated and downregulated genes, respectively,
with statistical significance. In F, box plot shows the differential expression of a cancer marker PIM3 in HBx- versus
GFP-treated mice. *P<.05.
(G) Bar plots showing the relative proportion of the indicated cell populations in HBx- and GFP-treated mice.

51
P-23 - How yeast go multicellular
Valentina Madár, Tünde Gaizer, Bíborka Pillér, Csaba I. Pongor, Andrea Ciliberto,
János Juhász, Attila Csikász-Nagy

Pázmány Péter Catholic University, Faculty of Information Technology and Bionics, Budapest, Hungary

Plethora of evolutionary innovation created the world we know today. Several lifestyle
strategies have given advantage to organisms to adopt to continuously changing
environment. One of these is the emergence of multicellularity, which provided an
opportunity for more complex organisms to evolve. The way from unicellularity to
multicellularity was a long journey. In this study we want to explore this process with the widely
used unicellular model organism: baker’s yeast (Saccharomyces cerevisiae).

Due to starvation or in insufficient environmental conditions yeasts can form facultative

multicellular secondary structures (e.g. pseudohyphae, flocs), that helps the colony to gain
nutrients and reduce the deficient environmental impact. Our goal is to mutate this
facultative multicellularity to obligate multicellularity and evolve a stay-together strategy in
yeast.

ACE2 is a DNA-binding transcription factor involved in positive regulation of septum digestion

after cytokinesis. Deletion of this gene results a multicellular „snowflake” phenotype in yeast
(Ratcliff et al. 2015). Combined with other modifications (e.g. Flo genes, Septin genes, Wnt
signaling pathway) can result in a newer structure and phenotype of a permanent
multicellular colony. Through these mutations, the evolutionary development of
multicellularity can be better understood.

1 Ratcliff, W., Fankhauser, J., Rogers, D. et al. Origins of multicellular evolvability in snowflake yeast.
Nat Commun 6, 6102 (2015). https://doi.org/10.1038/ncomms7102

52
P-24 - Integrated stress response facilitates
mucoprotective reprogramming against acute
renointestinal distress
Yuseok Moon

Laboratory of Mucosal Exposome and Biomodulation, Department of Integrative Biomedical Sciences, Pusan
National University, Yangsan, Korea

The integrated stress response (ISR) plays a pivotal role in the cellular response to stress,
primarily through global translational arrest and the upregulation of cellular adaptation-
linked molecules. Herein, we assessed whether ISR-driven cellular stress contributes to
pathophysiological outcomes in the renointestinal distress. Clinical transcriptome analysis
demonstrated that several ISR signals were positively associated with the renal injury in
patients. In particular, genetic ablation of NAG as a target of ISR aggravated chemical-
induced lesions and muco-foragers in renal tissues and the gut barrier. Moreover, stress-
responsive NAG facilitated mucus production and cellular survival via reorganization of the
autophagy regulatory network. Collectively, ISR-activated NAG counteracted pathological
processes via the protective reprogramming of the autophagic network, thereby providing
robust predictive biomarkers and interventions against acute renointestinal distress

(This research was supported by the Basic Science Research Program through the National Research
Foundation of Korea (NRF), funded by the Ministry of Education (2018R1D1A3B05041889), and the
framework of international cooperation program managed by the National Research Foundation of
Korea (NRF-2022K2A9A1A01098067, FY2022)).

53
P-25 - AutophagyNet: High-resolution data source
for the analysis of autophagy and its regulation
Luca Csabai*, Balázs Bohár*, Dénes Türei, Sowmya Prabhu, László Földvári-Nagy,
Matthew Madgwick, Dávid Fazekas, Dezső Módos, Márton Ölbei, Themis Halka,
Martina Poletti, Polina Kornilova, Tamás Kadlecsik, Amanda Demeter,
Máté Szalay-Bekő, Orsolya Kapuy, Katalin Lenti, Tibor Vellai, Lejla Gul,
Tamás Korcsmáros

Imperial College London, London, UK

Autophagy is a highly-conserved catabolic process eliminating unnecessary, dysfunctional

cellular components and invading pathogens. Autophagy malfunction contributes to
disorders such as cancer, neurodegenerative and inflammatory diseases. Understanding
autophagy regulation in health and disease has been the focus of the last decades. The
recent advent of omics technologies made precise analysis of autophagy a reality on a
systems-level. We previously provided an integrated database for autophagy research, the
Autophagy Regulatory Network (ARN). For the last seven years, this resource has been used
by thousands of users. Here, we present a new and upgraded resource, AutophagyNet. It
builds on the previous database but contains major improvements to address user feedback
and novel needs due to the advancement in omics data availability. AutophagyNet
contains updated interaction curation and integration of over 280,000 experimentally
verified interactions between core autophagy proteins and their protein, transcriptional and
post-transcriptional regulators as well as their potential upstream pathway connections.
AutophagyNet provides annotations for each core protein about their role: 1) in different
types of autophagy (mitophagy, xenophagy, etc.); 2) in distinct stages of autophagy
(initiation, elongation, termination, etc); 3) with subcellular and tissue-specific localization.
These annotations can be used to filter the dataset, providing customizable download
options tailored to the user’s needs. The resource is available in various file formats (e.g., CSV,
BioPAX and PSI-MI), and data can be analyzed and visualized directly in Cytoscape. The
multi-layered regulation of autophagy can be analyzed by combining AutophagyNet with
tissue- or cell type-specific using (multi-)omics datasets (e.g. transcriptomic or proteomic
data). The resource is publicly accessible at http://autophagynet.org.

54
P-26 - A systems biological study of oscillatory
characteristic of autophagy induction under cellular
stress
Bence Hajdú1, Marianna Holczer1, Margita Márton1, Luca Csabai2,
Tamás Korcsmáros2, Orsolya Kapuy1,

1 Department of Molecular Biology, Semmelweis University, Budapest, Hungary

2 Imperial College London, London, UK

Keywords: Autophagy, mTOR, AMPK, systems biology, ODE

Autophagy-dependent survival is an essential cellular process to respond various stress

events. The main element of autophagy activator complex, called ULK1 is regulated by
AMPK and mTORC1 kinases. mTORC1 is a key controller of cellular homeostasis in nutrient rich
environment and it inhibits autophagy trough the phosphorylation of ULK1. On the other
hand, under cellular stress (e.g. starvation), AMPK activates autophagy via ULK1. mTORC1
and AMPK are mutual antagonists, while ULK1 also effects their activity, namely, it inhibits
both AMPK and mTORgenerating a negative and ta double negative feedback loops in the
control network. Recently, a freely available mathematical model we developed to confirm
that feedback loops of AMPK- mTORC1-ULK1 regulatory triangle and investigate their roles in
guaranteeing the switch-like behaviour of autophagy induction. Meanwhile, an oscillatory
characteristic was also demonstrated in the presence of rapamycin treatment.

In this study we introduce a theoretical analysis to explore the dynamical characteristic of

both negative and double negative feedback loops of ULK1-controlled autophagy
induction paying particular attention to understanding how the periodic activation of
autophagy with the help of AMPK and mTORC1 kinases upon cellular stress. Parameter
estimation and sensitivity analysis are also carried out to validate our model. We suggest an
extra regulatory molecule in the control network acting like the key sensor of autophagy
induction. Our theoretical analysis explores that the inclusion of this extra protein induced by
AMPK ensures the proper dynamics of the control network by up-regulating ULK1 and down-
regulating mTORC1 upon cellular stress. The Autophagy Regulatory Network has been used
to identify a good number of proteins with similar connections, which could later be
important therapeutic targets in various diseases such as inflammatory bowel diseases.

Funding: Supported by the Richter Gedeon Talentum fundation

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P-27 - Reversal of epithelial-mesenchymal transition
in a compartmentalized in silico Boolean model
Márk Kerestély1, Péter Mendik1, Sebestyén Kamp2, Dávid Deritei1, Nina Kunši1,
Péter Csermely1, Daniel V. Veres1,2

1 Department of Molecular Biology, Semmelweis University, Budapest, Hungary

2 Turbine Ltd., Budapest, Hungary

It is a major challenge to reverse the epithelial-mesenchymal transition in cancer cells and

achieve mesenchymal-epithelial transition (MET) for therapeutic benefit. EMT is involved in
the metastasis of a wide range of cancerous diseases including colorectal carcinoma. In
silico Boolean modelling of EMT signalling is a cost-effective way to gain therapeutically
relevant information about its regulation. Subcellular compartmentalization of these Boolean
models improves their accuracy by simulating the regulatory role of distinct compartments
(e.g., cytoplasm, nucleus) in signalling. Signalling pathways involved in the regulation of both
EMT and MET, like the LIF/KLF4 pathway, can be incorporated into these models to model
the two-way dynamic of the epithelial-mesenchymal spectrum.

Aims: A limiting factor of current Boolean EMT models is that the stability of their attractors is
skewed towards the mesenchymal attractor. We have aimed to assess the effect of
compartmentalization (that we had applied to an established Boolean TGFB mediated EMT
model) on the stability of the epithelial attractor and its effect on the facilitation of MET by
comparing the compartmentalized and original versions of the same model.

Results: In our compartmentalized model, the epithelial attractor was found to be 4 times
more stable compared to the original model. (The mesenchymal attractor remained a lot
more stable than the epithelial in our model, as expected.) Compared to the 7 perturbations
required to restore the epithelial state in the original model, the number of perturbations
required to restore the epithelial state was reduced to 5 in the compartmentalized model.
By incorporating elements of the LIF/KLF4 signalling pathway into our model, a partial MET
was achieved following the activating perturbation of the nuclear GSK3B node. Our
compartmentalized approach to modelling EMT increased the stability of the epithelial
attractor and shifted the signal transduction towards MET.

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