Studies on immune tumour microenvironment in colorectal cancer

Studies on immune tumour microenvironment in colorectal cancer (PI Diana Domanska and Frode Jahnsen)

The use of immunotherapy has revolutionized cancer treatment by modulating immune responses against tumours. The first generation of antibody-based immunotherapies – immune checkpoint blockade (ICB) – acts by blocking receptor and/or ligand interacting molecules, such as PD-1 and CTLA-4, molecules that are involved in dampening T cell activation. ICB was the first tissue-agnostic approval of a cancer therapy based on the presence of a single biomarker, microsatellite instability (MSI) or deficient mismatch repair (dMMR). However, although patient subgroups within various cancer types have experienced durable clinical responses with ICB treatment, most cancer patients do not respond to ICB and approximately half of the cancer patients eligible for ICB have primary resistance.
Retrospective studies of patients receiving ICB have shown that the immune tumour microenvironment (iTME) consists of distinct subclasses where some subclasses are associated responsiveness to ICB, whereas others are not. The classification of iTME is mainly based on medium-resolution data of bulk RNA sequencing and immunohistochemistry using techniques such as CYBERSORT, XCell )and Immunoscore. Due to the nature of the datasets being used, the information regarding cellular proportions, cellular heterogeneity and deeper spatial distribution are very limited. The iTME is very diverse and complex and a deeper analysis of this complexity will help us to better identify the patients that will benefit from ICB and guide the search for novel targets for immunotherapeutic intervention.
Colorectal cancer (CRC) is one of the most common types of cancer worldwide. CRC has very limited clinical benefit of ICB. In metastatic CRC, only a small proportion of patients are eligible for ICB treatment: ≤5% of patients with metastatic CRC have MSI/dMMR tumours, and only half of these respond. It is therefore an unmet clinical need to develop new immune-oncology strategies for CRC.
In this project, we will develop an integrated approach to reconstruct cancer tissue architecture by combining single cell technologies and spatial transcriptomics with high dimensional immunoimaging. Computationally integrating these data will allow us to generate a whole-transcriptome map of the cancer tissue at single cell resolution. In combination with clinical and tumour-genomic data from large patient cohorts of CRC we will i) develop a classification system of the iTME with unprecedented resolution, ii) use our high resolution data to predict new immunotherapeutic targets and establish “mini-tumours” to validate our predictions, iii) develop strategies to personalized treatment.

Specific aims
Aim 1: Integrating technologies to produce whole transcriptome single cell resolution of cancer tissue. We will perform single cell (sc) RNA sequencing (seq) and spatial transcriptomics (10X Genomics Visium chips) to generate cellular-resolution spatiotemporal data of the iTME of CRC.
Aim 2: High-resolution spatial analysis of cancer tissue from patients with different clinical outcome. We will apply Visium chips on archival material of cancer tissue from clinically well-characterized CRC patients, selected to represent short and long-term survivors. We will integrate these data with results from Aim 1 to propose a high-resolution classification system of iTME related to clinical outcome (discovery phase).
Aim 3: Develop marker panels of iTME to stratify cancer patients for personalized treatment.
Based on data from Aim 1&2 we will develop panels of antibodies and RNA probes to identify subclasses of iTME on tissue sections (test phase). The panels will be validated on tissue microarrays (TMA) of large patient cohorts designed to consider tumour heterogeneity (validation phase).
Aim 4: Establish mini-tumours for ex vivo functional proof-of-concept of new immune-oncology treatment strategies. We will establish 3D patient-derived organoids (mini-tumours) co-cultured with tumour infiltrating immune cells from patient tumour tissue for in vitro functional validation of novel immunotherapeutic strategies based on results from Aim 1&2. Drug testing of patient-derived organoids will be used to identify novel treatment strategies.

Immunofluorescence staining of tumor macrophages in CRC with CD68 (green), CD163 (red) and calprotectin (blue)
UMAP plot of tumour macrophages in CRC

Frode Jahnsen (Group leader)

Frode is professor of medicine at the University of Oslo and senior consultant in clinical gastrointestinal pathology. He obtained his PhD in immunology under the supervision of Prof. Per Brandtzæg’s lab in 1997. He did a postdoc partly in the Brandtzæg lab and partly in Pat Holt’s lab in Perth, Australia. Returning from Australia in 2001 he started his training in Pathology and at the same time started to build his own research group. He became group leader in Centre for Immune Regulation (CIR), a Centre of Excellence funded by The Norwegian Research Council from 2007-2017. Until 2015 the lab had particular focus on immunopathology in allergic diseases in the airways. However, over the last 6 years the focus has shifted to mucosal immunology in the gut, and currently the lab has several ongoing projects studying the immune system in the gut in health as well as in diseases such as celiac disease, inflammatory bowel disease, graft versus host disease, Hirschsprung disease, and colorectal cancer.

Tuva Høst Brunsell (Postdoc)

Tuva started in January 2021 in a shared position as a pathologist in training and a postdoc in the lab. After completing her medical studies and internship she obtained a PhD focusing on the genomics of colorectal liver metastases at the Department of Molecular Oncology, Institute of Cancer Research. She is now establishing a method of high-resolution spatial transcriptomics in our lab which will be used to study immune cells in a morphological context in normal intestine and colorectal cancer.

Espen Bækkevold (Researcher)

Espen is molecular cell biologist and has a PhD in immunology from the University of Oslo. Following a postdoc at Harvard Medical School and Boston Children’s Hospital and a researcher appointment at the Norwegian School of Veterinary Science, he joined the lab in 2007. He is also a Professor at the Faculty of Dentistry, University of Oslo.
Espen has a “wet lab” background, and is interested in applying single-cell technologies to understand the composition and development of immune cell networks in human mucosal tissues.

Raquel Bartolome Casado (Postdoc)

Raquel is interested in studying the immune cells that are lodged in the human intestinal mucosa at single-cell resolution. After obtaining her degree in Biotechnology at the University of Salamanca (Spain), Raquel worked at the Cancer Research Center in Salamanca and completed her MSc studies. While working in this project, she realized research stays at the lab of Prof. Fritjof Lund-Johansen at the University of Oslo, where she acquired experience in novel multiplex bead-based immunoassays for large scale proteomic analysis. Then, Raquel went on to do her PhD in Prof. Frode Jahnsen’s lab at the Faculty of Medicine, University of Oslo. Her PhD work was focused on the longevity of the adaptive immune cell compartment in the human small intestine, with special focus on characterizing resident memory CD8+ and CD4+ T cells. Raquel obtained a Three-year Researcher Project grant with International Mobility from the Research Council of Norway and recently joined the Teichmann lab at Wellcome Sanger Institute (Cambridge, UK). She is currently studying the development and long-term maintenance of resident memory T cells in the human gut using single-cell multi-omics approaches.

Diana Domanska (Researcher)

Diana is a bioinformatician and matematician. She received her PhD in computer science from University of Silesia in Katowice (Poland) in 2014. After PhD, she did her postdoc at the University in Oslo in Biomedical Informatics. She worked on statistical analysis of genomics data, interactive visualizations and method development for genome-wide studies. She joined the lab in 2019, where she started working with single cell data and spatial transcriptomics. Current interests are in methods development for genomic data and their analysis.

Kjersti Thorvaldsen Hagen (Laboratory Scientist)

Kjersti is a biomedical laboratory scientist from Oslo Metropolitan University, and Kjersti joined the lab in 2008. Her main expertise is immunohistochemistry- and immunofluorescence methods. She also has genuine interests in molecular biology, especially in the working methods in single cell technologies.

Hanna Johannessen (PhD student)

Hanna joined the lab in February 2021 after completing her medical studies at the University of Oslo. Hanna is interested in the development of the mucosal immune system in the gut and in her PhD project she studies the relationship between the enteric nervous system and the immune system of children with Hirschsprungs disease. Her studies also include clinical aspects of Hirschsprungs disease, and she has collaborate closely with the pediatric surgeons at Oslo University Hospital.

Sol Lim (Postdoc)

Sol is a postdoc currently based in Inouye lab, department of Public Health and Primary Care, University of Cambridge. She received her BSc in Mathematics, MSc in Interdisciplinary program in Cognitive Sciences,  and PhD in Computational Neuroscience from Seoul National University, South Korea in 2015. During her PhD, she studied Connectomics with Dr Kaiser (Seoul, South Korea and Newcastle, UK),  regarding the spatial and topological characteristics of the brain network and its development both microscopically between synapses and macroscopically using neuroimaging. After her PhD, she moved to Indiana University (Bloomington, USA) to work with Dr Sporns and network scientists at the Indiana University Network Institute on multi-scale community detection and multi-layer networks applied to human brain networks. She then came back to the UK to join the Bullmore group in the department of psychiatry, University of Cambridge where she worked on the structural and functional network changes in the adolescent brain.  In April 2020, she joined the JahnsenLab to investigate multi-omic characteristics as well as the B cell receptor repertoire of the long-lived plasma cells in the human intestine at both bulk and single-cell levels.