High-dimensional molecular analysis of tissue-resident macrophages and tier interactions with cancer

Primary Supervisor: Toby Lawrence, King’s College London

Secondary supervisor: Chris Tape, UCL

Project

Macrophages play critical roles in cancer progression and resistance to therapy through both immune-regulatory functions, linked to suppression of anti-tumour immunity, and trophic functions supporting angiogenesis, tissue remodelling, invasion and metastasis.
Recent research has revealed there are two distinct lineages of macrophages that populate adult tissues; long-lived embryo-derived tissue-resident macrophages (TRM) and short-lived monocyte-derived macrophages (MDM) from adult bone marrow. Current research suggests there is a functional divergence between TRM and MDM that may have important implications in cancer (1-3); TRM are aligned with trophic functions and tissue homeostasis, while MDM are enriched for immune functions. We recently showed that embryo-derived TRM form a specific niche that promotes the metastatic spread of cancer cells in a mouse model of ovarian cancer (3), suggesting TRM have specific functions linked to tumour progression. We hypothesise that TRM maintain ?hard-wired? trophic functions that support the malignant progression of cancer cells and tumorigenesis.
We have developed protocols to derive human TRM from induced pluripotent stem cells (iPSC) that are amenable to genome editing (4). In this project, we will develop heterocellular patient-derived tumour organoids incorporating iPSC-derived TRM to study their impact of malignant progression. We will perform high-dimensional single cell analysis of organoids with and without TRMs using state-of-the-art proteogenomic approaches including single cell RNA-sequencing, mass cytometry and spatial transcriptomics (3,5). Integrated analysis of these datasets will allow us to infer intercellular communication networks between TRM and cancer cells associated with malignant progression. Genome editing in iPSC-derived TRM and cancer cells will validate the contribution of specific pathways to malignant progression and identify viable targets for therapeutic intervention.

The main objectives of this project are:

• The main objectives of this project are: Establish heterocellular patient derived organoids incorporating TRM.
• Perform high-dimensional proteogenomic analysis of heterocellular organoids.
• Integrated analysis of proteogenomic datasets to delineate intercellular communication pathways.
• Functional validation of communication pathways between TRM and cancer cells using genome editing.

These studies will give new insights into the biology of TRM and their roles cancer that may reveal new therapeutic targets for cancer treatment.

Candidate background

This project will combine immunology and cell biology approaches to decipher cellular communication networks in a heterotypic three-dimensional setting. This project would suit a candidate with a background in either immunology and/or cancer biology and a keen interest in immunocology and the tumour microenvironment. We would be particularly interested in candidates with experience or a special interest in high-dimensional single cell analysis techniques, such as scRNA-seq and CyTOF.

Potential Research Placements

1. Alessandro Di Tullio, GSK
2. Nathalie Auphan-Anezin, CIML, Marseille (F)
3. Lazarous Fotopoulos, CSCRM, King’s College London
4. Chris Tape, UCL Cancer Institute

References

1. Tissue-Resident Macrophages in Pancreatic Ductal Adenocarcinoma Originate from Embryonic Hematopoiesis and Promote Tumor Progression. Zhu Y, Herndon JM, Sojka DK, Kim KW, Knolhoff BL, Zuo C, Cullinan DR, Luo J, Bearden AR, Lavine KJ, Yokoyama WM, Hawkins WG, Fields RC, Randolph GJ, DeNardo DG. Immunity. 2017 Sep 19;47(3):597.
2. Specific targeting of CD163⁺ TAMs mobilizes inflammatory monocytes and promotes T cell-mediated tumor regression. Etzerodt A, Tsalkitzi K, Maniecki M, Damsky W, Delfini M, Baudoin E, Moulin M, Bosenberg M, Graversen JH, Auphan-Anezin N, Moestrup SK, Lawrence T. J Exp Med. 2019 Oct 7;216(10):2394-2411.
3. Tissue-resident macrophages in omentum promote metastatic spread of ovarian cancer. Etzerodt A, Moulin M, Doktor TK, Delfini M, Mossadegh-Keller N, Bajenoff M, Sieweke MH, Moestrup SK, Auphan-Anezin N, Lawrence T. J Exp Med. 2020 Apr 6;217(4):e20191869.
4. Induced-Pluripotent-Stem-Cell-Derived Primitive Macrophages Provide a Platform for Modeling Tissue-Resident Macrophage Differentiation and Function. Takata K, Kozaki T, Lee CZW, Thion MS, Otsuka M, Lim S, Utami KH, Fidan K, Park DS, Malleret B, Chakarov S, See P, Low D, Low G, Garcia-Miralles M, Zeng R, Zhang J, Goh CC, Gul A, Hubert S, Lee B, Chen J, Low I, Shadan NB, Lum J, Wei TS, Mok E, Kawanishi S, Kitamura Y, Larbi A, Poidinger M, Renia L, Ng LG, Wolf Y, Jung S, Önder T, Newell E, Huber T, Ashihara E, Garel S, Pouladi MA, Ginhoux F. Immunity. 2017 Jul 18;47(1):183-198.e6.
5. Multiplexed single-cell analysis of organoid signaling networks. Sufi J, Qin X, Rodriguez FC, Bu YJ, Vlckova P, Zapatero MR, Nitz M, Tape CJ. Nat Protoc. 2021 Oct;16(10):4897-4918.