Unveiling the cellular heterogeneity of cancer metastasis

Technologies within single-cell omics have revolutionized our ability to explore cellular heterogeneity with remarkable precision. Encompassing a range of methods that can analyze the molecular characteristics of individual cells, single- cell omics promise to provide valuable insights into the DNA, RNA, and protein levels at a single-cell resolution. In particular, single-cell RNA-sequencing (scRNA- seq) and spatial-omics stand out as pivotal tools providing insights into gene expression profiles, transcriptional states, and the spatial organization of cancer cells thereby providing leveraged to reveal the cellular heterogeneity of cancer cells and the tumour microenvironment (TME). Especially in the context of cancer metastasis, which remains a therapeutic enigma, the use of scRNA-seq and spatial-omics can be used to delineate the complex cellular landscapes of tumours and identify the interactions within the TME, providing crucial information for developing targeted therapies and improving patient outcomes.

In Paper I we investigate clear cell renal cell carcinoma (ccRCC) using scRNA-seq to analyze primary tumours and their metastatic counterparts. A distinct transcriptional signature was identified in tumour cells that predict metastatic potential and patient survival and highlights the role of the TME, particularly vascular remodelling and an immunosuppressive microenvironment in promoting metastasis. Finally, we highlight potential therapeutic targets, such as the CXCL9/CXCL10-CXCR3 and CD70-CD27 axes, as potential targets for treatments.

In Paper II, building on the insights of Paper I, we use scRNA-seq to analyze the TME of primary and bone metastatic ccRCC with a unique comparison to tumour involved-, benign- and healthy- bone marrow. Our findings highlight a population of tumour-associated mesenchymal stromal cells promoting epithelial-to- mesenchymal transition and bone remodelling as well as an immunosuppressive microenvironment with exhausted CD8+ T cells and tumour-associated macrophages that aids the metastatic process to bone. Finally, we show that tumour-associated mesenchymal cells exert their effects on bone remodelling via the RANK/RANKL/OPG signalling pathway, crucial for regulating bone resorption and remodelling in metastatic sites and suggest the pathway as a therapeutic target.

In Paper III, we investigated spatially resolved chromosomal aberrations in high- risk neuroblastoma (NB) patient samples and cell lines using spatial omics. We describe the tumour clonal landscape in patient samples and the evolutionary trajectories of cells in response to chemotherapy in NB cell lines. We reveal that targeting both proliferation and DNA damage response pathways via a combination treatment with doxorubicin, gemcitabine, and an ATM inhibitor, can effectively reduce tumour growth and inhibit regrowth both in vitro and in vivo, highlighting the importance of addressing genetic and phenotypic heterogeneity in NB.

Overall, this thesis provides novel insights into the intricate cellular landscape of primary and metastatic tumours as well as their surrounding microenvironments, revealing potential culprits of the metastatic process. Using high-resolution single-cell omics technologies, we enable the identification of key therapeutic targets and the development of more effective, personalized treatment strategies to combat cancer metastasis.

List of scientific papers

I. Adele M. Alchahin*, Shenglin Mei*, Ioanna Tsea, Taghreed Hirz, Youmna Kfoury, Douglas Dahl, Chin-Lee Wu, Alexander O. Subtelny, Shulin Wu, David T. Scadden, John H. Shin, Philip J. Saylor, David B. Sykes, Peter V. Kharchenko & Ninib Baryawno. A transcriptional metastatic signature predicts survival in clear cell renal cell carcinoma. Nat Commun 13, 5747 (2022). https://doi.org/10.1038/s41467-022-33375-w

II. Shenglin Mei*, Adele M. Alchahin*, Ioanna Tsea*, Youmna Kfoury, Taghreed Hirz, Nathan Elias Jeffries, Ting Zhao, Yanxin Xu, Hanyu Zhang, Hirak Sarkar, Shulin Wu, Alexander O. Subtelny, John Inge Johnsen, Yida Zhang, Keyan Salari, Chin-Lee Wu, Mark A. Randolph, David T. Scadden, Douglas M. Dahl, John Shin, Peter V. Kharchenko, Philip J. Saylor, David B. Sykes & Ninib Baryawno. Single-cell analysis of immune and stroma cell remodelling in renal cell carcinoma primary tumours and bone metastatic lesions. Genome Med 16, 1 (2024). https://doi.org/10.1186/s13073-023-01272-6

III. Ioanna Tsea*, Xiaoze Li Wang*, Yuwei Lin, Sen Li, Agnes Luise Sorteberg, Maja Lundström, Alexandra Johannesson, Pranauti Panshikar, Eleonor O'Brien, Kristina Ihrmark Lundberg, Ingrid Lilienthal, Quentin Verron, Nikolas Herold, Susanne Fransson, Tommy Martinsson, Per Kogner, Jacob Stenman, Malin Wickström, John Inge Johnsen, Ninib Baryawno, Charlotte Stadler, Magda Bienko & Shahrzad Shirazi Fard. Spatially resolved chromosomal aberrations are sensitive towards targeted therapy against proliferation and DNA damage response. [Manuscript]

*Equal contribution