Temporal and spatial topography of cell proliferation in cancer

Abstract

Proliferation is a fundamental trait of cancer cells but is poorly characterized in tumors by classical histologic methods. We use multiplexed tissue imaging to quantify the abundance of multiple cell cycle regulating proteins at single-cell level and develop robust multivariate proliferation metrics. Across cancers, the proliferative architecture is organized at two distinct spatial scales: large domains, and local niches enriched for specific immune lineages. A subset of tumor cells express cell cycle regulators in canonical patterns consistent with unrestrained proliferation, a phenomenon we refer to as “cell cycle coherence”. By contrast, the cell cycles of other tumor cell populations are skewed toward a specific phase or characterized by non-canonical (incoherent) marker combinations. Coherence varies across space, with changes in oncogene activity, and with therapeutic intervention, and is associated with aggressive behavior. Multivariate measures capture clinically significant features of cancer proliferation, a fundamental step in enabling more precise use of anti-cancer therapies.

Multiplexed and reproducible high content screening of live and fixed cells using the Dye Drop method

“…These states are not distinguished by any single marker in our antibody panel, but rather are by high dimensional features. This complexity in cell cycle arrest states is consistent with recent evidence from human tumors 37 and reveals how CyCIF can be used to discriminate drug-induced cell states that appear similar by lower-plex assays. It seems likely that such data, when collected at scale, will assist in identifying drug mechanism of action and response biomarkers.…”

“…However, these anticipated relationships masked dramatic variation in basal cell cycle state: under conditions of normal growth, G1 fraction varied from 15% to 86%, G2 fraction from 6% to 40%, and S phase fraction from 4% to 63% with no obvious association with subtype. The distribution of cell cycle states in actual tumors has also been shown to vary within and across cancers 37 and clearly warrants additional study.…”

Lymphocyte networks are dynamic cellular communities in the immunoregulatory landscape of lung adenocarcinoma

“…Recent advances in single-cell and multiplexed spatial analysis of tissues are driving large scale inter-institutional and international efforts to systematically characterize the spatial organization of human tumor and immune cells during cancer development and in response to therapy (Rajewsky et al, 2020; Rozenblatt-Rosen et al, 2020). Recurrent spatial features of human cancers are being identified, for example i) active immune surveillance of proliferating tumor cells by cytotoxic T cells (Gaglia et al, 2022; Launonen et al, 2022), ii) chemokine-organized tumor-immune architecture (Nirmal et al, 2022; Pelka et al, 2021), and iii) and cell-cell interactions involved in generating extracellular metabolites such as adenosine, an immunosuppressive purine metabolite of ATP hydrolysis by the CD39 and CD73 ectoenzymes (Coy et al, 2022). These early insights into the tissue cellular neighborhoods and cellular architectures of human cancer tissues have revealed a pressing need for experimental and analytical approaches to investigate the mechanistic underpinnings of the anti-cancer immune response.…”

“…FFPE sections were prepared and stained with a 24-plex antibody panel according to the previously described t-CyCIF protocols (Burger et al, 2021; Gaglia et al, 2022; Lin et al, 2018) (see Table S1 ). This CyCIF panel has been validated across many different sample types in accordance with standards defined by our group (Du et al, 2019).…”

Single cell spatial analysis reveals the topology of immunomodulatory purinergic signaling in glioblastoma

“…Cyclic immunofluorescence (CyCIF) 9 is one such method, enabling quantification of up to 60 antigens at single-cell resolution and generation of maps of functional neighborhoods. Integrating data from scRNA-seq and multiplexed tissue imaging has begun to reveal substantial spatial and molecular variation within human tumors [13][14][15] , and populationlevel regulation of tumor-immune interactions 16 . Such studies promise to reveal novel vulnerabilities in difficult to treat cancers.…”