Highlights in Cancer Research: August 2023

The EACR's 'Highlights in Cancer Research' is a regular summary of the most interesting and impactful recent papers in cancer research, curated by the Board of the European Association for Cancer Research (EACR). The list below appears in no particular order, and the summary information has been provided by the authors unless otherwise indicated. Use the dropdown menu or ‘Previous’ and ‘Next’ buttons to navigate the list. Epigenetic plasticity cooperates with cell-cell interactions to direct pancreatic tumorigenesis Burdziak, C., Alonso-Curbelo, D. et al. Science. 380 (6645): eadd5327 (2023). doi: 10.1126/science.add5327. Summary of the findings Pancreatic cancer is typically diagnosed late, with few treatment options, motivating a search for early intervention strategies to improve outcomes. In this paper, the authors leveraged genetically engineered mouse models to obtain a high-resolution view of pancreatic tissue during the earliest stages of cancer progression. Single-cell transcriptomic sequencing identified cellular phenotypes that are absent from normal pancreatic epithelia, but emerge following oncogenic Kras mutation. Exposure of these cells to inflammation—a condition known to provoke the onset of rapid tumorigenesis—triggers a transition toward neoplastic states from several distinct cellular origins. Among these, a highly plastic, Nestin-expressing progenitor-like population serves as the precursor for neoplastic states that predominate in the pancreas weeks or months later. By integrating epigenetic data, the authors revealed that highly plastic populations undergo global chromatin reprogramming, heightened in the vicinity of cell-cell communication genes, which alter the way these cells send and receive signals from their environment. They developed a computational approach to catalogue the set of receptors and ligands that define the communication capabilities of each plastic epithelial state and linked these ‘communication modules’ with relevant modules in tissue immune cells to define a pre-malignant cell-cell interaction network. This analysis identified a feedback loop between epithelial cells and regulatory T cells in the microenvironment, which drives the exit from plastic states toward neoplastic endpoints. [caption id="attachment_7213" align="alignnone" width="696"] A genetically engineered mouse model harboring mutant Kras in the pancreatic epithelium is subject to inflammation, inducing pancreatitis-driven tumorigenesis. Within 48 hours, chromatin opening near cell-cell communication genes opens channels of communication in plastic cells. Emergent signaling from gastric-like populations to progenitor-like cells involves multiple receptor-ligand pairs. Mouse illustration was created with BioRender (https://biorender.com/).[/caption] Future impact This work sheds light on the earliest events driving cancer progression, focusing on how genetic mutation cooperates with environmental factors such as inflammation to initiate disease. The cellular plasticity and cell-cell communication mechanisms that are shown to underly disease onset and early progression provide several potential targets for cancer therapeutics. Read more in Science Dysregulated Lipid Synthesis by Oncogenic IDH1 Mutation Is a Targetable Synthetic Lethal Vulnerability Thomas, D. et al. Cancer Discovery. 13 (2): 496–515 (2023). doi: 10.1158/2159-8290.CD-21-0218. Summary of the findings The genes encoding isocitrate dehydrogenase 1 and 2 (IDH1/2) are mutated in multiple cancers and drive the production of the oncometabolite (R)-2-hydroxyglutarate (R-2HG). However, specific differences between these two mutations with targetable implications have not been described. In the paper by Thomas et al, we discover a novel susceptibility specifically for IDH1 mutation (mIDH1) by identifying the lipid synthesis enzyme ACC1 (acetyl CoA carboxylase 1) as a synthetic lethal target. By analyzing the metabolome of primary acute myeloid leukaemia (AML) blasts, we identified a mIDH1-specific reduction in fatty acids compared to healthy progenitor cells that was not observed in IDH2-mutant AML. Moreover, mIDH1 cells exhibited an increase in acyl-carnitine linked fatty acids destined for the mitochondria, indicating a switch to beta-oxidation. Overall, our data show that mIDH1 cancer cells have a higher dependency on both exogenous and de novo fatty acids than mIDH2 AML. This suggests that differences in intracellular localization between cytoplasmic IDH1 and mitochondrial IDH2 can have profound effects on metabolic phenotypes. Strikingly, mIDH1 AML cells exhibited a defect in reductive carboxylation involved in de novo lipid synthesis, which was not reversible by the mIDH1-specific inhibitor ivosidenib, suggesting this defect is R-2HG independent, and nominating a mechanism for the mIDH1 specificity. In xenograft models, a lipid-free diet markedly slowed the growth of mIDH1 AML, but not healthy CD34+ stem and progenitor cells or IDH2-mutant AML suggesting the potential for precision dietary modification for IDH1-mutant cancers. Genetic and pharmacologic targeting of ACC1 resulted in growth inhibition of mIDH1 cancers, again not reversible by ivosidenib. Finally, pharmacologic targeting of ACC1 with ND-646, an ACC1-selective inhibitor, improved sensitivity of mIDH1 AML to venetoclax, a BH3 mimetic which is the current standard of care for older patients with AML. Future impact This paper is important because it demonstrates novel targets for IDH1 mutant cancers beyond the production of the oncometabolite (R)-2-hydroxyglutarate, and offers new insights for designing an ultra-precision approach encompassing diet and targeted therapy for cancer patients with IDH1, but not IDH2, mutant cancers. This is clinically relevant because emerging results from clinical trials testing mutant IDH inhibitors, such as ivosidenib, do not always result in tumour regression despite marked decreases in the oncometabolite. The pre-clinical data presented here suggests some patients with IDH1 mutant cancers, including AML in remission, cholangiocarcinoma, oligodendroglioma, and chondrosarcoma may benefit from general lipid-lowering and/or a lipid-free diet. This paper suggests other metabolic dependencies beyond the Warburg effect, depending on somatic mutation context, such as mitochondrial-driven beta oxidation are also involved in cancer metabolism. This paper reinforces other recent studies supporting the notion that many cancers are not dependent on ATP or carbon supply for growth, but are desperate for an adequate supply of re-usable NADPH (via NADH) and are prepared to sacrifice both de novo and exogenous fatty acids to guarantee this. Several new targets based on this work (AMPK, NAD kinase, beta-oxidation enzymes) deserved to be explored in future studies in both AML and other solid tumour models, contrasting IDH1 with IDH2. Read more in Cancer Discovery Single-cell spatial immune landscapes of primary and metastatic brain tumours Karimi, E., Yu, M.W., Maritan, S.M., Peruset, L. J. M. et al. Nature. 614: 555–563 (2023). doi: 10.1038/s41586-022-05680-3. Summary of the findings Glioma and brain metastases are invariably fatal tumours of the central nervous system that respond poorly to currently available treatment options. Poor treatment response is influenced, in part, by the unique nature of the local microenvironment, including the diverse populations of immune cells found near and within brain tumours. However, little is known about the complex spatial organization and cell-cell relationships of the brain tumour microenvironment and how it can be leveraged for therapeutic discovery. In this work, highly multiplexed imaging mass cytometry (IMC) was used to profile 139 primary gliomas and 46 brain metastases from patients at the single-cell level with spatial resolution. More than 1.1 million cells were profiled and categorized into 20 distinct cell populations, which revealed unique cellular landscapes between primary and secondary brain tumours. Moreover, spatial analyses revealed cell-cell interactions and cellular neighbourhoods that were common across disease states and associated with clinical outcomes. Cellular neighbourhoods that were present in brain metastases from different primary sites, as well as macrophage-enriched cellular neighbourhoods associated with prolonged survival of patients with glioblastoma, were described. Deeper spatial interrogation of macrophages in glioblastoma samples uncovered a population of monocyte-derived macrophages expressing myeloperoxidase (MPO) that were associated with an unexpected survival benefit. Future impact This work provides a high-dimensional, spatially resolved map of the tumour microenvironment within both primary and secondary brain tumours, serving as a critical resource for the cancer research community. Moreover, the discovery of MPO+ monocyte-derived macrophages in the brain tumour microenvironment and their association with improved outcomes warrants further investigation into the potential therapeutic roles of this cell type. Overall, this work adds to the growing evidence that the spatial architecture of the tumour microenvironment is a crucial component of the underlying tumour biology and can aid in therapeutic discovery. Read more in Nature Multiplexed 3D atlas of state transitions and immune interaction in colorectal cancer Lin, J., Wang, S., Coy, S. et al. Cell. 186(2): 363-381 (2023). doi: 10.1016/j.cell.2022.12.028. **Summary, future impact and graphical abstract by Alexandra Boitor** Summary of the findings Solid tumour cancers are heterogeneous in nature and encompass immune and stromal cells in addition to tumour cells. Lin, Wang, Coy et al. used multiplexed imaging coupled with 3D tissue reconstruction, spatial statistics and machine learning in an attempt to characterise tumour composition and morphological traits of diagnostic and prognostic importance in colorectal cancer.

The authors show that the molecular state and tissue morphology change gradually within the tumour and are characterised by gradient changes in the expression of various markers such as E-cadherin, PCNA, cytokeratin 20, cytokeratin 18, and epigenetic markers such as histone acetylation and trimethylation.

The authors also show that common histopathological features, often seen as individual structures are in fact part of larger, interconnected 3D structures. For instance, 3D reconstruction of the tissue suggests that tumour buds in the invasive margin of the tumour, adjacent to normal mucosa may in fact be cross-sections through the distal tips of larger, 3D fibrillar structures characterised by a graded EMT-like transition. Similarly, the authors observed that often secondary lymph organs and tertiary lymphoid structures are interconnected forming 3D networks that can be found along the invasive front of the tumour, inside the tumour or in deeper layers.

Substantial differences in immune activity have been noticed at the invasive front of the tumour. The invasive margin adjacent to normal mucosa presents the greatest density of immune cells, although it shows strong immunosuppressive characteristics (rich in T reg and PDL1+ cells). PD1+ - PDL1+ cell interactions are enriched in proximity to the tumour buds in the stroma. The “mucinous invasive margin” is characterised by the least infiltration of immune cells, whilst the “pushing invasive margin” presented few PDL1+ cells in comparison to the invasive margin adjacent to normal mucosa but was enriched in T regs. Tumour buds are characterised by low cell proliferation whilst cell proliferation in the deep invasive margin is high. Differences in active signalling pathways have also been noticed. [caption id="attachment_7399" align="alignnone" width="696"] The panels showing examples of molecular and morphologic gradients, 3D structures and tumour-immune interactions have been replicated from Lin, Jia-Ren, et al. "Multiplexed 3D atlas of state transitions and immune interaction in colorectal cancer." Cell 186.2 (2023): 363-381.[/caption] Future impact By analysing the tumour microenvironment concomitantly from morphological and signalling perspectives, this study enriches the current understanding of tumour biology in general and tumour heterogeneity in particular. The authors challenge the definition and perception of some commonly used morphological features with prognostic value and highlight the gradual changes in molecular states and morphological features within the tumour. Read more in Cell A microbiota-modulated checkpoint directs immunosuppressive intestinal T cells into cancers Fidelle, M., Rauber, C., Alves Costa Silva, C. et al. Science. 380 (6649): eabo2296 (2023). doi: 10.1126/science.abo2296. Summary of the findings In Fidelle, Rauber & Alves Costa et al., we demonstrate a mechanistic link between antibiotics (ABX) and compromised cancer treatment effectiveness using programmed cell death protein 1 (PD-1) blockade. The study reveals that ABX can suppress the immune system by downregulating a gut-specific cell adhesion molecule called "mucosal addressin cell adhesion molecule 1 (MAdCAM-1)" in the ileum, leading to the emigration of suppressive immune cells away from the intestine into distant tumours, where they inhibit PD-1 antibody efficacy. These immunosuppressive T cells were characterized by a Treg/Th17 phenotype. Enterocloster species, which thrive after ABX use, were found responsible for triggering MAdCAM-1 suppression and migration of these suppressive immune cells. Faecal microbiota transplantation aimed at restoring gut microbiota eubiosis or interleukin-17A neutralization was shown to prevent ABX-induced immunosuppression. In cancer patients treated with PD-1 blockade, low serum levels of soluble MAdCAM-1 were associated with poor clinical outcomes (compared with normal levels) in lung, kidney, and bladder cancer patients, supporting the impact of the MAdCAM-1-α4β7 axis in cancer immunosurveillance. [caption id="attachment_7214" align="alignnone" width="696"] The figure was kindly created by Stefan Homentcovschi.[/caption] Future impact These findings shed light on the complex interactions between gut bacteria, antibiotics, and cancer immunotherapy. Serum soluble MAdCAM holds promise as a potential biomarker to identify patients at high risk of gut microbiota dysbiosis and PD-1 blockade treatment failure, paving the way to stratify patients for microbiota-centered interventions. Read more in Science Tissue memory relies on stem cell priming in distal undamaged areas Levron, C. L., Watanabe, M., Proserpio, V. et al. Nature Cell Biology. 25: 740–753 (2023). doi: 10.1038/s41556-023-01120-0. Summary of the findings The skin functions as a barrier that senses and adapts to environmental changes while protecting us against mechanical injuries but also from genomic instability triggered by ultraviolet (UV) radiation. Although wound healing and cancer share many hallmarks and individuals with frequent skin injuries/inflammation (i.e. psoriasis or epidermolysis bullosa patients) are more prone to develop skin tumours, the functional connection between epithelial adaptations to skin damage and squamous cell carcinoma (SCC) onset is unknown. A combination of lineage tracing, single-cell transcriptomic and chromatin accessibility assay was used to evaluate the adaptation of multiple epidermal cell populations to wounds and their long-term consequences on the tissue. The authors found that epidermal stem cells acquire a memory of the injury, that allows them to faster respond to future challenges. In particular, specific memory cells are primed through a transcriptional pre-activation of metabolic- and migration-related genes, led by chromatin de-repression. The impact on the skin is profound from both spatial and temporal perspectives: the memory involves an unexpectedly wide area of cells surrounding the wound and lasts many months, with beneficial but also detrimental consequences. Indeed, the epigenetic adaptations that characterise the memory establish a field cancerization that promotes SCCs onset upon UVB exposure. Future impact In our life, we are subjected to injuries and UV rays. The study demonstrates that the memory of an injury increases susceptibility to UV-induced pre-cancerous lesions and SCCs. Future studies to identify druggable targets involved in this process might impact preventive medicine. Indeed, understanding the transcriptional and chromatin adaptations that cause field cancerization, is crucial to decipher the earliest steps of tumorigenesis when pre-neoplastic cells still morphologically resemble “normal” unaffected cells. The knowledge of the molecular mechanisms behind epigenetic field cancerization might offer new strategies of prevention, as well as new classes of biomarkers of cancer risk. Read more in Nature Cell Biology Stepwise activities of mSWI/SNF family chromatin remodeling complexes direct T cell activation and exhaustion Battistello, E., Hixon, K.A., Comstock, D.E. et al. Molecular Cell. 83(8): 1216-1236 (2023). doi: 10.1016/j.molcel.2023.02.026. **Summary, future impact and graphical abstract by Alexandra Boitor** Summary of the findings T-cell activation and exhaustion are underlined by changes in gene expression. Whilst several transcription factors involved in this process have been identified, the regulatory mechanisms of the T-cell activation state are not fully understood. In their paper, Battistello, Hixon, Comstock et all characterised these changes in gene expression and the mechanisms by which such changes are regulated, with a focus on mSWI/SNF.

Comprehensive profiling of genome-wide occupancy revealed increases in histone peaks and total mSWI/SNF occupancy at T cell activation. Chromatin accessibility and mSWI/SNF occupancy steadily decrease from T-cell early activation to late activation and exhaustion, with progressively fewer mSWI/SNF-bound sites characterising the accessible chromatin. Each state is also characterised by the binding of specific transcription factors and stepwise changes in gene expression. Gene loci for differentially upregulated genes between T-cell activation states are increasingly occupied by mSWI/SNF complexes from T-cell activation (23% of upregulated loci) to exhaustion (40%), highlighting an important role for mSWI/SNF in controlling transcriptional processes responsible for T-cell exhaustion. Depletion of any components of the mSWI/SNF complex in vitro leads to increased T-cell persistence and a slight increase in the number of T-cells that present a memory-like phenotype further highlighting the important role the mSWI/SNF complexes play in T-cell exhaustion. [caption id="attachment_7398" align="alignnone" width="696"] The panels showing the experimental design, chromatin occupancy of mSWI/SNF for each T cell activation stage and pharmacological disruption of mSWI/SNF have been replicated from Battistello, Elena, et al. "Stepwise activities of mSWI/SNF family chromatin remodelling complexes direct T cell activation and exhaustion." Molecular cell 83.8 (2023): 1216-1236.[/caption] Future impact Pharmacological perturbations of the mSWI/SNF complex by using small-molecule allosteric inhibitors of SMARCA4/2 ATPase activity or degraders of SMARCA4/2 ATPase subunit has the ability to attenuate T-cell activation status and thus inhibit T-cell exhaustion and promote the proliferative memory-like state by modulating chromatin accessibility. This is particularly relevant in the context of CAR-T therapy, as CAR-Ts with increased persistence are believed to exhibit enhanced anti-tumour activity. Read more in Molecular Cell Distant antimetastatic effect of enterotropic colon cancer-derived α4β7+CD8+ T cells Feliu, V., Gomez-Roca, C. et al . Science Immunology. 8 (84): eadg8841 (2023). doi: 10.1126/sciimmunol.adg8841. Summary of the findings In metastatic colorectal cancer (mCRC), metastases are resistant to treatment, thus representing a pivotal challenge for therapy improvement. In addition, the gut immune response develops locally, for instance with the priming of CD8 T lymphocytes expressing the “gut-homing” α4β7 integrin (α4β7 CD8 TL), but may also impact extra-intestinal sites such as the liver in the context of inflammatory bowel disease. To investigate the systemic influence of the local colon tumour immune response, we used a mCRC orthotopic mouse model, in which colon tumour cells are grafted in the colon simultaneously with extra-intestinal locations. In mice, the colon-derived immune response exerted an antimetastatic effect, provoking the elimination of distant, normally progressive, liver or subcutaneous metastases. Immunophenotyping, single-cell RNA and TCR sequencing, as well as cell tracking analyses, uncovered that, once primed by colon tumours, enterotropic tumour-neoantigen specific α4β7 CD8 TL were able to emigrate and infiltrate extra-intestinal tumors. α4β7 CD8 TL then exerted anti-metastatic activities which could be reverted using α4β7 blocking antibodies and could improve the control of liver lesions by anti-PD-L1 immunotherapy. We confirmed the relevance of α4β7 CD8 TL in a cohort of mCRC patients in whom higher expression of α4β7 integrin in metastases and higher numbers of circulating α4β7 CD8 TL were associated with response to immunotherapy. Our findings bring to light the central role of gut-derived α4β7 CD8 TL in systemic cancer immunosurveillance and their potential as biomarkers of responsiveness to immunotherapy in mCRC patients. Future impact We uncovered an unexpected “exodus” of enterotropic CD8 TL from the gut toward extra-intestinal tumours, where, in addition, they exhibit superior antitumor abilities as compared to non-intestinal metastases-infiltrating CD8 TL. We will explore which gut-specific components favour the effective priming of antitumor enterotropic α4β7 CD8 TL as well as the mechanisms leading to their gut emigration and extraintestinal trafficking, thus paving the way for new therapeutic strategies aiming to exploit the systemic antitumor activity of intestinal immunity. α4β7 CD8 TL may represent a new predictive biomarker of mCRC response to immunotherapy. For the majority of mCRC patients, who remain unresponsive to current immunotherapies, elicitation of tumour-specific enterotropic α4β7 CD8 TL, through vaccine strategies, involving a “gut-driver”, such as retinoic acid as an adjuvant, could be considered. Read more in Science Immunology Tumour extracellular vesicles and particles induce liver metabolic dysfunction Wang, G., Li, J. et al. Nature. 618: 374–382 (2023). doi: 10.1038/s41586-023-06114-4. Summary of the findings Cancer is a systemic disease where primary tumours disrupt host homeostasis through metastasis and the release of soluble factors, such as proteins, metabolites, hormones, and extracellular vesicles and particles (EVPs) into the circulation, affecting both local and distant tissues and organs. Wang and colleagues discovered that tumour-derived EVPs containing saturated fatty acids, in particular palmitic acid, can be transported to liver resident macrophages, Kupffer cells, triggering the release of TNF via TLR4. TNF-induced immune responses and fatty liver generation occurred in both tumour-bearing mice and cancer patients with extrahepatic metastasis. TNF also suppressed the expression of genes encoding the cytochrome P450 enzymes crucial for drug metabolism, thereby impairing drug metabolism in the livers of tumour-bearing mice. Importantly, the livers of pancreatic cancer patients with extrahepatic metastasis also exhibited downregulated cytochrome P450 enzymes. Treatment of mice with tumour-derived EVPs increased chemotoxicity, providing valuable insights into the diminished effectiveness and reduced tolerance to chemotherapy observed in cancer patients, even in the absence of liver metastasis. Notably, the abundant, non-membranous tumour-derived EVP subpopulation first described by the Lyden group in 2018, the exomeres, had a greater impact on promoting fatty liver disease than exosomes, suggesting that exomeres play a major role in dysregulating liver metabolic function. [caption id="attachment_7223" align="alignleft" width="292"] EVPs derived from cancers with extrahepatic metastatic tropism induce lipid droplet accumulation and suppress cytochrome P450 gene expression in the liver, leading to fatty liver generation and impaired liver drug metabolism, respectively. KC, Kupffer cell. TLR4, Toll-like receptor 4. LD, lipid droplet. CYP, cytochrome P450 enxymes. PA, palmitic acid, SFAs, saturated fatty acids.[/caption] Future impact This groundbreaking study unveils a novel perspective on the systemic effects of cancer, showing that multiple types of cancers with extrahepatic metastatic tropism can induce fatty liver generation and diminish drug metabolism in the liver. These findings suggest that blocking TNF locally in the liver or inhibiting palmitic acid production and thus preventing its packaging in tumour-derived EVPs could prevent fatty liver disease, improving drug metabolism and chemotherapy efficacy in cancer patients. Overall, this study has expanded our understanding of the mechanisms through which cancer exerts its systemic effects and presents potential avenues for enhancing anti-cancer treatment. Read more in Nature A neutrophil response linked to tumor control in immunotherapy Gungabeesoon, J., Gort-Freitas, N.A., Kiss, M.et al. Cell. 186(7): 1448-1464 (2023). doi: 10.1016/j.cell.2023.02.032. **Summary, future impact and graphical abstract by Alexandra Boitor** Summary of the findings Neutrophils are circulating leukocytes commonly found associated with a wide range of tumour types and that can exhibit both pro- and anti-tumour functions. In their paper Gungabeesoon, Gort-Freitas, Kiss et. al investigate the role that tumour-associated neutrophils play in tumour response to immunotherapy.

The authors focused on analysing in depth the effects that anti-CD40 therapy has on the neutrophil population associated with lung adenocarcinoma and anti-CD40 and anti-PD1 therapy have on colon adenocarcinoma. Any of these treatments in orthotopic mouse models induced an increase in the number of tumour-associated neutrophils, specifically in a subset of neutrophils characterised by high L-selectin expression, whilst the population of pro-tumour neutrophils (characterised by high expression of sialic acid binding Ig-like lectin F) seemingly disappeared. The neutrophil population enriched by effective anti-cancer treatments was characterised by gene signatures associated with cytotoxicity and interferon stimulation, gene signatures that were further enriched by treatment. Further on, the authors showed that neutrophil response to therapy relies on key components of anti-tumour immunity such as IL-12 and interferon secretion, BATF3-dependent dendritic cells and CXCR3 chemokine receptor . Future impact Upon inspection of treatment response to various anti-cancer treatments in orthotopic lung and colon adenocarcinoma in mice, the authors noticed that neutrophil accumulation characterised the response to various effective anti-cancer therapies that modulate the immune response but was not noticed upon administration of treatments known to be ineffective for the specific tumour type investigated. This suggests that neutrophil accumulation might be a feature common to different tumour types and treatment options that trigger the adaptive immune response. Read more in Cell

Highlights in Cancer Research: August 2023

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Highlights in Cancer Research: August 2023

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