The EACR’s ‘Highlights in Cancer Research’ is a regular summary of the most interesting and impactful recent papers in cancer research. Previously known as our Top 10 Cancer Research Publications, it is 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.

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2H3K27me3 conditions chemotolerance in triple-negative breast cancer

Marsolier J, Prompsy P, et al. Nat Genet. 54(4):459-468. (2022). 
doi: 10.1038/s41588-022-01047-6. 

Summary of the findings

Persistence of cancer cells to therapy remains a major clinical challenge. In triple-negative breast cancer, resistance to chemotherapy results in the highest recurrence risk among breast cancer subtypes. The drug-tolerant state seems largely defined by nongenetic features, but the underlying mechanisms are poorly understood. Marsolier et al. show that repressive histone modifications – H3K27me3 – condition the ability of a cancer cell to tolerate chemotherapy. Combining single-cell epigenomic and transcriptomic approaches to lineage tracing strategies, authors map the initial epigenomic events driving tolerance to chemotherapy in triple-negative breast cancer in patient-derived xenografts, cell lines and patient samples. They show that the repressive histone mark H3K27me3 is a lock to the activation of a drug-persistent expression program in breast cancers. Under chemotherapy, very few cells can survive the treatment, and these cells have a remodeled repressive epigenome, with targeted loss at key promoters. Using demethylase inhibitor in combination to chemotherapy, they show the possibility to improve response rate and delay recurrence both in vitro and in vivo.
 
“This paper shows that, at least in triple-negative breast cancer, the H3K27me3 landscape is a key determinant in the development of chemoresistance” EACR Board
At the onset of chemotherapy treatment, the majority of cancer cells die, while a rare fraction of cells can tolerate chemotherapy, so-called persister cells. The epigenome of persister cells is marked by an organized loss of repressive histone marks (H3K27me3) at genes that already poised for activation (decorated with H3K4me3/H3K27me3).

Future impact

These results highlight how chromatin landscapes shape the potential of cancer cells to respond to initial therapy. Locking the plasticity of the cell, here with a demethylase inhibitor, impairs their ability to escape treatment. Understanding epigenomic tumor evolution at single cell resolution was instrumental to design a combinatory treatment scheme to enhance response with an epigenetic compound. Mapping response to treatment in patients will now be essential to further understand the epigenomic evolution of the tumor and its microenvironment in response to various cancer therapies.

3Spatially resolved clonal copy number alterations in benign and malignant tissue

Erickson, A., He, M., Berglund, E. et al. Nature 608, 360–367 (2022). 
doi: 10.1038/s41586-022-05023-2.

Summary of the findings

Defining the transition from benign to malignant tissue by molecular principles will be fundamental to improving the early diagnosis of cancer. In the paper by Erickson A. et al., we describe the first step to generate a view of the genome integrity in situ using spatial transcriptomics. Spatial transcriptomics provides a high-resolution map of the entire transcriptome over thousands of areas (spots), enabling us to infer gains and losses of genomic information at unprecedented spatial resolution. Our approach provided comprehensive insights into clonal relationships focused on prostate cancer. Excitingly, we reveal using spatial genome-wide copy number variation (CNVs) analysis that distinct clonal patterns exist not only within tumors, but also in nearby healthy tissue. This allowed us to establish evolutionary clone trees from healthy benign tissue, via altered benign to multiclonal tumors. Importantly the phylogenetic tree could be overlayed on tissue architecture. Our results suggest a model for how genomic instability arises in histologically benign tissue that may represent early events in cancer evolution. The study also demonstrated the spatial landscape of CNVs in breast, brain, and skin cancer.
 
Spatial inferred copy number variation (siCNV) analysis of several tissues permitted interrogation of heterogeneity and establishment of clonal hierarchies encompassing a spectrum from mostly benign to mostly malignant cells. This analysis is contingent upon organwide spatial transcriptomics, spatial inferred genomics, and is underpinned by very detailed ‘spot-level’ consensus pathology.

Future impact

We highlight the power of an unsupervised approach to capture molecular and spatial continuums in a tissue context and challenge the rationale for treatment paradigms. Our spatially resolved analysis of clonal dynamics overcomes many of the shortcomings of previous ‘bulk’ sequencing analyses of tissue specimens, with particular applications in the diagnostic space. When linked to metastatic disease, we believe this holds the power to predict at near cellular resolution which clones have the potential to spread, thereby informing prognosis and treatment selection, for example with selection of regions for targeting with focal therapies, or monitoring with MRI imaging.
 

Read more in Nature

4Lymph node colonization induces tumor-immune tolerance to promote distant metastasis

Reticker-Flynn NE et al. Cell185(11):1924-1942 (2022). 
doi: 10.1016/j.cell.2022.04.019.

Lymph node metastatic tumours are epigenetically rewired, enabling lymph node colonization, suppression of anti-tumor immunity, and ultimately the generation of metastasis-promoting tumor-specific immune tolerance.

Summary of the findings

For over a century, scientists and clinicians have appreciated that solid tumors typically spread to lymph nodes before metastasizing to other vital organs, yet the relevance of this nodal involvement has been unclear. While clinicians such as William Halsted suggested that the lymphatics serve as convenient conduit amenable to gradual dissemination throughout the host where the lymph nodes provide transiently hospitable microenvironments for the acquisition of additional metastatic traits, others have suggested that nodal involvement is a red herring, providing only diagnostic utility, but serving no functional role in subsequent metastasis. The latter stance has been informed more recently by sequencing approaches enabling phylogenetic reconstruction of metastatic clonal architecture, in some instances implicating distinct clonal origins of lymph node and distant metastases. In their recent manuscript, Reticker-Flynn, et al. discovered that lymph node colonization plays a critical step in metastasis not because the tumor cells therein are clonal precursors of distant metastases, but rather because such colonization promotes the generation of systemic tumor-specific immune tolerance that renders distant tissues amenable to metastatic seeding. They show that colonization of lymph nodes is aided by chronic exposure to interferons facilitating epigenetic reprogramming and the upregulation of molecules that confer resistance to Natural Killer (NK) cells and cytotoxic T cells. Once the tumors colonize the nodes, they induce differentiation of regulatory T cells (Tregs), an immunosuppressive subset of T cells, which bear T cell receptors (TCRs) that recognize tumor antigens. These Tregs play critical roles in the generation of systemic tumor-immune tolerance. These findings raise critical questions about the appropriate approach to management of patients with lymph node involvement. The authors suggest that while lymphadenectomy may aid in removal of tolerance-inducing metastases, it may also prevent the recognition of tumors by the immune system and inhibit the generation of anti-tumor immunity. Thus, future work on therapies that reverse tolerance and boost anti-tumor immunity following lymph node metastasis is needed, and the mechanisms that they have uncovered will serve as an informative blueprint for the development of such therapies.
 

Read more in Cell

5Mex3a marks drug-tolerant persister colorectal cancer cells that mediate relapse after chemotherapy

Álvarez-Varela, A., Novellasdemunt, L., Barriga, F.M. et al. Nat Cancer 3, 1052–1070 (2022).
doi: 10.1038/s43018-022-00402-0.

“This is a great example how using organoids systems can predict responses of cancer patients or in this case, relapse after treatment.” EACR Board 

Summary of findings

Nearly 2 million new cases of colorectal cancer (CRC) are diagnosed worldwide each year. Chemotherapy is part of the standard of care for patients with advanced CRC. In many cases, this treatment is initially effective yet many patients relapse after intended curative therapeutic regimes. Tumor cells capable of resisting chemotherapy, the so-called Drug Tolerant Persister cells (DTPs), are the culprits of disease relapse after treatment but the identity and features of these tumor cell population remain poorly characterized.

In this Nature Cancer paper, Álvarez-Varela et al. from the Batlle lab at IRB Barcelona reveal the identity of a group of chemotherapy resistant cells in both murine tumor models and human CRC patients. These DTPs express the gene Mex3a, are stem cell-like cells and, as a result of adaptation to a suboptimal niche environment, they reside in a state of latency that spares them from death by conventional chemotherapy. Lineage tracing experiments combined with single-cell profiling showed that upon treatment, Mex3a+ DTPs adopt a state reminiscent of intestinal fetal progenitors and regenerate the tumor once chemotherapy treatment ceases.

Mex3a encodes an RNA-binding protein that regulates protein translation and Álvarez-Varela and colleagues demonstrate that CRCs lacking the Mex3a gene are unable to transition to the fetal-like state. Instead, they differentiate towards a secretory intestinal phenotype that is vulnerable to chemotherapy. Overall, these findings open up the possibility of improving the outcome of chemotherapy in CRC by implementing strategies that target Mex3a+ DTPs.

Future Impact 

A large proportion of CRC patients relapse after treatment with chemotherapy. This work paves the way for the development of drugs to eliminate dormant Mex3a+ cells, which would have a synergistic effect with chemotherapy to improve survival rates.
Additionally, since the MEX3A gene is required for tumour cells to relapse after chemotherapy, eradication of Mex3a+ cells could be done by targeting the MEX3A protein. Therefore, this paper offers candidate strategies to improve the clinical benefit of standard chemotherapy.

Read more in Nature Cancer

6Genome-wide mapping of somatic mutation rates uncovers drivers of cancer

Sherman, M.A., Yaari, A.U., Priebe, O. et al. Nat Biotechnol (2022).
doi: 10.1038/s41587-022-01353-8.

Summary of findings 

The search for mutations that cause cancer has focused primarily on the 2% of the genome that codes for proteins. We developed a computational tool, Dig, that enables the entire genome – coding and noncoding alike – to be searched for mutations that may drive cancer.

Dig uses deep learning to map cancer-specific somatic mutation rates across the whole genome based on the epigenetic organization of DNA. The number of mutations observed in a cohort of tumors can then be compared against Dig’s maps to pinpoint regions of the genome with unexpected mutational patterns, a crucial signal that the region may be driving cancer.

We created mutation rate maps for 37 types of cancer and applied them to find potential drivers. Across all types of cancer, we found that mutations within gene introns likely account for 5% of single nucleotide driver mutations in tumor suppressor genes by inducing cryptic alternative splicing. We also found that tumor suppressor genes may be inhibited by rare mutations in 5’ UTRs. Finally, by examining large cohorts profiled with targeted sequencing panels, we found that genes that commonly drive one type of cancer can infrequently drive other types of cancer as well.

Future impact 

The discovery of cancer-causing mutations within protein-coding DNA paved the way for targeted therapies. Now, our method together with the application of whole genome sequencing to tumor samples may open up therapeutic avenues within the noncoding genome. For example, antisense oligonucleotides, which can reverse cryptic splicing, may be effective treatment options for some patients with intronic driver mutations. More broadly, our work demonstrates the power of deep-learning to provide insights into cancer biology. As the volume of genomics data continues to increase, we believe these techniques will be important tools to unravel the complexities of cancer.

Read more in Nature Biotechnology

7Protein phosphatase 2A inactivation induces microsatellite instability, neoantigen production and immune response

Yen, YT., Chien, M., Wu, PY. et al. Nat Commun 12, 7297 (2021). 
doi: 10.1038/s41467-021-27620-x.

“This paper shows that we can make MSS tumors MSI with a small molecule PP2A inhibitor and thereby sensitize to checkpoint therapy. This could be a great synergy with immuno-oncology drugs.” EACR Board

Summary of findings

Microsatellite instability (MSI), a predictive biomarker of immune checkpoint blockade (ICB) response, is caused by mismatch repair deficiency (MMRd) through epigenetic silencing of the MMR genes. MSI is the first FDA-approved tissue-agnostic therapy, an anti-cancer treatment that targets a common genetic biomarker of cancer, regardless of tumour type. However, MSI tumours with MMRd account for only 15% of sporadic colorectal cancer, the tumour type with the highest prevalence of MSI, suggesting most cancer patients do not respond to ICB. Here, we report a mechanism of MMRd and demonstrate that protein phosphatase 2A (PP2A) deletion or inactivation converts microsatellite stability (MSS) tumours into MSI tumours through two orthogonal pathways: (i) by increasing retinoblastoma protein phosphorylation that leads to E2F and DNMT3A/3B expression with subsequent DNA methylation, and (ii) by increasing histone deacetylase (HDAC)2 phosphorylation that subsequently decreases H3K9ac levels and histone acetylation, which induces epigenetic silencing of MLH1. In mouse models of MSS and MSI colorectal cancers, triple-negative breast cancer and pancreatic cancer, PP2A inhibition triggers neoantigen production, cytotoxic T cell infiltration and ICB sensitization. Human cancer cell lines and tissue array confirm these signaling pathways. These data indicate the dual involvement of PP2A inactivation in silencing MLH1 and inducing MSI.

A cartoon showing the mechanism by which PP2A deletion or inactivation converts cold MSS tumours to MSI tumours through: (i) increasing phosphorylation of Rb to cause E2F and DNMT3A/3B expression and subsequent DNA Methylation, and (ii) increasing phosphorylation of HDAC2 to decreases H3K9ac levels and histone acetylation, and subsequent epigenetic silencing of MLH1.

Future impact 

Recent advances in immunotherapy have led to real breakthroughs in developing more effective and less toxic treatments for many cancers. Unfortunately, most cancer patients do not respond to ICB. There are widespread efforts to find pharmacologic and/or immunologic ways to turn unresponsive (‘cold’) tumours into responsive (‘hot’) tumours. Our data demonstrate that defective MMR can be induced by targeting PP2A both in vitro and in vivo, which leads to accumulation of mutational burden and increased neoantigens, which in turn trigger anti-tumour immune surveillance and sensitize tumours to ICB. Moreover, this strategy can be applied to multiple human tumour types.

Read more in Nature Communication

8The metastatic spread of breast cancer accelerates during sleep

Diamantopoulou, Z., Castro-Giner, F., Schwab, F.D. et al. Nature 607, 156–162 (2022).
doi: 10.1038/s41586-022-04875-y.

Summary of findings

Distant metastasis is achieved by the hematogenous dissemination of circulating tumor cells (CTCs). However, the temporal dynamics that dictate the generation of metastasis-competent CTCs have been often neglected, assuming that CTCs are constantly shed from growing tumors or shed as a consequence of mechanical insults. We observe a striking and unexpected pattern of CTC generation dynamics in both patients with breast cancer and mouse models, highlighting that the vast majority of spontaneous CTC intravasation events occur during sleep. We demonstrate that rest-phase CTCs are highly metastasis-prone compared to CTCs that are generated during the active phase. Mechanistically, single cell-resolution RNA sequencing analysis of CTCs reveals a dramatic upregulation of mitotic genes during the rest phase in both patients and mouse models, enabling metastasis proficiency. At the systemic level, we find that key circadian rhythm hormones such as melatonin, testosterone and glucocorticoids dictate CTC generation dynamics, and as a consequence, that insulin directly promotes tumor cell proliferation in vivo, yet in a time-dependent manner. Thus, the spontaneous generation of CTCs with a high metastatic ability does not occur continuously, but it is concentrated within the rest phase of the host, providing a new rationale for time-controlled interrogation and treatment of metastasis-prone cancers.

Graphical representation of the human circadian rhythm. The white and black bars represent environmental light (active period) and dark conditions (rest period), respectively (left). The radial histograms show the percent of single CTCs, CTC clusters and CTC-WBC clusters isolated during the rest or active phase in early- or late-stage breast cancer patients. n=21 early-stage and n=9 late-stage patients. The vast majority of CTCs are detected during the rest phase.

Read more in Nature 

9Genome-wide identification and analysis of prognostic features in human cancers

Smith J.C. and Sheltzer J.M., Cell Reports 38. 13 (2022). 
doi: 10.1016/j.celrep.2022.110569.

“This paper has many thought-provoking concepts challenging the very frequent (over)use of survival curves as indicators of importance of genes in cancer.” EACR Board

**Summary, future impact and graphical abstract by Alexandra Boitor**

Summary of findings

In addition to disease progression, cancer-associated mortality can also be caused by both under- and overtreatment. Treatment decisions are based on patient risk prediction which at the moment heavily relies on histopathological and radiological tumour classification. These methods require subjective judgements and cannot always unambiguously predict clinical outcomes. In this paper, the authors conducted a pan-cancer analysis across the 33 cancer types profiled by TCGA seeking to identify the genomic features that underlie patient outcomes. The following features were analysed for each tumour: point mutations, CNAs, gene expression, microRNA expression, DNA methylation, and protein expression. This analysis identified new prognostic features that may add prognostic value to methods currently used and challenges the value of mutations in cancer driver genes as biomarkers or treatment targets.

In this study, pan-cancer outcome-linked biomarkers were identified based on genomic data such as gene expression, copy number, methylation and mutation from more than 10.000 patients.

Future impact 

By identifying 100 features/ cancer type that strongly correlate with patient outcomes, this paper paves the way to the identification of new biomarkers that could improve prognosis and could be used for treatment decisions in ambiguous clinical situations. In addition, this paper has the potential to reform drug target selection for anti-cancer therapeutic development by casting light on a couple of reasons why many anti-cancer drugs fail in clinical trials.

Read more in Cell Reports 

10A pan-cancer compendium of chromosomal instability

Drews, R.M., Hernando, B., Tarabichi, M. et al. Nature 606, 976–983 (2022).
doi: 10.1038/s41586-022-04789-9.

Summary of findings

Chromosomal instability (CIN) is an umbrella term used to describe the accumulation of large-scale losses, gains and rearrangements of DNA. The broad genomic complexity caused by CIN is a hallmark of cancer; however, until now there has been no systematic framework to measure different types of CIN and their effect on clinical phenotypes across different cancer types. In our publication we evaluated the extent, diversity and origin of CIN across 7,880 tumours representing 33 cancer types. We presented a compendium of 17 copy number signatures that characterised specific types of CIN, with putative aetiologies supported by multiple independent data sources. Labelled CX1 to CX17 according to pan-cancer prevalence, the signatures measure the four main drivers of CIN in human cancers: errors during mitosis (CX1, CX6, CX14), failures in DNA repair (CX2, CX3, CX5, CX10), replication stress (CX8, CX9, CX11, CX13) and tolerance of whole-genome duplication (CX4). We showed the signatures to be predictive of drug response and able to identify new drug targets, reporting 44 potential drug response biomarkers and 49 new drug targets. Of particular therapeutic importance are three signatures indicative of problems with homologous recombination repair (CX2, CX3, CX5), which allowed us to define different levels of impaired homologous recombination (IHR). In its extreme form, IHR becomes clinically relevant as well-known homologous recombination deficiency (HRD), but we found that less severe forms of IHR also leave their telltale marks in many other cancers. This extension to the classical HRD model allowed us to predict response to platinum-based chemotherapies by dividing patients into non-clinically-relevant IHR and clinically-relevant IHR. Taken together, our results illuminate a fundamental structure underlying genomic complexity in human cancers and provide a resource to guide future CIN research.

The workflow of the study. Copy number aberrations were used to derive pan-cancer copy number signatures. Additional data, shown on the left and right, were incorporated into the analysis to support the signature aetiologies and the insights provided.

Read more in Nature 

11Structure of the MRAS-SHOC2-PP1C phosphatase complex

Hauseman, Z.J., Fodor, M., Dhembi, A. et al. Nature 609, 416–423 (2022). 
doi: 10.1038/s41586-022-05086-1.

Summary of findings

Given its central role in cell signaling and oncogenesis, Ras is one of the most studied molecules in biology and many RAS-interacting effector proteins have been described. However, only a handful of structures are available for RAS/effector complexes, limiting our understanding of intricate RAS functions in pathogenic conditions. In a recent Nature paper, Hauseman et al. provide a high-resolution X-ray structure of the SHOC2-MRAS-PP1 (SMP) holophosphatase complex responsible for an essential step in the activation of the MAPK signaling pathway, via dephosphorylation of a key regulatory site in RAF proteins that enables RAF dimerization and subsequent activation. The importance of the SMP complex has been discovered in the context of germline gain-of-function mutations that cause Rasopathies, a family of developmental syndromes with aberrant MAPK pathway activation. Recently, the SMP complex has become the focus of intense interest as a potential pharmacologic target in oncology. The authors reveal a highly cooperative assembly between the three members of the complex, with Rasopathy mutations mapping to protein-protein interfaces resulting in increased complex formation, RAF de-phosphorylation and MAPK pathway activity. Significantly, they show that not only the preferred non-canonical MRAS but also the canonical RAS isoforms can also form, albeit with reduced cooperativity, functional ternary complexes with SHOC2-PP1. Since the SMP complex assembly is dependent on the nucleotide-loading state of RAS, which is influenced by upstream pathway activation but also, in a constitutive manner, by oncogenic mutations on canonical RAS proteins, the authors suggest that in such conditions the activated or oncogenic canonical RAS isoforms can substitute for the non-canonical wild-type MRAS in the complex.

The crystal structure of the MRAS-SHOC2-PP1C complex, with potential therapeutic implications for MAPK-dependent tumour cells.

Future Impact of the Findings

An important implication arising from this work is that constitutively activated RAS-mutant proteins could simultaneously act on and recruit separate subunits of RAF and SHOC2-PP1 to sustain oncogenic proliferation. Publicly available large cancer genetic screens support these findings showing significant co-dependencies between SHOC2 and canonical RAS proteins within cancer models expressing RAS oncogenic mutations. In summary, this publication provides molecular insights on important aspects of RAS biology and offer a resource for possible therapeutic interventions in both Rasopathies and RAS-mutated cancers.

Read more in Nature 

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