The EACR’s Top 10 Cancer Research Publications is a regular summary of the most interesting and impactful recent papers in cancer research. 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. Use the ‘Next’ and ‘Previous’ buttons to navigate.

1Adaptive Immune Resistance Emerges from Tumor-Initiating Stem Cells

Y. Miao et al., Cell Volume 177, Issue 5, 16 May 2019, Pages 1172-1186.e14

Summary of the findings

Cancer treatments have been revolutionized by the development of immunotherapies. Adoptive T cell transfer (ACT)-based immunotherapy is a major current strategy in which a cancer patient’s cytotoxic T cells are engineered to recognize a tumor-specific neoantigen, then are reintroduced into the body to selectively attack the tumor.

Unfortunately, the majority of patients receiving ACT therapy experience tumor relapse, the nature of which is still poorly understood but vital for advancing clinical outcomes. To understand why, we designed a skin squamous cell carcinoma (SCC) mouse model that can be effectively targeted by ACT. Transcriptome profiling and lineage tracing revealed that a subset of TGFβ-responding cells, with characteristics of tumor-initiating stem cells, are refractory to the immunotherapy treatment and are the root of tumor relapse. We discovered that these TGFβ-responding cells survive by selectively acquiring CD80, a surface immune modulatory ligand previously thought to be exclusive to immune cells. Moreover, upon contact with CTLA4 expressed by the cytotoxic T cells, the CD80-expressing cancer cells directly dampened their activity. Our findings place tumor-initiating stem cells at the crux of how immune checkpoint pathways are activated.

Future impact of the findings

This study unraveled an unrecognized intrinsic mechanism that protects cancer-causing cells from anti-tumor immunity. The work represents a major conceptual advance in the cancer immunology field, with clinical ramifications. Although CTLA4 has been a target of current cancer immune checkpoint blockade therapies, it has long been assumed that it targets the regulatory T cell in the tumor-periphery. The finding that CD80 can be expressed by TGFβ-responding, tumor-initiating stem cells exposes a new target for CTLA4 blocking antibodies, and suggests their possible potency in conjunction with TGFβ-inhibitors.

Read more in Cell

2Visualizing Engrafted Human Cancer and Therapy Responses in Immunodeficient Zebrafish

C. Yan et al., Cell 177, 1903–1914 June 13, 2019

Summary of the findings

Xenograft cell transplantation into immunodeficient mice has become the gold standard for assessing pre-clinical efficacy of cancer drugs, yet direct visualization of single-cell phenotypes is difficult. Here, we report an optically-clear prkdc−/−, il2rga−/− zebrafish that lacks adaptive and natural killer immune cells, can engraft a wide array of human cancers at 37°C, and permits the dynamic visualization of single engrafted cells. For example, photoconversion cell-lineage tracing identified migratory and proliferative cell states in human rhabdomyosarcoma, a pediatric cancer of muscle. Additional experiments identified the preclinical efficacy of combination olaparib PARP inhibitor and temozolomide DNA-damaging agent as an effective therapy for rhabdomyosarcoma and visualized therapeutic responses using a four-color FUCCI cell-cycle fluorescent reporter. These experiments identified that combination treatment arrested rhabdomyosarcoma cells in the G2 cell cycle prior to induction of apoptosis. Finally, patient-derived xenografts could be engrafted into our model, opening new avenues for developing personalized therapeutic approaches in the future.

Read more in Cell

3Patient-derived organoids can predict response to chemotherapy in metastatic colorectal cancer patients

S.N. Ooft, F. Weeber et al., Science Translational Medicine Vol 11, Issue 513 09 October 2019

“This paper shows that organoids can be used to predict response to chemotherapy.” Alberto Bardelli, EACR President 2018-20

Summary of the findings

Chemotherapy is effective in only a subset of colorectal cancer (CRC) patients, and therefore many patients are treated to no avail while still experiencing toxic side effects. There are currently no good biomarkers that can identify non-responding patients. Patient-derived tumor organoids (PDOs) are three-dimensional cultures of tumor cells derived from individual patients, and CRC PDOs can be established with high efficiency. We therefore carried out a multi-center, prospective, observational clinical study testing the potential of organoids to predict response to chemotherapy. The primary objective was to develop an in vitro test based on PDOs from metastatic lesions to identify non-responders to standard-of-care chemotherapy in CRC. Pre-treatment tumor biopsies were used to establish organoids, and test chemosensitivity to the same treatment that the patient received.

We correctly predicted response of the biopsied lesion for >80% patients treated with irinotecan-based therapies. Importantly, using this test, we did not misclassify any patients who would have benefited from treatment. In contrast, organoids failed to predict response to treatment with 5-fluorouracil and oxaliplatin, indicating that the potential of organoids to predict response to chemotherapy differs between treatment lines.

Patient-derived organoids: The EACR’s Top 10 Cancer Research Publications

Future impact of the findings

Our data suggest that there is potential to use PDOs to prevent treatment of patients who are resistant to irinotecan-based therapies. Our findings should be validated in future studies with larger independent patient cohorts.

Read more in Science Translational Medicine

4Human colon mucosal biofilms from healthy or colon cancer hosts are carcinogenic

S. Tomkovich et al., Journal of Clinical Investigation 2019;129(4):1699–1712

Summary of the findings

Mucosal-associated polymicrobial biofilms were previously identified in ~50% of colorectal cancer (CRC) patients and ~13% of healthy patients, however whether this microbial organization contributed to carcinogenesis was unclear. We administered biofilm-associated microbes obtained from CRC or healthy patients undergoing screening colonoscopy to three Wnt-based CRC mouse models (germ-free ApcMinΔ850/+;Il10–/– or ApcMinΔ850/+ and specific pathogen–free ApcMinΔ716/+ mice) to test their functional role in CRC. In contrast to bacteria derived from biofilm-negative colon mucosa of healthy patients, mucosal bacterial biofilm communities from either CRC or healthy patients promoted tumorigenesis in genetically-susceptible mice. Furthermore, human mucosa biofilm communities induced biofilm formation in the mouse colon and the mucosal-associated tumorigenic biofilm communities were transmissible and promoted CRC when administered to a new cohort of germ-free ApcMinΔ850/+;Il10–/– mice. Our findings suggest that, at least some, human colon mucosal biofilms are carcinogenic in CRC mouse models, implicating both microbiota organization and composition as drivers of CRC.

Future impacts of the findings

These findings highlight the importance of evaluating the organization and location of microbial communities within the host in addition to determining microbiota composition. Beyond examining microbiota community composition and organization in the context of CRC, there is a need to determine how these communities interact with the host at a functional level.  A deeper understanding of temporal biofilm formation and associated functions will be critical for CRC prevention and treatment. An essential next step will be conducting prospective longitudinal studies in human populations to characterize biofilm assembly and to determine key biofilm microbial members that predict individual CRC risk.

Figure Caption: Bacteria derived from human colon mucosal biofilms identified on mucosal biopsies from healthy patients and tumor or paired normal tissue resected from CRC patients promoted tumorigenesis in CRC mouse models. In mice, biofilm communities expressed genes associated with bacterial secretion systems, sporulation, peptidoglycan synthesis and cytoskeletal proteins.

Read more in The Journal of Clinical Investigation

5Intraclonal Plasticity in Mammary Tumors Revealed through Large-Scale Single-Cell Resolution 3D Imaging

A.C. Rios et al., Cancer Cell 35, 618–632 April 15, 2019

“This paper was great reading. It presents a pipeline for studying breast tumor heterogeneity and plasticity using 3D models from the Visvader lab.” Therese Sørlie, EACR Board member

Cancer biology: LSR-3D imaging to unveil the clonal landscape of breast cancer in mouse models

Summary of the findings

Unraveling the inherent 3D cellular organization of biological specimens is essential for understanding developmental and disease processes, including cancer. While modern microscopy ideally requires the visualization of both fine cellular details and overall tissue architecture within a single biological sample, this remains technically very challenging. We have developed a method of sample preparation and immunofluorescent labeling that enables visualization of intact organs and importantly, tumoral tissues in 3D which enable for Large-scale, Single-cell Resolution 3D (LSR-3D) imaging. Combined with advanced multi-colored lineage tracing in mouse models of tumorigenesis, we observed that even when harboring the same cancer-driving mutations, only a few cellular clones contribute to cancer progression.

Despite this profound clonal competition and restriction, however, breast tumors remain highly heterogenous. We managed to reconcile these seemingly contrasting observations by providing proof of intraconal plasticity evolving over time during tumor development, with clonal cells displaying varying levels of EMT transition. As a result, some cells from the same clone remained epithelial, while others progressed towards mesenchymal identity. Strikingly, most clones harbored cells that had undergone EMT, suggesting both widespread clonal plasticity, as well as an important role for EMT in carcinogenesis (Cancer Cell 2019).

LSR-3D imaging: The EACR’s Top 10 Cancer Research Publications

Read more in Cancer Cell

6Partner-independent fusion gene detection by multiplexed CRISPR/Cas9 enrichment and long-read Nanopore sequencing

C. Stangl et al., bioRxiv 807545

Summary of the findings

Fusion genes are hallmarks of various cancer types and important determinants for diagnosis, prognosis and treatment possibilities. The promiscuity of fusion genes with respect to partner choice and exact breakpoint-positions restricts their detection in the diagnostic setting, even for known and recurrent fusion gene configurations. To accurately identify these gene fusions in an unbiased manner, we developed FUDGE: a FUsion gene Detection assay from Gene Enrichment. FUDGE couples target-selected and strand-specific CRISPR/Cas9 activity for enrichment and detection of fusion gene drivers – without prior knowledge of fusion partner or breakpoint-location – to long read Nanopore sequencing (Figure 1A).

FUDGE encompasses a dedicated bioinformatics approach (NanoFG) to detect fusion genes from Nanopore sequencing data (Figure 1B). Our strategy is flexible with respect to target choice and enables multiplexed enrichment for simultaneous analysis of several genes in multiple samples in a single sequencing run. We demonstrate that FUDGE effectively identifies fusion genes in cancer cell lines, tumor samples and on whole genome amplified DNA irrespective of partner gene or breakpoint-position in 100% of cases – all within two days.

Partner-independent fusion gene detection: The EACR’s Top 10 Cancer Research Publications

Future impact of the findings

Fusion detection techniques such as FUDGE will enable faster diagnosis of cancer patients, facilitating immediate initiation of appropriate treatment protocols. The precise genomic breakpoint location of a fusion gene – as detected and reported by FUDGE – provides a patient-specific biomarker that can trace minimal residual disease and tumor dynamics from liquid biopsies. Additionally, by detecting fusion partners in an unbiased manner, previously unidentified or less frequent partners can be identified in addition to known rearrangements. This will aid in the understanding of fusion gene biology and offer opportunities to explore treatment stratification based on fusion (partner) status.

Read the Preprint in BioRxiv

7Quantitative evidence for early metastatic seeding in colorectal cancer

Z. Hu et al., Nature Genetics volume 51, pages 1113–1122(2019)

Summary of the findings

Hu et al. described a novel theoretical and analytical framework to enable quantitative in vivo measurement of the timing of metastasis from exome sequencing of paired primary colorectal cancers and distant metastases. By applying this evolutionary framework to patients with liver or brain metastases, they demonstrate that metastatic seeding commonly occurs early (17/21 patients), when the cancer is clinically undetectable (~104-108 cells or 0.0001-1 cm3), irrespective of the site of metastasis. These data suggest that some colorectal cancers are born to be bad, wherein their invasive and metastatic potential is specified early.

In order to define molecular features associated with metastasis, they further analyzed an independent cohort of 2,751 colorectal cancers with targeted sequencing data. The authors found that specific combinations of mutations (many of which arise early) that collectively promote niche independence were associated with metastasis.  Since many of these mutations overlap with drivers of initiation, these data may help to explain why relatively few drivers of metastasis have been identified to date.

Early metastatic seeding in colorectal cancer: The EACR’s Top 10 Cancer Research Publications
Specific combinations of somatic alterations that promote niche independence can confer metastatic competence in early-stage adenocarcinomas resulting in dissemination and, in some cases, seeding of distant metastases, while the lesion is small and clinically undetectable. The shift from immune surveillance to immune evasion presumably dictates whether disseminated tumor cells result in clinically manifest metastatic outgrowths.

Implications and future outlook

This study demonstrates that human colorectal cancers can disseminate and seed distant metastases before the primary tumor is clinically detectable. Moreover, this effort identifies specific combinations of early driver mutations that are associated with metastasis. These findings challenge the long-held view that metastasis is a late event in the evolution of a cancer. Moreover, they highlight opportunities for improved patient stratification and the earlier detection of aggressive disease — for example by profiling circulating cell free DNA. Clearly not all colorectal cancers will metastasize and it will be important to identify determinants of favorable prognosis and the role of immune surveillance during disease progression.

Read more in Nature Genetics

8Metabolic landscape of the tumor microenvironment at single cell resolution

Z. Xiao et al., Nature Communications volume 10, Article number: 3763 (2019)

Summary of the findings

Solid tumors consist of malignant cells along with stromal and immune cells that together form the tumor microenvironment (TME). Each of these cells faces a unique nutritional environment and has a unique genotypic background, resulting in cell-specific wiring of metabolism.

In this study, we characterized the metabolic landscape of the TME using single-cell RNA-seq data from two human cancers, melanoma and head and neck. The goal of this study was to answer two important questions: (1) what is the nature of metabolic reprogramming in single malignant and non-malignant cells in the TME; (2) what processes contribute most to the metabolic heterogeneity in each cell type. Neither could be answered with bulk measurements.

We found that single malignant cells exhibit higher metabolic plasticity and activity compared to non-malignant cells, possibly enabling these cells to adapt to specific genotypic and environmental contexts and satisfy demands for biomass and energy. Notably, the metabolic features of single malignant cells differ greatly from those of bulk tumors.  We also find that mitochondrial activity is the major contributor to the metabolic heterogeneity in all cell types. Finally, we identify the metabolic signatures that distinguish different immune and stromal cell subtypes.

Metabolic landscape of the tumor microenvironment: The EACR’s Top 10 Cancer Research Publications

Future impact of the findings

This study advances our understanding of the metabolic heterogeneity of the TME to reach single-cell resolution in vivo, highlights the importance of single-cell measurements in understanding cancer cell metabolism, and unravels the essential role of mitochondria in mediating intratumoral metabolic heterogeneity. It is thus intriguing to determine whether these properties are applicable to other tumor types and altered by cancer therapeutics. The computational framework can also be applied in studying other tumor types and physiological processes.  One limitation is that metabolic features are inferred from gene expression.  While it has some predictive capacity for estimating metabolic flux, single cell metabolomics technologies will ultimately be needed to get further insights into metabolism at the single-cell level.

Read more in Nature Communications

9Flower isoforms promote competitive growth in cancer

Madan, E., Pelham, C.J., Nagane, M. et al. Nature 572, 260–264 (2019)

“Great paper, fundamental research finding from Drosophila.” Ruth Palmer, EACR Board member

Summary of the findings

In humans, the adaptive immune system uses the exchange of information between cells to detect and eliminate foreign or damaged cells; however, the removal of unwanted cells does not always require an adaptive immune system. For example, cell selection in Drosophila uses a cell selection mechanism based on ‘fitness fingerprints’, which allow it to delay ageing, prevent developmental malformations and replace old tissues during regeneration. At the molecular level, these fitness fingerprints consist of combinations of Flower membrane proteins.

Proteins that indicate reduced fitness are called Flower-Lose, because they are expressed in cells marked to be eliminated. However, the presence of Flower-Lose isoforms at a cell’s membrane does not always lead to elimination, because if neighbouring cells have similar levels of Lose proteins, the cell will not be killed. Humans could benefit from the capability to recognize unfit cells, because accumulation of damaged but viable cells during development and ageing causes organ dysfunction and disease. However, in Drosophila this mechanism is hijacked by premalignant cells to gain a competitive growth advantage. This would be undesirable for humans because it might make tumours more aggressive. It is unknown whether a similar mechanism of cell-fitness comparison is present in humans.

Here we show that two human Flower isoforms (hFWE1 and hFWE3) behave as Flower-Lose proteins, whereas the other two isoforms (hFWE2 and hFWE4) behave as Flower-Win proteins. The latter give cells a competitive advantage over cells expressing Lose isoforms, but Lose-expressing cells are not eliminated if their neighbours express similar levels of Lose isoforms; these proteins therefore act as fitness fingerprints. Moreover, human cancer cells show increased Win isoform expression and proliferate in the presence of Lose-expressing stroma, which confers a competitive growth advantage on the cancer cells. Inhibition of the expression of Flower proteins reduces tumour growth and metastasis, and induces sensitivity to chemotherapy. Our results show that ancient mechanisms of cell recognition and selection are active in humans and affect oncogenic growth.

Read more in Nature

10Tumor Microbiome Diversity and Composition Influence Pancreatic Cancer Outcomes

E. Riquelme et al., Cell Volume 178, Issue 4, 8 August 2019, Pages 795-806.e12

“Our study represents the first report to explore the influence of the tumor microbiome on clinical outcomes”

Summary of the findings

Pancreatic ductal adenocarcinoma (PDAC) is a disease with very prognosis. Most of PDAC patients have an overall survival (OS) shorter than 5 years. However, a minor subset of PDAC patients (9%) survive more than 5 years after surgery. The factors that determine such enigmatic long-term survival remain unknown. We investigated the role of the tumor microbiota and the immune system in influencing this long-term survival.

Using 16S ribosomal RNA gene sequencing, we analyzed the tumor microbiome composition in two independent cohorts of PDAC patients with long-term survival (LTS; OS >5 years) and short-term survival (STS; OS < 5 years). We found that alpha-diversity of the tumor microbiome was significantly higher in LTS patients compared with STS, suggesting the potential influence of tumor microbiome diversity in mediating pancreatic cancer progression. Furthermore, we identified an intra-tumoral microbiome signature (Pseudoxanthomonas-Streptomyces-Saccharopolyspora-Bacillus clausii) highly predictive of long-term survivorship in both discovery and validation cohorts. We also assessed the immune infiltrate infiltration by multiplex immunostaining. LTS tumors showed greater densities of CD3, CD8 T cells and granzyme B (GzmB)-positive cells compared with the STS tumors. Combining both results, we found a strong association between CD8 and GzmB tissue densities with microbiome diversity, suggesting that the tumor microbiome diversity may contribute to anti-tumor immune response by favoring recruitment and activation of CD8+ T cells.

We then aimed to learn where was the pancreatic tumors bacteria coming from and by comparing microbial composition of stools, pancreatic tumors and adjacent pancreatic area we did find a specific migration of bacteria from gut into tumors. This suggested that fecal microbial transplantation could modulate tumor microbiome and immune status, ultimately affecting tumor growth. Based on this premise, we then proceeded with human-into-mice fecal microbiota transplantation (FMT) from STS, LTS, and healthy controls onto mice that were then challenged with pancreatic tumors.  Results from these experiments showed that the tumor immune activation status as well as tumor growth can be modulated by the gut-tumor microbial axis.

In short, our study demonstrates that PDAC microbiome composition, which partially migrated from the gut, influences the host immune response and potentially the natural course of the disease. The FMT experiments represent an immense therapeutic opportunity to manipulate the microbiome and the tumor immune microenvironment to improve the life expectancy of PDAC patients in whom few therapeutic options exist.

Read more in Cell

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