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.

1Cross-reactivity between tumor MHC class I–restricted antigens and an enterococcal bacteriophage

A. Fluckiger et al. Science 21 Aug 2020: Vol. 369, Issue 6506, pp. 936-942

“This report shows for the first time ‘molecular mimicry’ between microbial peptides and melanoma epitopes leading to T cell reactivity and associated with improved survival after PD1 immunotherapy.” Yardena Samuels, EACR Board Member

Summary of the findings

Our gut contains at least one thousand of different bacterial species. Bacteria can be infected by so-called phages, which are small virus-like objects that require bacterial hosts to replicate. In this Science paper, Fluckiger et al. describe the identification of a particular phage species, a Siphoviridae, that infects a class of intestinal bacteria called Enterococci. As it infects its bacterial host, this phage causes the expression of a protein that elicits a phage-specific immune response by the host immune system. Importantly, T cells that recognize a specific phage antigen also recognize cancer cells, as shown for laboratory mice as well as patients with lung or kidney cancer. Oncological patients carrying the Siphoviridae phage in their gut exhibit a better response to cancer immunotherapy than patients who lack them. Of note, the tumour antigen that is cross-reactive with the phage is non-mutated, both in mouse and human cancer cells. Fluckiger et al. also show that human T lymphocytes specific for non-mutated tumour antigens can be cross-reactive with microbial antigens. These results suggest that the microbiota can shape the immune repertoire, thus profoundly influencing anticancer immune responses that target non-mutated tumour-associated antigens.

Immunological significance of the molecular mimicry between cancer and microbiota antigens. Enterococcus Tape Measure Protein Phage sequence harbouring antigenic MHC class I-restricted peptides sharing molecular mimicry with PSMB4 oncogenic driver induce and/or amplify memory Tc1 immune responses beneficial against tumors overexpressing PSMB4. Enterococcus hirae bearing the Siphoviridae phage can lysogenize E. gallinarum in the ileum that in turn may contribute to antigenic epitope spreading.

Future impact of the findings

It is now established that prolonged treatments with broad-spectrum antibiotics abolish the efficacy of anticancer immunotherapies, supporting the idea that immunostimulatory bacteria must be present in the gut for an optimal treatment outcome. Indeed, it will be possible in the future to administer specific bacterial strains to cancer patients with the objective to ameliorate the control of tumours by the immune system. Probably, such immunostimulatory bacteria will be orally administered to patients in a personalized fashion so that they complement the microbial ecosystem and elicit the correct pattern of immune responses.

Read more in Science

2A Potent and Selective Small-Molecule Degrader of STAT3 Achieves Complete Tumor Regression In Vivo

L. Bai et al. Cancer Cell 36, 498–511 November 11, 2019

Summary of the findings

Transcription factor signal transducer and activator of transcription 3 (STAT3) has long been pursued as a drug target but yet to be successful. Many previous efforts have focused on inhibiting the canonical activity of dimerized STAT3, which is mediated by dimerization of two phosphorylated STAT3 monomers through its Src homology 2 (SH2) domain. However, such strategy is unable to completely block the functions of STAT3 as monomeric STAT3 protein also possesses non-canonical activities. Employing the proteolysis targeting chimera (PROTAC) technology, we successfully developed SD-36 as a potent and selective STAT3 degrader. SD-36 potently and selectively degrades STAT3 protein in human normal and cancer cells in vitro, xenograft tumor tissues and mouse tissues in vivo. Comparing to its corresponding SH2 domain inhibitor, SD-36 is >1,000 times more potent in suppressing STAT3-dependent gene transcription and has much more profound effect on STAT3 target genes in cancer cells. SD-36 exerts potent growth inhibitory activities in a subset of leukemia and lymphoma cell lines with high levels of phosphorylated STAT3 protein. Importantly, SD-36 achieves complete and long-lasting tumor regression in mouse tumor models of leukemia and lymphoma cell lines  and is well tolerated in animals.

Development of SD-36 as a highly potent and selective STAT3 PROTAC degrader for cancer treatment

Future impact of the findings

  1. Degradation of STAT3 protein is a promising cancer therapeutic strategy.

2. STAT3 degraders warrant clinical testing for the treatment of human cancers.

3. The PROTAC strategy can be used to develop highly selective degraders for one protein from non-selective inhibitors of homologous proteins;

4. The PROTAC strategy may be used to target other traditionally undruggable or difficult drug targets.

Read more in Cancer Cell

3Discovering functional evolutionary dependencies in human cancers

M. Mina, A. Iyer, D. Tavernari. et al. Nat Genet 521198–1207 (2020)

“This study delves into the functional relationships among genomic alterations observed in human tumors.” Elisa Oricchio, EACR Board Member

Summary of the findings

The development and progression of human tumors is driven by the continuous emergence of new alterations, such as DNA mutations. Cancer cells can harbor dozens, sometimes hundreds of alterations, a small fraction of which are believed to confer a fitness advantage. The functional effect of a given alteration can vary however in different tumors: a mutation can boost tumor cells only if originating in a specific tissue or only if another alteration is present (or absent). As a result, cancer alterations are often “paired”: some frequently observed together, while others rarely or never found in the same tumor. We termed these pairings evolutionary dependencies. Although, evolutionary dependencies exist among several cancer alterations, their effect on tumor growth and treatment is largely unknown.

Here, we designed a computational framework to integrate molecular profiles of >9,000 cancer patients with large-scale genetic screenings, which inactivate one gene at a time across multiple cancer cell lines. These analyses allowed us to infer and validate a set of functional alterations and test the effect of inactivating a gene when it is mutated alone or with specific others. Results showed that alteration pairs that we predicted to act synergistically increased the effect of single gene knock-out (Figure 1A). Conversely, alterations that we predicted to be redundant rescued the phenotype of single gene knock-out (Figure 1B). Similarly, we show that the effectiveness of a drug inactivating a specific gene does not only depend on whether or not that gene is activated in the tumor, but also by which other alterations are present.

Future impact of the findings

Precision medicine approaches in cancer are based on the principle that tumors exhibiting mutations activating specific cancer-associated genes will benefit from drugs that inactivate those genes. However, the success of these approaches is often inconsistent across patients. We argue that tumor phenotypes and response to treatment are not determined by individual and independent mutations, but by the concerted action of multiple alterations. Our study provides a framework combining computational predictions, experimental evidence and clinical data to understand the combinatorial functional effect of cancer genomic alterations.

Read more in Nature Genetics

4High-dose vitamin C enhances cancer immunotherapy

A. Magrì et al. Sci Transl Med. 2020 Feb 26;12(532):eaay8707

Summary of the findings

Vitamin C (also known as ascorbic acid) is an essential dietary nutrient, and its chronic deficiency contributes to impaired immunity. The anticancer effect of VitC has been investigated for decades with controversial results. While several studies have tested the efficacy of combining VitC with chemotherapy or targeted agents, the potential of combining VitC with immune modulators for anticancer purposes has not been explored.

Proposed mechanisms of anticancer activity of vitamin C

In this Science Translational Medicine paper, Magrì and colleagues analyzed the possibility that VitC could exert its effects not only directly on tumor cells but also through modulation of anti-tumor immunity. The authors found that a fully competent immune system is required to maximize the anti-proliferative effect of VitC against several types of mouse tumors including breast, colorectal, melanoma and pancreatic cancers.  When administered at high-dose, VitC increased the arrival at the tumor site of immune cells and delayed cancer growth. Excitingly, treatment with VitC improved the efficacy of immunotherapies. The combination was particularly effective against a subset of tumors, molecularly classified as microsatellite unstable or mismatch repair deficient. In conclusion the study of Magrì and colleagues shows that VitC can stimulate anticancer adaptive immunity and improves the efficacy of immune checkpoint inhibitors.

Future impact of the findings

In the late 70’ Ewan Cameron (a physician) and dr Linus Pauling (winner of the chemistry Nobel prize) first reported that concomitant intravenous and oral supplementation of VitC prolonged survival of terminal cancer patients. These findings were not confirmed when VitC was given only orally. The discrepant results may be explained by subsequent studies revealing that the administration route strongly affects VitC pharmacokinetics. The study by Magrì and colleagues supports these concepts and shows that VitC can be effective in mice when administered intravenously with immune modulators. These results support the design of clinical trials combining VitC and immunotherapy.

Read more in Science Translational Medicine

5Circulating tumour cell clustering shapes DNA methylation to enable metastasis seeding

Artistic coloration of a human circulating tumor cell cluster, isolated from the blood of a patient with cancer using a microfluidic device, by Martin Oeggerli (Micronaut).
Circulating tumor cells are cancer cells that detach from the primary tumor and enter the blood circulation, on their way to initiate a metastasis at a distant site. When traveling in the blood as clusters, circulating tumor cells are endowed with an extraordinary potential to efficiently initiate a metastasis. While very rare compared to blood cells in the bloodstream (1 circulating tumor cell per billion blood cells), capturing of circulating tumor cell clusters is now possible through the use of specialized microfluidic technologies, thus enabling scientists to study their biology and vulnerabilities.

S. Gkountela et al. Cell. 2019 Jan 10;176(1-2):98-112.e14.

Summary of the findings

A better understanding of the molecular features that characterize metastatic cancer cells is of exceptional importance for the development of new cancer therapies. We set out to perform a genome-wide DNA methylation analysis of circulating tumor cells (CTCs) from both breast cancer patients and mouse models, aiming to define the methylation landscape of metastatic precursors in circulation. Surprisingly, when comparing the methylome of single and clustered CTCs, we found that highly metastatic CTC clusters display hypomethylation at binding sites for critical stemness- and proliferation-associated transcription factors such as OCT4, SOX2, NANOG and SIN3A. These results suggest that CTC clustering is linked to DNA methylation remodeling, with significant impact on metastasis-seeding ability. Importantly, when dissociating CTC clusters through CRISPR-mediated cell-cell junction knockout or treatment with CTC cluster-dissociating compounds (identified through a screen with 2’486 FDA-approved molecules), we observed re-methylation of critical transcription factor binding sites and suppression of metastasis-forming ability in mouse models. Our findings clearly link cell-cell junction formation with changes in DNA methylation that promote stemness and metastasis, and highlight an opportunity for anti-cluster therapies in the treatment of metastatic cancers. These results are rapidly translating into the clinical setting, as we conducting a proof-of-concept clinical trial to evaluate CTC cluster dissociation approaches in breast cancer patients.

Read more in Cell

6Peripheral CD8+ T cell characteristics associated with durable responses to immune checkpoint blockade in patients with metastatic melanoma

Fairfax, B.P., Taylor, C.A., Watson, R.A. et al. Nature Medicine volume 26, pages 193–199(2020)

Summary of the findings

We are interested in the inter-individual variation in response to checkpoint immunotherapy for the treatment of metastatic melanoma. Markers of response that are detectable in the periphery have the potential to be clinically relevant as they can be assayed without recourse to biopsy. CD8 T cells show the most pronounced response to checkpoint immunotherapy and we set out to characterise the transcriptomic responses of these cells with treatment, and also determine markers of long-term clinical benefit.

We found that patients with a continued clinical response to therapy at six months had relative upregulation of genes involved in T cell receptor signalling. Using this insight, we categorised patients according to the T cell clonal response 21 days after their first treatment. We found that patients with more separate large peripheral CD8 clones (those >0.5% total repertoire) had a improved long-term outcomes, an observation we replicated in a further cohort. The number of large clones associated with both progression free and overall survival. We proceeded to use single cell sequencing to demonstrate that larger CD8 T cell clones express increased levels of cytotoxic markers and the number of large clones is strongly correlated with CD8 effector cell counts; providing mechanistic insight into our findings.

Going forward we want to assess how clonal size relates with cellular responsive to immunotherapy and deduce other factors involved in this process.

Read more in Nature Medicine

7Immune-awakening revealed by peripheral T cell dynamics after one cycle of immunotherapy

Analysis of TCR evolution in cell free DNA and identification of specific T cell subsets in the blood of melanoma patients after only 3 weeks on ICB drugs reveals immune-awakening in patients who will go on to mount an effective response.

S. Valpione et al. Nature Cancer vol. 1,2 (2020): 210-221

Summary of the findings

Immunotherapy with cytotoxic T lymphocyte associated protein-4 (CTLA4) and programmed death-1 (PD1) immune-checkpoint blockade (ICB) is increasingly utilised to treat solid tumours both in the metastatic and the neoadjuvant/adjuvant setting. Unfortunately, most patients do not respond to these drugs and some experience significant toxicity without benefit. New strategies are therefore needed to identify which patients will benefit from these treatments and to improve the chance of response in the majority of patients. To advance knowledge of the response dynamics induced by ICB, we analysed T cell phenotypes and T cell receptor (TCR) repertoire evolution under the selective pressure of ICB. We identified a subset of circulating T cells that early during treatment identifies the patients with better outcomes, and we discovered cell-free DNA-based TCR signatures that can track effective responses. The immune-signatures we identified have all the advantages associated with minimally invasive liquid biopsies, can identify responders after the first cycle of therapy and shed a light onto T cell dynamics associated with effective immune-responses in patients receiving ICB drugs.

Future perspectives

Our results will allow development of new strategies to improve cancer care, by highlighting how TCR repertoires evolve during effective responses and by identifying the T cell subset that expands early during treatment. This will guide the design of new immune-biomarkers for future clinical development and has also contributed to our understanding of the mechanisms underlying effective immune-response induced by ICB drugs.

Read more in Nature Cancer

8The next entry on the list is two linked papers:

MLH1 Deficiency-Triggered DNA Hyperexcision by Exonuclease 1 Activates the cGAS-STING Pathway

J. Guan et al. Cancer Cell Volume 39, Issue 1, P109-121.E5, January 11, 2021

DNA Sensing in Mismatch Repair-Deficient Tumor Cells Is Essential for Anti-tumor Immunity

C. Lu et al. Cancer Cell Volume 39, Issue 1, P96-108.E6, January 11, 2021

Summary of the findings

The great success of anti-PD-1 therapy against tumors defective in DNA mismatch repair (dMMR) highlights the role of tumor mutational burden (TMB) as a predictive biomarker in onco-immunotherapy. However, primary resistance exists in about 50% of dMMR tumor patients. Consistently, half of dMMR tumors with TMB-High have low level of T-cell infiltration. The mechanism concerning the neoantigen-independent immune profile in dMMR tumors is largely unknown. Given that innate sensing-mediated costimulatory signal is required for T-cell-dependent immune checkpoint blockade, we hypothesize that dMMR may trigger certain DNA sensing to benefit the aforementioned clinical outcome. By screening the DNA sensing pathways correlative to dMMR patients’ prognosis, we found that patients with lower cGAS/STING expression in their tumor tissues were more likely to survive their cancers shorter than those with higher expression. We confirmed this in dMMR mouse models. We show that depleting the cGAS-STING pathway in tumor cells defective in MMR factor MLH1 (dMLH1) badly impairs tumor-infiltration of T cells. Our mechanistical studies reveal that dMLH1, which is seen in about half of dMMR tumors, induces aberrantly hyperactive DNA excision by exonuclease 1 (Exo1), prompting the severely damaged DNA to release to the cytoplasm. This activates the cGAS-STING pathway and stimulates IFN production, leading to T-cell proliferation and tumor infiltration. Radiation further stimulates the immune signaling response. Correspondingly, dMLH1 cancer patients who resist anti-PD-1 therapy express low levels of cGAS/STING. These studies refine our understanding of the mechanisms underlying immunotherapy sensitivity and identify new biomarkers for predicting efficacy in dMMR patients.

MLH1 deficiency-triggered DNA sensing contributes to immunotherapy

Future impact of the findings

The findings in our study suggest that TMB-mediated neo-antigens in dMMR tumors is not enough for effective immunotherapy. The newly identified biomarkers of the factors involved in the cGAS-STING pathway could steer how dMMR tumors are treated in the future. Thus, evaluating the status of tumors’ cGAS-STING pathway factors could decide whether patients will benefit from immunotherapy. Additionally, since radiation stimulates the cGAS-STING immune signaling in dMLH1 tumor cells, delivering radiation before immunotherapy could further enhance the effectiveness of these therapies in dMMR patients.

Read more in Cancer Cell: Article 1 / Article 2

9MTOR signaling orchestrates stress-induced mutagenesis, facilitating adaptive evolution in cancer

A. Cipponi et al. Science 05 Jun 2020: Vol. 368, Issue 6495, pp. 1127-1131

“This paper provides evidence that cancer cells (alike bacteria) active adaptive mutability to escape targeted therapies.” Alberto Bardelli, EACR Board Member

Summary of the findings

Genetic variability is central to adaptability and evolution of human cancer.

Mutagenesis may occur incrementally or in transient bursts, triggered in response to environmental or pharmacological pressures, when genetic diversity is most needed to create evolutionary opportunities.

Conserved mechanisms underpinning stress-induced mutagenesis (SIM) have been extensively described in microorganisms. Analogous processes may underpin progression and therapeutic failure in human malignancies.

We developed in vitro model systems of intense drug selection and we undertook a genome-wide functional screen to identify common mechanisms driving SIM. These studies implicate the MTOR signaling pathway in mediating a stress-related repression of accurate DNA repair, generating new mutational landscapes which facilitate the emergence of resistance to targeted anticancer agents (Figure 1).

Figure 1. Selection with targeted anticancer therapies results in genetic diversity. Single cell-derived clonal populations obtained from untreated and early-phase drug-resistant cancer cell lines, have been expanded through an equal number of generations and subjected to whole genome sequencing. Mutation rates, measured as the percentage of de novo single nucleotide variants (SNVs), were significantly higher in the drug-resistant populations.

These observations, together with the reduction of clonogenic potential early during adaptation, are consistent with a two-phase model for drug resistance. Initially, the rapid expansion of genetic diversity is counterbalanced by an intrinsic fitness penalty. Subsequently, normalization of SIM and fixation of stably resistant genomic configurations establish a new adaptive equilibrium.

Collectively, these data reveal conserved programs of mutagenesis as prominent contributors to therapeutic failure and provide a rational framework for synthetic lethal combinations of cytostatic agents with genotoxic therapies. Such combinations could potentially generate a lethal mutational load during the initial phase of adaptive evolution, thereby reducing therapeutic failure.

Read more in Science

10Colorectal Cancer Cells Enter a Diapause-like DTP State to Survive Chemotherapy

S. Rehman, J. Haynes, E. Collignon et al. Cell Volume 184, Issue 1, P226-242.E21, January 07, 2021

“This paper shows evidence that cancer cells which survive therapy enter an embional like state.” Rene Bernards, EACR Board Member

Summary of the findings

Cancer cells enter a reversible drug-tolerant persister (DTP) state to evade death from chemotherapy and targeted agents. It is increasingly appreciated that DTPs are important drivers of therapy failure and tumor relapse. We combined cellular barcoding and mathematical modeling in patient-derived colorectal cancer models to identify and characterize DTPs in response to chemotherapy. Barcode analysis revealed no loss of clonal complexity of tumors that entered the DTP state and recurred following treatment cessation. Our data fit a mathematical model where all cancer cells, and not a small subpopulation, possess an equipotent capacity to become DTPs. Mechanistically, we determined that DTPs display remarkable transcriptional and functional similarities to diapause, a reversible state of suspended embryonic development triggered by unfavorable environmental conditions. Our study provides insight into how cancer cells use a developmentally conserved mechanism to drive the DTP state, pointing to novel therapeutic opportunities to target DTPs.

Read more in Cell

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