The EACR’s Top 10 Cancer Research Publications: February 2022

Correia, A.L., Guimaraes, J.C., Auf der Maur, P. et al. Nature 594, 566–571 (2021).

Summary of findings

Tumor cells that spread beyond the primary tumor can enter a dormant state upon arrival at the distant site, only to awaken years (or even decades) later to form deadly metastases. What drives these cells in and out of dormancy is yet to be fully understood. In this Nature paper, Correia et al. developed a tool to follow dormant disseminated tumor cells (DTCs), and surveyed the anatomical distribution of dormant reservoirs in spontaneous metastasis models of breast cancer. They discovered that DTCs lay preferentially dormant in the liver, and spatially distinct liver ts thsub-microenvironments allow coexistence of dormant DTCs and rare growing metastases even within the same tissue. It is the size of the endogenous pool of natural killer (NK) cells within these sub-microenvironmenat controls breast cancer progression. When abundant, NK cells sustain dormancy through interferon-γ signaling, preventing hepatic metastases and prolonging survival. If there is a liver injury, such as liver fibrosis mediated by the accumulation of activated hepatic stellate cells, NK cell proliferation is inhibited and metastases emerge. These findings show that NK cells put cancer cells to sleep, and suggest that therapies aimed at normalizing the NK cell pool might succeed in preventing liver metastases.

“Dormancy in breast cancer is a critical problem and in this study it is shown that NK cells play a critical role in this process.”

EACR Board

Future impacts of the findings

These results yielded direct druggable targets with already approved agents that can be repurposed and readily translated into the clinical setting. For this, the authors are already setting up two clinical trials at the University Hospital of Basel. The first will trace the levels of NK cells in breast cancer patients at high risk of developing metastases, and examine whether those levels correlate with the outcome of these patients. And the second will be an intervention trial to evaluate the potential of adjuvant NK cell immunotherapy to prevent metastatic disease in breast cancer patients.

Read more in Nature

Pernigoni, Zagato, Calcinotto et al. Science, Volume 374 | Issue 6564 8 October 2021

Summary of the findings

Despite significant therapeutic advances, prostate cancer is a leading cause of male cancer mortality, with metastatic castration-resistant prostate cancer (mCRPC) remaining fatal. Androgens influence the growth of prostate tumor cells, and androgen deprivation therapy (ADT) is the standard of care for advanced prostate cancer. The microbiota comprises the organisms that live in close contact with the host, with mutual benefit for both counterparts. In this Science paper, Pernigoni et al. investigated the role of the gut microbiota and its association with the emergence of endocrine-resistance in prostate cancer. They discovered that ADT in mice and prostate cancer patients selects a peculiar “unfavorable” microbiota. In brief, “unfavorable” bacteria over abundant in ADT-resistant individuals can produce androgens forms starting from precursors. These microbes-derived androgens (DHEA and Testosterone) are absorbed into the systemic circulation and promote the development of castration- and endocrine therapy-resistant states. These results suggest that the microbiota can hinder the efficacy of prostate cancer standard of therapy.

Future impact of the findings

Current therapies for CRPC therapy are not elusive, so finding new treatments that delay or revert CRPC remains an urgent and unmet clinical need. Given the pivotal role of microbiota in prostate cancer, it is now fundamental to leverage thinking of novel therapeutics targeting gut microbiota in prostate cancer patients. Pre-, pro-, post-biotics, and antibiotics treatments that can target the gut microbiota shifting its composition from an “unfavorable” to a “favorable” composition may have tremendously beneficial effects in delaying or reverting CRPC, also increasing therapy responsiveness.

Read more in Science

Rossman, Zabka et al. Mol Cancer Ther 2021;20:2177–88

Summary of the findings

BRAF gene mutations, especially BRAF^V600E, drive up to 8% of all human cancer across cancer types. Drugs targeting BRAF mutations can induce dramatic remissions in human cancer patients, however, drug resistance consistently develops. There is considerable interest in identifying clinically-relevant, immunocompetent animal models to test strategies to overcome drug resistance and advance BRAF-targeted therapies. This work focused on naturally-occurring canine urothelial carcinoma, a heterogenous aggressive cancer which interestingly, harbors the dog homologue of BRAF^V600E. In a canine phase I/II clinical trial of the BRAF-targeted drug, vemurafenib, remission occurred in 38% of dogs. As in humans, drug resistance developed with median progression free interval of 6 months. Transcriptomic analyses of tumor tissues collected by cystoscopic biopsy before, during, and at relapse on therapy were very informative. Upregulation of genes in the classical and alternative MAPK-related pathways occurred in subsets of dogs at cancer progression, providing important clues to mechanisms contributing to drug resistance. The most consistent transcriptomic changes, however, were the increase in patterns of immune infiltration during the first month of vemurafenib, and immune failure at relapse. The results support the inclusion of dogs with BRAF-mutated cancer to complement experimental models in research to improve BRAF-targeted therapies in humans.

Future impact of the findings

The canine model can be used in research to improve BRAF-targeted therapy. Insights into transcriptomic changes in tumor signaling and immune activity with therapy can be leveraged to develop better therapies, especially targeted drug-immunotherapy combinations. The transcriptomic, pharmacokinetic, and case data have been deposited in the US National Cancer Institute’s Integrated Canine Data Commons with expected release by March 2022. This data can be analyzed in parallel with human cancer data to test emerging hypotheses. In addition to work aimed at helping humans, the work is expected to lead to new cancer therapies for pet dogs with cancer.

Read more in Molecular Cancer Therapeutics

Pascual, G., Domínguez, D., Elosúa-Bayes, M. et al. Nature 599, 485–490 (2021).

Summary of the findings

Fatty acid uptake and an altered metabolism are hallmarks of metastasis. In this work, we describe how dietary palmitic acid (and not oleic or linoleic acids) induces a more aggressive profile in tumour cells and how this remains as a form of cellular “memory”. Tumours from mice fed a short-term diet rich in palm oil and tumour cells
briefly exposed to palmitic acid in vitro remained highly metastatic even after being
successively transplanted (without further exposure to high levels of this fatty acid).

The prometastatic profile is related to the capacity of the tumour cells to establish a neural network around the tumour. The palmitic acid-induced prometastatic memory, which is dependent on the fatty acid transporter CD36, the transcription factor EGR2 and the glial-cell-stimulating peptide galanin, promotes a pro-regenerative state of tumour-activated Schwann cells, which secrete a specialized extracellular matrix. Intratumoural Schwann cells and innervation are parameters that strongly correlate with metastasis.

Using a variety of approaches to block the formation of the neural network surrounding the tumour, we were able to prevent the development of metastases.

Future impact of the findings

Our findings provide a novel insight into the metastasis initiation process and may drive new approaches to tackle cancer. In this regard, the mechanisms detailed in our work pave the way for the development of therapies that specifically block metastasis, which is the main cause of death by cancer.

Read more in Nature

Haas, L., Elewaut, A., Gerard, C.L. et al. Nat Cancer 2, 693–708 (2021).

“This article shows the importance of preclinical studies to identify the best combination strategy of targeted and immuno-therapies.”

EACR Board

Summary of the findings

The combination (or sequential application) of different cancer therapies represents a powerful opportunity to increase response and cure rates for cancer patients. However, how cancer cells and the crosstalk within the tumor microenvironment change upon different therapeutic challenges, and how this might influence the outcome of subsequent therapies is poorly understood.

In this study we show that when tumors relapse after targeted therapy with MAPK pathway inhibitors, they are cross-resistant to immunotherapies, despite the different modes of action of these therapies. We found that cross-resistance is mediated by a cancer cell–instructed, immunosuppressive tumor microenvironment that lacks functional CD103⁺ dendritic cells, precluding an effective T cell response. Restoring the numbers and functionality of CD103⁺ dendritic cells can re-sensitize cross-resistant tumors to immunotherapy. We showed that cross-resistance is controlled by a reactivated and rewired MAPK signaling pathway, which not only restores its cancer cell-intrinsic oncogenic functions but, in addition, drives an immune-evasive gene expression program that establishes a completely different immune phenotype conferring resistance to immunotherapy. Importantly, this rewired state not only dominates RAFi and RAFi/MEKi-resistant tumors but is already present in a subset of therapy-naïve tumors that respond poorly to immunotherapy. Our work provides mechanistic evidence for cross-resistance between two unrelated therapies, and a scientific rationale for treating patients with immunotherapy before they acquire resistance to targeted therapy.

Future impact of the findings

Currently, more than half of BRAF-mutant patients initially receive targeted therapy, often until they acquire resistance. Our data, together with other work and data from prospective phase III clinical trials e.g. DREAMseq/NCT02224781, provide a strong scientific rationale for using immunotherapy as a first-line treatment. The concept of targeted-therapy/immunotherapy cross-resistance in BRAF-mutant melanoma may also extend to other tumor types and therapies, which should be evaluated. Collectively, our work highlights the importance of understanding the complex and dynamic biology of cancer cells and the tumor microenvironment in all three phases of therapy, i.e., the therapy-naïve, the responding/adapting, and the therapy-resistant state in order to guide the rational combination and optimal sequence of therapies.

Read more in Nature Cancer

Vernieri et al., Cancer Discov January 1 2022 (12) (1) 90-107

Summary of the findings

In preclinical models, cyclic calorie restriction, in the form of fasting or fasting-mimicking diets (FMDs), has been shown to potentiate the antitumor effects of standard antineoplastic therapies, such as chemotherapy, endocrine therapy and immunotherapy, by affecting host/tumor metabolism and by boosting antitumor immunity. However, the applicability of this approach in clinical setting remains unclear.

In our Cancer Discovery paper, we reported the results of a first-in-human, phase Ib clinical trial in 101 cancer patients. We showed that a severely calorie-restricted 5-day FMD regimen is safe and well tolerated when repeated every three/four weeks in combination with standard antineoplastic treatments. The FMD resulted in a significant and consistent reduction of blood glucose, insulin and IGF-1 concentration, thus recapitulating the metabolic effects that were found to mediate in part the antitumor activity of calorie restriction in preclinical studies.

More importantly, the FMD produced a global and desirable reshaping of systemic and intratumor immunity, with a reduction of immunosuppressive immune cell subsets, including myeloid-derived suppressor cells, regulatory T cells and exhausted T cells, paralleled by an increase in cytotoxic/activated T cells, activated dendritic cells, cytolytic Natural Killer cells and memory T cells. Some of these immune modifications were maintained more than 30 days after the completion of the FMD.

Future impact of the findings

Based on 1) solid preclinical evidence showing consistent and synergistic antitumor effects of cyclic FMD and standard antitumor therapies and 2) our results demonstrating safety and desirable metabolic and immunologic effects of cyclic FMD in cancer patients, our group and other groups have recently initiated phase II clinical trials to investigate if cyclic FMD can improve the antitumor activity/efficacy of standard chemotherapy in selected cancer patient populations, such as in patients with LKB1-inactive advanced lung adenocarcinoma (FAME trial, NCT03709147) or in patients with early-stage triple-negative breast cancer (TNBC) (BREAKFAST trial, NCT04248998). These trials may provide first clinical evidence of antitumor activity of cyclic FMD in cancer patients.

Read more in Cancer Discovery

Westcott, P.M.K., Sacks, N.J., Schenkel, J.M. et al. Nat Cancer 2, 1071–1085 (2021).

“This is an excellent paper that uses several model systems to decipher neoantigen characteristics that affect their immunogenicity as well as their cross priming. It has strong ramifications on our understanding of immune evasion and therapy response.”

EACR Board

Summary of the findings

Immune checkpoint blockade immunotherapy is remarkably effective in patients with DNA mismatch repair-deficient colorectal cancer owing to a high burden of somatic mutation-derived antigens, or “neoantigens”. Unfortunately, most colorectal cancer—so called mismatch repair-proficient—is not responsive to these therapies. While these tumors harbor a lower burden of neoantigens than their mismatch repair-deficient counterparts, we showed that they are not devoid of neoantigens, harboring more mutations on average than some cancers that are responsive to immunotherapy. Interestingly, we found that neoantigens in mismatch repair-proficient colorectal cancer are expressed at lower levels on average, raising the possibility that neoantigen expression is also an important determinant of immunity. To functionally test this, we developed a versatile platform for modulating neoantigen expression in colorectal cancer organoids and transplanted these into the distal colons of mice. We showed that low expression of model neoantigens drove suboptimal T-cell cross-priming, and while neoantigen-specific T cells were observed infiltrating tumors, they underwent immediate functional impairment and failed to restrain tumorigenesis. Immune checkpoint blockade was minimally effective in the model, suggesting that this type of T-cell dysfunction is distinct from T-cell “exhaustion”. In contrast, therapies that boost priming (i.e., vaccination and agonistic anti-CD40) were highly efficacious.

Future impact of the findings

A major takeaway from this study is that not all T-cell dysfunction in cancer is the same. The dysfunction we observed is consistent with tolerogenic priming, which will require a different therapeutic approach. Neoantigen expression level (and likely other variables that affect MHC-I presentation) really tunes the quality of the initial T-cell response. This has important therapeutic implications, as immune “cold” tumors may harbor “Trojan horse” neoantigens that never primed productive T-cell responses and thus fly under the radar of functional tumor-infiltrating lymphocyte assays. But if priming can be rescued, these same neoantigens may render tumors vulnerable to killing.

Read more in Nature Cancer

Sammut, SJ., Crispin-Ortuzar, M., Chin, SF. et al. Nature 601, 623–629 (2022).

Summary of the findings

Despite great strides in understanding the biology of cancer, we still cannot reliably predict response to chemotherapy (plus HER2-targeted therapy for ERBB2 amplified tumours). In this study, we aimed to: (a) understand the biological processes associated with response to chemotherapy in breast cancer and (b) build a machine learning framework that combines pre-therapy molecular and digital pathology data to predict response.

We molecularly profiled breast tumour biopsies obtained at diagnosis from 168 women using exome and RNA sequencing and analysed their histological architecture using digital pathology. Women received 18 weeks of pre-operative chemotherapy and response was assessed at surgery using the Residual Cancer Burden score.

The baseline pre-therapy features were monotonically associated with response. DNA features associated with response related to genomic instability, including tumour mutation and neoantigen burden, homologous recombination deficiency and TP53 mutations. Response to therapy was also modulated by the tumour immune microenvironment. Specifically, high lymphocyte density, lack of T-cell dysfunction and exclusion, and absence of HLA class I loss of heterozygosity were associated with a better outcome.

Combining these molecular and digital pathology features into a multi-omic machine learning model predicted a pathological complete response in an external validation cohort with an area under curve of 0.87.

A tweetorial describing this study can be found at: https://twitter.com/stephensammut/status/1468251380586590216

Future impact of the findings

By integrating highly dimensional multi-omic data generated by profiling the tumour ecosystem, we have increased our understanding of the biology of breast cancer and developed a framework that will transform the way we treat it. In the future, this framework could be used to determine which patients can be treated with standard of care therapies (if they are predicted to respond) or treated using novel therapies in clinical trials (if predicted to be resistant to standard therapies). Perhaps more importantly, this approach has demonstrated a new way of thinking about forecasting therapy response which could be adapted for use in other cancer types.

Read more in Nature

Garciaz et al., Cancer Discov January 26 2022 DOI: 10.1158/2159-8290.CD-21-0522

Brief summary of the findings

Identifying new mechanisms inducing cancer cell death is critical for improving clinical outcomes. Ironomycin is a salinomycin-derivative drug that sequesters iron into the lysosomes and induces a non-apoptotic death in cancer cells. Using unbiased CRISPR screening, we studied the effect of ironomycin in acute myeloid leukemia (AML) cells. We surprisingly found that mitochondrial metabolism was the main modulator of ironomycin efficacy. Using a multidisciplinary systems biology approach including metabolomics, RNA sequencing, video-microscopy ICP-mass spectrometry and functional testing, we observed that the drug induced a strong depletion in mitochondrial iron triggering a defect in mitochondrial respiration and a mitochondrial stress response. Ironomycin treatment induced a BAX/BAK-dependent mitochondrial outer membrane permeabilization (MOMP) leading to cell death. Contrary to venetoclax, a BH3-mimetics commonly used for AML treatment, BAX and BAK activation was independent on the anti-apoptotic protein BCL-2 or the BH3-only pro-apoptotic proteins. Interestingly, this non-canonical new cell death modality potentiated the effect of venetoclax in vivo and was independent of AML cells TP53 status. Finally, the drug was active in venetoclax resistant leukemia cells derived from patients. In conclusion, ironomycin inexorably links mitochondrial metabolism to cell death and represents a new therapeutics for treating cancer cells resistant to BH3-mimetics.

Future impact of the findings

Acute myeloid leukemia patients with AML blasts that are resistant to the BH3-mimetics venetoclax have an extremely poor outcome. Ironomycin reduces mitochondrial iron, starves mitochondria and provokes a BAX/BAK dependent cell death non-redundant with BH3-mimetics. Triggering this new cell death modality can resensitize resistant AML cells to the BH3-mimetics venetoclax and overcome BH3-mimetics resistance. Ironomycin represents a new bullet in the fight against aggressive leukemias, by inducing non-canonical cell death in AML patients resistant to BH3-mimetics.

Read more in Cancer Discovery

Baruch et al., Science Vol 371, Issue 6529 pp. 602-609

“This is the first time that it is demonstrated that the combination of fecal microbiota transplantation with anti-PD-1 therapy in metastatic melanoma is feasible and effective.”

EACR Board

The composition of the gut microbiome influences the response of cancer patients to immunotherapies. Baruch et al. and Davar et al. report first-in-human clinical trials to test whether fecal microbiota transplantation (FMT) can affect how metastatic melanoma patients respond to anti–PD-1 immunotherapy (see the Perspective by Woelk and Snyder). Both studies observed evidence of clinical benefit in a subset of treated patients. This included increased abundance of taxa previously shown to be associated with response to anti–PD-1, increased CD8⁺ T cell activation, and decreased frequency of interleukin-8–expressing myeloid cells, which are involved in immunosuppression. These studies provide proof-of-concept evidence for the ability of FMT to affect immunotherapy response in cancer patients.

Read more in Science