Our group focuses on the interplay between cellular plasticity, stem cells and cancer. Cellular plasticity is recognized today as a critical feature of cancer cells that enables them to transit between different cellular states, including reversible transitions between mesenchymal and epithelial phenotypes, or stem cell-like and differentiated states. In tumors, the acquisition of stem cell properties correlates with increased malignancy and poor prognosis, and Cancer Stem Cells (CSCs) sustain the tumor bulk and contribute to treatment resistance and disease relapse post-therapy.
In this respect, we have reported that inducing dedifferentiation with the so-called Yamanaka factors can lead to the development of a variety of tumors. We have also demonstrated that tissue damage, as the main driver of cancer, triggers cell dedifferentiation and the acquisition of stem cell properties in vivo.
These observations have important therapeutic implications given that chemotherapy and radiotherapy – cornerstones for the treatment of most cancers – could have the side effect of inducing stemness in non-stem cancer cells and, in turn, possibly contribute to tumor recurrence and metastasis.
Our main objective is to better understand the mechanisms and players implicated in this process, with the ultimate goal of developing novel therapies based on the inhibition of cancer cell plasticity.
Recent findings have demonstrated that some genomic regions, previously considered as non-coding (including lncRNAs), contain small open reading frames encoding for evolutionary conserved, unannotated micropeptides. The few that have been identified to-date play key functions in elemental cellular processes, leading to a new level of complexity with major implications – from basic research to the clinical setting.
Over the past three years we have focused on identifying and characterizing novel cancer micropeptides that could represent novel actors in carcinogenesis.We have discovered six new cancer micropeptides and have obtained compelling evidence in vitro and in vivo that four of them act as novel tumor suppressors, inducing cell cycle arrest, differentiation or inhibition of mesenchymal traits in cancer cells.
The identification of tumor-micropeptides could be crucial in advancing insights into cancer physiopathology. Moreover, they could also serve as new cancer biomarkers for the early detection of disease and patient stratification for tailored therapies, as well as therapeutic targets.
In 2019, we have expanded our micropeptides studies and embarked on a new project that aims to identify novel secreted micropeptides that act as crucial cellular messengers for pancreatic cancer metastasis.
Our laboratory seeks to better understand how epigenetics and chromatin structure and dynamics affect cell behavior, with a specific focus on cancer. Through our comprehensive studies, we aim to dissect the role of epigenetic changes in cancer, identify mechanisms of response and resistance to anti-cancer medicines, and explore new therapeutic opportunities.
Over the last few years, we have elucidated epigenetic changes during EMT and cancer progression, and discovered a new histone H3 modification (oxidized H3) enriched in heterochromatin that is implicated in chromatin condensation and the transition to a metastatic cell fate (published in Mol. Cell, FEBS J., and Oncogene). We have also discovered an important role for lamin B1 in the reorganization of 3D chromatin structure during EMT (published 2018, Nat. Commun.).
Dedicated to fully applying these insights to the epigenetic landscape and 3D structure during this malignant transformation, we have adopted chromosome conformation–based techniques together with ChIP-seq, ATAC-seq and RNA-seq. By combining these data with excellent computational and statistical tools in standard cancer models, such as cancer cell lines, and in a large and unique collection of patient-derived xenograft (PDX) models, we will continue to navigate this largely uncharted area which shows great promise in the early diagnosis of disease.
We are equally committed to describing the association of chromatin conformation modifications with the acquisition of malignant traits and evaluating the functional consequences of these developments in genes and pathways. Next steps will involve deciphering how these alterations occur at the molecular level and more precisely identifying these putative culprits for future targeted therapy
VHIO’s Experimental Therapeutics Group conducts bench-to-bedside preclinical research in breast cancer to advance insights into biomarkers of response to targeted therapies. To do so, we generate preclinical models such as patient-derived xenografts (PDXs) and patient-derived cultures (PDCs) from breast cancer patient samples.
Our group has significantly contributed to the field of PI3K inhibitor resistance and we continue to explore mechanisms of resistance to CDK4/6 inhibitors, FGFR inhibitors, AKT inhibitors and AR modulators (SARMs) in breast tumors in greater depth.
Using clinically relevant PDXs we provided data to further support that loss of G1-cell cycle checkpoint control, such as mutation/loss of RB1 or CCND1-amplification, is associated with lack of response to CDK4/6 blockade in estrogen receptor positive breast cancer. We have also generated a collection of PDXs containing FGFR amplification to study biomarkers of sensitivity to FGFR inhibitors; both pan-FGFR1-4 and Multi-targeted Tyrosine Kinase Inhibitors (MTKIs).
Encouraged by the early success of DNA damage repair inhibitors in germline BRCA1/2 mutated tumors, we initiated a project aimed at identifying response biomarkers of PARP inhibitors (PARPi) as well as other DNA damage repair inhibitors including those targeting WEE1 or ATR.
Our studies underpin the capacity of germline BRCA mutant tumors to recover HRR functionality and develop resistance to PARPi. We have developed an assay, the RAD51predict test, which accurately identifies germline BRCA tumors that have restored HRR functionality and become resistant to these drugs. Importantly, this test also identifies tumors that are sensitive to PARPi through HRR alterations beyond the germline BRCA condition. We filed a patent (EU application in 2017 and PCT in 2018), and we are currently validating the use of this test in tumor samples from breast, ovarian and prostate cancer patients.
Finally, we are also studying the effects of PARPi on the tumor immune environment. HRR-deficient tumors have been shown to accumulate cytosolic DNA, which can elicit an innate immune signal (the STING pathway) and upregulate interferon-related genes, leading to lymphocytic infiltration and PD-L1 expression. We are testing the hypothesis that treatment of HRR-deficient tumors with PARPi elicits a DNA damage response that results in upregulation of PD-L1 and might limit the antitumor immune-mediated cytotoxicity by lymphocytes, but sensitizes to anti-PD-L1 treatments.
In short, working closely together with Cristina Saura’s Breast Cancer Group, and Judith Balmaña’s Hereditary Cancer Genetics Group, our team has significantly advanced the understanding of the mode of action of novel targeted therapies, identified new response biomarkers and developed a biomarker-based assay with potential clinical application. We have also demonstrated the efficacy of hypothesis-based drug combinations.
Reflective of VHIO’s purely multidisciplinary and translational approach, our research is also carried out through collaborations with other groups including VHIO’s Molecular Oncology, and Oncology Data Science – OdysSey Groups directed by Paolo Nuciforo and Rodrigo Dienstmann, respectively.
We study primary brain tumors and brain metastasis; some of the most aggressive of all cancers. Both glioblastoma and brain metastasis are dismal diseases with limited therapeutic options. Advancing progress in this field towards improving outcomes for these patients is therefore critical.
Evolving heterogeneity is among one of the major challenges that are currently hampering our efforts aimed at more effectively treating brain cancers. We focus on inter-tumor heterogeneity and evolution that includes genomic heterogeneity, cancer initiating cells and stroma/immune cell heterogeneity – including the study of TGF-β and LIF.
Tumors are composed of a mosaic of cell subclones that differ in their genomic alterations. Our group explores the genomic diversity present in glioblastoma and analyzes intratumor genomic heterogeneity as it evolves over time in response to therapy. We are designing tools to monitor evolving genomic heterogeneity, and studying the use of liquid biopsies for brain cancer through the study of circulating cell free tumor DNA in cerebrospinal fluid from patients.
Specifically, we are driving cerebrospinal fluid as liquid biopsy for the real time policing of brain cancer closer to the clinic. Reflective of our expertise in developing this novel approach, we recently first-authored an article (Seoane et al. Ann Oncol. 2019), analyzing several studies on the use of liquid biopsy in primary and metastatic brain tumors for the diagnosis and follow-up of disease as well as the detection of mechanisms of resistance or susceptible mutations.
While no biomarker derived from liquid biopsy against these tumor types has yet been validated and integrated into clinical practice, there is an increasing body of evidence in the literature, including our findings, that points to its efficacy in the real time evaluation of malignant disease and potential in better guiding the therapeutic management of patients.
We are as equally committed to furthering insights into the role of the tumor microenvironment which, in the case of brain cancers, assumes a crucial role in cancer progression. Advancing discovery into the tumor microenvironment promises a way of combating cancer independently of its heterogeneity.
By eliminating the niche where tumors reside and thrive should help us to develop more effective anti-cancer compounds. In this context, we have reported that the cytokine LIF assumes an essential role in the tumor microenvironment and is consequently a promising therapeutic target.
Building on our previous LIF studies, where we were the first to establish a link between this multi-functional protein and cancer, as well as show that LIF blockade eliminates cancer stem cells and prevents disease progression and recurrence, subsequent research has led to the publication of a further article this year directed by our Group (Pascual-García et al. Nat Commun. 2019.)
We have now shown that the novel agent MSC-1, developed by VHIO, inhibits LIF and has now been shown to have a dual mechanism of action. In tumors expressing high levels of LIF, this protein promotes the proliferation of cancer stem cells. LIF blockade eliminates these tumor-initiating stem cells, putting the brakes on metastatic cell spread and cancer recurrence.
Additionally, elevated LIF expression disables the anti-tumor alarm system and stops the immune system from thwarting cancer’s plans. Blocking LIF reactivates the alarm to call an anti-tumoral immune response.
During 2019, we continued our research line on novel immune therapies by generating novel CARs (chimeric antigen receptors). With the knowledge accumulated during the development and characterization of bispecific antibodies, we have been able to efficiently develop our CARS that are directed against the p95HER2 protein; only present in some mammary and gastric tumors, and completely absent in normal tissues. Importantly, this project has been funded by the Spanish Association Against Cancer (AECC) for the next five years.
In addition, our ever-expanding platform of breast and pancreatic cancer patient-derived experimental models led to us establishing several fruitful collaborations with several national and international groups. These partnerships have enabled us to identify novel mechanisms of resistance to anti-cancer therapies (Lambies et al., Diaz-Rodriguez et al., and Gomez-Miragaya et al.) as well as biomarkers of sensitivity to precision medicines (Kang et al., and Blasco-Benito et al.).
Our group has also contributed to the characterization of a novel antibody drug conjugate that is effective against some pancreatic tumors and triple negative breast cancers (Merlino et al.). Finally, we have also collaborated in identifying drugs targeting senescent cells which, under certain circumstances, majorly contribute to tumor progression. At VHIO, we have worked with several groups on research led by Sandra Peiró, Principal Investigator of our Chromatin Dynamics in Cancer Group, to unveil mechanisms that govern gene expression in triple negative breast cancer (Cebria Costa et al.).
Our highly collaborative approach has also allowed us to participate in several large-scale projects funded by the European Union this year, including the Immune-Image project supported by the Innovative Medicines Initiative (IMI). This large-scale consortium aims to develop novel tracers to monitor the immune response to anti-tumor therapies for research into patient-derived cancer xenografts. We are also participating in the COLOSSUS multi-center European Commission Horizon 2020-supported project; Advancing a Precision Medicine Paradigm in metastatic Colorectal Cancer: Systems based patient stratification solutions, for which our group is developing humanized mouse models.
Mention must also be made regarding the continued backing and support received from the Breast Cancer Research Foundation (BCRF), for which we are extremely grateful.
Several of our young talents have been awarded in 2019 including Veronica Rodilla who received a Stop Fuga de Cerebros grant from Roche, and Irene Rius and Faiz Bilal who defended their PhD theses on novel therapies against breast and pancreatic cancers, respectively.
Lastly, it has been an extremely productive year for the Centro de Investigación Biomédica en Red (CIBER-ONC: Center for the Biomedical Research Network in Oncology), under the scientific direction of our Principal Investigator, Joaquín Arribas. This recently established network is comprised of several of the most active cancer research groups across Spain, including three at VHIO.
Our group focuses on the pleiotropic and ubiquitous Myc oncoprotein, whose deregulation is implicated in almost all human cancers. The technical challenges of targeting nuclear transcription factors such as Myc –and the concern regarding potential side effects– had until recently precluded any preclinical validation of Myc inhibition as a possible therapeutic strategy.
Over the past few years, we have demonstrated in several mouse models that Myc inhibition has a dramatic therapeutic impact across several tumor types, with very mild and reversible side effects in normal tissue.
Encouraged by our results in mice, we are now interested in developing viable, non-toxic pharmacological options for Myc targeting in the clinic. To do so, we have created a spin-off company, Peptomyc S.L., for the development of Myc-inhibiting peptides for cancer therapy. Our laboratory in partnership with Peptomyc is currently validating our novel approach against notoriously difficult-to-treat cancers that are resistant to standard treatments and in dire need of new therapeutic avenues (i.e. KRAS-driven Non-Small Cell Lung Cancer, glioblastoma, and metastatic triple negative breast cancer).
Our group has continued to contribute to groundbreaking science by publishing in journals of international prestige. One particular highlight for 2019 is a paper describing key studies for advancing our Myc inhibitor mini-protein Omomyc towards the clinic (Beaulieu et al. Intrinsic cell-penetrating activity propels Omomyc from proof of concept to viable anti-Myc therapy. Sci Trans Med. 2019). This publication was very well received by the scientific community and highlighted in Nature Reviews Cancer and Nature Reviews Drug Discovery as a potential seminal milestone towards the clinical application of our first-in-class Myc inhibitor.
Laura Soucek and first author Marie-Eve Beaulieu also had the opportunity to add their authors’ views regarding this important achievement thanks to a publication in Molecular & Cellular Oncology, in which they summarized the main take-home messages of their publication in Science Translational Medicine on Myc biology and inhibition.
This year has also celebrated several collaborative successes:
Our work with Rajeev Vibhakar’s laboratory led to a publication in International Journal of Cancer, demonstrating the therapeutic potential of Myc inhibition in childhood rhabdoid tumors. In addition, results of our collaborative studies with teams led by Esther Vazquez, Ibane Abasolo and Antonio Villaverde, were published in Advanced Science and demonstrate the potential of therapeutic proteins delivered in the form of inclusion bodies to treat breast cancer.
Last but not least, we contributed to an excellent manuscript headed by Jordi Alcaraz and published in Cancer Research, showing that epigenetic SMAD3 repression in tumor-associated fibroblasts reduces fibrosis and sensitivity to the antifibrotic drug nintedanib in lung squamous cell carcinoma.
We have also had the privilege of hosting a Fulbright Scholar (as part of the U.S. Department of Education’s International Exchange Program), Jessica Chambers, who graduated from Princeton University.
Hector G. Palmer and his Stem Cells & Cancer Group are studying the mechanisms that permit tumors to escape from effective treatments and progress to advanced stages, when patients’ lives are at risk.
His team uses multi-omic approaches for revealing unexpected alterations related with tumor phenotypes. The group also pairs gene editing (CRISPR/Cas) with classical signalling biochemistry in cancer cell lines as well as genetically modified mice, patient-derived organoids and xenografts (PDX) to study the functional relevance of these newly identified alterations in patients' response to therapies.
The group is also part of a global multidisciplinary task force that includes oncologists, surgeons, radiologists and nurses. This strong collaboration means that laboratory results have a rapid clinical interpretation and translation to the bedside.
Main research lines include:
Tumor cell dormancy
We study the intriguing biology of cancer cell dormancy that is responsible for chemoresistance, formation of minimal residual disease and relapse of patients. The team discovered a core epigenetic network governing dormancy of tumor cells (J Clin Invest. 2018), and is now studying the function of TET2, DPPA3 and other epigenetic factors governing dormancy in further depth. Importantly, we are rapidly progressing in developing drugs that modulate dormancy drivers including TET2 and defining novel biomarkers to detect chemo-resistant dormant tumor cells (DTC).
Response to target-directed drugs
Our group works in close collaboration with oncologists and pharmaceutical companies to identify molecular mechanisms responsible for the sensitivity or resistance to drugs blocking Wnt/beta-catenin, Notch, PI3K/AKT, EGFR/LGR5 or BRAF/MEK/ERK oncogenic signals (Nat Med. 2012; Clin Can Res. 2014; Clin Can Res. 2019). Based on our discoveries we are designing new pre-screening tests for a genetic-guided enrolment of patients in clinical trials. Crucially, our findings are helping to define new rational drug combinations to treat cancer patients with progressive disease.
Advanced pre-clinical models of cancer
We are expanding and characterizing our PDX collections (CRC, neuroendocrine, hepatic tumors and peritoneal pseudomyxoma), and improving their potential to evaluate drug efficacy and metastasis by orthotopic injection and live imaging (TC, PET and Echography).
We are developing ambitious projects through the EuroPDX Consortium, a collaboration that VHIO co-founded incorporating the main reference groups working with PDX in Europe.
Tumor cell communication with its microenvironment plays an important role in tumor initiation and progression. Cancer cells hijack the tumor microenvironment ecosystem via paracrine signaling to promote a pro-oncogenic microenvironment that is crucial for the development of primary and metastatic tumors.
Our main aim is to characterize the mechanisms adopted by these cells to communicate amongst themselves as well as with their microenvironment during tumorigenesis. We aim to exploit these data to advance biomarker and drug target discovery.
Our team’s working hypothesis is that cellular signaling pathways undergo alterations during the tumorigenesis process and that these changes are translated into differential protein secretion, which can also potentially be used to identify secreted markers. Furthermore, some of the differentially regulated proteins could be direct extracellular messengers of intracellular signaling pathways contributing to fundamental stages implicated in cancer initiation and progression, therefore representing potential therapeutic targets.
The methodological focus of our group centers on profiling the secreted sub-proteome (‘secretome’) of cells by quantitative mass spectrometry. Most secreted proteins contain a signal peptide that directs their sorting to the extracellular space through the endoplasmic reticulum (ER)–Golgi secretory pathway. One of the most striking observations when secretome profiles are carefully produced and analyzed is that they contain hundreds of theoretical intracellular proteins.
Recent reports showing intracellular proteins with alternative extracellular functions suggest that new protein functions associated with alternative subcellular localizations could implicated in tumorigenesis. In line with this notion, our recent efforts within the context of therapeutics and tumor invasion have led us to hypothesize that the characterization of non-classical protein secretion could lead to the development of novel anti-cancer therapies.