Krisztian Homicsko

The consensus molecular subtypes of colorectal cancer

Colorectal cancer (CRC) is a frequently lethal disease with heterogeneous outcomes and drug responses. To resolve inconsistencies among the reported gene expression–based CRC classifications and facilitate clinical translation, we formed an international consortium dedicated to large-scale data sharing and analytics across expert groups. We show marked interconnectivity between six independent classification systems coalescing into four consensus molecular subtypes (CMSs) with distinguishing features: CMS1 (microsatellite instability immune, 14%), hypermutated, microsatellite unstable and strong immune activation; CMS2 (canonical, 37%), epithelial, marked WNT and MYC signaling activation; CMS3 (metabolic, 13%), epithelial and evident metabolic dysregulation; and CMS4 (mesenchymal, 23%), prominent transforming growth factor–β activation, stromal invasion and angiogenesis. Samples with mixed features (13%) possibly represent a transition phenotype or intratumoral heterogeneity. We consider the CMS groups the most robust classification system currently available for CRC—with clear biological interpretability—and the basis for future clinical stratification and subtype-based targeted interventions.

RAD001 (Everolimus) Improves the Efficacy of Replicating Adenoviruses that Target Colon Cancer

Selectively replicating adenoviruses have the potential to cure cancer but have shown little efficacy in clinical trials. We have tested the ability of the mTOR kinase inhibitor RAD001 (everolimus) to enhance the response of xenografts to an oncolytic adenovirus. The virus has Tcf sites inserted in the early viral promoters and replicates selectively in cells with activation of the Wnt signaling pathway. To enhance tumor cell infection, an integrin targeting peptide (CDCRGDCFC) was inserted into the fiber gene of the virus. RAD001 combines three useful properties: it inhibits tumor cell growth directly, blocks angiogenesis, and suppresses the immune response. RAD001 does not block viral protein expression, DNA replication, or cytopathic effect in tumor cells in vitro. After 6 weeks of daily RAD001 treatment, ongoing viral DNA replication could be detected in tumor xenografts, showing that RAD001 does not inhibit virus replication in vivo. I.v. injection of virus alone produced a small delay in xenograft growth, whereas combination therapy substantially prolonged the survival of the mice. We suggest that collapsing the tumor vasculature after the initial infection traps the virus and facilitates local spread within the tumor. Unlike conventional drugs, which require continued access to the tumor through the vascular system, oncolytic viruses are in principle less sensitive to late reductions in perfusion because they are produced locally within the tumor.

Tumor lymphangiogenesis promotes T cell infiltration and potentiates immunotherapy in melanoma

Tumor lymphangiogenesis, a driver of immunosuppression and metastasis, also potentiates immunotherapy. Unintentional immunotherapy inhibition Metastatic spread depends on lymphangiogenesis, and mediators of this pathway are targeted clinically for cancer treatment. Fankhauser et al. used mouse models of melanoma to show that blocking lymphangiogenesis actually disrupted recruitment of naïve T cells and subsequent antitumor immunity. Data from patients enrolled in clinical trials confirmed that indicators of lymphangiogenesis were associated with robust T cell responses. These findings have important implications for the use and predictions of response to immunotherapy. In melanoma, vascular endothelial growth factor–C (VEGF-C) expression and consequent lymphangiogenesis correlate with metastasis and poor prognosis. VEGF-C also promotes tumor immunosuppression, suggesting that lymphangiogenesis inhibitors may be clinically useful in combination with immunotherapy. We addressed this concept in mouse melanoma models with VEGF receptor–3 (VEGFR-3)–blocking antibodies and unexpectedly found that VEGF-C signaling enhanced rather than suppressed the response to immunotherapy. We further found that this effect was mediated by VEGF-C–induced CCL21 and tumor infiltration of naïve T cells before immunotherapy because CCR7 blockade reversed the potentiating effects of VEGF-C. In human metastatic melanoma, gene expression of VEGF-C strongly correlated with CCL21 and T cell inflammation, and serum VEGF-C concentrations associated with both T cell activation and expansion after peptide vaccination and clinical response to checkpoint blockade. We propose that VEGF-C potentiates immunotherapy by attracting naïve T cells, which are locally activated upon immunotherapy-induced tumor cell killing, and that serum VEGF-C may serve as a predictive biomarker for immunotherapy response.

Dramatic response of vemurafenib-induced cutaneous lesions upon switch to dual BRAF/MEK inhibition in a metastatic melanoma patient.

BRAF inhibitory therapy is the mainstream treatment for BRAF mutant advanced melanoma. However vemurafenib, a type I mutant BRAF V600 inhibitor, induces an array of proliferative skin disorders from keratosis pilaris-like and keratoacanthoma-like lesions to locally aggressive cutaneous squamous cell carcinoma (cuSCC). Dual BRAF/MEK inhibition is known to lower the incidence of such manifestations, but it is not known whether it can counteract established lesions. Here we show, for the first time, a dramatic response and a restitution ad integro upon dual inhibition of a widespread proliferative affection induced by BRAF monotherapy. A 75-year-old woman was diagnosed with a BRAF V600E mutated metastatic melanoma. Following dacarbazine (DTIC) and ipilimumab, the patient was started on 960 mg twice daily vemurafenib (Zelboraf), which resulted in complete response, but the patient also developed grade IV skin toxicity. Despite dose-reduction to 720 mg twice daily the side effects persisted. We hypothesized that a switch to double inhibition of the mitogen-activated protein kinase pathway with dabrafenib and trametinib could lead to improvement of the skin lesions, while preserving tumor control. The patient was closely followed for changes in skin lesions. We witnessed a rapid regression followed by complete disappearance of all side effects of vemurafenib except for grade I fatigue. The biopsied skin lesions show regression of established keratoacanthoma-like lesions with signs of apoptosis. Switching from the current standard of care vemurafenib therapy to the double BRAF/MEK inhibition in BRAF mutant melanoma patients results in rapid disappearance of established proliferative skin disorders.

Targeting Programmed Cell Death 1 in Ovarian Cancer

Reference EPFL-ARTICLE-216550doi:10.1200/Jco.2015.63.7785View record in Web of Science Record created on 2016-02-16, modified on 2016-08-09

T cell–induced CSF1 promotes melanoma resistance to PD1 blockade

T cells promote immunosuppression in melanoma through CSF1 induction and macrophage recruitment. CSF1 curbs immunotherapy efficacy in melanoma Although melanoma is one of the cancer types best targeted by checkpoint blockade, many patients are refractory to therapy. One likely culprit is the persistence of tumor-associated macrophages, which can be immunosuppressive. Neubert and colleagues examined patient samples and performed coculture experiments that implicated CD8+ T cell induction of tumor-derived CSF1, which could then promote immunosuppressive macrophages. Addition of CSF1 signaling blockade to anti-PD1 treatment improved responses in transplantable mouse melanoma models. These results uncover the biology of hurdles that still need to be overcome in immunotherapy, and also suggest a solution. Colony-stimulating factor 1 (CSF1) is a key regulator of monocyte/macrophage differentiation that sustains the protumorigenic functions of tumor-associated macrophages (TAMs). We show that CSF1 is expressed in human melanoma, and patients with metastatic melanoma have increased CSF1 in blood compared to healthy subjects. In tumors, CSF1 expression correlated with the abundance of CD8+ T cells and CD163+ TAMs. Human melanoma cell lines consistently produced CSF1 after exposure to melanoma-specific CD8+ T cells or T cell–derived cytokines in vitro, reflecting a broadly conserved mechanism of CSF1 induction by activated CD8+ T cells. Mining of publicly available transcriptomic data sets suggested co-enrichment of CD8+ T cells with CSF1 or various TAM-specific markers in human melanoma, which was associated with nonresponsiveness to programmed cell death protein 1 (PD1) checkpoint blockade in a smaller patient cohort. Combination of anti-PD1 and anti–CSF1 receptor (CSF1R) antibodies induced the regression of BRAFV600E-driven, transplant mouse melanomas, a result that was dependent on the effective elimination of TAMs. Collectively, these data implicate CSF1 induction as a CD8+ T cell–dependent adaptive resistance mechanism and show that simultaneous CSF1R targeting may be beneficial in melanomas refractory to immune checkpoint blockade and, possibly, other T cell–based therapies.

Combine and Conquer: Double CTLA-4 and PD-1 Blockade Combined with Whole Tumor Antigen Vaccine Cooperate to Eradicate Tumors

Visit the Cancer Research 75th Anniversary [timeline][1]. See related article by Duraiswamy et al., [Cancer Res 2013;73:3591–603][2] . Cancers hijack the normal regulatory pathways of normal inflammatory reactions. Dysregulation of fundamental immune checkpoints is present virtually in all

Serum protein predictors of long term survival from combined ipilimumab and nivolumab therapy in metastatic melanoma patients.

e21513Background: Combined ipilimumab (IPI) and nivolumab (NIVO) is the most advanced immune therapy for metastatic melanoma patients. However, high response rates can be achieved at the price of i...

Molecular Classification of Colon Cancer: Perspectives for Personalized Adjuvant Therapy

Although surgery for early-stage colorectal cancer (CRC) is often curative, many patients require adjuvant chemotherapy to treat micrometastatic disease and to reduce the risk of recurrence. Targeted therapies have improved outcomes for patients with metastatic disease but, in the adjuvant setting, options are limited to a fluoropyrimidine alone or in combination with oxaliplatin. There is an unmet need for new predictive biomarkers to personalise treatment in the adjuvant setting. With goals to address this gap and to better characterise disease heterogeneity, several groups including our own have identified three to six gene expression subtypes that were later consolidated into consensus molecular subtypes as part of the Colorectal Cancer Subtyping Consortium (CRCSC) effort. In this review, we discuss the differences and similarities between these subtypes and their potential prognostic and predictive values. We question whether a personalised treatment approach based on CRC subtypes might be beneficial in the adjuvant setting to improve treatment options and ultimately patient outcomes.

Abstract 603: Consensus molecular subtyping through a community of experts advances unsupervised gene expression-based disease classification and facilitates clinical translation

Background: Gene expression-based subtyping is widely accepted as a relevant source of disease stratification. Despite the widespread use, its translational and clinical utility is hampered by discrepant results, likely related to differences in data processing and algorithms applied to diverse patient cohorts, sample preparation methods, and gene expression platforms. In the absence of a clear methodological gold standard to perform such analyses, a more general framework that integrates and compares multiple strategies is needed to define common disease patterns in a principled, unbiased manner. Methods: We formed a consortium of 6 independent experts groups - each with a previously published CRC classifier, ranging from 3 to 6 subtypes - to understand similarities and differences of their subtyping systems. Sage Bionetworks functioned as neutral party to aggregate public and proprietary data (Synapse platform) and perform meta-analysis. Each group applied its CRC subtyping signature to the collection of data sets with gene expression (n = 4,151, predominantly stage II and III). Using the resulting subtype labels, we developed a network-based model and applied a Markov cluster algorithm to detect robust network substructures that would indicate recurring subtype patterns and therefore a consensus subtyping system. Correlative analyses using clinico-pathological, genomic and epigenomic features was performed to robustly characterize the identified subtypes. Results: This analytical framework revealed significant interconnectivity between the six independent classification systems, leading to the identification of four biologically distinct consensus molecular subtypes (CMS) enriched for key pathway traits: CMS1 (MSI Immune), hypermutated, microsatellite unstable, with strong immune activation; CMS2 (Canonical), epithelial, chromosomally unstable, with marked WNT and MYC signaling activation; CMS3 (Metabolic), epithelial, with evident metabolic dysregulation; and CMS4 (Mesenchymal), prominent TGFβ activation, angiogenesis, stromal invasion. Patients diagnosed with MSI Immune tumors had worse survival after relapse and those with mesenchymal tumors had increased risk of metastasis and worse overall survival. Discussion: We describe a novel methodological paradigm for deriving benchmarks of disease subtyping. Our work represents the first example of a community of experts identifying and advocating for a single reproducible model for cancer subtyping, effectively unifying previous classifiers. In the CRC domain, the uniformity afforded by this new classification system and its application to a large data set revealed important subtype-specific biological associations that were previously unnoticed or marginally significant, supporting a new taxonomy of the disease. Citation Format: Justin Guinney, Rodrigo Dienstmann, Xin Wang, Aurelien de Reynies, Andreas Schlicker, Charlotte Soneson, Laetitia Marisa, Paul Roepman, Gift Nyamundanda, Paolo Angelino, Brian Bot, Jeffrey S. Morris, Iris Simon, Sarah Gerster, Evelyn Fessler, Felipe de Sousa e Melo, Edoardo Missiaglia, Hena Ramay, David Barras, Krisztian Homicsko, Dipen Maru, Ganiraju Manyam, Bradley Broom, Valerie Boige, Ted Laderas, Ramon Salazar, Joe W. Gray, Josep Tabernero, Rene Bernards, Stephen Friend, Pierre Laurent-Puig, Jan P. Medema, Anguraj Sadanandam, Lodewyk Wessels, Mauro Delorenzi, Scott Kopetz, Louis Vermeulen, Sabine Tejpar. Consensus molecular subtyping through a community of experts advances unsupervised gene expression-based disease classification and facilitates clinical translation. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 603. doi:10.1158/1538-7445.AM2015-603