EGFR Mutant Structural Database: computationally predicted 3D structures and the corresponding binding free energies with gefitinib and erlotinib

published_or_final_versio

Identification of immune-related gene signatures to evaluate immunotherapeutic response in cancer patients using exploratory subgroup discovery

Phenotypic and genotypic heterogeneity are characteristic features of cancer patients. To tackle patients[trademark] heterogeneity, immune checkpoint inhibitors (ICIs) represent one of the most promising therapeutic approaches. However, approximately 50 percent of cancer patients that are eligible for treatment with ICIs will not respond well, which motivates the exploration of immunotherapy in combination with either targeted treatments or chemotherapy. Over the years, multiple patient stratification techniques have been developed to identify homogenous patient subgroups, although, matching patient subgroup to treatment option that can improve patients[trademark] health outcome remains a challenging task. We extend our exploratory subgroup discovery algorithm to identify patient subpopulations that can potentially benefit from immuno-targeted combination therapies or chemoimmunotherapy in five cancer types: Head and Neck Squamous Carcinoma (HNSC), Lung Adenocarcinoma (LUAD), Lung Squamous Carcinoma (LUSC), Skin Cutaneous Melanoma (SKCM) and Triple-Negative Breast Cancer (TNBC). We employ various regression models to identify immune-related gene signatures and drug targets that increase the likelihood of partial remission on combination therapies, either immunotargeted regimen or chemoimmunotherapy. Moreover, our pipelines can pinpoint adverse drug effects associated with predicted drug combinations. In addition, we uncovered distinct immune cell populations (T-cells, B-cells, Myeloid, NK-cells) for TNBC patients that differentiate patients with partial remission from patients with progressive disease after chemoimmunotherapy. Finally, we incorporate our methodological developments on Mutational Forks Formalism that enable an assessment of patient-specific flow by leveraging information from multiple single-nucleotide alterations to adjust the transitional likelihoods that are solely based on the canonical view of a disease. Our suit of methods can help to better select responders for combination therapies and improve health outcome for cancer patients with limited treatment options.Includes bibliographical references

The Era of Radiogenomics in Precision Medicine: An Emerging Approach to Support Diagnosis, Treatment Decisions, and Prognostication in Oncology

With the rapid development of new technologies, including artificial intelligence and genome sequencing, radiogenomics has emerged as a state-of-the-art science in the field of individualized medicine. Radiogenomics combines a large volume of quantitative data extracted from medical images with individual genomic phenotypes and constructs a prediction model through deep learning to stratify patients, guide therapeutic strategies, and evaluate clinical outcomes. Recent studies of various types of tumors demonstrate the predictive value of radiogenomics. And some of the issues in the radiogenomic analysis and the solutions from prior works are presented. Although the workflow criteria and international agreed guidelines for statistical methods need to be confirmed, radiogenomics represents a repeatable and cost-effective approach for the detection of continuous changes and is a promising surrogate for invasive interventions. Therefore, radiogenomics could facilitate computer-aided diagnosis, treatment, and prediction of the prognosis in patients with tumors in the routine clinical setting. Here, we summarize the integrated process of radiogenomics and introduce the crucial strategies and statistical algorithms involved in current studies

MAPK-pathway inhibition mediates inflammatory reprogramming and sensitizes tumors to targeted activation of innate immunity sensor RIG-I.

Kinase inhibitors suppress the growth of oncogene driven cancer but also enforce the selection of treatment resistant cells that are thought to promote tumor relapse in patients. Here, we report transcriptomic and functional genomics analyses of cells and tumors within their microenvironment across different genotypes that persist during kinase inhibitor treatment. We uncover a conserved, MAPK/IRF1-mediated inflammatory response in tumors that undergo stemness- and senescence-associated reprogramming. In these tumor cells, activation of the innate immunity sensor RIG-I via its agonist IVT4, triggers an interferon and a pro-apoptotic response that synergize with concomitant kinase inhibition. In humanized lung cancer xenografts and a syngeneic Egfr-driven lung cancer model these effects translate into reduction of exhausted CD8+ T cells and robust tumor shrinkage. Overall, the mechanistic understanding of MAPK/IRF1-mediated intratumoral reprogramming may ultimately prolong the efficacy of targeted drugs in genetically defined cancer patients

MAPK-pathway inhibition mediates inflammatory reprogramming and sensitizes tumors to targeted activation of innate immunity sensor RIG-I

Kinase inhibitors suppress the growth of oncogene driven cancer but also enforce the selection of treatment resistant cells that are thought to promote tumor relapse in patients. Here, we report transcriptomic and functional genomics analyses of cells and tumors within their microenvironment across different genotypes that persist during kinase inhibitor treatment. We uncover a conserved, MAPK/IRF1-mediated inflammatory response in tumors that undergo stemness- and senescence-associated reprogramming. In these tumor cells, activation of the innate immunity sensor RIG-I via its agonist IVT4, triggers an interferon and a pro-apoptotic response that synergize with concomitant kinase inhibition. In humanized lung cancer xenografts and a syngeneic Egfr-driven lung cancer model these effects translate into reduction of exhausted CD8(+) T cells and robust tumor shrinkage. Overall, the mechanistic understanding of MAPK/IRF1-mediated intratumoral reprogramming may ultimately prolong the efficacy of targeted drugs in genetically defined cancer patients

Development of targeted therapeutic strategies for metastatic lung cancer

El cáncer de pulmón es el cáncer que se diagnostica con más frecuencia y la principal causa de muerte por cáncer en todo el mundo. Es importante destacar que alrededor del 75% de los pacientes son diagnosticados en estadios metastásicos avanzados, cuando la cirugía ya no es posible, lo que supone una caída dramática de la tasa de supervivencia a 5 años al 6%. El principal objetivo de esta tesis es definir nuevas estrategias terapéuticas inspiradas en la biología para pacientes con cáncer de pulmón metastásico. Para ello, se exploraron diferentes estrategias terapéuticas inspiradas en la biología del tumor, una de ellas proviene de los exosomas tumorales y la otra de las células que diseminan desde el tumor primario para formar las metástasis

Modulation of Immune Checkpoints by Tumour Extracellular Vesicles

Melanoma extracellular vesicles (EVs) are endowed with pro-tumourigenic features and can condition immunity, favouring immune escape. Immune checkpoints (IC), expressed by immune and cancerous cells, regulate immune responses. BRAF and MEK inhibitors, a standard treatment for BRAF-mutated melanoma patients, can condition tumour cell IC expression. I investigated the IC expression in melanoma specimens, cell lines and EVs, in association with drug resistance, a common event during treatment, to uncover potential targets for immunotherapy. IC were studied in melanoma and immune cells interacting with melanoma EVs from drug sensitive and resistant cell line pairs with CD81GFP-tagged EVs. IC were determined by qRT-PCR, western blot and latex beads flow cytometry on cell line and plasma EVs, isolated by ultracentrifugation and commercial kits. EVs were measured by Nanoparticle Tracking Analysis in whole plasma and after isolation from cell lines. In melanoma lesions CD155, HVEM and GAL9 transcripts displayed a modulation in association with drug resistance. In cell lines, PDL1, PDL2 and CD155 increased, while GAL9 and HVEM decreased with resistance. PDL1, PDL2 and GAL9 modulations were influenced by IFNγ and regulated by CCL2 and specific miRNAs. EVs carried IC and reflected the IC expression pattern of originating melanoma cells. EVs from resistant melanoma cells transferred drug resistance-associated features to sensitive counterparts; while EVs from both, sensitive and resistant melanoma cells induced in monocytes a myeloid-derived suppressor cell phenotype accompanied with the increase of PDL1 and HVEM expression. During therapy patients’ plasma EVs displayed modulations in number and size. Their IC, as protein and transcripts, associated with response to treatment. BRAF and MEK inhibitors modulate melanoma IC expression and cognate EVs reflect originating cells, potentially representing surrogates of melanoma resistance status. The effects of IC-carrying EVs on interacting cells suggest their involvement in tumour immune escape, and their modulations may reflect immune activation during therapy

Exploiting tumour cell dependency on pro-survival BCL2 proteins with BH3 mimetics

The RAS-RAF-MEK1/2-ERK1/2 signalling pathway is one of the most frequently deregulated pathways in human cancer, with mutations in KRAS and BRAF commonly occurring in cancers of the pancreas, skin, and colon, among others. Indeed, BRAF and MEK1/2 inhibitors are approved for the treatment of BRAF-mutant malignant melanoma and are improving patient outcomes. However, the development of acquired resistance to these agents is inevitable, highlighting the need for strategies to enhance their primary efficacy in the clinic. Inhibition of ERK1/2 signalling increases the abundance of pro-apoptotic BH3-only proteins such as BIM and BMF. However, despite this, responses to ERK1/2 pathway inhibitors are typically cytostatic, reflecting the residual activity of pro-survival BCL2 proteins. In this thesis, we determined that melanoma cells had a high MCL1:BCL-XL ratio, and as a result were biased towards MCL1 due to low expression of BCL-XL. Consequently, melanoma cells were uniquely dependent on MCL1 to restrain the pro-apoptotic BH3-only proteins induced by ERK1/2 pathway inhibition. The BH3 mimetic AZD5991, a selective MCL1 inhibitor, combined with ERK1/2 pathway inhibitors to drive striking synergistic apoptosis in vitro and robust tumour regressions in vivo. CRISPR/Cas9 gene editing of BIM and BMF in two melanoma cell lines showed that the cell death was substantially BIM/BMF-dependent, and required BAK and BAX to execute. In contrast to melanoma, colorectal cancer (CRC) cells exhibit increased expression of BCL-XL, with a low MCL1:BCL-XL ratio. The combination of MEK1/2 inhibitors with pan-BH3 mimetics that target BCL2, BCL-w and BCL-XL (such as ABT-263) has previously been explored in CRC cells. However, results in this thesis demonstrated that BCL-XL was the critical pro-survival protein in CRC cells responsible for buffering the pro-apoptotic effects of ERK1/2 pathway inhibition. CRC cell lines were completely refractory to BCL2 inhibition when combined with the MEK1/2 inhibitor selumetinib. MEK1/2 inhibitors primed CRC cells for rapid BAX-dependent apoptosis upon BCL-XL antagonism. BH3 mimetics combined with the ERK1/2 inhibitors SCH772984 or AZ6197 in a model of acquired resistance to BRAF and/or MEK1/2 inhibitors in A375 melanoma cells to drive striking apoptosis in vitro and in vivo. Combined BRAF and MCL1 inhibition delayed the onset of acquired resistance to BRAF inhibitor monotherapy in melanoma cells. In SW620 (CRC) cells, combined MEK1/2 and BCL-XL inhibition caused substantial cell death and did not result in the outgrowth of resistant clones; this combination possibly induced senescence in the residual “persister” cells. Finally, in addition to apoptosis, an alternate temporally-distinct cell death modality occurred in CRC cells treated with combined MEK1/2 and BCL-XL inhibition, and this was amplified when caspases were inhibited. This caspase-independent cell death was subsequently determined to be RIPK1-dependent necroptosis, which was reversed by inhibition of RIPK1 by necrostatin-1. BCL-XL may directly inhibit necroptosis induction at the level of the necrosome through the binding of the effector protein MLKL, which was displaced upon BCL-XL inhibition. BH3 mimetics are effective as single agents for the treatment of haematological malignancies, but their application in solid tumours needs to be refined. The results presented here demonstrate that BH3 mimetics harness the apoptotic potential of ERK1/2 pathway inhibitors to drive striking, synergistic cell death in melanoma and CRC cells. The ratio of pro-survival proteins could represent a potential clinical biomarker, and be informative in the clinic to drive BH3 mimetic combination choices.Cambridge International Trust scholarship AstraZenec