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1.
Int J Mol Sci ; 25(3)2024 Feb 01.
Article in English | MEDLINE | ID: mdl-38339019

ABSTRACT

The advent of immune checkpoint inhibitors (ICIs) has represented a breakthrough in the treatment of many cancers, although a high number of patients fail to respond to ICIs, which is partially due to the ability of tumor cells to evade immune system surveillance. Non-coding microRNAs (miRNAs) have been shown to modulate the immune evasion of tumor cells, and there is thus growing interest in elucidating whether these miRNAs could be targetable or proposed as novel biomarkers for prognosis and treatment response to ICIs. We therefore performed an extensive literature analysis to evaluate the clinical utility of miRNAs with a confirmed direct relationship with treatment response to ICIs. As a result of this systematic review, we have stratified the miRNA landscape into (i) miRNAs whose levels directly modulate response to ICIs, (ii) miRNAs whose expression is modulated by ICIs, and (iii) miRNAs that directly elicit toxic effects or participate in immune-related adverse events (irAEs) caused by ICIs.


Subject(s)
MicroRNAs , Neoplasms , Humans , MicroRNAs/genetics , Immune Checkpoint Inhibitors/pharmacology , Immune Checkpoint Inhibitors/therapeutic use , Immune Evasion , Immunologic Surveillance , Neoplasms/drug therapy , Neoplasms/genetics
2.
Lab Chip ; 24(7): 2025-2038, 2024 Mar 26.
Article in English | MEDLINE | ID: mdl-38410967

ABSTRACT

Patient-derived organoids (PDOs) serve as invaluable 3D tumor models, retaining the histological complexity and genetic heterogeneity found in primary tumors. However, the limitation of small sample volumes and the lack of tailored platforms have hindered the research using PDOs. Within the tumor microenvironment, cancer-associated fibroblasts play a pivotal role in influencing drug sensitivity. In this study, we introduce an agarose microwell platform designed for PDO-based tumor and tumor microenvironment models, enabling rapid drug screening and resistance studies with small sample volumes. These microwells, constructed using 3D printing molds, feature a U-shaped bottom and 200 µm diameter. We successfully generated co-culture spheroids of non-small cell lung carcinoma (NSCLC) cells, including NCI-H358 or A549, and NSCLC PDOs F231 or F671 with fibroblast cell line, WI-38. Our results demonstrate the production of uniformly-sized spheroids (coefficient of variation <30%), high viability (>80% after 1 week), and fibroblast-induced drug resistance. The PDOs maintained their viability (>81% after 2 weeks) and continued to proliferate. Notably, when exposed to adagrasib, a KRASG12C inhibitor, we observed reduced cytotoxicity in KRASG12C-mutant spheroids when co-cultured with fibroblasts or their supernatant. The fibroblast supernatant sustained proliferative signals in tumor models. Taking into account the physical features, viability, and drug resistance acquired through supernatants from the fibroblasts, our platform emerges as a suitable platform for in vitro tumor modeling and the evaluation of drug efficacy using patient-derived tissues.


Subject(s)
Carcinoma, Non-Small-Cell Lung , Lung Neoplasms , Humans , Carcinoma, Non-Small-Cell Lung/drug therapy , Carcinoma, Non-Small-Cell Lung/metabolism , Sepharose , Proto-Oncogene Proteins p21(ras) , Lung Neoplasms/pathology , Drug Resistance , Organoids/metabolism , Fibroblasts/metabolism , Tumor Microenvironment
3.
Int J Mol Sci ; 24(17)2023 Aug 31.
Article in English | MEDLINE | ID: mdl-37686342

ABSTRACT

Activation of the aryl hydrocarbon receptor (AhR) has been shown to be important in physiological processes other than detoxification, including vascular homeostasis. Although AhR is highly expressed in the endothelium, its function has been poorly studied. This systematic review aims to summarise current knowledge on the AhR role in the endothelium and its cardiovascular implications. We focus on endogenous AhR agonists, such as some uremic toxins and other agonists unrelated to environmental pollutants, as well as studies using AhR knockout models. We conclude that AhR activation leads to vascular oxidative stress and endothelial dysfunction and that blocking AhR signalling could provide a new target for the treatment of vascular disorders such as cardiovascular complications in patients with chronic kidney disease or pulmonary arterial hypertension.


Subject(s)
Environmental Pollutants , Vascular Diseases , Humans , Receptors, Aryl Hydrocarbon/genetics , Familial Primary Pulmonary Hypertension , Endothelium
4.
Nurs Open ; 10(8): 5211-5224, 2023 08.
Article in English | MEDLINE | ID: mdl-37084014

ABSTRACT

AIMS AND OBJECTIVES: To assess the effects of intensive follow-up by primary care nurses on cardiovascular disease self-management and compliance behaviours after myocardial infarction. BACKGROUND: Although cardiovascular disease prevention and cardiac rehabilitation take place in hospital settings, a nurse-led approach is necessary in primary care during the first few months after a myocardial infarction. Therefore, it is important to assess self-management of cardiovascular disease and levels of compliance with the prescribed diet, physical activity, and medication. DESIGN: The study used a multicentre, quasi-experimental, pre-post design without a control group. METHODS: Patients with acute coronary syndrome from 40 healthcare facilities were included in the study. A total of 212 patients participated in a programme including 11 interventions during the first 12-18 months after myocardial infarction. The following Nursing Outcomes Classification (NOC) outcomes were assessed at baseline and at the end of the intervention: Self-management: Cardiac Disease (1617) and Compliance Behaviour: Prescribed Diet (1622), Compliance Behaviour: Prescribed Activity (1632), and Compliance Behaviour: Prescribed Medication (1623). Marjory Gordon's functional health patterns and a self-care notebook were used in each intervention. Pre-post intervention means were compared using Student's t-tests for related samples. The results of the study are reported in compliance with the TREND Statement. RESULTS: A total of 132 patients completed the intervention. The indicators for each NOC outcome and the variations in scores before and after the intensive follow-up showed a statistically significant improvement (p-value = 0.000). Compliance Behaviour: Prescribed Diet (pre = 3.7; post = 4.1); Compliance Behaviour: Prescribed Activity (pre = 3.9; post = 4.3); Compliance Behaviour: Prescribed Medication (pre = 3.9; post = 4.7). CONCLUSION: Intensive, immediate follow-up after myocardial infarction improves compliance behaviours and self-management of heart disease. A combined self-care and family care approach should be encouraged to empower post-myocardial infarction patients. To facilitate patients' self-efficacy, the use of health education tools such as a cardiovascular self-care notebook can also be helpful. RELEVANCE TO CLINICAL PRACTICE: This study highlights the benefits of intensive, protocolised, comprehensive patient follow-up in primary care during the first few months after an acute myocardial infarction (AMI). Primary care nurses train patients in cardiovascular self-care. PATIENT OR PUBLIC CONTRIBUTION: Patients were not involved in either the design or the carrying out of the study. However, at the end of the study, they participated in an evaluation process about the utility of the research study and their satisfaction with it. This process was carried out using an ad hoc survey consisting of 10 questions assessing the nursing care and follow-up inputs that were received.


Subject(s)
Heart Diseases , Myocardial Infarction , Self-Management , Humans , Follow-Up Studies , Nurse's Role , Myocardial Infarction/rehabilitation , Primary Health Care
5.
Genome Biol ; 23(1): 252, 2022 12 09.
Article in English | MEDLINE | ID: mdl-36494864

ABSTRACT

BACKGROUND: JUNB transcription factor contributes to the formation of the ubiquitous transcriptional complex AP-1 involved in the control of many physiological and disease-associated functions. The roles of JUNB in the control of cell division and tumorigenic processes are acknowledged but still unclear. RESULTS: Here, we report the results of combined transcriptomic, genomic, and functional studies showing that JUNB promotes cell cycle progression via induction of cyclin E1 and repression of transforming growth factor (TGF)-ß2 genes. We also show that high levels of JUNB switch the response of TGF-ß2 stimulation from an antiproliferative to a pro-invasive one, induce endogenous TGF-ß2 production by promoting TGF-ß2 mRNA translation, and enhance tumor growth and metastasis in mice. Moreover, tumor genomic data indicate that JUNB amplification associates with poor prognosis in breast and ovarian cancer patients. CONCLUSIONS: Our results reveal novel functions for JUNB in cell proliferation and tumor aggressiveness through regulation of cyclin E1 and TGF-ß2 expression, which might be exploited for cancer prognosis and therapy.


Subject(s)
Neoplasms , Transforming Growth Factor beta2 , Mice , Animals , Transforming Growth Factor beta2/genetics , Transcription Factor AP-1 , Cell Division , Cell Cycle Checkpoints , Carcinogenesis , Transcription Factors/genetics
6.
Int J Mol Sci ; 23(13)2022 Jun 21.
Article in English | MEDLINE | ID: mdl-35805895

ABSTRACT

Pulmonary fibrosis (PF) is characterized by aberrant extracellular matrix (ECM) deposition, activation of fibroblasts to myofibroblasts and parenchymal disorganization, which have an impact on the biomechanical traits of the lung. In this context, the balance between matrix metalloproteinases (MMPs) and their tissue inhibitors of metalloproteinases (TIMPs) is lost. Interestingly, several MMPs are overexpressed during PF and exhibit a clear profibrotic role (MMP-2, -3, -8, -11, -12 and -28), but a few are antifibrotic (MMP-19), have both profibrotic and antifibrotic capacity (MMP7), or execute an unclear (MMP-1, -9, -10, -13, -14) or unknown function. TIMPs are also overexpressed in PF; hence, the modulation and function of MMPs and TIMP are more complex than expected. EMMPRIN/CD147 (also known as basigin) is a transmembrane glycoprotein from the immunoglobulin superfamily (IgSF) that was first described to induce MMP activity in fibroblasts. It also interacts with other molecules to execute non-related MMP aactions well-described in cancer progression, migration, and invasion. Emerging evidence strongly suggests that CD147 plays a key role in PF not only by MMP induction but also by stimulating fibroblast myofibroblast transition. In this review, we study the structure and function of MMPs, TIMPs and CD147 in PF and their complex crosstalk between them.


Subject(s)
Basigin , Pulmonary Fibrosis , Extracellular Matrix/pathology , Humans , Matrix Metalloproteinases , Pulmonary Fibrosis/drug therapy , Pulmonary Fibrosis/pathology , Tissue Inhibitor of Metalloproteinases
7.
Biomedicines ; 10(5)2022 May 19.
Article in English | MEDLINE | ID: mdl-35625914

ABSTRACT

Patients with high cholesterol and glucose levels are at high risk for cardiovascular disease. The Sterol Regulatory Element Binding Protein (SREBP) system regulates genes involved in lipid, cholesterol and glucose pathways. Autosomal Dominant Hypercholesterolemias (ADHs) are a group of diseases with increased cholesterol levels. They affect 1 out of every 500 individuals. About 20-30% of patients do not present any mutation in the known genes (LDLR, APOB and PCSK9). ADHs constitute a good model to identify the genes involved in the alteration of lipid levels or possible therapeutic targets. In this paper, we studied whether a mutation in the SREBP system could be responsible for ADH and other metabolic alterations present in these patients. Forty-one ADH patients without mutations in the main responsible genes were screened by direct sequencing of SREBP system genes. A luciferase reporter assay of the found mutation and an oral glucose tolerance test in carriers and non-carriers were performed. We found a novel mutation in the SREBF2 gene that increases transcription levels and cosegregates with hypercholesterolemia, and we found increased glucose levels in one family. SREBP2 is known to be involved in cholesterol synthesis, plasma levels and glucose metabolism in humans. The found mutation may involve the SREBF2 gene in hypercholesterolemia combined with hyperglycemia.

8.
Article in English, Spanish | MEDLINE | ID: mdl-34492375

ABSTRACT

INTRODUCTION: Mental health (MH) care has important challenges, especially in the field of humanization. Our objectives were to identify the humanization measures in MH plans of the Spanish autonomous communities (CCAA) and the priorities to be developed in this area. MATERIAL AND METHODS: A large and multidisciplinary group of people involved in MH care participated in a consensus, according to a modified Delphi method, based on «design thinking¼, in three phases: (1) identification of humanization measures in MH plans of CCAA; (2) analysis of the implementation of these measures; and (3) identification of humanization priorities in MH. RESULTS: Fourteen of the 17 CCAA have current MH plans. They contained four types of humanization measures: (1) improvement of the quality of care; (2) promotion of user participation; (3) campaigns against stigma and discrimination; (4) caring for especially vulnerable people. Implementation of measures ranged from 6.3% (i.e.: specific budget) to 100%, with an average of 64.1%. We identified priority issues, operationalized in 5 proposals: (1) information campaigns; (2) multidisciplinary meeting forums; (3) platforms of support entities; (4) strategies on MH education; (5) humanization in study plans. CONCLUSIONS: Some MH plans include humanization among their objectives, but partially. The implementation of humanization proposals such as those identified in this study is essential to achieve a high-quality MH care.

9.
Cancers (Basel) ; 12(12)2020 Dec 10.
Article in English | MEDLINE | ID: mdl-33321963

ABSTRACT

Mammalian SWI/SNF (SWitch/Sucrose Non-Fermentable) complexes are ATP-dependent chromatin remodelers whose subunits have emerged among the most frequently mutated genes in cancer. Studying SWI/SNF function in cancer cell line models has unveiled vulnerabilities in SWI/SNF-mutant tumors that can lead to the discovery of new therapeutic drugs. However, choosing an appropriate cancer cell line model for SWI/SNF functional studies can be challenging because SWI/SNF subunits are frequently altered in cancer by various mechanisms, including genetic alterations and post-transcriptional mechanisms. In this work, we combined genomic, transcriptomic, and proteomic approaches to study the mutational status and the expression levels of the SWI/SNF subunits in a panel of 38 lung adenocarcinoma (LUAD) cell lines. We found that the SWI/SNF complex was mutated in more than 76% of our LUAD cell lines and there was a high variability in the expression of the different SWI/SNF subunits. These results underline the importance of the SWI/SNF complex as a tumor suppressor in LUAD and the difficulties in defining altered and unaltered cell models for the SWI/SNF complex. These findings will assist researchers in choosing the most suitable cellular models for their studies of SWI/SNF to bring all of its potential to the development of novel therapeutic applications.

10.
Nutrients ; 12(10)2020 Oct 14.
Article in English | MEDLINE | ID: mdl-33066385

ABSTRACT

Macronutrients represent risk factors for hyperlipidemia or diabetes. Lipid alterations and type 2 diabetes mellitus are global health problems. Overexpression of sterol regulatory element-binding factor (Srebf2) in transgenic animals is linked to elevated cholesterol levels and diabetes development. We investigated the impact of increased Srebf2 locus expression and the effects of control and high-fat, high-sucrose (HFHS) diets on body weight, glucose and lipid metabolisms in transgenic mice (S-mice). Wild type (WT) and S-mice were fed with both diets for 16 weeks. Plasma glucose, insulin and lipids were assessed (n = 25). Immunostainings were performed in liver, pancreas and fat (N = 10). Expression of Ldlr and Hmgcr in liver was performed by RT-PCR (N = 8). Control diet: S-mice showed reduced weight, insulin, total and HDL cholesterol and triglycerides (TG). HFHS diet widened differences in weight, total and HDL cholesterol, insulin and HOMA index but increased TG in S-mice. In S-mice, adipocyte size was lower while HFHS diet produced lower increase, pancreatic ß-cell mass was lower with both diets and Srebf2, Ldlr and Hmgcr mRNA levels were higher while HFHS diet produced a rise in Srebf2 and Hmgcr levels. Srebf2 complete gene overexpression seems to have beneficial effects on metabolic parameters and to protect against HFHS diet effects.


Subject(s)
Blood Glucose , Cholesterol/blood , Diet, High-Fat/adverse effects , Dietary Sucrose/adverse effects , Gene Expression , Sterol Regulatory Element Binding Protein 2/genetics , Sterol Regulatory Element Binding Protein 2/metabolism , Animals , Body Weight , Diabetes Mellitus, Type 2/etiology , Diabetes Mellitus, Type 2/metabolism , Female , Insulin/blood , Lipid Metabolism , Male , Mice, Inbred C57BL , Mice, Transgenic
11.
Cancer Res ; 80(19): 4224-4232, 2020 10 01.
Article in English | MEDLINE | ID: mdl-32747363

ABSTRACT

Progression on therapy in non-small cell lung carcinoma (NSCLC) is often evaluated radiographically, however, image-based evaluation of said therapies may not distinguish disease progression due to intrinsic tumor drug resistance or inefficient tumor penetration of the drugs. Here we report that the inhibition of mutated EGFR promotes the secretion of a potent vasoconstrictor, endothelin-1 (EDN1), which continues to increase as the cells become resistant with a mesenchymal phenotype. As EDN1 and its receptor (EDNR) is linked to cancer progression, EDNR-antagonists have been evaluated in several clinical trials with disappointing results. These trials were based on a hypothesis that the EDN1-EDNR axis activates the MAPK-ERK signaling pathway that is vital to the cancer cell survival; the trials were not designed to evaluate the impact of tumor-derived EDN1 in modifying tumor microenvironment or contributing to drug resistance. Ectopic overexpression of EDN1 in cells with mutated EGFR resulted in poor drug delivery and retarded growth in vivo but not in vitro. Intratumoral injection of recombinant EDN significantly reduced blood flow and subsequent gefitinib accumulation in xenografted EGFR-mutant tumors. Furthermore, depletion of EDN1 or the use of endothelin receptor inhibitors bosentan and ambrisentan improved drug penetration into tumors and restored blood flow in tumor-associated vasculature. Correlatively, these results describe a simplistic endogenous yet previously unrealized resistance mechanism inherent to a subset of EGFR-mutant NSCLC to attenuate tyrosine kinase inhibitor delivery to the tumors by limiting drug-carrying blood flow and the drug concentration in tumors. SIGNIFICANCE: EDNR antagonists can be repurposed to improve drug delivery in VEGFA-secreting tumors, which normally respond to TKI treatment by secreting EDN1, promoting vasoconstriction, and limiting blood and drug delivery.


Subject(s)
Carcinoma, Non-Small-Cell Lung/drug therapy , Drug Resistance, Neoplasm/genetics , Endothelin-1/metabolism , Lung Neoplasms/drug therapy , Animals , Antineoplastic Agents/pharmacology , Biological Availability , Carcinoma, Non-Small-Cell Lung/genetics , Cell Line, Tumor , Drug Resistance, Neoplasm/drug effects , Endothelin-1/genetics , ErbB Receptors/genetics , Erlotinib Hydrochloride/pharmacology , Gefitinib/pharmacokinetics , Humans , Lung Neoplasms/genetics , Mice , Mutation , Protein Kinase Inhibitors/pharmacology , Vascular Endothelial Growth Factor A/metabolism , Vasoconstriction/drug effects , Vasoconstriction/physiology , Xenograft Model Antitumor Assays
12.
PLoS One ; 15(2): e0228909, 2020.
Article in English | MEDLINE | ID: mdl-32049991

ABSTRACT

BACKGROUND/OBJECTIVE: Patients with non-small cell lung cancer (NSCLC) develop resistance to antitumor agents by mechanisms that involve the epithelial-to-mesenchymal transition (EMT). This necessitates the development of new complementary drugs, e.g., cannabinoid receptors (CB1 and CB2) agonists including tetrahydrocannabinol (THC) and cannabidiol (CBD). The combined use of THC and CBD confers greater benefits, as CBD enhances the effects of THC and reduces its psychotropic activity. We assessed the relationship between the expression levels of CB1 and CB2 to the clinical features of a cohort of patients with NSCLC, and the effect of THC and CBD (individually and in combination) on proliferation, EMT and migration in vitro in A549, H460 and H1792 lung cancer cell lines. METHODS: Expression levels of CB1, CB2, EGFR, CDH1, CDH2 and VIM were evaluated by quantitative reverse transcription-polymerase chain reaction. THC and CBD (10-100 µM), individually or in combination (1:1 ratio), were used for in vitro assays. Cell proliferation was determined by BrdU incorporation assay. Morphological changes in the cells were visualized by phase-contrast and fluorescence microscopy. Migration was studied by scratch recolonization induced by 20 ng/ml epidermal growth factor (EGF). RESULTS: The tumor samples were classified according to the level of expression of CB1, CB2, or both. Patients with high expression levels of CB1, CB2, and CB1/CB2 showed increased survival reaching significance for CB1 and CB1/CB2 (p = 0.035 and 0.025, respectively). Both cannabinoid agonists inhibited the proliferation and expression of EGFR in lung cancer cells, and CBD potentiated the effect of THC. THC and CBD alone or in combination restored the epithelial phenotype, as evidenced by increased expression of CDH1 and reduced expression of CDH2 and VIM, as well as by fluorescence analysis of cellular cytoskeleton. Finally, both cannabinoids reduced the in vitro migration of the three lung cancer cells lines used. CONCLUSIONS: The expression levels of CB1 and CB2 have a potential use as markers of survival in patients with NSCLC. THC and CBD inhibited the proliferation and expression of EGFR in the lung cancer cells studied. Finally, the THC/CBD combination restored the epithelial phenotype in vitro.


Subject(s)
Cannabidiol/metabolism , Carcinoma, Non-Small-Cell Lung/metabolism , Cell Proliferation/physiology , Dronabinol/metabolism , Epithelial-Mesenchymal Transition/physiology , Lung Neoplasms/metabolism , Receptor, Cannabinoid, CB1/metabolism , Receptor, Cannabinoid, CB2/metabolism , A549 Cells , Adult , Aged , Aged, 80 and over , Cannabinoid Receptor Agonists/pharmacology , Cannabinoids/metabolism , Cell Line, Tumor , Cell Proliferation/drug effects , Epithelial-Mesenchymal Transition/drug effects , Female , Gene Expression/drug effects , Humans , Male , Middle Aged , Psychotropic Drugs/pharmacology
13.
Cancer Res ; 79(17): 4439-4452, 2019 09 01.
Article in English | MEDLINE | ID: mdl-31273063

ABSTRACT

Although EGFR mutant-selective tyrosine kinase inhibitors (TKI) are clinically effective, acquired resistance can occur by reactivating ERK. We show using in vitro models of acquired EGFR TKI resistance with a mesenchymal phenotype that CXCR7, an atypical G protein-coupled receptor, activates the MAPK-ERK pathway via ß-arrestin. Depletion of CXCR7 inhibited the MAPK pathway, significantly attenuated EGFR TKI resistance, and resulted in mesenchymal-to-epithelial transition. CXCR7 overexpression was essential in reactivation of ERK1/2 for the generation of EGFR TKI-resistant persister cells. Many patients with non-small cell lung cancer (NSCLC) harboring an EGFR kinase domain mutation, who progressed on EGFR inhibitors, demonstrated increased CXCR7 expression. These data suggest that CXCR7 inhibition could considerably delay and prevent the emergence of acquired EGFR TKI resistance in EGFR-mutant NSCLC. SIGNIFICANCE: Increased expression of the chemokine receptor CXCR7 constitutes a mechanism of resistance to EGFR TKI in patients with non-small cell lung cancer through reactivation of ERK signaling.


Subject(s)
Carcinoma, Non-Small-Cell Lung/drug therapy , Drug Resistance, Neoplasm , Lung Neoplasms/drug therapy , Protein Kinase Inhibitors/pharmacology , Receptors, CXCR/metabolism , Animals , Carcinoma, Non-Small-Cell Lung/metabolism , Carcinoma, Non-Small-Cell Lung/mortality , Cell Line, Tumor , Drug Resistance, Neoplasm/genetics , Epithelial-Mesenchymal Transition/genetics , ErbB Receptors/antagonists & inhibitors , Humans , Lung Neoplasms/metabolism , Lung Neoplasms/mortality , MAP Kinase Signaling System/drug effects , MAP Kinase Signaling System/genetics , Mice, Transgenic , Mutation , Neoplasms, Experimental/drug therapy , Neoplasms, Experimental/genetics , Receptors, CXCR/genetics , beta-Arrestins/metabolism
14.
Anal Chem ; 91(1): 836-845, 2019 01 02.
Article in English | MEDLINE | ID: mdl-30500173

ABSTRACT

High resolution LC-MS untargeted lipidomics using data independent acquisition (DIA) has the potential to increase lipidome coverage, as it enables the continuous and unbiased acquisition of all eluting ions. However, the loss of the link between the precursor and the product ions combined with the high dimensionality of DIA data sets hinder accurate feature annotation. Here, we present LipidMS, an R package aimed to confidently identify lipid species in untargeted LC-DIA-MS. To this end, LipidMS combines a coelution score, which links precursor and fragment ions with fragmentation and intensity rules. Depending on the MS evidence reached by the identification function survey, LipidMS provides three levels of structural annotations: (i) "subclass level", e.g., PG(34:1); (ii) "fatty acyl level", e.g., PG(16:0_18:1); and (iii) "fatty acyl position level", e.g., PG(16:0/18:1). The comparison of LipidMS with freely available data dependent acquisition (DDA) and DIA identification tools showed that LipidMS provides significantly more accurate and structural informative lipid identifications. Finally, to exemplify the utility of LipidMS, we investigated the lipidomic serum profile of patients diagnosed with nonalcoholic steatohepatitis (NASH), which is the progressive form of nonalcoholic fatty liver disease, a disorder underlying a strong lipid dysregulation. As previously published, a significant decrease in lysophosphatidylcholines, phosphatidylcholines and cholesterol esters and an increase in phosphatidylethanolamines were observed in NASH patients. Remarkably, LipidMS allowed the identification of a new set of lipids that may be used for NASH diagnosis. Altogether, LipidMS has been validated as a tool to assist lipid identification in the LC-DIA-MS untargeted analysis of complex biological samples.


Subject(s)
Lipidomics/methods , Lipids/blood , Tandem Mass Spectrometry/methods , Biomarkers/blood , Chromatography, Liquid/methods , Databases, Chemical , Humans , Non-alcoholic Fatty Liver Disease/blood , Tandem Mass Spectrometry/statistics & numerical data
15.
FASEB J ; : fj201800204, 2018 Jun 15.
Article in English | MEDLINE | ID: mdl-29906244

ABSTRACT

Oncogenic Kras mutations are one of the most common alterations in non-small cell lung cancer and are associated with poor response to treatment and reduced survival. Driver oncogenes, such as Kras are now appreciated for their ability to promote tumor growth via up-regulation of anabolic pathways. Therefore, we wanted to identify metabolic vulnerabilities in Kras-mutant lung cancer. Using the Kras LSL-G12D lung cancer model, we show that mutant Kras drives a lipogenic gene-expression program. Stable-isotope analysis reveals that mutant Kras promotes de novo fatty acid synthesis in vitro and in vivo. The importance of fatty acid synthesis in Kras-induced tumorigenesis was evident by decreased tumor formation in Kras LSL-G12D mice after treatment with a fatty acid synthesis inhibitor. Importantly, with gain and loss of function models of mutant Kras, we demonstrate that mutant Kras potentiates the growth inhibitory effects of several fatty acid synthesis inhibitors. These studies highlight the potential to target mutant Kras tumors by taking advantage of the lipogenic phenotype induced by mutant Kras.-Singh, A., Ruiz, C., Bhalla, K., Haley, J. A., Li, Q. K., Acquaah-Mensah, G., Montal, E., Sudini, K. R., Skoulidis, F., Wistuba, I. I., Papadimitrakopoulou, V., Heymach, J. V., Boros, L. G., Gabrielson, E., Carretero, J., Wong, K.-k., Haley, J. D., Biswal, S., Girnun, G. D. De novo lipogenesis represents a therapeutic target in mutant Kras non-small cell lung cancer.

16.
Genome Med ; 10(1): 41, 2018 05 31.
Article in English | MEDLINE | ID: mdl-29848362

ABSTRACT

BACKGROUND: Large-sequencing cancer genome projects have shown that tumors have thousands of molecular alterations and their frequency is highly heterogeneous. In such scenarios, physicians and oncologists routinely face lists of cancer genomic alterations where only a minority of them are relevant biomarkers to drive clinical decision-making. For this reason, the medical community agrees on the urgent need of methodologies to establish the relevance of tumor alterations, assisting in genomic profile interpretation, and, more importantly, to prioritize those that could be clinically actionable for cancer therapy. RESULTS: We present PanDrugs, a new computational methodology to guide the selection of personalized treatments in cancer patients using the variant lists provided by genome-wide sequencing analyses. PanDrugs offers the largest database of drug-target associations available from well-known targeted therapies to preclinical drugs. Scoring data-driven gene cancer relevance and drug feasibility PanDrugs interprets genomic alterations and provides a prioritized evidence-based list of anticancer therapies. Our tool represents the first drug prescription strategy applying a rational based on pathway context, multi-gene markers impact and information provided by functional experiments. Our approach has been systematically applied to TCGA patients and successfully validated in a cancer case study with a xenograft mouse model demonstrating its utility. CONCLUSIONS: PanDrugs is a feasible method to identify potentially druggable molecular alterations and prioritize drugs to facilitate the interpretation of genomic landscape and clinical decision-making in cancer patients. Our approach expands the search of druggable genomic alterations from the concept of cancer driver genes to the druggable pathway context extending anticancer therapeutic options beyond already known cancer genes. The methodology is public and easily integratable with custom pipelines through its programmatic API or its docker image. The PanDrugs webtool is freely accessible at http://www.pandrugs.org .


Subject(s)
Antineoplastic Agents/therapeutic use , Computational Biology/methods , Genomics , Neoplasms/drug therapy , Neoplasms/genetics , Precision Medicine , Computer Simulation , Genome, Human , Humans
17.
J Thorac Oncol ; 12(8): 1268-1279, 2017 08.
Article in English | MEDLINE | ID: mdl-28483607

ABSTRACT

INTRODUCTION: Proinflammatory cytokine interleukin-17A (IL-17A) is overexpressed in a subset of patients with lung cancer. We hypothesized that IL-17A promotes a protumorigenic inflammatory phenotype and inhibits antitumor immune responses. METHODS: We generated bitransgenic mice expressing a conditional IL-17A allele along with conditional KrasG12D and performed immune phenotyping of mouse lungs, a survival analysis, and treatment studies with antibodies either blocking programmed cell death 1 (PD-1) or IL-6 or depleting neutrophils. To support the preclinical findings, we analyzed human gene expression data sets and immune profiled patient lung tumors. RESULTS: Tumors in IL-17:KrasG12D mice grew more rapidly, resulting in a significantly shorter survival as compared with that of KrasG12D mice. IL-6, granulocyte colony-stimulating factor (G-CSF), milk fat globule-EGF factor 8 protein, and C-X-C motif chemokine ligand 1 were increased in the lungs of IL17:Kras mice. Time course analysis revealed that levels of tumor-associated neutrophils were significantly increased, and lymphocyte recruitment was significantly reduced in IL17:KrasG12D mice as compared with in KrasG12D mice. In therapeutic studies PD-1 blockade was not effective in treating IL-17:KrasG12D tumors. In contrast, blocking IL-6 or depleting neutrophils with an anti-Ly-6G antibody in the IL17:KrasG12D tumors resulted in a clinical response associated with T-cell activation. In tumors from patients with lung cancer with KRAS mutation we found a correlation between higher levels of IL-17A and colony- stimulating factor 3 and a significant correlation among high neutrophil and lower T-cell numbers. CONCLUSIONS: Here we have shown that an increase in a single cytokine, IL-17A, without additional mutations can promote lung cancer growth by promoting inflammation, which contributes to resistance to PD-1 blockade and sensitizes tumors to cytokine and neutrophil depletion.


Subject(s)
Interleukin-17/biosynthesis , Lung Neoplasms/immunology , Neutrophils/immunology , Programmed Cell Death 1 Receptor/immunology , Animals , Disease Progression , Gene Expression , Humans , Interleukin-17/immunology , Lung Neoplasms/genetics , Lung Neoplasms/pathology , Mice , Mice, Transgenic , Mutation , Neutrophils/pathology , Programmed Cell Death 1 Receptor/antagonists & inhibitors , Proto-Oncogene Proteins p21(ras)/genetics , Proto-Oncogene Proteins p21(ras)/immunology
18.
Clin Cancer Res ; 23(12): 3203-3213, 2017 Jun 15.
Article in English | MEDLINE | ID: mdl-28302866

ABSTRACT

Purpose: We aimed to maximize the performance of detecting genetic alterations in lung cancer using high-throughput sequencing for patient-derived xenografts (PDXs).Experimental Design: We undertook an integrated RNA and whole-exome sequencing of 14 PDXs. We focused on the genetic and functional analysis of ß2-microglobulin (B2M), a component of the HLA class-I complex.Results: We identified alterations in genes involved in various functions, such as B2M involved in immunosurveillance. We extended the mutational analysis of B2M to about 230 lung cancers. Five percent of the lung cancers carried somatic mutations, most of which impaired the correct formation of the HLA-I complex. We also report that genes such as CALR, PDIA3, and TAP1, which are involved in the maturation of the HLA-I complex, are altered in lung cancer. By gene expression microarrays, we observed that restitution of B2M in lung cancer cells upregulated targets of IFNα/IFNγ. Furthermore, one third of the lung cancers lacked the HLA-I complex, which was associated with lower cytotoxic CD8+ lymphocyte infiltration. The levels of B2M and HLA-I proteins correlated with those of PD-L1. Finally, a deficiency in HLA-I complex and CD8+ infiltration tended to correlate with reduced survival of patients with lung cancer treated with anti-PD-1/anti-PD-L1.Conclusions: Here, we report recurrent inactivation of B2M in lung cancer. These observations, coupled with the mutations found at CALR, PDIA3, and TAP1, and the downregulation of the HLA-I complex, indicate that an abnormal immunosurveillance axis contributes to lung cancer development. Finally, our observations suggest that an impaired HLA-I complex affects the response to anti-PD-1/anti-PD-L1 therapies. Clin Cancer Res; 23(12); 3203-13. ©2016 AACR.


Subject(s)
Genomics , Histocompatibility Antigens Class I/genetics , Lung Neoplasms/genetics , beta 2-Microglobulin/genetics , Animals , B7-H1 Antigen/antagonists & inhibitors , B7-H1 Antigen/immunology , CD8-Positive T-Lymphocytes/immunology , Gene Expression Regulation, Neoplastic , Histocompatibility Antigens Class I/immunology , Humans , Lung Neoplasms/drug therapy , Lung Neoplasms/immunology , Lung Neoplasms/pathology , Mice , Mutation , Programmed Cell Death 1 Receptor/antagonists & inhibitors , Programmed Cell Death 1 Receptor/immunology , Exome Sequencing , Xenograft Model Antitumor Assays , beta 2-Microglobulin/antagonists & inhibitors , beta 2-Microglobulin/immunology
19.
Cancer Discov ; 6(9): 1006-21, 2016 09.
Article in English | MEDLINE | ID: mdl-27312177

ABSTRACT

UNLABELLED: As a master regulator of chromatin function, the lysine methyltransferase EZH2 orchestrates transcriptional silencing of developmental gene networks. Overexpression of EZH2 is commonly observed in human epithelial cancers, such as non-small cell lung carcinoma (NSCLC), yet definitive demonstration of malignant transformation by deregulated EZH2 remains elusive. Here, we demonstrate the causal role of EZH2 overexpression in NSCLC with new genetically engineered mouse models of lung adenocarcinoma. Deregulated EZH2 silences normal developmental pathways, leading to epigenetic transformation independent of canonical growth factor pathway activation. As such, tumors feature a transcriptional program distinct from KRAS- and EGFR-mutant mouse lung cancers, but shared with human lung adenocarcinomas exhibiting high EZH2 expression. To target EZH2-dependent cancers, we developed a potent open-source EZH2 inhibitor, JQEZ5, that promoted the regression of EZH2-driven tumors in vivo, confirming oncogenic addiction to EZH2 in established tumors and providing the rationale for epigenetic therapy in a subset of lung cancer. SIGNIFICANCE: EZH2 overexpression induces murine lung cancers that are similar to human NSCLC with high EZH2 expression and low levels of phosphorylated AKT and ERK, implicating biomarkers for EZH2 inhibitor sensitivity. Our EZH2 inhibitor, JQEZ5, promotes regression of these tumors, revealing a potential role for anti-EZH2 therapy in lung cancer. Cancer Discov; 6(9); 1006-21. ©2016 AACR.See related commentary by Frankel et al., p. 949This article is highlighted in the In This Issue feature, p. 932.


Subject(s)
Enhancer of Zeste Homolog 2 Protein/genetics , Gene Expression Regulation, Neoplastic , Lung Neoplasms/genetics , Animals , Antineoplastic Agents/chemistry , Antineoplastic Agents/pharmacology , Cell Line, Tumor , Cell Transformation, Neoplastic/genetics , Cell Transformation, Neoplastic/metabolism , Chromatin/genetics , Chromatin/metabolism , Disease Models, Animal , Drug Design , Enhancer Elements, Genetic , Enhancer of Zeste Homolog 2 Protein/antagonists & inhibitors , Enhancer of Zeste Homolog 2 Protein/metabolism , Gene Expression , Gene Expression Profiling , Gene Expression Regulation, Neoplastic/drug effects , Humans , Lung Neoplasms/diagnosis , Lung Neoplasms/drug therapy , Lung Neoplasms/metabolism , Magnetic Resonance Imaging , Mice , Models, Molecular , Molecular Conformation , Molecular Targeted Therapy , Promoter Regions, Genetic , Structure-Activity Relationship , Xenograft Model Antitumor Assays
20.
Cancer Res ; 75(20): 4372-83, 2015 Oct 15.
Article in English | MEDLINE | ID: mdl-26282169

ABSTRACT

Non-small cell lung cancers (NSCLC) that have developed resistance to EGF receptor (EGFR) tyrosine kinase inhibitor (TKI), including gefitinib and erlotinib, are clinically linked to an epithelial-to-mesenchymal transition (EMT) phenotype. Here, we examined whether modulating EMT maintains the responsiveness of EGFR-mutated NSCLCs to EGFR TKI therapy. Using human NSCLC cell lines harboring mutated EGFR and a transgenic mouse model of lung cancer driven by mutant EGFR (EGFR-Del19-T790M), we demonstrate that EGFR inhibition induces TGFß secretion followed by SMAD pathway activation, an event that promotes EMT. Chronic exposure of EGFR-mutated NSCLC cells to TGFß was sufficient to induce EMT and resistance to EGFR TKI treatment. Furthermore, NSCLC HCC4006 cells with acquired resistance to gefitinib were characterized by a mesenchymal phenotype and displayed a higher prevalence of the EGFR T790M mutated allele. Notably, combined inhibition of EGFR and the TGFß receptor in HCC4006 cells prevented EMT but was not sufficient to prevent acquired gefitinib resistance because of an increased emergence of the EGFR T790M allele compared with cells treated with gefitinib alone. Conversely, another independent NSCLC cell line, PC9, reproducibly developed EGFR T790M mutations as the primary mechanism underlying EGFR TKI resistance, even though the prevalence of the mutant allele was lower than that in HCC4006 cells. Thus, our findings underscore heterogeneity within NSCLC cells lines harboring EGFR kinase domain mutations that give rise to divergent resistance mechanisms in response to treatment and anticipate the complexity of EMT suppression as a therapeutic strategy.


Subject(s)
Antineoplastic Agents/pharmacology , Carcinoma, Non-Small-Cell Lung/genetics , Drug Resistance, Neoplasm/genetics , Lung Neoplasms/genetics , Mutation , Protein Kinase Inhibitors/pharmacology , Animals , Carcinoma, Non-Small-Cell Lung/metabolism , Carcinoma, Non-Small-Cell Lung/pathology , Cell Line, Tumor , Cluster Analysis , Epithelial-Mesenchymal Transition/drug effects , Epithelial-Mesenchymal Transition/genetics , Gefitinib , Gene Expression Profiling , Humans , Lung Neoplasms/metabolism , Lung Neoplasms/pathology , Mice , Phenotype , Quinazolines/pharmacology , Receptors, Transforming Growth Factor beta/metabolism , Signal Transduction/drug effects , Smad Proteins/metabolism , Transforming Growth Factor beta1/metabolism , Transforming Growth Factor beta1/pharmacology
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