Adenocarcinoma of the lung is the leading cause of cancer death worldwide. Here we report molecular profiling of 230 resected lung adenocarcinomas using messenger RNA, microRNA and DNA sequencing integrated with copy number, methylation and proteomic analyses. High rates of somatic mutation were seen (mean 8.9 mutations per megabase). Eighteen genes were statistically significantly mutated, including RIT1 activating mutations and newly described loss-of-function MGA mutations which are mutually exclusive with focal MYC amplification. EGFR mutations were more frequent in female patients, whereas mutations in RBM10 were more common in males. Aberrations in NF1, MET, ERBB2 and RIT1 occurred in 13% of cases and were enriched in samples otherwise lacking an activated oncogene, suggesting a driver role for these events in certain tumours. DNA and mRNA sequence from the same tumour highlighted splicing alterations driven by somatic genomic changes, including exon 14 skipping in MET mRNA in 4% of cases. MAPK and PI(3)K pathway activity, when measured at the protein level, was explained by known mutations in only a fraction of cases, suggesting additional, unexplained mechanisms of pathway activation. These data establish a foundation for classification and further investigations of lung adenocarcinoma molecular pathogenesis.

https://cdr.lib.unc.edu/downloads/2z10ws24x

Comprehensive molecular profiling of lung adenocarcinoma: The cancer genome atlas research network

Epigenetic mechanisms are essential for normal development and maintenance of tissue-specific gene expression patterns in mammals. Disruption of epigenetic processes can lead to altered gene function and malignant cellular transformation. Global changes in the epigenetic landscape are a hallmark of cancer. The initiation and progression of cancer, traditionally seen as a genetic disease, is now realized to involve epigenetic abnormalities along with genetic alterations. Recent advancements in the rapidly evolving field of cancer epigenetics have shown extensive reprogramming of every component of the epigenetic machinery in cancer including DNA methylation, histone modifications, nucleosome positioning and non-coding RNAs, specifically microRNA expression. The reversible nature of epigenetic aberrations has led to the emergence of the promising field of epigenetic therapy, which is already making progress with the recent FDA approval of three epigenetic drugs for cancer treatment. In this review, we discuss the current understanding of alterations in the epigenetic landscape that occur in cancer compared with normal cells, the roles of these changes in cancer initiation and progression, including the cancer stem cell model, and the potential use of this knowledge in designing more effective treatment strategies.

/pdf/epigenetics-in-cancer-53kplki7aw.pdf

Epigenetics in Cancer

https://www.hal.inserm.fr/inserm-00561753/document

International Association for the Study of Lung Cancer/American Thoracic Society/European Respiratory Society International Multidisciplinary Classification of Lung Adenocarcinoma

The release of negative regulators of immune activation (immune checkpoints) that limit antitumor responses has resulted in unprecedented rates of long-lasting tumor responses in patients with a variety of cancers. This can be achieved by antibodies blocking the cytotoxic T lymphocyte–associated protein 4 (CTLA-4) or the programmed cell death 1 (PD-1) pathway, either alone or in combination. The main premise for inducing an immune response is the preexistence of antitumor T cells that were limited by specific immune checkpoints. Most patients who have tumor responses maintain long-lasting disease control, yet one-third of patients relapse. Mechanisms of acquired resistance are currently poorly understood, but evidence points to alterations that converge on the antigen presentation and interferon-γ signaling pathways. New-generation combinatorial therapies may overcome resistance mechanisms to immune checkpoint therapy.

Cancer immunotherapy using checkpoint blockade

Adenocarcinoma of the lung is the leading cause of cancer death worldwide. Here we report molecular profiling of 230 resected lung adenocarcinomas using messenger RNA, microRNA and DNA sequencing integrated with copy number, methylation and proteomic analyses. High rates of somatic mutation were seen(mean 8.9 mutations per megabase). Eighteen genes were statistically significantly mutated, including RIT1 activating mutations and newly described loss-of-function MGA mutations which are mutually exclusive with focal MYC amplification. EGFR mutations were more frequent in female patients, whereas mutations in RBM10 were more common in males. Aberrations in NF1, MET, ERBB2 and RIT1 occurred in 13% of cases and were enriched in samples otherwise lacking an activated oncogene, suggesting a driver role for these events in certain tumours. DNA and mRNA sequence from the same tumour highlighted splicing alterations driven by somatic genomic changes, including exon 14 skipping in MET mRNA in 4% of cases. MAPK and PI(3)K pathway activity, when measured at the protein level, was explained by known mutations in only a fraction of cases, suggesting additional, unexplained mechanisms of pathway activation. These data establish a foundation for classification and further investigations of lung adenocarcinoma molecular pathogenesis.

Comprehensive molecular profiling of lung adenocarcinoma

Ultrasensitive immunosensor for multiplex detection of cancer biomarkers carcinoembryonic antigen (CEA) and yamaguchi sarcoma viral oncogene homolog 1 (YES1) based on eco-friendly synthesized gold nanoparticles.


 Immune checkpoint inhibitors (ICIs) targeting PD-L1/PD-1 have dramatically improved the management of NSCLC patients. Nevertheless, more than 50% patients will present primary resistance or will develop secondary resistance within 12-25 months after treatment initiation. The mechanisms of resistance to ICIs may depend on tumor-intrinsic molecular/genetic alterations that generate an immunosuppressive tumor microenvironment (isTME). Using In silico analyses (TCGA and AACR-GENIE cohorts), and protein expression analysis in our institutional CIMA-CUN cohort, we have shown that >50% LUSC and ~28% LUAD tumors exhibited reduced PTEN mRNA/protein levels. Patients with PTEN-low tumors had higher levels of CXCL10, PD-L1 and PD-L2. In a cohort of stage IV NSCLC patients treated with ICIs, we found that patients with low tumor PTEN levels were significantly associated with worse OS (p=0.021). We have developed and characterized a Pten-null LUSC model using UN680 cells, which was also refractory to anti-PD-1 when implanted in syngeneic mice. Pten loss led to a deregulation of multiple pathways related to immunosuppression, with a positive enrichment in “IL-6/JAK/STAT3” and “TNF-α via NFkB” hallmarks, identified by GSEA. Tumors from the Pten-null LUSC model were highly metastatic and fibrotic, and secreted TGF-β/CXCL10, thus favoring conversion of CD4+ lymphocytes into Tregs. Human/mouse PTEN-low tumors were enriched in Tregs and immunosuppressive genes. Importantly, treatment of mice bearing Pten-null tumors with TLR agonists+anti-TGF-β, aimed to alter this isTME, led to tumor rejection and immunological memory in 100% of mice. Our results demonstrate that lack of PTEN causes immunotherapy resistance in LUSC by establishing an isTME that can be reversed therapeutically.
 Citation Format: Francisco Exposito, Miriam Redrado, Maeva Houry, Katherine Hastings, Magdalena Molero-Abraham, Teresa Lozano, Jose L. Solorzano, Julian Sanz Ortega, Vera Andradas, Ramon Amat, Esther Redin, Sergio Leon, Naroa Legarra, Javier García, Diego Serrano, Karmele Valencia, Camila Robles-Oteiza, Giorgia Foggetti, Enriqueta Felip, Juan J. Lasarte, Luis Paz-Ares, Jon Zugazagoitia, Katerina Politi, Luis M Montuenga, Alfonso Calvo. PTEN loss confers resistance to anti-PD-1 therapy in NSCLC by increasing tumor infiltration of T regulatory cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1124.

Abstract 1124: PTEN loss confers resistance to anti-PD-1 therapy in NSCLC by increasing tumor infiltration of T regulatory cells

Background: While lung cancer low-dose computed tomography (LDCT) screening is being rolled out in many regions around the world, differentiation of indeterminate pulmonary nodules between malignant and benign remains to a challenge for screening programs. We conducted one of the first systematic investigations of circulating protein markers for their ability to assess the risk of malignancy for screen-detected pulmonary nodules. Methods: Based on four LDCT screening studies in the United States, Canada and Europe, we assayed 1078 unique protein markers in pre-diagnostic samples based on a nested case-control design with a total of 1253 participants. Protein markers were measured using proximity extension assays and the data were analyzed using multivariate logistic regression, random forest, and penalized regressions. Results: We identified 36 potentially informative markers differentiating malignant nodules from benign nodules. Pathway analysis revealed a tightly connected network based on the 36 protein-coding genes. We observed a differential mRNA expression profile of the corresponding 36 mRNAs between lung tumors and adjacent normal tissues using data from The Cancer Genomic Atlas. We prioritized a panel of 9 protein markers through 10-fold nested cross-validations. We observed that circulating protein markers can increase sensitivity to 0.80 for nodule malignancy compared to the Brock model (p-value<0.001). Two additional markers were identified that were specific for lung tumors diagnosed within one year. All 11 protein markers showed general consistency in improving prediction across the four LDCT studies. Conclusions: Circulating protein markers can help to differentiate between malignant and benign pulmonary nodules. Validating these results in an independent CT-screening study will be required prior to clinical implementation.

Circulating Proteome for Pulmonary Nodule Malignancy

Background: Cytologic examination of specimens obtained from the respiratory tract is a lung cancer diagnostic procedure with high specificity, but moderate sensitivity. The use of molecular biomarkers may enhance the sensitivity of cytologic examination in the detection of lung cancer. Methods: Complement factor H, a protein secreted by lung cancer cells, was quantified in a series of bronchoalveolar lavage supernatants from lung cancer patients and patients with non-malignant respiratory diseases. Albumin, total protein content, and hemoglobin were also analyzed. Results were validated in independent sets of bronchoalveolar lavage and sputum supernatants. Results: There was a significantly higher concentration of factor H in bronchoalveolar lavage samples from lung cancer patients. The sensitivity and specificity of the factor H test was 82% and 77%, respectively. These results were validated in an independent set of patients with nearly identical results. Furthermore, 70% and 45% of bronchoalveolar lavage fluids from central and peripheral tumors, respectively, reported as cytologically negative were classified as positive using this marker. Finally, the test was evaluated in a series of sputum supernatants from lung cancer patients and controls. The sensitivity and specificity of the factor H test in this series was 80% and 88%, respectively.

sputum from patients with lung cancer

Maria J. Pajares, Luis M. Montuenga and Ruben PioLasarte, Jose I. Riezu-Boj, John D. Lambris, Ana Rouzaut, Leticia Corrales, Daniel Ajona, Stavros Rafail, Juan J.ol.1201654http://www.jimmunol.org/content/early/2012/10/01/jimmunJ Immunol€ published online 1 October 2012MaterialSupplementary4.DC1.htmlhttp://www.jimmunol.org/content/suppl/2012/10/01/jimmunol.120165Subscriptionshttp://jimmunol.org/subscriptionsInformation about subscribing to The Journal of Immunology is online at: Permissionshttp://www.aai.org/ji/copyright.htmlSubmit copyright permission requests at: Email Alertshttp://jimmunol.org/cgi/alerts/etocReceive free email-alerts when new articles cite this article. Sign up at:

Luis M. Montuenga

Papers

Ultrasensitive immunosensor for multiplex detection of cancer biomarkers carcinoembryonic antigen (CEA) and yamaguchi sarcoma viral oncogene homolog 1 (YES1) based on eco-friendly synthesized gold nanoparticles.

Abstract 1124: PTEN loss confers resistance to anti-PD-1 therapy in NSCLC by increasing tumor infiltration of T regulatory cells

Circulating Proteome for Pulmonary Nodule Malignancy

sputum from patients with lung cancer

Progression for Lung Cancer Anaphylatoxin C5a Creates a Favorable