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

Characterization of pancreatic endocrine cells of the European common frog Rana temporaria.

Recent studies highlight the importance of baseline functional immunity for efficacious immune checkpoint blockade therapies. Extensive systemic immune profiling was performed in a discovery cohort of 112 non-small cell lung cancer patients undergoing PD-L1/PD-1 blockade immunotherapy. Responders showed high baseline phenotypic diversity of myeloid cell types in peripheral blood, in which elevated activated monocytic cells and decreased granulocytic phenotypes were potent prognostic factors. A high-throughput profiling of soluble factors in plasma was carried out that identified fractalkine (FKN), a chemokine involved in adhesion and chemotactic attraction of immune cells, as a biomarker of myeloid cell diversity in human patients and in murine models, which was found significantly increased in objective responders. Secreted FKN inhibited adenocarcinoma and squamous cell carcinoma growth in vivo through a prominent contribution of systemic effector NK cells, enhanced tumor infiltration with immunostimulatory immune cells and inhibition of MDSCs within tumors. A synergy between FKN and PD-L1/PD-1 blockade immunotherapy was found in murine lung cancer models refractory to anti-PD-L1/anti-PD-1 treatment. Transcriptional data from human lung adenocarcinoma samples independently confirmed the data from the discovery cohort. Importantly, recombinant FKN and tumor expressed-FKN were efficacious in delaying tumor growth in vivo with significant abscopal effects, indicating a potential therapeutic use of FKN in combination with immunotherapies.

/pdf/potent-clinical-prognostic-and-systemic-adjuvant-therapeutic-e098llfo.pdf

Potent clinical prognostic and systemic adjuvant therapeutic value of plasma fractalkine in PD-L1/PD-1 blockade immunotherapy for lung cancer

Lung cancer is the most common fatal type of cancer in the developed world. Less than a quarter of new cases of lung cancer diagnosed every year are amenable to curative surgery, and even with the best therapeutic approach, less than 10% survive 5 years (1). Significantly better lung cancer clinical management approaches are urgently required. The most promising avenue to reduce lung cancer is the implementation of comprehensive preventive strategies. The overwhelming majority of this disease is caused by exposure to tabacco combustion products (2). Unfortunately, despite any level of success of primary smoking prevention measures, the current burden of tobacco consumption in the world today and the long incubation time of lung cancer augue that the high death rate from this disease will not change for decades. Effective reduction in lung cancer mortality, especially in the near term, will require more than primary (anti-smoking) prevention measures. The present review deals with the tools and tec...

/pdf/new-molecular-strategies-for-early-lung-cancer-detection-30mo6w3hsy.pdf

New molecular strategies for early lung cancer detection.

RNA-seq is a reference technology for determining alternative splicing at genome-wide level. Exon arrays remain widely used for the analysis of gene expression, but show poor validation rate with regard to splicing events. Commercial arrays that include probes within exon junctions have been developed in order to overcome this problem.

We compare the performance of RNA-seq (Illumina HiSeq) and junction arrays (Affymetrix Human Transcriptome array) for the analysis of transcript splicing events. Three different breast cancer cell lines were treated with CX-4945, a drug that severely affects splicing. To enable a direct comparison of the two platforms, we adapted EventPointer, an algorithm that detects and labels alternative splicing events using junction arrays, to work also on RNA-seq data. Common results and discrepancies between the technologies were validated and/or resolved by over 200 PCR experiments.

As might be expected, RNA-seq appears superior in cases where the technologies disagree, and is able to discover novel splicing events beyond the limitations of physical probe-sets. We observe a high degree of coherence between the two technologies, however, with correlation of EventPointer results over 0.90. Through decimation, the detection power of the junction arrays is equivalent to RNA-seq with up to 60 million reads. Our results suggest, therefore, that exon-junction arrays are a viable alternative to RNA-seq for detection of alternative splicing events when focusing on well-described transcriptional regions.

/pdf/comparison-of-rna-seq-and-microarray-platforms-for-splice-2v5f20jmjr.pdf

Comparison of RNA-seq and Microarray Platforms for Splice Event Detection using a Cross-Platform Algorithm

SummaryPhysiological and histochemical studies have recently supported the notion that nitric oxide (NO) is the transduction signal responsible for the non-adrenergic, non-cholinergic relaxation of the vasculature as well as the airways of the mammalian lung. We report the presence of immunoreactivity to NO synthase (NOS) in nerve cell bodies and nerve fibres in the neural plexus of the buccal cavity and lungs of the frog, Rana temporaria, using the indirect immunocytochemical technique of avidin-biotin and the NADPH-diaphorase technique. The neural ganglia located next to the muscle layer and within the connective tissue of the buccal cavity were partially immunoreactive for NOS. In the lungs, NOS immunoreactivity occurred in nerve cell bodies, as well as in both myelinated and unmyelinated nerve fibres. Fine nerve fibres immunoreactive to NOS were observed within the muscle fibre bundles and next to the respiratory epithelium. Both the presence of NOS immunoreactivity and the positive histochemical reaction for NADPH-diaphorase in the neural plexus of amphibian respiratory tract suggests a broad evolutionary role for NO as a peripheral neurotransmitter.

Luis M. Montuenga

Papers

Characterization of pancreatic endocrine cells of the European common frog Rana temporaria.

Potent clinical prognostic and systemic adjuvant therapeutic value of plasma fractalkine in PD-L1/PD-1 blockade immunotherapy for lung cancer

New molecular strategies for early lung cancer detection.

Comparison of RNA-seq and Microarray Platforms for Splice Event Detection using a Cross-Platform Algorithm

Neuronal nitric oxide synthase immunoreactivity in the respiratory tract of the frog, Rana temporaria