• clinical
• molecular
• pathology
• renal cell carcinoma
• treatment

• xjj2018zyts34 The Fundamental Research Funds for the Central Universities of China
• 2020SF-119 The Research Funds on Social Development from the Department of Science and Technology of Shaanxi Province of China

The aim of the current study was to investigate the prevalence and clinicopathologic characteristics of ROS1‐rearranged non‐small cell lung cancer (NSCLC) in routine genotypic screening in conjunction with the study of PD‐L1 expression, a biomarker for first‐line treatment decisions.

Reflex simultaneous genotypic screening for EGFR by peptide nucleic acid clamping, and ALK and ROS1 by fluorescence in situ hybridization (FISH) was performed on consecutive NSCLC cases at the time of initial pathologic diagnosis. We evaluated genetic aberrations, clinicopathologic characteristics, and PD‐L1 tumor proportion score (TPS) using a PD‐L1 22C3 assay kit.

In 407 consecutive NSCLC patients, simultaneous genotyping identified 14 (3.4%) ROS1 and 19 (4.7%) ALK rearrangements, as well as 106 (26%) EGFR mutations. These mutations were mutually exclusive and were found in patients with similar clinical features, including younger age, a prevalence in women, adenocarcinoma, and advanced stage. The PD‐L1 assay was performed on 130 consecutive NSCLC samples. High PD‐L1 expression (TPS ≥ 50%) was observed in 29 (22.3%) tumors. PD‐L1 expression (TPS ≥ 1%) was significantly associated with wild type EGFR, while ROS1 rearrangement was associated with high PD‐L1 expression. Of the 14 cases with ROS1 rearrangement, 12 (85.7%) showed PD‐L1 expression and 5 (35.7%) showed high PD‐L1 expression.

In the largest consecutive routine Asian NSCLC cohort analyzed to date, we found that high PD‐L1 expression frequently overlapped with ROS1 rearrangement, while it negatively correlated with EGFR mutations.

• Biomarker
• epidermal growth factor receptor
• human ROS1 protein
• non-small cell lung carcinoma
• programmed death 1 ligand 1

• cancer
• drug toxicity
• epidermal growth factor receptor
• molecular targeted therapy
• tumor response criteria
• vascular endothelial growth factor

• ALK
• EGFR
• Non-small-cell lung cancer
• afatinib
• alectinib
• ceritinib
• crizotinib
• epidermal growth factor receptor
• immunotherapy
• nivolumab
• nsclc
• osimertinib
• pembrolizumab
• tkis
• tyrosine kinase inhibitors

• Brain Neoplasms/diagnosis
• Brain Neoplasms/drug therapy
• Brain Neoplasms/secondary
• Carcinoma, Non-Small-Cell Lung/diagnosis
• Carcinoma, Non-Small-Cell Lung/drug therapy
• Carcinoma, Non-Small-Cell Lung/pathology
• Drug Resistance, Neoplasm/drug effects
• Genes, cdc/drug effects
• Genes, cdc/immunology
• Humans
• Lung Neoplasms/diagnosis
• Lung Neoplasms/drug therapy
• Lung Neoplasms/pathology
• Neoplasm Staging
• Prognosis
• Protein Kinase Inhibitors/classification
• Protein Kinase Inhibitors/therapeutic use

• Lung cancer stem cells
• Lung neoplasms
• Molecular targeted therapy
• Neoplastic stem cells

• ALK (anaplastic lymphoma kinase) oncogene
• anaplastic large cell lymphoma (ALCL)
• autophagic switch
• combined therapy
• cytoprotective autophagy
• cytotoxic autophagy
• neuroblastoma (NB)
• non-small cell lung carcinoma (NSCLC)
• rhabdomyosarcoma (RMS)
• tyrosine kinase inhibitor (TKI)

With an incidence of 68 new cases per 100,000 people per year, an estimated total number of up to 350,000 new non-small-cell lung cancer (NSCLC) cases are diagnosed each year in the European Union. Up to 10% of NSCLC patients are eligible for therapy with novel ALK (anaplastic lymphoma kinase) inhibitors, as they have been diagnosed with a mutation in the gene coding for ALK. The ALK inhibitor therapy costs add up to approx. 9000 € per patient per month, with treatment durations of up to one year. Recent studies have shown that up to 10% of ALK cases are misdiagnosed by nearly 40% of pathologic investigations. The current state-of-the-art ALK diagnostic procedure comprises a Fluorescent in situ Hybridization (FISH) assay accompanied by ALK inhibitor therapy (Crizotinib). The therapy success ranges between a full therapy failure and the complete remission of the tumor (i.e., healing), but the biomedical and systemic reasons for this range remain unknown so far. It appears that the variety of different ALK mutations and variants contributes to the discrepancy in therapy results. Although the major known fusion partner for ALK in NSCLC is the Echinoderm microtubule-associated protein-like 4 (EML4), of which a minimum of 15 variants have been described, an additional 20 further ALK fusion variants with other genes are known, of which three have already been found in NSCLC. We hypothesize that the wide variety of known (and unknown) ALK mutations is associated with a variable therapy success, thus rendering current companion diagnostic procedures (FISH) and therapy (Crizotinib) only partly applicable in ALK-related NSCLC treatment. In cell culture, differing sensitivity to Crizotinib has been shown for some fusion variants, but it is as yet unknown which of them are really biologically active in cancer patients, and how the respective variants affect the response to Crizotinib treatment. Moreover, it has been demonstrated that translocated ALK genes can also be observed in healthy tissues and are not compulsorily associated with tumors. Therefore, it is important to keep in mind that even for the known variants of ALK fusion genes, the biological function is not known for all variants, and that no information is available on the homogeneity of ALK fusion variants within a single tumor. These facts, in concert with data for ALK mutation prevalence and therapy outcomes of a German cohort of NSCLC patients, support the hypothesis that, by using novel companion diagnostic tools in combination with therapy outcome predictions, massive cost savings could be possible in European Health Care systems without a loss of patient care.

• ALK
• NSCLC
• cost saving
• crizotinib
• lung cancer

• adult
• anaplastic lymphoma kinase
• cytogenetics
• renal cell carcinoma

Traditionally tumors were classified based on anatomic location but now specific genetic mutations in cancers are leading to treatment of tumors with molecular targeted therapies. This has led to a paradigm shift in the classification and treatment of cancer. Tumors treated with molecular targeted therapies often show morphological changes rather than change in size and are associated with class specific and drug specific toxicities, different from those encountered with conventional chemotherapeutic agents. It is important for the radiologists to be familiar with the new cancer classification and the various treatment strategies employed, in order to effectively communicate and participate in the multi-disciplinary care. In this paper we will focus on lung cancer as a prototype of the new molecular classification.

• ALK rearrangement
• Adenocarcinoma
• EGFR mutation
• Lung cancer
• NSCLC

• Cisplatin
• Combination therapy
• Crizotinib
• Non-small cell lung cancer
• cMET

• Lung cancer
• Mucinous
• Prognosis
• Stage IV
• Treatment outcome

• anaplastic lymphoma kinase
• cancer
• inhibitor
• resistance
• therapy
• tyrosine kinase

Clinical outcomes of anaplastic lymphoma kinase (ALK)-rearranged non-small cell lung cancer according to ALK fusion variants are not clear. We aimed to investigate the prevalence of ALK fusion variants and to compare clinical outcomes according to ALK fusion variants.

A retrospective analysis was conducted on patients with advanced ALK-rearranged adenocarcinoma treated with chemotherapy and ALK inhibitors. ALK rearrangement was identified by fluorescence in situ hybridization and confirmed by immunohistochemistry. Peptide nucleic acid-mediated quantitative polymerase chain reaction assays, designed to detect 28 types of echinoderm microtubule-associated protein-like 4 (EML)-ALK rearrangements, were performed. Clinicopathological analysis and treatment outcomes with platinum-based chemotherapy, pemetrexed therapy, and ALK inhibitors—including crizotinib and ceritinib—were evaluated.

A total of 52 patients with ALK-rearranged lung adenocarcinoma were enrolled. EML4-ALK variant 1 (v1) was the most common variant (38.5 %) followed by the non-EML4 variant (36.5 %), EML4-ALK variant 3a/b (19.2 %), and EML4-ALK variant 2 (5.8 %). No clinicopathological distinction was found between the different ALK fusion variants. Treatment response rates for each therapeutic agent did not differ according to ALK fusion variant. However, EML4 variants, especially v1, showed significantly longer progression-free survival (PFS) on pemetrexed treatment than did non-EML4 variants (median 31.1 months versus 5.7 months, P = 0.003). PFS with platinum-based chemotherapy and ALK inhibitors did not differ according to ALK fusion variant. Multivariate survival analysis using Cox’s regression model revealed v1 as the only predictive factor for prolonged PFS on pemetrexed.

Among ALK fusion variants, v1 is the most common subtype. It showed superior progression-free survival on pemetrexed than did non-EML4 variants. No survival difference was demonstrated between variants treated with crizotinib or ceritinib.

The online version of this article (doi:10.1186/s12967-016-1061-z) contains supplementary material, which is available to authorized users.

• Anaplastic lymphoma kinase
• Anaplastic lymphoma kinase inhibitor
• EML4-ALK fusion
• Non-small cell lung cancer
• Pemetrexed

Cancer cells exhibit altered metabolism including aerobic glycolysis that channels several glycolytic intermediates into de novo purine biosynthetic pathway. We discovered increased expression of phosphoribosyl amidotransferase (PPAT) and phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole succinocarboxamide synthetase (PAICS) enzymes of de novo purine biosynthetic pathway in lung adenocarcinomas. Transcript analyses from next-generation RNA sequencing and gene expression profiling studies suggested that PPAT and PAICS can serve as prognostic biomarkers for aggressive lung adenocarcinoma. Immunohistochemical analysis of PAICS performed on tissue microarrays showed increased expression with disease progression and was significantly associated with poor prognosis. Through gene knockdown and over-expression studies we demonstrate that altering PPAT and PAICS expression modulates pyruvate kinase activity, cell proliferation and invasion. Furthermore we identified genomic amplification and aneuploidy of the divergently transcribed PPAT-PAICS genomic region in a subset of lung cancers. We also present evidence for regulation of both PPAT and PAICS and pyruvate kinase activity by L-glutamine, a co-substrate for PPAT. A glutamine antagonist, 6-Diazo-5-oxo-L-norleucine (DON) blocked glutamine mediated induction of PPAT and PAICS as well as reduced pyruvate kinase activity. In summary, this study reveals the regulatory mechanisms by which purine biosynthetic pathway enzymes PPAT and PAICS, and pyruvate kinase activity is increased and exposes an existing metabolic vulnerability in lung cancer cells that can be explored for pharmacological intervention.

• amplification
• glutamine
• lung adenocarcinoma
• purine biosynthesis
• xenograft

• FISH
• c-MET
• heterogeneity
• immunohistochemistry
• non-small-cell lung cancer

• Cancer stem cells
• Cell signaling
• Chemotherapy
• Lung cancer
• Resistance

• EML4–ALK fusion
• ROS1
• acquired resistance
• brain metastases
• c-Met
• crizotinib
• non-small-cell lung cancer

• PI3K-Akt-mTOR pathway
• non-small cell lung cancer (NSCLC)

Oncogenic fusion genes underlie the mechanism of several common cancers. Next-generation sequencing based RNA-seq analyses have revealed an increasing number of recurrent fusions in a variety of cancers. However, absence of a publicly available gene-fusion focused RNA-seq data impedes comparative assessment and collaborative development of novel gene fusions detection algorithms. We have generated nine synthetic poly-adenylated RNA transcripts that correspond to previously reported oncogenic gene fusions. These synthetic RNAs were spiked at known molarity over a wide range into total RNA prior to construction of next-generation sequencing mRNA libraries to generate RNA-seq data.

Leveraging a priori knowledge about replicates and molarity of each synthetic fusion transcript, we demonstrate utility of this dataset to compare multiple gene fusion algorithms’ detection ability. In general, more fusions are detected at higher molarity, indicating that our constructs performed as expected. However, systematic detection differences are observed based on molarity or algorithm-specific characteristics. Fusion-sequence specific detection differences indicate that for applications where specific sequences are being investigated, additional constructs may be added to provide quantitative data that is specific for the sequence of interest.

To our knowledge, this is the first publicly available synthetic RNA-seq data that specifically leverages known cancer gene-fusions. The proposed method of designing multiple gene-fusion constructs over a wide range of molarity allows granular performance analyses of multiple fusion-detection algorithms. The community can leverage and augment this publicly available data to further collaborative development of analytical tools and performance assessment frameworks for gene fusions from next-generation sequencing data.

The online version of this article (doi:10.1186/1471-2164-15-824) contains supplementary material, which is available to authorized users.

• ALK
• EGFR
• KRAS
• Met
• ROS-1
• biomarkers
• lung adenocarcinoma

• Biomarker analysis
• Biopsy
• Cytology
• Individualized medicine
• Targeted therapy

• ALK
• autophagy
• crizotinib
• drug resistance
• lung cancer

• Anaplastic Lymphoma Kinase
• Animals
• Antineoplastic Agents/therapeutic use
• Caenorhabditis elegans Proteins/physiology
• Cell Transformation, Neoplastic/genetics
• Clinical Trials as Topic
• Crizotinib
• Drosophila Proteins/physiology
• Drug Resistance, Neoplasm
• Enzyme Induction
• Gene Expression Regulation, Developmental
• Gene Expression Regulation, Neoplastic
• Humans
• Lymphoma, Large-Cell, Anaplastic/enzymology
• Lymphoma, Large-Cell, Anaplastic/genetics
• Mice
• Models, Biological
• Models, Molecular
• Mutation
• Neoplasm Proteins/biosynthesis
• Neoplasm Proteins/chemistry
• Neoplasm Proteins/genetics
• Neoplasm Proteins/physiology
• Neoplasms/drug therapy
• Neoplasms/enzymology
• Neoplasms/genetics
• Oncogene Proteins, Fusion/genetics
• Oncogene Proteins, Fusion/physiology
• Protein Conformation
• Protein-Tyrosine Kinases/physiology
• Pyrazoles/therapeutic use
• Pyridines/therapeutic use
• Receptor Protein-Tyrosine Kinases/biosynthesis
• Receptor Protein-Tyrosine Kinases/chemistry
• Receptor Protein-Tyrosine Kinases/genetics
• Receptor Protein-Tyrosine Kinases/physiology
• Signal Transduction
• Translocation, Genetic
• Zebrafish Proteins/physiology

Lung cancer is a heterogeneous and complex disease. Genomic and transcriptomic profiling of lung cancer not only further our knowledge about cancer initiation and progression, but could also provide guidance on treatment decisions. The fact that targeted treatment is most successful in a subset of tumors indicates the need for better classification of clinically related molecular tumor phenotypes based on better understanding of the mutations in relevant genes, especially in those oncogenic driver mutations. EGFR gene mutations, KRAS gene mutations, EML4-ALK rearrangements and altered MET signaling are widely recognized alterations that play important roles in both the biological mechanisms and the clinical sensitivity to treatment in lung cancer. In this article, we reviewed the discovery of the clinical values of these oncogenic driver mutations and the clinical studies revealing the prognostic and predictive values of these biomarkers for clinical sensitivity and resistance to anti-EGFR therapy or other targeted therapies. These form the basis of personalized treatment in lung cancer based on biomarker profiles of individual tumor, leading to therapeutic advancement and betterment.

• ALK
• Driver mutations
• EGFR
• Lung cancer

• Adult
• Aged
• Aged, 80 and over
• Anaplastic Lymphoma Kinase
• Carcinoma, Non-Small-Cell Lung/drug therapy
• Carcinoma, Non-Small-Cell Lung/enzymology
• Carcinoma, Non-Small-Cell Lung/mortality
• Crizotinib
• Female
• Humans
• Lung Neoplasms/drug therapy
• Lung Neoplasms/enzymology
• Lung Neoplasms/mortality
• Male
• Middle Aged
• Protein Kinase Inhibitors/adverse effects
• Protein Kinase Inhibitors/therapeutic use
• Pyrazoles/adverse effects
• Pyrazoles/therapeutic use
• Pyridines/adverse effects
• Pyridines/therapeutic use
• Receptor Protein-Tyrosine Kinases/analysis
• Receptor Protein-Tyrosine Kinases/antagonists & inhibitors

• P30 CA046934 NCI NIH HHS
• P50 CA090578 NCI NIH HHS

RET encodes the tyrosine kinase receptor of growth factors belonging to the glial-derived neurotrophic factor family. Recently, RET gene rearrangements with N-terminal of KIF5B gene were identified in lung adenocarcinomas from large-scale sequencing. We investigated RET mRNA expression by real-time reverse-transcriptase polymerase chain reaction (RT-PCR) assay using LightCycler, and KIF5B/RET gene rearrangements using newly established fluorescence in situ hybridization (FISH) analysis in surgically treated nonsmall cell lung cancer (NSCLC) cases. RET protein expression was also investigated by immunohistochemistry (IHC). This study included 157 surgically removed NSCLC cases for mRNA level analyses. The RET/β actin mRNA levels were not significantly different between lung cancer (6.359 ± 15.268) and adjacent normal lung tissues (8.205 ± 28.931, P = 0.6332). Tumor/normal (T/N) ratio of RET/β actin mRNA levels was not different within gender, stage, smoking status, and pathological subtypes. T/N ratio of RET/β actin mRNA levels was significantly higher in KIF5B/RET rearrangement samples (161.763 ± 123.488) than in wild-type samples (5.9013 ± 17.148, P = 0.044). Although RET IHC positivity was not perfectly correlated with KIF5B/RET arrangement, we have detected the KIF5B/RET rearrangements using FISH analysis. Thus, we have successfully introduced FISH for diagnosing KIF5B/RET positive lung adenocarcinoma. This method facilitates the molecular evaluation for RET fusions and could be applicable in clinical practice to detect lung cancer that may be responsive to RET inhibitors.

• FISH
• KIF5B/RET
• RET expression
• lung cancer

• Adult
• Aged
• Aged, 80 and over
• Anaplastic Lymphoma Kinase
• Brazil
• Carcinoma, Non-Small-Cell Lung/enzymology
• Carcinoma, Non-Small-Cell Lung/genetics
• Female
• Gene Rearrangement/genetics
• Humans
• Immunohistochemistry
• In Situ Hybridization, Fluorescence
• Lung Neoplasms/enzymology
• Lung Neoplasms/genetics
• Male
• Middle Aged
• Receptor Protein-Tyrosine Kinases/genetics