MicroRNA Expression and Clinical Outcome of Small Cell Lung Cancer

The role of microRNAs in small-cell lung carcinoma (SCLC) is largely unknown. miR-34a is known as a p53 regulated tumor suppressor microRNA in many cancer types. However, its therapeutic implication has never been studied in SCLC, a cancer type with frequent dysfunction of p53. We investigated the expression of a panel of 7 microRNAs (miR-21, miR-29b, miR-34a/b/c, miR-155, and let-7a) in 31 SCLC tumors, 14 SCLC cell lines, and 26 NSCLC cell lines. We observed significantly lower miR-21, miR-29b, and miR-34a expression in SCLC cell lines than in NSCLC cell lines. The expression of the 7 microRNAs was unrelated to SCLC patients' clinical characteristics and was neither prognostic in term of overall survival or progression-free survival nor predictive of treatment response. Overexpression or downregulation of miR-34a did not influence SCLC cell viability. The expression of these 7 microRNAs also did not predict in vitro sensitivity to cisplatin or etoposide in SCLC cell lines. Overexpression or downregulation of miR-34a did not influence sensitivity to cisplatin or etoposide in SCLC cell lines. In contrast to downregulation of the miR-34a target genes cMET and Axl by overexpression of miR-34a in NSCLC cell lines, the intrinsic expression of cMET and Axl was low in SCLC cell lines and was not influenced by overexpression of miR-34a. Our results suggest that the expression of the 7 selected microRNAs are not prognostic in SCLC patients, and miR-34a is unrelated to the malignant behavior of SCLC cells and is unlikely to be a therapeutic target

Copy number aberrations of genes regulating normal thymus development in thymic epithelial tumors

PURPOSES: To determine whether the deregulation of genes relevant for normal thymus development can contribute to the biology of thymic epithelial tumors (TET). EXPERIMENTAL DESIGN: Using array comparative genomic hybridization, we evaluated the copy number aberrations of genes regulating thymus development. The expression of genes most commonly involved in copy number aberrations was evaluated by immunohistochemistry and correlated with patients' outcome. Correlation between FOXC1 copy number loss and gene expression was determined in a confirmation cohort. Cell lines were used to test the role of FOXC1 in tumors. RESULTS: Among 31 thymus development-related genes, PBX1 copy number gain and FOXC1 copy number loss were presented in 43.0% and 39.5% of the tumors, respectively. Immunohistochemistry on a series of 132 TETs, including those evaluated by comparative genomic hybridization, revealed a correlation between protein expression and copy number status only for FOXC1 but not for PBX1. Patients with FOXC1-negative tumors had a shorter time to progression and a trend for a shorter disease-related survival. The correlation between FOXC1 copy number loss and mRNA expression was confirmed in a separate cohort of 27 TETs. Ectopic FOXC1 expression attenuated anchorage-independent cell growth and cell migration in vitro. CONCLUSION: Our data support a tumor suppressor role of FOXC1 in TETs

Whole Genome and Transcriptome Sequencing of a B3 Thymoma

<div><p>Molecular pathology of thymomas is poorly understood. Genomic aberrations are frequently identified in tumors but no extensive sequencing has been reported in thymomas. Here we present the first comprehensive view of a B3 thymoma at whole genome and transcriptome levels. A 55-year-old Caucasian female underwent complete resection of a stage IVA B3 thymoma. RNA and DNA were extracted from a snap frozen tumor sample with a fraction of cancer cells over 80%. We performed array comparative genomic hybridization using Agilent platform, transcriptome sequencing using HiSeq 2000 (Illumina) and whole genome sequencing using Complete Genomics Inc platform. Whole genome sequencing determined, in tumor and normal, the sequence of both alleles in more than 95% of the reference genome (NCBI Build 37). Copy number (CN) aberrations were comparable with those previously described for B3 thymomas, with CN gain of chromosome 1q, 5, 7 and X and CN loss of 3p, 6, 11q42.2-qter and q13. One translocation t(11;X) was identified by whole genome sequencing and confirmed by PCR and Sanger sequencing. Ten single nucleotide variations (SNVs) and 2 insertion/deletions (INDELs) were identified; these mutations resulted in non-synonymous amino acid changes or affected splicing sites. The lack of common cancer-associated mutations in this patient suggests that thymomas may evolve through mechanisms distinctive from other tumor types, and supports the rationale for additional high-throughput sequencing screens to better understand the somatic genetic architecture of thymoma.</p> </div

Transcriptome sequencing data of tier 1 mutations.

<p>The expression of tier1 genes was estimated using Transcriptome sequencing data. For each gene, identified by a unique Ensembl identity (ID) code, the estimation of expression was calculated using Cufflinks and reported as FPKM (number of fragments per kilobase of exon per million fragments mapped: Cufflinks FPKM). Each FPKM value was calculated with a confidence interval ranging between Low CI and High CI values. Mutated allele expression summarizes the percentage of mutated reads covering the mutation site.</p

Features of the B3 thymoma.

<p>(A) Preoperative Chest CT-scan showing a mediastinal mass protruding in the left hemithorax. (B) Haematoxylin and Eosin staining of postoperative tumor section showing the lobular aspects typical of B3 thymomas, the almost complete absence of intratumoral thymocytes and the presence of cancer cells characterized by polygonal shape and round nuclei. (C) Whole-genome sequencing results showing (1) Sanger sequencing-confirmed SNVs and INDELs, (2) reference genomic coordinates, (3) copy number gain (green) and loss (red), and (4) structural variations.</p

Candidate structural variations identified by complete genome sequencing.

<p>Structural variations such as large deletions, insertions inversions or translocations were predicted using whole genome sequencing data. Structural variations were hypothesized in the presence of a junction sequence: a hybrid sequence composed of two non-adjacent fragment of DNA. In the table are reported the candidate structural variations of this B3 thymoma: the extremity position of the 2 joint sequences and the strand of orientation. Among these candidates only the translocation t(11;X) was confirmed by PCR.</p