Characterization of Fibroblast Growth Factor Receptor 1 in Small-Cell Lung Cancer

Introduction:There remains a significant therapeutic need for small-cell lung cancer (SCLC). We and others have reported high frequency of copy number gains in cytogenetic bands encoding fibroblast growth factor receptor 1 (FGFR1) in SCLC tumors and cell lines.Methods:Thirteen SCLC cell lines and 68 SCLC patient tumor samples were studied for FGFR1 amplification. Growth inhibition assays were performed using PD173074, a pan-FGFR inhibitor to determine the correlation between FGFR1 expression and drug sensitivity.Results:We did not detect FGFR1 mutations in SCLC cell lines. Focal amplification of FGFR1 gene was found in five tumor samples (7%), with high-level focal amplification in only one tumor sample (1%). Amplification owing to polysomy of chromosome 8, where FGFR1 locates, was observed in 22 tumor samples (32%). There was no correlation between FGFR1 gene copy number and messenger RNA expression or protein expression in SCLC cells. FGFR inhibitor sensitivity correlated with FGFR1 copy number determined by real-time polymerase chain reaction assay (r= −0.79; p = 0.01).Conclusion:FGFR1 gene mutations and focal amplification are rare in SCLC, but polysomy of chromosome 8 is relatively common. FGFR1 copy number gain predicts sensitivity to FGFR inhibition, and FGFR expression correlates inversely with chemosensitivity

NUP98-PHF23 Is a Chromatin-Modifying Oncoprotein That Causes a Wide Array of Leukemias Sensitive to Inhibition of PHD Histone Reader Function

In this report, we show that expression of a NUP98-PHF23 (NP23) fusion, associated with acute myeloid leukemia (AML) in humans, leads to myeloid, erythroid, T-cell, and B-cell leukemia in mice. The leukemic and pre-leukemic tissues display a stem cell-like expression signature including Hoxa, Hoxb, and Meis1 genes. The PHF23 PHD domain is known to bind H3K4me3 residues, and chromatin immunoprecipitation experiments demonstrated that the NP23 protein bound chromatin at a specific subset of H3K4me3 sites, including Hoxa, Hoxb, and Meis1. Treatment of NP23 cells with disulfiram, which inhibits the binding of PHD domains to H3K4me3 residues, rapidly and selectively killed NP23 myeloblasts; cell death was preceded by decreased expression of Hoxa, Hoxb, and Meis1. Furthermore, AML driven by a related fusion gene, NUP98-JARID1A (NJL), was also sensitive to disulfiram. Thus, the NP23 mouse provides a platform to evaluate compounds that disrupt binding of oncogenic PHD proteins to H3K4me3

Interaction between the microbiome and TP53 in human lung cancer.

BACKGROUND: Lung cancer is the leading cancer diagnosis worldwide and the number one cause of cancer deaths. Exposure to cigarette smoke, the primary risk factor in lung cancer, reduces epithelial barrier integrity and increases susceptibility to infections. Herein, we hypothesize that somatic mutations together with cigarette smoke generate a dysbiotic microbiota that is associated with lung carcinogenesis. Using lung tissue from 33 controls and 143 cancer cases, we conduct 16S ribosomal RNA (rRNA) bacterial gene sequencing, with RNA-sequencing data from lung cancer cases in The Cancer Genome Atlas serving as the validation cohort. RESULTS: Overall, we demonstrate a lower alpha diversity in normal lung as compared to non-tumor adjacent or tumor tissue. In squamous cell carcinoma specifically, a separate group of taxa are identified, in which Acidovorax is enriched in smokers. Acidovorax temporans is identified within tumor sections by fluorescent in situ hybridization and confirmed by two separate 16S rRNA strategies. Further, these taxa, including Acidovorax, exhibit higher abundance among the subset of squamous cell carcinoma cases with TP53 mutations, an association not seen in adenocarcinomas. CONCLUSIONS: The results of this comprehensive study show both microbiome-gene and microbiome-exposure interactions in squamous cell carcinoma lung cancer tissue. Specifically, tumors harboring TP53 mutations, which can impair epithelial function, have a unique bacterial consortium that is higher in relative abundance in smoking-associated tumors of this type. Given the significant need for clinical diagnostic tools in lung cancer, this study may provide novel biomarkers for early detection

COMPLETE GENOME SEQUENCING OF A HUMAN B3 THYMOMA

Background: Molecular biology of thymomas is poorly understood. We sequenced the whole genome of one B3 thymoma and the matched normal DNA from blood sample of the same patient. Methods: Frozen primary tumor and blood were collected from a Caucasian 53 female with B3/stage IVA thymoma after surgery. DNA and RNA were extracted using All Prep kit (Qiagen). Array Comparative genomic hybridization (CGH) was performed on 180K array (Agilent) and Agilent platform. Transcriptome sequencing was performed using 72bp paired-end sequencing and 2 flow cell lanes of genome analyzer II (Illumina). Whole genome sequencing (WGS) was performed on tumor and normal DNA using Complete Genomic Inc platform. Results: In the WGS analysis, a total of 222.02 gigabases (Gb) of sequence were mapped (95.3% of genome called) for the tumor sample and 234.53 Gb (96.4% of genome called) for the matched normal control. Sequence reads were aligned to a human reference genome (NCBI Build 37) and a local de novo assembly was used to call and score variants. Both array CGH and copy number (CN) aberrations estimated from WGS showed CN imbalance patterns comparable with those previously described for B3 thymomas with CN gain of chromosomes 1q, 5, 7 and X and CN loss of 3p, 6, 11q42.2-qter and q13. We observed 3,096,049 single nucleotide variations (SNVs) in the tumor and 3,314,611 in the normal DNA. The transition/transversion ratio was 2.14 and 1.83 for germ line and somatic SNVs, respectively. Somatic SNVs were defined as those variations present in tumor but not normal matched DNA. We observed 5946 diploid somatic indels and 6530 SNVs, of which 43 and 83 were within exonic regions, respectively. 29 indels and 25 SNVs were not previously described as SNPs, nor in segmental duplication, or synonymous mutations. By comparison with the transcriptome sequencing data of the same tumor sample, we confirmed the expression of 6 mutated genes, while for 45 mutated genes there were not enough reads to confirm the calls. Conclusion: WGS and accompanying transcriptome sequencing offer an unprecedented view of the genome of a thymoma cancer patient sample. We are actively engaged in determining the potential functional significance of the genomic variants in the context of transcriptome sequencing and copy number variation to gather clues as to the underlying biology driving this relatively rare tumor type

The BRCA1 Ashkenazi founder mutations occur on common haplotypes and are not highly correlated with anonymous single nucleotide polymorphisms likely to be used in genome-wide case-control association studies

BackgroundWe studied linkage disequilibrium (LD) patterns at the BRCA1 locus, a susceptibility gene for breast and ovarian cancer, using a dense set of 114 single nucleotide polymorphisms in 5 population groups. We focused on Ashkenazi Jews in whom there are known founder mutations, to address the question of whether we would have been able to identify the 185delAG mutation in a case-control association study (should one have been done) using anonymous genetic markers. This mutation is present in approximately 1% of the general Ashkenazi population and 4% of Ashkenazi breast cancer cases. We evaluated LD using pairwise and haplotype-based methods, and assessed correlation of SNPs with the founder mutations using Pearson's correlation coefficient.ResultsBRCA1 is characterized by very high linkage disequilibrium in all populations spanning several hundred kilobases. Overall, haplotype blocks and pair-wise LD bins were highly correlated, with lower LD in African versus non-African populations. The 185delAG and 5382insC founder mutations occur on the two most common haplotypes among Ashkenazim. Because these mutations are rare, even though they are in strong LD with many other SNPs in the region as measured by D-prime, there were no strong associations when assessed by Pearson's correlation coefficient, r (maximum of 0.04 for the 185delAG).ConclusionSince the required sample size is related to the inverse of r, this suggests that it would have been difficult to map BRCA1 in an Ashkenazi case-unrelated control association study using anonymous markers that were linked to the founder mutations