Abstract 1133: Inactivation of BRG1 in non-small cell lung cancer (NSCLC) cell lines
Bibliographic record
Abstract
Abstract Purpose: To study the frequency and gene expression profile of BRG1 inactivation in NSCLC cell lines. Background: BRG1 is the catalytic subunit of SWI/SNF chromatin remodeling complex and provides ATPase activity necessary for transcriptional regulation of many genes. BRG1 is frequently inactivated in lung cancers and loss of BRG1 correlated with poor prognosis. Methods: Forty NSCLC cell lines containing various gene mutations were analyzed. BRG1 cDNA was sequenced and SNP analysis was used to confirm the large deletion mutants. Gene expression profile was determined by Illumina human WG-6 V3 beadchip (detecting ∼ 48,000 transcripts, ∼25,000 genes). BRG1 mRNA levels were determined by both RNA microarray and qPCR methods. BRG1 protein expression was analyzed by immuno-blotting. Results: Thirteen of forty (33%) NSCLC cell lines had no BRG1 protein expression (n =11) or expressed abnormal size of BRG1 (n =2). BRG1 cDNA was sequenced in these cell lines as well as control cell lines. While 10 control cell lines with normal BRG1 protein expression were not found to contain mutations, eleven cell lines without BRG1 protein expression and one containing abnormal size BRG1 protein were found to have mutations, including deletions, point mutations and insertion. The deletions and point mutations of BRG1 are homozygous. Mutant BRG1 expressed either no or lower than normal levels of BRG1 mRNA. BRG1 inactivation was found more frequent in smokers (50%) than non-smokers (15%), and coexisted with KRAS mutation, but was mutually exclusive to EGFR mutation. Furthermore, inactivation of BRG1 and LKB1, a tumor suppressor gene also located on chromosome 19p and adjacent to BRG1, showed 73% concordance (P=0.03). Finally, RNA microarray analysis showed nearly 800 transcripts (False Discovery Rate <5%) down or up regulated in NSCLC cell lines with BRG1 inactivation compared to cell lines with wild type BRG1. Conclusions: 1) BRG1 is frequently mutated in NSCLC cell lines by deletions or point mutations. 2) There is excellent concordance (98 %) between mutation status and loss of protein expression. 3) Inactivation of BRG1 shows concordance with smoking history and LKB1 mutation, and is negatively correlated with EGFR mutation. 4) Inactivation of BRG1 has a major impact on gene expression profile of NSCLC cell lines. These data indicate that BRG1 may play an important role in lung tumorigenesis. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1133.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".