Loss of chromosome arms 3p and 9p and inactivation of P16 (INK4a) in normal epithelium of patients with primary lung cancer

Identification of somatic copy number variations in plasma cell free DNA correlating with intrinsic resistances to EGFR targeted therapy in T790M negative non-small cell lung cancer

Background

About 20–30% EGFR-mutant non-small lung cancer show intrinsic resistance to EGFR targeted therapies. Compared to T790M positive in acquired resistance patients, little is known about EGFR-TKI intrinsic resistance for T790M negative patients.

Methods

Thirty-one patients with advanced stage lung cancer, including 18 patients with intrinsic resistance (PFS <6 months) and 13 patients with acquired resistance (PFS >36 months) but are negative for plasma T790M were recruited in the study. Plasma cell free DNA was profiled by low coverage whole genome sequencing with median genome coverage of 1.86X by Illumina X10. Sequencing coverage across chromosomes was summarized by samtools, and normalized by segmentation analysis as provided by R package ‘DNACopy’.

Results

The most frequent chromosomal changes were found on chr7, chr1 and chr8. Among them, chr7p gains were found in 12 (66.7%) intrinsic resistance and 4 (30.7%) acquired resistance patients. The gene EGFR was found located on the focal amplification peak of chr7p. The performance of 7p gain to predict intrinsic resistance reaches AUC =0.902. Similarly, focal amplifications were also found on chromosome 5, 16 and 22, where tumor related gene PCDHA^@, ADAMTS18 and CRKL were located. Focal deletions were also found in chr1, 8, 10 and 16, where genes SFTPA1/2, DLC1, PTEN and CDH1 are located.

Conclusions

The results suggest cell free DNA copy number might be a useful peripheral blood tumor biomarker for predicting intrinsic resistance of EGFR targeted therapy and prognosis.

The potential of genome-wide analyses to improve non-small-cell lung cancer care

SUMMARY 

Genomic technologies have revolutionized the way we study and understand cancer. The advent of next-generation sequencing technology in particular is now starting to change the clinical management of non-small-cell lung cancer. These technologies have helped us to refine prognostication and identify new driver mutations that can allow subselection of patients for therapeutic intervention. However, several limitations and challenges must be overcome before these technologies are widely accepted in diagnostic laboratories. It will be important for clinicians and diagnostic laboratories to consider sample type, analytical platform, cost, data security and ethics, and the bioinformatics challenges associated with 'big data', before widespread integration to the clinic. If these challenges can be overcome, then genomics has the potential to change clinical management of lung cancer.

Genetically abnormal circulating cells in lung cancer patients: an antigen-independent fluorescence in situ hybridization-based case-control study

PURPOSE

We performed a study to determine if a fluorescence in situ hybridization (FISH)-based assay using isolated peripheral blood mononuclear cells (PBMCs) with DNA probes targeting specific sites on chromosomes known to have abnormalities in non-small cell lung cancer (NSCLC) cases could detect circulating genetically abnormal cells (CACs).

EXPERIMENTAL DESIGN

We evaluated 59 NSCLC cases with stage I through IV disease and 24 controls. PBMCs and matched tumors were hybridized with 2 two-color [3p22.1/CEP3 and 10q22.3 (SP-A)/CEP10) and 2 four-color [CEP3, CEP7, CEP17, and 9p21.3 (URO); and EGFR, c-MYC, 6p11-q11, and 5p15.2 (LAV)] FISH probes. Percentages of cytogenetically abnormal cells (CACs) in peripheral blood and in matched tumor specimens were quantified by using an automated fluorescent scanner. Numbers of CACs were calculated based on the percentage of CACs (defined as PBMCs with genetic abnormalities) per milliliter of blood and expressed per microliter of blood.

RESULTS

Patients with NSCLC had significantly higher numbers of CACs than controls. Mean number of CACs ranged from 7.23 +/- 1.32/microL for deletions of 10q22.3/CEP10 to 45.52 +/- 7.49/microL for deletions of 3p22.1/CEP3. Numbers of CACs with deletions of 3p22.1, 10q22.3, and 9p21.3, and gains of URO, increased significantly from early to advanced stage of disease.

CONCLUSIONS

We have developed a sensitive and quantitative antigen-independent FISH-based test for detecting CACs in peripheral blood of patients with NSCLC, which showed a significant correlation with the presence of cancer. If this pilot study can be validated in a larger study, CACs may have a role in the management of patients with NSCLC.

Effects of Exogenous Wild-Type P16 Gene Transfection on the Expression of Cell Cycle-Related Proteins in Bladder Cancer Cell Line

Cell cycle regulatory proteins are important indicators in determining progression through the cell cycle. Recent experimental evidence shows that active Cdk4-Cyclin D1 complexes help cells to pass through the R point, a point of no return, after which the cells become committed to a new round of replication. It is widely known that P16INK4a can arrest cells in the G1 phase, but how the expression of exogenous P16INK4 gene can affect the activity of Cdk4-Cyclin D1 remains unclear. In this study, using exogenous wild-type P16 gene, antibodies for P16, Cdk4, Cyclin D1 and Rb proteins, and primers for these genes, we examined the expression of exogenous wild-type P16 gene and the changes of cell cycle regulatory genes (Cdk4, Cyclin D1, and Rb) in human bladder cancer cells. The cell cycle analysis revealed that the proliferation of P16 gene-transfected cancer cells was inhibited after the transfection of exogenous wild P16 gene. The immunocytochemical results indicated that after the transfection of exogenous wild-type P16 gene, the expression of Cdk4, Cyclin D1, and Rb were negative in the nuclei, whereas the expression of P16 significantly increased in the nuclei and the cytoplasm. The RT-PCR results showed that the transcription of P16 gene increased significantly after the transfection, whereas the transcription of Cdk4, Cyclin D1, and Rb decreased. Our results suggest that the transfection of exogenous wild P16 gene induces the bladder cancer cells arrested in G0/G1 phase, and the increasing expression of P16 inhibits the expression of Cdk4, Cyclin D1, and Rb in nuclei. As a consequence, exogenous P16 has negative effects on the malignant proliferation of the bladder cancer cells, and it may be considered as target for potential anticancer drugs.

Chromosome 9 instability and alterations of p16 gene in squamous cell carcinoma of the lung and in adjacent normal bronchi: FISH and immunohistochemical study

AIMS

p16, a tumour suppressor gene located at 9p21 chromosome and involved in cell cycle regulation, is often inactivated in lung carcinoma. Inactivation is also supported by the loss of p16 protein, a strong inhibitor of cyclin-dependent kinase (CDK) 4 and 6. The aim of this study was to examine alterations of p16 both in pulmonary squamous cell carcinoma (SCC) and in morphological normal bronchi contiguous with neoplasia.

METHODS AND RESULTS

p16 gene and chromosome 9 alterations were examined by fluorescence in situ hybridization and the expression of p16 protein by immunohistochemistry in pulmonary surgical specimens from 31 patients with SCC. As controls, surgical specimens from 13 patients with non-neoplastic pathology were examined. Tumours showed molecular alterations for p16 gene and chromosome 9 abnormalities in, respectively, 29/31 and 19/31 cases respectively. p16 protein was unexpressed in 29/31 cases. In morphologically normal bronchi p16 gene and chromosome 9 alterations occurred in, respectively, 13/31 and 4/31 cases respectively; loss of protein immunoreactivity occurred in 14/31 cases. No alterations were seen in any of the control cases.

CONCLUSIONS

Inactivation of p16 gene in histologically normal bronchi could aid the identification of individuals at risk of developing SCC of the lung.

Multi-target interphase fluorescence in situ hybridization assay increases sensitivity of sputum cytology as a predictor of lung cancer

Survival rates for lung cancer are low because patients have disseminated disease at diagnosis; therefore tests for early diagnosis are highly desirable. This pilot study investigated occurrence of chromosomal aneusomy in sputum from a 33 case-control cohort matched on age, gender, and date of sample collection. Subjects had chronic obstructive pulmonary disease and > or = 30 pack-years of tobacco use, and aneusomy was tested using a multi-target DNA FISH assay (LAVysion, Abbott/Vysis). In specimens collected within 12 months of lung cancer diagnosis, abnormality was more frequent among the 18 cases (41%) than the 17 controls (6%; P = 0.04). Aneusomy had no significant association with cytologic atypia, which might indicate that molecular and morphological changes could be independent markers of tumorigenesis. Combining both tests, abnormality was found in 83% of the cases and 20% of the controls (P = 0.0004) suggesting that FISH may improve the sensitivity of cytologic atypia as a predictor of lung cancer.

Cyclin D1 overexpression in bronchial epithelia of patients with lung cancer is associated with smoking and predicts survival

PURPOSE

Cyclin D1 is overexpressed in almost 60% of resectable non-small-cell lung cancer (NSCLC). In the absence of cyclin D1 gene amplification, overexpression is characterized by allelic imbalanced transcript levels.

METHODS

The aims were to study cyclin D1 expression by immunohistochemistry and allelic balance of transcripts in tumor-free bronchial epithelia from patients with resectable NSCLC by using monoclonal antibodies (48 patients and 288 sites), microdissection/reverse transcriptase polymerase chain reaction/restriction fragment length polymorphism analyses (24 patients and 144 sites). Derived data were related to patient characteristics-in particular, smoking habits.

RESULTS

In 167 (58%) of 288 sites, cyclin D1 was overexpressed, with cytoplasmic and nuclear sublocalization in 53% and 7% of all sites, respectively. Nuclear overexpression was more frequent in premalignant versus normal or hyperplastic epithelia (55% v 3%; P <.0001). Allele-specific expression imbalances were found in 69 (48%) of 144 sites; in particular, those in which cyclin D1 was overexpressed (P =.004). In 14 (58%) of 24 patients, balanced or imbalanced transcript ratios and degree of expression were consistent at all sites for the same patient, whereas in another 10 patients, transcript balances and cyclin D1 expression patterns varied across the sites. Nuclear cyclin D1 expression in at least one site (14 of 48 patients) was linked to heavy smoking (> 40 pack-years; P =.02) and shorter overall survival (P =.01).

CONCLUSION

Allele-specific, probably damage-driven, deregulation of the cyclin D1 gene may precede and perhaps facilitate the spread of preneoplastic clones across the bronchial epithelial surface in a significant number of patients. Cyclin D1 expression at multiple bronchial sites may identify a subgroup of heavy-smoking patients with poor outcome.

Genetic and epigenetic mosaicism in cancer precursor tissues

The concept of field effects in cancer is old, but recent molecular data have substantiated it. Clones of cells that carry well-defined genetic or epigenetic aberrations, but which have not yet acquired the morphological hallmarks of neoplasia, have been documented in the precursor tissues of some of the most common pediatric and adult malignancies. Here I review this evidence, focusing on loss of heterozygosity (LOH) and gain of DNA methylation.

Loss of heterozygosity analysis of mouse pulmonary adenomas induced by coal tar

Manufactured gas plant (MGP) residues, commonly known as coal tars, were generated several decades ago as a byproduct of residential and industrial gas production from the distillation of coal. Previous short-term exposure studies have shown MGP residues to be tumorigenic in mouse liver and lung. In order to gain further insight into carcinogenesis by complex mixtures of environmental chemicals containing known carcinogenic polycyclic aromatic hydrocarbons, we investigated mouse pulmonary tumors for loss of heterozygosity (LOH) as a result of multiple exposure to MGP residues. Twenty mouse lung adenomas produced in (C57BL/6 x C3H)F1 hybrid mice and manually microdissected were selected to examine genome-wide allelic losses at 58 microsatellite loci. Regions of chromosomes 1, 4, 5, 8, and 11 were affected in 30-40% of tumors. The elevated rates of allelic imbalance in these chromosomes may indicate the location of unknown tumor suppressor genes significant to neoplastic transformation in mouse lung tissues. Laser capture microdissection-based LOH analysis of pulmonary adenomas showed that contamination of nonneoplastic tissues was not masking the allelic losses in the manually microdissected tumor analysis. The low frequency of chromosome instability in these tumors, measured by means of inter-simple sequence repeat PCR, suggests the presence of discrete regions of LOH instead of extensive structural rearrangements.

A case-control analysis of lymphocytic chromosome 9 aberrations in lung cancer

Cytogenetic aberrations on chromosome 9 have been reported to be one of the most frequent genetic changes in lung tumorigenesis. Although many of these changes have been detected in lung carcinoma specimens, there is growing evidence showing the concordance between chromosomal alterations in primary lung tumors and peripheral blood lymphocytes (PBLs). We investigated whether spontaneous aberrations on chromosome 9 in PBLs are associated with the presence of lung cancer and with a family history of cancer. A personal interview, to construct a detailed epidemiologic profile including family history of cancer, was conducted on 174 lung cancer cases and 162 matched controls. One hundred metaphases from PBLs of each subject were analyzed for chromosome 9 aberrations using the whole chromosome painting technique. Overall, the mean proportion of individuals with chromosome 9 abnormalities in their PBLs was significantly higher in cases (96.0%) than in controls (60.5%) (p < 0.05). After adjustment by age, gender, ethnicity, family size, and pack-years, there was a 16.63-fold significantly elevated odds ratio (OR) for lung cancer associated with chromosome 9 aberrations. When subjects were categorized by frequencies of the chromosome 9 lesions, we observed significantly increased odds ratios of 11.13 (4.66, 26.58) and 27.45 (11.15, 67.54) for individuals with 1 chromosome 9 aberration and >/=2 chromosome 9 aberrations, respectively. By performing family history analyses, we further observed that control individuals with chromosome 9 aberrations were more likely to report a family history of any cancer (OR = 1.67 [0.84, 3.32]) and lung cancer (OR = 2.49 [0.81, 7.67]). Our findings suggest that chromosome 9 aberrations in PBLs might be considered a marker of lung cancer predisposition and may be associated with familial aggregation of cancer.

Recent advances in the molecular diagnosis of lung cancer

Despite extensive effort in improvement of diagnosis and treatment of patients with lung cancer in past three decades, the overall survival of patients with the disease remains dismal. Because the development of lung cancer takes a few decades, early diagnosis of the disease or identification of truly high-risk populations may provide us opportunity to successfully cure or prevent the disease. Recent advances in understanding biological basis of lung tumorigenesis provide new tools for detecting malignant cells or the process of malignant transformation and progression. Along with identification of molecular abnormalities in the early lung tumorigenesis, advanced molecular analytic technologies have been emerged, which may facilitate development of rapid and effective methods for early diagnosis and risk assessment. Here, I discuss recent progresses in understanding of early molecular abnormalities in lung cancer, efforts of translating laboratory findings to clinical tests, and prospective of biomarkers in lung cancer diagnosis and risk assessment.

Tumor suppressor genes on chromosome 3p involved in the pathogenesis of lung and other cancers

Loss of heterozygosity (LOH) involving several chromosome 3p regions accompanied by chromosome 3p deletions are detected in almost 100% of small (SCLCs) and more than 90% of non-small (NSCLCs) cell lung cancers. In addition, these changes appear early in the pathogenesis of lung cancer and are found as clonal lesions in the smoking damaged respiratory epithelium including histologically normal epithelium as well as in epithelium showing histologic changes of preneoplasia. These 3p genetic alterations lead to the conclusion that the short arm of human chromosome 3 contains several tumor suppressor gene(s) (TSG(s)). Although the first data suggesting that 3p alterations were involved in lung carcinogenesis were published more than 10 years ago, only recently has significant progress been achieved in identifying the candidate TSGs and beginning to demonstrate their functional role in tumor pathogenesis. Some of the striking results of these findings has been the discovery of multiple 3p TSGs and the importance of tumor acquired promoter DNA methylation as an epigenetic mechanism for inactivating the expression of these genes in lung cancer. This progress, combined with the well known role of smoking as an environmental causative risk factor in lung cancer pathogenesis, is leading to the development of new diagnostic and therapeutic strategies which can be translated into the clinic to combat and prevent the lung cancer epidemic. It is clear now that genetic and epigenetic abnormalities of several genes residing in chromosome region 3p are important for the development of lung cancers but it is still obscure how many of them exist and which of the numerous candidate TSGs are the key players in lung cancer pathogenesis. We review herein our current knowledge and describe the most credible candidate genes.

Prognostic significance of p16INK4a alterations and 9p21 loss of heterozygosity in locally advanced laryngeal squamous cell carcinoma

The p16INK4a gene, localized within chromosome 9p21, has been identified as a cyclin-dependent kinase inhibitor and may negatively regulate the cell cycle acting as a tumor suppressor. Genetic alterations involving the 9p21 region are common in human cancers. A consecutive series of 64 untreated patients (median of follow up 53 months) undergoing surgical resection for locally advanced laryngeal squamous-cell carcinomas (LSCCs) has been studied prospectively. Our purpose was to investigate p16 alterations (9p21 allelic loss, hypermethylation and point mutations) and their possible association with clinico-pathological data and flow cytometric variables (DNA-ploidy and S-phase fraction (SPF)), and to determine the possible prognostic role of this gene in these tumors. PCR-based techniques were used for investigating 9p21 loss of heterozygosity (LOH) and methylation promoter status of the p16 gene. p16 mutations were detected by PCR-SSCP (single strand conformation polymorphism) and sequencing. 9p21 LOH was detected in 16/62 (26%) informative tumors, point mutations in 5% (3/64) and hypermethylation in 9% (6/64) of the cases. p16 alterations were significantly associated with high SPF and DNA-aneuploidy. By univariate analysis, poor histologic differentiation, stage IV, DNA-aneuploidy and p16 point mutations proved to be significantly related to quicker relapse, whereas these same factors, and in addition high SPF, 9p21 LOH and any p16 alterations were significantly related to shorter overall survival. By Cox proportional hazards analysis only histologic grade (G3) and p16 point mutations were independently related to both disease relapse and death. Our study has identified p16 point mutations as important biomolecular indicators in LSCCs.