Differential DNA sequence deletions from chromosomes 3, 11, 13, and 17 in squamous-cell carcinoma, large-cell carcinoma, and adenocarcinoma of the human lung

A comprehensive study of p53 protein

The protein p53 has been extensively investigated since it was found 43 years ago and has become a "guardian of the genome" that regulates the division of cells by preventing the growth of cells and dividing them, that is, inhibits the development of tumors. Initial proof of protein existence by researchers in the mid-1970s was found by altering and regulating the SV40 big T antigen termed the A protein. Researchers demonstrated how viruses play a role in cancer by employing viruses' ability to create T-antigens complex with viral tumors, which was discovered in 1979 following a viral analysis and cancer analog research. Researchers later in the year 1989 explained that in Murine Friend, a virus-caused erythroleukemia, commonly found that p53 was inactivated to suggest that p53 could be a "tumor suppressor gene." The TP53 gene, encoding p53, is one of human cancer's most frequently altered genes. The protein-regulated biological functions of all p53s include cell cycles, apoptosis, senescence, metabolism of the DNA, angiogenesis, cell differentiation, and immunological response. We tried to unfold the history of the p53 protein, which was discovered long back in 1979, that is, 43 years of research on p53, and how p53's function has been developed through time in this article.

Improving the Subtype Classification of Non-small Cell Lung Cancer by Elastic Deformation Based Machine Learning

Non-invasive image-based machine learning models have been used to classify subtypes of non-small cell lung cancer (NSCLC). However, the classification performance is limited by the dataset size, because insufficient data cannot fully represent the characteristics of the tumor lesions. In this work, a data augmentation method named elastic deformation is proposed to artificially enlarge the image dataset of NSCLC patients with two subtypes (squamous cell carcinoma and large cell carcinoma) of 3158 images. Elastic deformation effectively expanded the dataset by generating new images, in which tumor lesions go through elastic shape transformation. To evaluate the proposed method, two classification models were trained on the original and augmented dataset, respectively. Using augmented dataset for training significantly increased classification metrics including area under the curve (AUC) values of receiver operating characteristics (ROC) curves, accuracy, sensitivity, specificity, and f1-score, thus improved the NSCLC subtype classification performance. These results suggest that elastic deformation could be an effective data augmentation method for NSCLC tumor lesion images, and building classification models with the help of elastic deformation has the potential to serve for clinical lung cancer diagnosis and treatment design.

The Glucose-Regulated MiR-483-3p Influences Key Signaling Pathways in Cancer

The hsa-mir-483 gene, located within the IGF2 locus, transcribes for two mature microRNAs, miR-483-5p and miR-483-3p. This gene, whose regulation is mediated by the the CTNNB1/USF1 complex, shows an independent expression from its host gene IGF2. The miR-483-3p affects the Wnt/β-catenin, the TGF-β, and the TP53 signaling pathways by targeting several genes as CTNNB1, SMAD4, IGF1, and BBC3. Accordingly, miR-483-3p is associated with various tissues specific physiological properties as insulin and melanin production, as well as with cellular physiological functions such as wounding, differentiation, proliferation, and survival. Deregulation of miR-483-3p is observed in different types of cancer, and its overexpression can inhibit the pro-apoptotic pathway induced by the TP53 target effectors. As a result, the oncogenic characteristics of miR-483-3p are linked to the effect of some of the most relevant cancer-related genes, TP53 and CTNNB1, as well as to one of the most important cancer hallmark: the aberrant glucose metabolism of tumor cells. In this review, we summarize the recent findings regarding the miR-483-3p, to elucidate its functional role in physiological and pathological contexts, focusing overall on its involvement in cancer and in the TP53 pathway.

A network-based method to evaluate quality of reproducibility of differential expression in cancer genomics studies

BACKGROUND

Personalized cancer treatments depend on the determination of a patient's genetic status according to known genetic profiles for which targeted treatments exist. Such genetic profiles must be scientifically validated before they is applied to general patient population. Reproducibility of findings that support such genetic profiles is a fundamental challenge in validation studies. The percentage of overlapping genes (POG) criterion and derivative methods produce unstable and misleading results. Furthermore, in a complex disease, comparisons between different tumor subtypes can produce high POG scores that do not capture the consistencies in the functions.

RESULTS

We focused on the quality rather than the quantity of the overlapping genes. We defined the rank value of each gene according to importance or quality by PageRank on basis of a particular topological structure. Then, we used the p-value of the rank-sum of the overlapping genes (PRSOG) to evaluate the quality of reproducibility. Though the POG scores were low in different studies of the same disease, the PRSOG was statistically significant, which suggests that sets of differentially expressed genes might be highly reproducible.

CONCLUSIONS

Evaluations of eight datasets from breast cancer, lung cancer and four other disorders indicate that quality-based PRSOG method performs better than a quantity-based method. Our analysis of the components of the sets of overlapping genes supports the utility of the PRSOG method.

Association between IL-1A single nucleotide polymorphisms and chronic beryllium disease and beryllium sensitization

OBJECTIVE

To determine if single nucleotide polymorphisms (SNPs) in interleukin (IL) IL-1A, IL-1B, IL-1RN, IL-2, IL-9, and IL-9R were associated with chronic beryllium disease (CBD) and beryllium sensitization (BeS).

METHODS

Forty SNPs in six IL genes were evaluated in 85 individuals with CBD, 61 individuals with BeS, and 730 individuals without BeS or CBD (nonsensitized) using a 5' nuclease polymerase chain reaction assay. Logistic regression was used to evaluate the association between IL SNPs, CBD, and BeS, adjusting for plant-site and HLA-DPB1Glu69 in additive, dominant, and recessive inheritance models.

RESULTS

IL-1A-1142, IL-1A-3769, and IL-1A-4697 were significantly associated with CBD in both the additive and dominant models compared to individuals with BeS or the nonsensitized.

CONCLUSIONS

These results indicate that genetic variations in the IL-1A gene may play a role in the development of CBD but not BeS.

Oncogenic role of miR-483-3p at the IGF2/483 locus

hsa-mir-483 is located within intron 2 of the IGF2 locus. We found that the mature microRNA (miRNA) miR-483-3p is overexpressed in 100% of Wilms' tumors. In addition, colon, breast, and liver cancers exhibit high or even extremely high levels of miR-483-3p in approximately 30% of the cases. A coregulation with IGF2 mRNA was detected, although some tumors exhibited high expression of miR-483-3p without a concomitant increase of IGF2. These findings suggested that miR-483-3p could cooperate with IGF2 or act as an autonomous oncogene. Indeed, here we prove that an anti-miRNA oligonucleotide against miR-483-3p could inhibit the miRNAs without affecting IGF2 mRNA and it could suppress tumorigenicity of HepG2 cells, a cell line that overexpresses miR-483-3p and IGF2. Conversely, no antitumor effect was elicited by inhibition of IGF2. The oncogenic mechanism of miR-483-3p was at least partially clarified by the finding that it could modulate the proapoptotic protein BBC3/PUMA and miR-483-3p enforced expression could protect cells from apoptosis. Our results indicate that miR-483-3p could function as an antiapoptotic oncogene in various human cancers and reveal a new, potentially important target for anticancer therapy.

Annulate Lamellae in a Large Cell Lung Carcinoma Cell Line with High Expression of Tyrosine Kinase Receptor and Proto-Oncogenes

The morphology, karyotype, in vitro growth properties, and expression of tyrosine kinase receptors and proto-oncogenes are reported for a newly established large cell undifferentiated lung carcinoma cell line (RVH-6849). The results were analyzed concomitantly with those for two well-established cell lines from an adenocarcinoma of the lung (A549) and a squamous cell carcinoma (A431). All three cell lines demonstrated common ultrastructural features of epithelial cells, but only RVH-6849 had frequent aggregates of centrioles and annulate lamellae (AL) and was polyploid, having five to seven copies of chromosome 7 by karyotype analysis. All three cell lines expressed transforming growth factor alpha (TGF-alpha), epidermal growth factor receptor (EGFR), c-erb B-2, and c-met genes. RVH-6849 cells, however, expressed the most messenger RNA (mRNA) for TGF-alpha, c-erb B-2, and c-met. Only EGFR mRNA was expressed more in the other two cell lines, especially in A431 cells. AL represent an exaggerated form of the nuclear membrane-pore complex that is found in actively proliferating cells such as germ and some neoplastic cells. AL are suspected to be involved in the deposition or processing of mRNA: The enhanced coexpression of AL and mRNAs of three tyrosine kinase-containing receptors in RVH-6849 cells may represent such a relationship.

TNF-alpha polymorphisms in chronic beryllium disease and beryllium sensitization

OBJECTIVE

Tumor necrosis factor-alpha (TNF-alpha) is a potent cytokine involved in normal immune functions. The aim of this study was to investigate if there is an association between chronic beryllium disease or beryllium sensitization and two variants of the TNF-alpha gene located at -308 and -238 called TNF-alpha-308*02 and TNF-alpha-238*02.

METHODS

TNF-alpha-308 and TNF-alpha-238 genotyping was conducted in a large, population-based cohort consisting of 886 beryllium workers (92 individuals with chronic beryllium disease, 64 who were beryllium sensitized, and 730 individuals without sensitization or disease).

RESULTS

The odds of chronic beryllium disease in the presence of at least one TNF-alpha-308*02 or TNF-alpha-238*02 allele was not significant (OR=1.0; 95% CI=0.7, 1.7 and OR=0.8; 95% CI=0.4, 1.6). This was true regardless of whether a worker was homozygous or heterozygous for TNF-alpha-308*02 or TNF-alpha-238*02. Similarly, neither allele was associated with sensitization (P>0.05).

CONCLUSIONS

Unlike an earlier report, there was no association between these specific TNF-alpha alleles and either chronic beryllium disease or sensitization to beryllium.

Reduced expression of the Tslc1 gene and its aberrant DNA methylation in rat lung tumors

TSLC1 gene inactivation due to promoter methylation has been reported in several human cancers. Here, we investigated the expression of the Tslc1 gene and its methylation pattern in lung adenocarcinomas induced by N-nitrosobis(2-hydroxypropyl)amine (BHP). Six-week-old male Wistar rats were given 2000 ppm BHP in their drinking water for 12 weeks and maintained without further treatment until they were sacrificed at 25 weeks. Total RNA was extracted from a total of 11 lung adenocarcinomas and their Tslc1 gene expressions were analyzed by real-time quantitative reverse transcription-polymerase chain reaction. Tslc1 expression was significantly reduced in the lung adenocarcinomas compared with three normal lung tissues (p < 0.05). Bisulfite sequence analysis of four lung adenocarcinomas and two normal lung tissues revealed that the 5' upstream region of the Tslc1 gene was highly methylated in the four lung adenocarcinomas, but unmethylated in the two normal lung tissues. These results suggest that aberrant Tslc1 gene methylation may be involved in BHP-induced development of lung adenocarcinomas in rats.

Exfoliative cytologic evaluation of primary cultured lung carcinomas

This paper describes a tissue culture and exfoliative cell culture system that enables one to (1) evaluate the adequacy of primary lung carcinoma cultures for cytogenetic analysis, and (2) predict the likelihood of viable cells and type of differentiation present in the primary lung tumor cultures used for cytogenetics. Primary lung carcinomas were established from explant outgrowths and maintained in serum supplemented or serum free media on plastic or basement membrane associated protein coated dishes in order to obtain cells for karyotypic analysis (Miura et al., 1990). The media from these cultures that would ordinarily have been discarded was aspirated at each media change and used to prepare cytocentrifuge cytology preparations. Papanicolaou stained cells from the preparations were evaluated by cytotechnologists in order to assess (1) the cellularity and presence of cancer cells in the sample, (2) cytology preparations of cell and explant outgrowth cultures from primary lung tumors are reliable method for screening and evaluating the suitability of primary lung carcinoma cultures for cytogenetic analysis.

Wilms' tumour: connecting tumorigenesis and organ development in the kidney

Wilms' tumour, or nephroblastoma, is a common childhood tumour that is intimately linked to early kidney development and is often associated with persistent embryonic renal tissue and other kidney abnormalities. WT1, the first gene found to be inactivated in Wilms' tumour, encodes a transcription factor that functions as both a tumour suppressor and a critical regulator of renal organogenesis. Our understanding of the roles of WT1 in tumour formation and organogenesis have advanced in parallel, providing a striking example of the intersection between tumour biology, cellular differentiation and normal organogenesis.

The association between HLA-DPB1Glu69 and chronic beryllium disease and beryllium sensitization

BACKGROUND

Several case-control studies have found an association between chronic beryllium disease (CBD) and HLA-DPB1 gene variants. However, the relationship between HLA-DPB1 and beryllium sensitization, and whether the presence of one or two HLA-DPB1(Glu69) alleles is differentially associated with CBD and beryllium sensitization have not been completely resolved.

METHODS

Restriction fragment length polymorphism (RFLP) analysis was used to address these questions in a large population-based cohort consisting of 884 beryllium workers (90 with CBD, 64 beryllium sensitized).

RESULTS

HLA-DPB1(Glu69) was associated with both CBD (OR = 9.4; 95% CI = 5.4, 16.6) and sensitization (OR = 3.3, 95% CI = 1.9, 5.9). Further, workers with CBD and sensitization were more likely to be homozygous HLA-DPB1(Glu69) compared to workers without disease or sensitization (P < 0.001).

CONCLUSIONS

Follow-up of this cohort, scrutiny of HLA-DPB1 haplotypes, and evaluation of gene-environment and gene-gene interactions will be important for fully understanding the immunogenetic nature of this occupational disease.

RRM1 and PTEN as prognostic parameters for overall and disease-free survival in patients with non-small-cell lung cancer

PURPOSE

RRM1 has important functions in the determination of the malignant phenotype. It controls cell proliferation through deoxynucleotide production and metastatic propensity through PTEN induction. It is located in a region of loss of heterozygosity in non-small-cell lung cancer (NSCLC), which is a predictor of poor survival. We hypothesized that RRM1 expression would be a significant predictor of outcome in NSCLC.

PATIENTS AND METHODS

A retrospective data set of 49 patients and a prospective data set of 77 patients with resectable NSCLC were studied. RNA was extracted from tumor and normal lung tissue, and expression of the genes RRM1, PTEN, and RRM2 was determined by real-time quantitative polymerase chain reaction.

RESULTS

RRM1 expression was significantly correlated with PTEN and RRM2 expression in tumor tissue. RRM1 and PTEN expression in tumor tissue was highly predictive of overall (P =.011 and.018, respectively) and disease-free survival (P =.002 and.026, respectively). Patients with high levels of expression lived longer and had disease recurrence later than patients with low levels of RRM1 and PTEN. In a multivariate analysis, high RRM1 expression was predictive of long survival independent of tumor stage, performance status, and weight loss.

CONCLUSION

RRM1 is a biologically and clinically important determinant of malignant behavior in NSCLC. Knowing the level of expression of this gene adds significant information to management decisions independent of the currently used outcome predictors of tumor stage, performance status, and weight loss. Future clinical trials should stratify patients based on expression of this gene to avoid unwanted biases.

Promoter methylation of the TSLC1 gene in advanced lung tumors and various cancer cell lines

We previously identified TSLC1, a tumor suppressor gene in human nonsmall cell lung cancer (NSCLC). TSLC1 belongs to immunoglobulin superfamily molecules and is involved in cell adhesion. Loss of TSLC1 expression was strongly correlated with the promoter hypermethylation in several NSCLC cell lines. Here, we examined the methylation status of the TSLC1 gene promoter in 48 primary NSCLC tumors by bisulfite SSCP in combination with bisulfite sequencing. Six CpG sites around the promoter regions were significantly methylated in 21 of 48 primary NSCLC tumors (44%). Promoter methylation was more likely to be observed in relatively advanced tumors with TNM classification of pT2, pT3 or pT4 (19 of 33, 58%) than in those with pT1 (2 of 15, 13%), suggesting that alteration of TSLC1 would be involved in the progression of human NSCLC. Loss of TSLC1 expression was also observed in 20 of 46 (43%) human cancer cell lines, including those from esophageal (3 of 3), gastric (8 of 9), ovarian (2 of 5), endometrial (2 of 2), breast (1 of 3), colorectal (2 of 8) and small cell lung cancers (2 of 10). Combined analysis of promoter methylation and the allelic state in these cell lines indicated that the TSLC1 gene was often silenced not only by mono-allelic methylation associated with loss of the other allele but also through bi-allelic methylation. These results suggest that alteration of TSLC1 would be involved in advanced NSCLC as well as in many other human cancers.

Clinical implication and prognostic significance of the tumor suppressor TSLC1 gene detected in adenocarcinoma of the lung

BACKGROUND

Recently, the TSLC1 (tumor suppressor in lung cancer 1) gene has been identified as a novel tumor suppressor in human nonsmall cell lung carcinoma. To the authors' knowledge, the clinical relevance of TSLC1 gene expression has not been studied using patient data and surgical samples. The current study was designed to evaluate whether the TSLC1 gene can serve as a target for the prognostic determination of patients with pulmonary adenocarcinoma.

METHODS

A total of 38 patients who were surgically treated for proven primary lung adenocarcinoma were enrolled in the current study. Surgical specimens were examined for TSLC1 protein expression immunohistochemically and by Western blot analysis. The correlation between levels of TSLC1 expression and pathologic characteristics, as well as prognosis, was investigated.

RESULTS

All patients underwent a potentially curative resection of their tumor. TSLC1 antigen expression as evaluated by immunohistochemistry was confirmed by immunoblotting. The expression of TSLC1 protein was found to be inversely correlated with advanced disease stage, lymph node involvement, lymphatic permeation, and vascular invasion. The 4-year overall survival rates of patients with a tumor demonstrating high (> 70% positive cells [n = 14 patients]), intermediate (20-70% positive cells [n = 10 patients]), and low (< 20% positive cells [n = 14 patients]) expression of the TSLC1 antigen were 84%, 28%, and 7%, respectively. In addition, the disease-free survival of patients with a tumor that demonstrated a high percentage of TSLC1 protein-positive cells was reported to be significantly better than that of patients with a tumor that showed a low percentage of TSLC1 protein-positive cells.

CONCLUSIONS

The loss or reduction of TSLC1 expression in resected lung adenocarcinoma cases was associated with a poor prognosis, indicating that TSLC1 represents a central effector gene for controlling the biologic aggressiveness of the tumor and that it is an essential biomarker for predicting patient prognosis. These data may help to detect those patients at high risk for recurrence who might benefit from additional therapeutic strategies such as adjuvant therapy.

Loss of heterozygosity on the long arm of chromosome 21 in non-small cell lung cancer

BACKGROUND

In Down syndrome, the incidence of solid tumors including lung cancer is considerably lower than that of the general population. The low risk of lung cancer in individuals with Down syndrome may be related to the gene-dosage effect of the extra chromosome 21. It may suggest that tumor suppressor genes playing a role in the pathogenesis of lung cancer may be present on chromosome 21.

METHODS

A total of 39 surgically resected non-small cell lung cancers were analyzed using nine microsatellite markers for 21q. Loss of heterozygosity was considered to be present when the signal intensity of the allele in tumor DNA was less than 50% of that in the corresponding normal DNA.

RESULTS

Loss of heterozygosity for at least one locus was detected in 22 of 39 tumors (56.4%). Allelic loss was frequently detected at three distinct regions: at the locus D21S1432 on 21q21.1, the region between D21S1435 and D21S1442 on 21q21.2 to 21.3, and the region between D21S1270 and D21S1445 on 21q22.1.

CONCLUSIONS

These results indicate that loss of heterozygosity on 21q may play an important role in the pathogenesis of non-small cell lung cancer.

Chromosomal imbalances in human lung cancer

A wealth of cytogenetic data has demonstrated that numerous somatic genetic changes are involved in the pathogenesis of human lung cancer. Despite the complexity of the genomic changes observed in these neoplasms, recurrent chromosomal patterns have emerged. In this review, we summarize chromosomal alterations identified in small cell and non-small cell lung cancer, using classical and molecular cytogenetic techniques. These analyses have uncovered a set of chromosome regions implicated in lung cancer development and progression. However, many of the target genes remain unknown. Newer technology, such as array-CGH, when combined with cDNA microarrays and tissue microarrays, will facilitate the integration of genomic and gene expression data and pave the way toward a molecular classification of lung carcinomas. The molecular implications of consistent chromosome imbalances found in lung cancer to date are also discussed.

Functional cloning of a tumor suppressor gene, TSLC1, in human non-small cell lung cancer

The identification of a tumor suppressor gene in non-small cell lung cancer (NSCLC) is one of the most important issues to elucidate the molecular mechanisms of this type of refractory cancer and to establish a novel strategy against it. Since NSCLC, like most other human cancers, develops as a sporadic disease, linkage analysis is not available for gene cloning. This review describes the functional cloning approaches to a tumor suppressor gene in sporadic cancers. Suppression of the malignant phenotype of cancer cells by fusion with a normal fibroblast was the first demonstration of the recessive phenotype of cancer cells in 1969. Evidence of tumor suppressor genes on the specific chromosomes was later provided by functional complementation of the cancer phenotype through microcell-mediated chromosome transfer. Further introduction of more restricted DNA fragments by YAC transfer provides a potent tool to localize the gene to a small segment, appropriate for the subsequent gene cloning. TSLC1, a novel tumor suppressor gene in NSCLC, was identified on chromosome 11q23.2 through a series of functional complementation of A549 cells in tumorigenicity. Two-hit inactivation of the TSLC1 by promoter methylation and gene deletion was observed in 40% of primary NSCLC tumors. The strong tumor suppressor activity of TSLC1, and its possible involvement in cell adhesion, suggest that the functional cloning approach could cast a new light on a group of genes that have not yet been characterized, but are important for general human carcinogenesis as well as tumor suppression.

Prognostic significance of molecular genetic aberrations on chromosome segment 11p15.5 in non-small-cell lung cancer

PURPOSE

The assessment of prognosis and decisions on treatment for patients with non-small-cell lung cancer (NSCLC) are determined on the basis of disease stage and performance status. NSCLC frequently manifests loss of heterozygosity (LOH) at chromosome segment 11p15.5. Whether LOH at 11p15.5 is an independent prognostic variable has yet to be determined.

PATIENTS AND METHODS

We developed five novel markers, which can be assessed by polymerase chain reaction and restriction enzyme digestion. LOH at 11p15.5 was assessed in 193 patients who underwent surgical resection for pathologic stage I and II of the disease.

RESULTS

LOH at 11p15.5 was associated with poor survival (P =.021). Multivariate logistic regression analysis showed that after disease stage, performance status, weight loss, sex, age at diagnosis, and smoking history were controlled for, patients with LOH were two times more likely to die than those without LOH (relative risk [RR] = 2.01, P =.021). Cox regression analysis with disease stage and LOH revealed that the survival of patients with stage I disease and LOH was similar to the survival of patients with stage II disease, and it was significantly worse than the survival of stage I patients without LOH (RR = 2.38, P =.038).

CONCLUSION

LOH in a 310-kb region on chromosome segment 11p15.5 that includes the gene for the regulatory subunit of the enzyme ribonucleotide reductase is highly predictive of poor survival from NSCLC. The future utility of analysis of the allelic status of this region may involve treatment decisions, such as the use of neoadjuvant and adjuvant chemotherapy for patients with stage I disease.

Transcript map and complete genomic sequence for the 310 kb region of minimal allele loss on chromosome segment 11p15.5 in non-small-cell lung cancer

Molecular, functional, and clinical analyses strongly suggest that chromosome segment 11p15.5 contains a gene involved in lung cancer pathogenesis. The critical region of allele loss is 310 kb in size. We used our contig of P1-phage artificial chromosome (PAC) clones together with newly identified bacterial artificial chromosome (BAC) clones and the draft human genome sequence to complete a contiguous string of 380 407 bp. Three PAC clones that span the region were used to identify transcripts by exon trapping. Computational gene prediction algorithms were used to query the sequence for potential genes and exons. Screening for expression was performed with tissue-specific and cell line derived mRNA arrays. The region contains the complete SSA/Ro52 and RRM1 genes, exons 7-12 of the GOK gene, and the psirad pseudo-gene. A cluster of six nearly identical genes with an intact open reading frame (ORF) of 585 bp that share 75% identity with the HSPC182 gene was found. In addition, five putative novel genes were identified. Sequence tagged sites (STS) and polymorphic markers were used to screen 117 lung cancer cell lines for homozygous deletions and none were identified. These data provide the basis for the identification of a lung cancer suppressor gene on 11p15.5.

Identification of tumor suppressor candidate genes by physical and sequence mapping of the TSLC1 region of human chromosome 11q23

Loss of heterozygosity for a locus on human chromosome 11q22-23 is observed at high frequency in non-small cell lung carcinoma (NSCLC). Introduction of a 1.1 Mb fragmented yeast artificial chromosome (YAC) mapping to this region completely suppresses the tumorigenic properties of a human NSCLC cell line, A549. Smaller fragmented YACs give partial but not complete suppression. To further localize the gene(s) responsible for this partial suppression, a bacterial artificial chromosome (BAC) and P1-based artificial chromosome (PAC) contig was constructed, completely spanning the candidate region. End sequence generated in the construction of the BAC/PAC contig identified a previously unmapped EST and served to order genomic sequence contigs from the publicly available Celera Genomics (CG) and Human Genome Project (HGP) efforts. Comparison showed that CG provided larger contigs, while HGP provided more coverage. Neither CG nor HGP provided complete sequence coverage, alone or in combination. The sequence was used to map 110 ESTs and to predict new genes, including two GenScan gene predictions that overlapped ESTs and were shown to be differentially expressed in tumorigenic and suppressed A549 cell lines.

Additional characterization of a hexanucleotide polymorphic site in the first intron of human H-ras gene: comparative study of its alterations in non-small cell lung carcinomas and sporadic invasive breast carcinomas

Intron 1 of the human H-ras gene possesses a polymorphism consisting of repetitions of the GGGCCT consensus. Three alleles have been reported at this locus. We confirmed that two, P1 and P2, display four and two repeats, respectively, with their internal sequence structure similar to that previously described. The third, P3, previously assigned as a three-unit repetition allele according to its electrophoretic mobility and with no other information regarding its internal structure, was also found. Sequence analysis of the P3 allele revealed that it consists of three perfect repeats of the GGGCCT consensus. This polymorphism is present only in human c-H-ras gene, although single hexanucleotide repeats are found scattered within intron 1 of this gene in rodents. Analysis of this locus in matched tumor/distant normal samples from: (i) 38 patients with non-small-cell lung carcinoma (NSCLC), and (ii) 35 patients with sporadic invasive breast carcinoma, revealed: (1) 6.6% and 19% loss of heterozygosity (LOH) respectively, and (2) 10.5% and 2.9% hexanucleotide instability (HI) respectively, detected by the presence of shifted in length alleles. Shifted alleles exhibited altered internal sequence structure in comparison to normal ones, suggesting complex mutational events. The same pattern of alterations was also detected in tissues adjacent to lung adenocarcinomas and dysplasias adjacent to squamous cell carcinomas (7.7% LOH, 5.9% HI), implying that abnormalities at this locus may be early events in lung carcinogenesis. The frequency of alterations (LOH vs. HI) was significantly different among NSCLC and breast cancer (P=.005), probably due to the different tumor biology of each system. Finally, altered mRNA expression of H-ras gene was detected in all cases with HI, but this finding was also observed in samples without HI. In view of reports showing that elements in intron 1 of H-ras gene potentially influence its transcriptional regulation, from our results we cannot exclude that the hexanucleotide locus could be an element with possible involvement in expressional regulation of this gene.

Biological considerations in lung cancer

Our understanding of lung cancer biology has rapidly expanded in recent years. Lung cancer, unlike most human cancers, can be traced to an environmental risk factor in the majority of cases, and this fact is reflected in the vast number of genetic alterations discovered in lung tumors whose pathogenesis is believed to be mediated by carcinogen exposure. The discovery of these alterations has led to a greater understanding of tumor development. The dramatic progress in the understanding of the genetic and molecular basis of oncogenesis and the induction of immunity has led to a rejuvenation of efforts to apply this new knowledge to this common and refractory disease. Further, the resurgent interest in cancer immunology and tumor-host interactions holds promise for the development of new approaches to treatment based on harvesting the immune systems ability to recognize these alterations. Hopefully, this understanding will lead to novel approaches with real and convincing clinical efficacy once some of these strategies are tested in carefully performed randomized clinical trials with appropriate power to detect meaningful differences.

Cloning, expression and localization of human BM88 shows that it maps to chromosome 11p15.5, a region implicated in Beckwith-Wiedemann syndrome and tumorigenesis

Porcine BM88 is a neuron-specific protein that enhances neuroblastoma cell differentiation in vitro and may be involved in neuronal differentiation in vivo. Here we report the identification, by Western blotting, of homologous proteins in human and mouse brain and the isolation of their respective cDNAs. Several human and mouse clones were identified in the EST database using porcine BM88 cDNA as a query. A human and a mouse EST clone were chosen for sequencing and were found both to predict a protein of 149 amino acids, with 79.9% reciprocal identity, and 76.4% and 70.7% identities to the porcine protein, respectively. This indicated that the clones corresponded to the human and mouse BM88 homologues. In vitro expression in a cell-free system as well as transient expression in COS7 cells yielded polypeptide products that were recognized by anti-BM88 antibodies and were identical in size to the native BM88 protein. Northern-blot analysis showed a wide distribution of the gene in human brain whereas immunohistochemistry on human brain sections demonstrated that the expression of BM88 is confined to neurons. The initial mapping assignment of human BM88 to chromosome 11p15.5, a region implicated in Beckwith-Wiedemann syndrome and tumorigenesis, was retrieved from the UniGene database maintained at the National Centre for Biotechnology Information (NCBI, Bethesda, MD, U.S.A.). We confirmed this localization by performing fluorescence in situ hybridization on BM88-positive cosmid clones isolated from a human genomic library. These results suggest that BM88 may be a candidate gene for genetic disorders associated with alterations at 11p15.5.

Chromosomal duplication involving the forkhead transcription factor gene FOXC1 causes iris hypoplasia and glaucoma

The forkhead transcription factor gene FOXC1 (formerly FKHL7) is responsible for a number of glaucoma phenotypes in families in which the disease maps to 6p25, although mutations have not been found in all families in which the disease maps to this region. In a large pedigree with iris hypoplasia and glaucoma mapping to 6p25 (peak LOD score 6.20 [recombination fraction 0] at D6S967), no FOXC1 mutations were detected by direct sequencing. However, genotyping with microsatellite repeat markers suggested the presence of a chromosomal duplication that segregated with the disease phenotype. The duplication was confirmed in affected individuals by FISH with markers encompassing FOXC1. These results provide evidence of gene duplication causing developmental disease in humans, with increased gene dosage of either FOXC1 or other, as yet unknown genes within the duplicated segment being the probable mechanism responsible for the phenotype.

Characterization of a 500-kb contig spanning the region between c-Ha-Ras and MUC2 on chromosome 11p15.5

The 11p15.5 region is associated with a broad range of diseases, including childhood acute myeloid leukemia; non-small cell lung carcinoma; arthrogryposis multiplex congenita, distal type 2B; and bladder cancer. Since targets for these diseases are unknown, we have constructed a physical map consisting of BAC and PAC clones spanning the region from the HRAS1 gene to the cluster of mucin genes on 11p15.5. The contig spans approximately 500 kb and includes 13 genes (9 novel), 9 STSs (5 novel), and 1 SNP and builds upon a published physical map spanning the region from the telomere to the HRAS gene. In addition, we expand the mucin gene cluster located on 11p15.5 to include a novel mucin-like gene (MUCDHL) located less than 250 kb telomeric to MUC6. The identification of potential disease genes within an organizational and evolutionary context provides valuable clues to function and as such will benefit our understanding of this region of the genome.

SSA/RO52gene and expressed sequence tags in an 85 kb region of chromosome segment 11p15.5

Frequent allelic loss in lung cancer has been described in a region on chromosome segment 11p15.5 (LOH11A). The region is approximately 650 kb in size and flanked by the markers D11S988 centromeric and D11S860 telomeric. Clinical and cell biological studies suggest that it contains a gene associated with metastatic tumor spread. One of the genes identified within this region is SSA/Ro52, which has a RING finger domain and may be involved in gene regulation. We studied this gene for mutations using SSCP analysis and for expression using RT-PCR and Western blotting on lung cancer cell lines and tumor-normal tissue pairs. No mutations and no differences in mRNA or protein expression between tumor tissue and normal tissue pairs were identified. We discovered a novel polymorphic site (SSA44C/T) within exon 1 of this gene. Among 141 primary lung cancers, allelic loss was observed in 16% of informative cases. Our analyses excluded SSA/Ro52 as a tumor-suppressor gene in lung cancer and newly defined the centromeric border of the LOH11A region from D11S988 previously to SSA44C/T. This reduced the region of the putative suppressor gene to 460 to 485 kb. A significant difference (p = 0.01) in the frequency of alleles for this polymorphism between Caucasians and African-Americans was observed. The "T" allele frequency was 0.12 in Caucasians and 0.23 in African-Americans. A genomic EcoRI map over 85 kb surrounding the SSA/Ro52 gene was constructed, and 4 expressed sequence tags were identified by sequencing and studied.

Structure, expression, and chromosome mapping of LATS2, a mammalian homologue of the Drosophila tumor suppressor gene lats/warts

We have cloned and characterized LATS2, a novel mammalian homologue of the Drosophila tumor suppressor gene lats/warts. Northern blot analysis showed ubiquitous expression of mouse LATS2 (MmLATS2) mRNA, whereas expression of human LATS2 (HsLATS2) mRNA was enhanced in skeletal muscle and heart. Immunoblotting analysis of fractionated cell lysates showed HsLats2 to be a nuclear protein. We mapped the MmLATS2 gene to mouse chromosome 14 by interspecific backcross analysis. We also mapped the HsLATS2 gene (by fluorescence in situ hybridization) to the 13q11-q12 region, in which a loss of heterozygosity has been frequently observed in many primary cancers and to which the tumor suppressor genes RB and BRCA2 have also been mapped.

Elucidation of the mechanism of homozygous deletion of 3p12-13 in the U2020 cell line reveals the unexpected involvement of other chromosomes

Homozygous deletions in tumor cells have been useful in the localization and validation of tumor suppressor genes. We have described a homozygous deletion in a lung cancer cell line (U2020) which is located within the most proximal of the three regions on the short arm of chromosome 3 believed to be lost in lung cancer development. Construction of a YAC contig map indicates that the deletion spans around 8 Mb, but no large deletion was apparent on conventional cytogenetic analysis of the cell line. To investigate this paradox, whole chromosome, arm-specific, and regional paints have been used. This analysis has revealed that genetic loss has occurred by complex rearrangements of chromosomes 3, rather than simple interstitial deletion. These studies emphasize the power of molecular cytogenetics to disclose unsuspected tumor-specific translocations within the extremely complex karyotypes characteristic of solid tumors.

Identification of novel bladder tumour suppressor genes

Many genetic alterations have recently been identified in transitional cell carcinoma (TCC) of the bladder. These include alterations to known proto-oncogenes and tumour suppressor genes and the identification of multiple sites of nonrandom chromosomal deletion which are predicted to define the location of as yet unidentified tumour suppressor genes. This review summarises recent efforts to define the location of novel bladder tumour suppressor genes using loss of heterozygositiy (LOH) and homozygous deletion analyses and to isolate the genes targeted by these deletions. For three of the four regions of deletion on chromosome 9, the most frequently deleted chromosome in TCC, candidate genes have been identified. It is anticipated that the identification of the genes and/or genetic regions which are frequently altered in TCC will provide useful tools for diagnosis, prediction of prognosis, patient monitoring and novel therapies.

A 1.4-Mb high-resolution physical map and contig of chromosome segment 11p15.5 and genes in the LOH11A metastasis suppressor region

The centromeric part of chromosome segment 11p15.5 contains a region of frequent allele loss in many adult solid malignancies. This region, called LOH11A, is lost in 75% of lung cancers and is thought to contain a gene that may function as a metastasis suppressor. Genetic complementation studies have shown suppression of the malignant phenotype including reduction of metastasis formation. We constructed a high-resolution physical map and contig over 1.4 Mb that includes the beta-hemoglobin gene cluster and the gene for the large subunit of ribonucleotide reductase (RRM1). Through sequencing and computerized analysis, we determined that this region contains an unusually large number of transposable elements, which suggests that double-stranded DNA breaks occur frequently here. Twenty-two putative genes were identified. Because of its location at the site of maximal allele loss in the 650-kb LOH11A region and previous functional studies, RRM1 is the most likely candidate gene with metastasis suppressor function. The malignant phenotype, in this case, results from a relative loss of function rather than a complete loss.

Characterization of two monoclonal antibodies against the RON tyrosine kinase receptor

RON is a receptor protein tyrosine kinase belonging to the hepatocyte growth factor (HGF) receptor family. Using Récepteur d'Origine Nantais (RON) transfected cell lines, Macrophage Stimulating Protein (MSP) was identified as the ligand of RON. RON is synthesized as a single chain precursor, which subsequently is cleaved to yield a disulfide-linked heterodimer, with a 40-kDa alpha chain and a 150-kDa beta chain. Activation of RON by MSP results in cell migration, shape change, and proliferation. The present work centers on the production and characterization of two monoclonal antibodies (MAbs) to RON called ID-1 and ID-2. Antibodies were generated by immunization of mice with Madin-Darby Canine Kidney (MDCK) cells expressing human RON (clone RE7). Both antibodies recognized the mature and precursor form of RON. The specificity of the anti-RON antibodies was confirmed using a hepatocarcinoma cell line HepG2 expressing both task MET and RON receptors. Specific immunoprecipitation with ID-1 and ID-2 or anti-MET antibody followed by Western blotting under reducing conditions with rabbit polyclonal antibodies against RON and MET showed that our anti-RON antibodies recognize specifically the RON receptor. Ligand binding experiments showed that both antibodies are able to block the binding of radiolabeled MSP to RON and showed also that the antibodies recognize two different epitopes in the molecule. The blocking of MSP binding to RON by the anti-RON antibodies was confirmed by inhibition of cell migration induced by MSP in HT-29-D4 cells. Significant immunostaining was not observed in any subpopulation of whole blood with either ID-1 or ID-2. We analyzed the expression of RON receptor in a number of human hematopoietic and nonhematopoietic cells lines by flow cytometry. We found a strong mean of fluorescence intensity (MFI) in colon adenocarcinoma cells SW620 and HT-29-D4, low MFI in SVK14 and HepG2 cells, and no immunostaining in melanoma, lymphoma, and leukemia cells. Immunohistochemistry revealed that RON was expressed in germinal centers of tonsil, in skin, small intestine, and colon. These antibodies defined RON as CDw136 during the last leucocyte typing VI.

Benzo[a]pyrene diol-epoxide DNA adducts and levels of polycyclic aromatic hydrocarbons in autoptic samples from human lungs

Benzo[a]pyrene (BaP) and other polycyclic aromatic hydrocarbons (PAHs) which are present in cigarette smoke, are common air and food genotoxic contaminants and possible human carcinogens. We measured the following PAH levels: benzo[a]anthracene, benzo[b]fluoranthene, benzo[k]fluoranthene, BaP, dibenzo[a,h]anthracene, benzo[g,h,i]perylene as well as (+/-) syn and anti BaP diol-epoxide (BPDE) DNA adducts in autopsy samples from the lungs of non-smokers, ex-smokers and smokers who had lived in Florence, Italy. PAH levels in lung tissue were similar in all groups, with the exception of dibenzo[a,h]anthracene (DBA), which was higher in lung samples from smokers (n = 10, 0.18+/-0.17 ng/g d.w, mean +/- S.D.) compared to non-smokers (n = 15, 0.046+/-0.025 ng/g d.w) (P < 0.05), whereas ex-smokers (n = 5), had intermediate levels (0.07+/-0.03 ng/g d.w). The average level of total BPDE-DNA adducts was 4.46+/-5.76 per 10(8) bases in smokers, 4.04+/-2.37 per 10(8) in ex-smokers and 1.76+/-1.69 per 10(8) in non-smokers. The levels of non-smokers were significantly different (P < 0.05) from the levels of the smokers and ex-smokers combined. Total BPDE-DNA adducts were correlated with BaP levels in the lung samples in which both determinations were obtained (r = 0.63). Our results demonstrate that the biological load of PAHs due to environmental pollution is similar in individuals who smoke and those who do not, but BPDE-DNA adducts are higher in smokers and ex-smokers compared to non-smokers. This study further confirms the usefulness of BPDE-DNA adduct levels determination in the lungs from autopsy samples for monitoring long-term human exposure to BaP, a representative PAH.

The human DENN gene: genomic organization, alternative splicing, and localization to chromosome 11p11.21-p11.22

We have previously isolated and sequenced the cDNA of a novel gene, DENN, that exhibits differential mRNA expression in normal and neoplastic cells. The open reading frame of 4761 nucleotides encodes a putative hydrophilic protein of 1587 amino acids with a calculated molecular mass of 176,431 Da. Within DENN cDNA lies an alternative exon segment of 129 nucleotides encoding 43 amino acids, which may be excluded from some transcripts by alternative splicing. The serine- and leucine-rich DENN protein possesses a RGD cellular adhesion motif and a leucine-zipper-like motif associated with protein dimerization, and shows partial homology to the receptor binding domain of tumor necrosis factor alpha. DENN is virtually identical to MADD, a human MAP kinase-activating death domain protein that interacts with type I tumor necrosis factor receptor. DENN displays significant homology to Rab3 GEP, a rat GDP/GTP exchange protein specific for Rab3 small G proteins implicated in intracellular vesicle trafficking. DENN also exhibits strong similarity to Caenorhabditis elegans AEX-3, which interacts with Rab3 to regulate synaptic vesicle release. Composed of 15 exons (ranging in size from 73 to 1230 bp) and 14 introns (varying from about 170 bp to 5.3 kb), the DENN gene is estimated to span at least 28 kb. The alternative splicing event was traced to an alternative 5' donor site involving exon 7. DENN was mapped to chromosome region 11p11.21-p11.22 by FISH. Using polyclonal antibodies against a synthetic peptide, Western blotting of MOLT-4 T-lymphoblastic leukemic cell proteins and immunoblotting of subcellular fractions of MOLT-4 cells and PLC/PRF/5 liver cancer cells yielded data corroborating the alternative splicing mechanism that generates two variant isoforms of the DENN protein that display differential expression in cells of different lineages.

Localization of tumor suppressor activity important in nonsmall cell lung carcinoma on chromosome 11q

Loss of heterozygosity on chromosome 11q23 is observed at high frequency in human nonsmall cell lung carcinomas (NSCLCs), suggesting the presence of a tumor suppressor gene. Previous analysis of DNA from 79 patients identified a commonly deleted segment of 5 centimorgans. Complementation analysis was used to further localize a putative tumor suppressor gene. Three yeast artificial chromosome (YAC) clones spanning the minimal loss of heterozygosity region were modified, and spheroplast fusion was used to transfer them into human A549 NSCLC or murine Lewis lung carcinoma (LLC) cell lines. The resulting yeast x human hybrid cell lines containing an intact copy of a 1.6-Mb YAC, 939b12, showed reduced growth in vitro. Injection of parental A549 cells into athymic (nu/nu) mice resulted in tumor formation at 27 of 28 injection sites. In contrast, two independent 939b12-containing cell lines formed tumors at only 3 of 20 injection sites. 939b12 also suppressed tumor formation by LLC NSCLC cells in nude mice, but YACs 785e12 and 911f2, which flank 939b12, had no suppressor activity. Further localization of tumor suppression activity on 939b12 was accomplished by introduction of defined fragmentation derivatives into A549 cells and by analysis of YACs that were broken on transfer into LLC cells. This complementation approach localized tumor suppression activity to the central 700 kb of 939b12 and provides a functional assay for positional cloning of this tumor suppressor gene.

Loss of heterozygosity on chromosome 11p15 during histological progression in microdissected ductal carcinoma of the breast

Microdissection of histologically identifiable components from formalin-fixed, paraffin-embedded tissue sections allows molecular genetic analyses to be correlated directly with pathological findings. In this study, we have characterized loss of heterozygosity (LOH) at chromosome 11p15 at different stages of progression in microdissected tumor components from 115 ductal carcinomas of the breast. Microdissected foci of intraductal, infiltrating, and metastatic tumors were analyzed to determine the stage of progression at which LOH at 11p15 occurs. LOH was detected in 43 (37%) of 115 cases. Foci of intraductal carcinoma could be microdissected from 85 cases, of which 30 (35%) showed LOH at some stage of progression. LOH was detected in the intraductal component in 26 of these 30 cases. Interstitial deletions were characterized by using a panel of 10 highly polymorphic markers. The smallest region of overlap (SRO) for LOH at 11p15 was bounded by the markers D11S4046 and D11S1758. LOH at 11p15.5 showed no correlation with estrogen receptor status, the presence of positive lymph nodes, tumor size, histological grade, or long-term survival. We conclude that 11p15 LOH usually occurs early in breast cancer development but less frequently does not develop until the infiltrating or metastatic stages of tumor progression.

Allelic imbalance and instability of microsatellite loci on chromosome 1p in human non-small-cell lung cancer

The mapping of allelic loss on the short arm of chromosome 1 has been performed in non-small-cell lung cancer. We used a set of 11 microsatellite loci spanning 1p to examine the frequency of allelic imbalance in a panel of 58 tumours. Fifty-one of 58 (87.9%) cases have shown somatic allelic loss at one or more loci tested. The two shortest regions of the overlap (SRO) of the deletions have been identified: SRO 1 at 1p13.1 and SRO 2 at 1p32-pter. Allelic losses at these regions have been compared among adenocarcinoma and squamous cell carcinoma and no difference has been found. In contrast to SRO 1, deletions at SRO 2 significantly correlated with advanced stage of the disease as well as post-operative metastasizing and relapse. These data may suggest that SRO 1 and SRO 2 can harbour tumour-supressor genes (TSGs) involved in different stages of NSCLC development. SRO 2 is still quite large and its refined mapping should help attempts to clone and identify the putative TSG(s). Microsatellite instability (replication errors) affecting only 6 (10.3%) of 58 tumour samples is an infrequent genetic alteration at the loci tested.

Disruption of the RB pathway and cell-proliferative activity in non-small-cell lung cancers

The pathway consisting of retinoblastoma protein (pRB), cyclin D1 and p16 (RB pathway) which is involved in the phosphorylation of pRB plays an important role in G1/S progression. The disruption of this RB pathway has been reported in several types of human neoplasm. An immunohistochemical study of 101 non-small-cell lung cancers (NSCLCs) showed loss of p16 is in 47 tumors (46.5%) and loss of pRB in 42 tumors (41.6%). In 79 of 101 NSCLCs (78.2%), the expression of p16 and pRB was complementary (p < 0.0001). Methylation of the cdkn2 gene was detected in 50% of p16-negative tumors and in 11% of p16-positive tumors. Aberrant expression of cyclin D1 was found in 45 tumors (44.5%). The cyclin-D1-positive tumors had significantly higher Ki-67 indices than the cyclin-D1-negative tumors irrespective of the tumor p16 or pRB expression. Thus, 91 (90%) of 101 NSCLCs showed disturbed expression of at least 1 of the 3 components of the RB pathway. Our results suggest that the disruption of the RB pathway plays an important role in tumorigenesis in NSCLCs and that increased cyclin-D1 expression leads to strong proliferative activity which may over-ride the suppressive effect of p16 and pRB.

Transcriptional map of 170-kb region at chromosome 11p15.5: identification and mutational analysis of the BWR1A gene reveals the presence of mutations in tumor samples

Chromosome region 11p15.5 harbors unidentified genes involved in neoplasms and in the genetic disease Beckwith-Wiedemann syndrome. The genetic analysis of a 170-kb region at 11p15.5 between loci D11S601 and D11S679 resulted in the identification of six transcriptional units. Three genes, hNAP2, CDKN1C, and KVLQT1, are well characterized, whereas three genes are novel. The three additional genes were designated BWR1A, BWR1B, and BWR1C. Full-length cDNAs for these three genes were cloned and nucleotide sequences were determined. While our work was in progress, BWR1C cDNA was described as IPL [Qian, N., Franck, D., O'Keefe, D., Dao, D. , Zhao, L., Yuan, L., Wang, Q., Keating, M., Walsh, C. & Tycko, B. (1997) Hum. Mol. Genet. 6, 2021-2029]. The cloning and mapping of these genes together with the fine mapping of the three known genes indicates that the transcriptional map of this region is likely to be complete. Because this region frequently is altered in neoplasms and in the genetic disease Beckwith-Wiedemann syndrome, we carried out a mutational analysis in tumor cell lines and Beckwith-Wiedemann syndrome samples that resulted in the identification of genetic alterations in the BWR1A gene: an insertion that introduced a stop codon in the breast cancer cell line BT549 and a point mutation in the rhabdomyosarcoma cell line TE125-T. These results indicate that BWR1A may play a role in tumorigenesis.

Cytogenetic findings in thirty lung carcinoma patients

Primary tissue cultures of human lung tumors were prepared from 30 cases of which 16 were diagnosed as squamous cell carcinoma, six adenocarcinoma, four adenosquamous cell carcinoma, three large cell carcinoma, and one small cell lung carcinoma. Chromosomal abnormalities were observed in 26 cases by cytogenetic studies with a GTG banding technique. Specific chromosome bands frequently involved in structural abnormalities were seen on 1p11, 1q11, 2p10, 6p10, 7q11, 7q22, 7q32, 8q22, 9q22, 11q11, 21q10, and Xq24. We assumed that especially i(2)(p10), i(9)(p10), i(21)(q10), t(11;12), t(14;15), del(X)(q24), and loss of the Y chromosome may play a role in the development of lung cancer as secondary changes. In this way, our cytogenetic findings provide evidence that multiple genetic lesions are associated with the pathogenesis of lung cancer.

p53 tumor-suppressor gene: clues to molecular carcinogenesis

The tumor-suppressor gene product p53 is clearly a component in several biochemical pathways, including transcription, DNA repair, genomic stability, cell-cycle control and apoptosis, that are central to human carcinogenesis. The p53 is functionally inactivated by mutational, viral, and cellular mechanisms in the majority of human cancers. Analysis of the spectrum of p53 mutations provides clues to the etiology and molecular pathogenesis of cancer. Recent insight into the p53-mediated biochemical pathways of cell-cycle arrest and apoptosis has provided further understanding of the mechanisms related to p53-mediated tumor suppression. This insight in turn may provide the potential molecular targets for the development of rational multimodality cancer therapy, including chemo-, immuno-, and gene-therapeutic strategies. The convergence of previously parallel lines of basic, clinical, and epidemiologic investigation may provide an opportunity to transfer research findings rapidly from the laboratory to the clinic.

Polymorphisms of H-ras-1 and p53 in breast cancer and lung cancer: a meta-analysis

Certain polymorphic variants of H-ras-1 and p53 have been investigated for an association between inheritance and cancer risk. The results of a metaanalysis, which reviews studies of H-ras-1 rare alleles and p53 codon 72 allelic variants in breast and lung cancer, are presented. The data constituted evidence for elevated risk of both breast and lung cancer with inheritance of rare H-ras-1 alleles. Calculated population attributable risks are 0.092 and 0.037 for breast and lung cancer, respectively. The frequency of the rare H-ras-1 alleles was observed to be greater in African Americans than in Caucasians, and a specific allele (A3.5) that is common in African Americans was found only at low frequency in Caucasians. For p53 a consensus has yet to be reached. Lung cancer studies conducted in Caucasian and African-American populations have found no evidence of risk associated with the proline variant of codon 72. Two similar studies conducted in Japanese populations suggested an association between p53 genotype distribution and lung cancer risk. However, one implicates the proline allele but the other implicates the arginine allele. The frequency of the proline variant is significantly dependent on race. Frequencies have been reported for control populations of Japanese (0.347 and 0.401), Caucasian (0.295, 0.284, and 0.214), African American (0.628 and 0.527), and Mexican American (0.263).

Delineation of the centromeric and telomeric chromosome segment 11p15.5 lung cancer suppressor regions LOH11A and LOH11B

We have reported frequent allele loss for two separate regions identified by the markers D11S12 and HRAS on chromosome 11p15.5. D11S12 allele loss was associated with tumor stage and type and HRAS allele loss with cigarette consumption, sex, and survival. To positionally clone the putative tumor suppressor genes located in these regions, we here report a reduction in the size of these intervals to approximately 250 kb. The markers used, ordered from centromere to telomere, were D11S932 -D11S1331-D11S1760-D11S1323-D11S4891 (HBB)-D11S1758-D11S12-D11S988-D11S860-D11S131 8-TH-HRAS-D11S1363-D11S2071. We analyzed 44 tissue pairs from patients with primary lung cancer. The smallest common regions of allele loss were located between D11S1758 and D11S12 in the centromeric region of chromosome segment 11p15.5 (region of LOH on chromosome 11 in lung cancer, LOH11A) and between HRAS and D11S1363 in the telomeric region (region of LOH on chromosome 11 in lung cancer, LOH11B). Loss of heterozygosity was observed in 24/39 (62%) primary lung cancers informative for LOH11A and in 17/34 (50%) informative for LOH11B. The pattern of allele loss strongly suggests that two lung cancer suppressor genes are located on chromosome segment 11p15.5, one between D11S1758 and D11S12 and the other between HRAS and D11S1363. The estimated physical size of each of these regions is 250 kb.

Deletions of the short arm of chromosome 3 in solid tumors and the search for suppressor genes

The concept that cells can become malignant upon the elimination of parts of chromosomes inhibiting cell division dates back to Boveri in 1914. Deletions occurring in tumor cells are therefore considered a first indication of possible locations of tumor suppressor gene. Approaches used to localize and identify the paradigm of tumor suppressors, RB1, have also been applied to localize tumor suppressor genes on 3p, the short arm of chromosome 3. This review discusses the methodological advantages and limitations of the various approaches. From a review of the literature on losses of 3p in different types of solid tumors it appears that some tumor types show involvement of the same region, while between others the regions involved clearly differ. Also discussed are results of functional assays of tumor suppression by transfer of part of chromosome 3 into tumor cell lines. The likelihood that a common region of deletions would contain a tumor suppressor is strongly enhanced by coincidence of that region with a chromosome fragment suppressing tumorigenicity upon introduction in tumor cells. Such a situation exists for a region in 3p21.3 as well as for one or more in 3p12-p14. The former region is considered the location of a lung cancer suppressor. The same gene or a different one in the same region may also play a role in the development of other cancers including renal cell cancer. In the latter cancer, there may be additional roles of the VHL region and/or a 3p12-p14 region. The breakpoint region of a t(3;8) originally found to be constitutively present in a family with hereditary renal cell cancer now seems to be excluded from such a role. Specific genes on 3p have been suggested to act as suppressor genes based on either their location in a common deletion region, a markedly reduced expression or presence of aberrant transcripts, their capacity to suppress tumorigenicity upon transfection in to tumor cells, the presumed function of the gene product, or a combination of several of these criteria. A number of genes are evaluated for their possible role as a tumor suppressor according to these criteria. General agreement on such a role seems to exist only for VHL. Though hMLH1 plays an obvious role in the development of specific mismatch repair-deficient cancers, it cannot revert the tumor phenotype and therefore cannot be considered a proper tumor suppressor. The involvement of VHL and MLH1 also in some specific hereditary cancers allowed to successfully apply linkage analysis for their localization. TGFBR2 might well have a tumor suppressor function. It does reduce tumorigenicity upon transfection. Other 3p genes coding for receptor proteins THRB and RARB, are unlikely candidates for tumor suppression. Present observations on a possible association of FHIT with tumor development leave a number of questions unanswered, so that provisionally it cannot be considered a tumor suppressor. Regions that have been identified as crucial in solid tumor development appear to be at the edge of synteny blocks that have been rearranged through the chromosome evolution which led to the formation of human chromosome 3. Although this may merely represent a chance occurrence, it might also reflect areas of genomic instability.

No evidence of microsatellite instability but frequent loss of heterozygosity in primary resected lung cancer

We examined microsatellite instability and loss of heterozygosity (LOH) in primary lung tumors from 93 cancer patients, using 16 microsatellite markers. The cases studied included 87 non-small-cell lung cancers (NSCLC) and six small-cell lung cancers (SCLC). All the patients except two were current or former smokers. The microsatellite markers were all dinucleotide repeat sequences from chromosomal locations 1p, 3p, 5q, 8p, 9p, 10p, 11p, 13q, and 17q. None of the tumors showed microsatellite instability (0/93). In NSCLC, 28% (24/87) of the cases showed LOH in at least one locus, whereas, in SCLC, 67% (4/6) had allelic losses. The frequency of LOH differed between the various cell types of NSCLC. The highest frequency was seen in large cell carcinoma (3/6, 50%) followed by squamous cell carcinoma (16/43, 37%) and adenocarcinoma (5/35, 14%). The most common site of LOH was 3p, where markers D3S1284, D3S659, D3S1289, D3S966, D3S647, and D3S1038 were studied. LOH, studied with 9p markers (D9S126, D9S171, D9S162), was less common. The present results, together with earlier reports, suggest that smoking-related primary lung cancers seldom show microsatellite instability but are characterized by frequent LOH.

Two regions of homozygosity on chromosome 3p in squamous cell carcinoma of the head and neck: comparison with cytogenetic analysis

BACKGROUND

Loss effecting the short arm of chromosome 3 occurs in nearly 60% of squamous cell carcinomas of the head and neck (SCCHN). Karyotype analysis indicated that these losses occur in two regions, 3p13-p14 and 3p21-p24. To test these findings, we examined tumor DNA from 38 SCCHN cell lines for heterozygosity and homozygosity at 6 polymorphic loci spanning this region.

METHODS

The polymerase chain reaction (PCR) was used to amplify polymorphic restriction sites on 3p, the amplified products were digested with the appropriate restriction enzyme, electrophoresed on agarose gels, and assessed for the presence of one or both alleles. The 38 SCCHN cell lines were established from 31 patients and included 16 that had been karyotyped. In 6 cases two or three tumor cell lines established from separate tumors in the same patients were studied.

RESULTS

The cell lines exhibited a very low frequency of heterozygosity for the regions 3p12-3p21 (D3S3, D3S30 and D3S2) and distal 3p21-3p24 (D3F15S2 and THRB), when compared with that observed in the normal population. In contrast, D3S32, located within 3p21, was heterozygous in 38% of the tumors which is close to the frequency seen in the normal population (50%). In most cases the PCR results were consistent with the cytogenetic predictions. However, in 4 cell lines 3p loss was predicted from the karyotype, but heterozygosity for D3S32 was present.

CONCLUSIONS

These experiments support cytogenetic data that indicate two regions of 3p loss in SCCHN tumors. The 3p regions that show a high frequency of homozygosity may contain tumor suppressor genes involved in the development and/or progression of squamous cancer. The region surrounding D3S32 may contain an essential gene that is conserved in two copies even when much of 3p is lost.

Multiple genetic abnormalities of 11p15 in Wilms' tumor

Wilms' tumor has served as a model of multiple genetic alterations in childhood cancer. This review summarizes work in our laboratory identifying several of these alterations. These include the localization to 11p15 of an embryonal tumor suppressor gene and at least one gene for Beckwith-Wiedemann syndrome, which predisposes to Wilms' tumor; as well as a novel mutational mechanism in man, loss of imprinting.