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Journal of Clinical Oncology, Vol 20, Issue 5 (March), 2002: 1353-1360
© 2002 American Society for Clinical Oncology

Prognostic Significance of Molecular Genetic Aberrations on Chromosome Segment 11p15.5 in Non–Small-Cell Lung Cancer

By Gerold Bepler, Ashish Gautam, Lauren M. McIntyre, Amy F. Beck, David S. Chervinsky, Young-Chul Kim, Diana M. Pitterle, Andrew Hyland

From the Lung Cancer Program, Roswell Park Cancer Institute, Buffalo, NY; Computational Genomics, Purdue University, West Lafayette, IN; Department of Internal Medicine, Chonnam University, Kwangju, South Korea; and Department of Medicine, Duke University Medical Center, Durham, NC.

Address reprint requests to Gerold Bepler, MD, PhD, Moffitt Cancer Center and Research Institute, Thoracic Oncology Program, MRC-MOLONC, 12902 Magnolia St, Tampa, FL 33612; email: beplerg@ moffitt.usf.edu.


    ABSTRACT
 TOP
 ABSTRACT
 INTRODUCTION
 PATIENTS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
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.


    INTRODUCTION
 TOP
 ABSTRACT
 INTRODUCTION
 PATIENTS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
IT IS ESTIMATED THAT 169,500 patients will be diagnosed with lung cancer in the United States in 2001, and 157,400 will die as a result of the disease. Lung cancer causes more death than colorectal cancer (56,700), breast cancer (40,600), and prostate cancer (31,500) combined.1 Five-year survival rates have improved from 8% in the early 1960s to 15% in the early 1990s. This doubling of the 5-year lung cancer survival rate is encouraging and has resulted in a shift from the previous nihilism associated with lung cancer treatment to a guarded optimism regarding outcome from treatment. Although locoregional control of non–small-cell lung cancer (NSCLC) can be achieved by surgery and radiation, more than 70% of relapses in patients with stage I disease occur at distant sites.2 Thus, most patients with NSCLC must have systemic disease, even at the earliest stages. Efforts at improving the management and outcome of patients with this disease are evolving. Recent efforts have been directed at chemoprevention to reduce incidence and at neoadjuvant and adjuvant chemotherapy to reduce the high systemic relapse rate.

Cytotoxic intervention strategies have associated toxicities, particularly in this target population where rates of comorbidities from atherosclerotic disease and chronic benign lung disease are high. Directing treatment strategies toward patients with NSCLC most likely to benefit has been guided by clinical variables such as disease stage, performance status, and weight loss. Other pathologic and molecular variables include submicroscopic metastases,3 metabolic activity by imaging,4 expression of proteins in various pathways regulating cellular growth and differentiation,5-7 mutations in oncogenes and tumor suppressor genes,8-12 expression of extracellular matrix proteinases and markers of angiogenesis,13-15 and genome instability. We have focused on genome instability.

The predominant type of genome instability in cancer is structural aberration of chromosomes (ie, deletions, translocations, and insertions). These are thought to arise as a result of impaired repair of DNA double-strand breaks by homologous recombination and nonhomologous end joining.16,17 Loss-of-heterozygosity (LOH) analysis is the most frequently used technique to assess genome instability, and allele loss often heralds the discovery of genes with key functions in tumor development and progression.18 Many chromosomal regions with frequent LOH have been described in lung cancer including the centromeric part of chromosome segment 11p15.5.19-24 This region, called LOH11A, has been mapped and sequenced,25,26 and a putative suppressor gene (RRM1) within this region has been identified.27 We investigated the frequency and clinical significance of LOH for this region by studying five polymorphic markers in 193 patients with pathologic stage I and II disease who underwent resection for NSCLC. These five markers are distributed over 310 kb and cover the smallest area of common allele loss (Fig 1).26



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Fig 1. Schematic representation of the region located on chromosome segment 11p15.5 between the beta-hemoglobin (ß-hbb) and insulin (ins) genes. The scale provides physical distances in kilobase-pairs (kb). Arrows indicate the exact position of the five polymorphic markers used. Bars depict the frequency of LOH.

 

    PATIENTS AND METHODS
 TOP
 ABSTRACT
 INTRODUCTION
 PATIENTS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
Specimen Collection and DNA Extraction
Paired tumor/normal specimens were obtained from patients undergoing curative surgery for pathologic stage I or stage II NSCLC as part of an institutional review board–approved research study from February 1985 to July 1996. Specimens were pulverized in liquid nitrogen, and DNA was extracted (Qiagen, Valencia, CA).

Data Collection
Demographic and clinical data were collected by chart review, telephone contact, or query of the social security death index. For each patient, these included the date of birth, diagnosis, sample collection, relapse, and death or last follow-up; tumor histology and grade of differentiation; pathologic disease stage according to the American Thoracic Society staging system28; performance status using the Eastern Cooperative Oncology Group (ECOG) scale (0 = no symptoms; 1 = minor symptoms; and 2 = symptoms present, out of bed or chair for > 50% of the waking hours); weight loss (>= or < 5% in the 3 months preceding diagnosis); sex and place of residence; and quantity of cigarette use over lifetime and current smoking status. Patients who smoked less than 100 cigarettes in their lifetime were classified as nonsmokers.29

Allele Loss Analysis
The five polymorphic markers analyzed for LOH are restriction site polymorphisms. DNA was amplified with primer pairs flanking the polymorphic site followed by restriction enzyme digestion. For this, one primer was end-labeled with gamma-[33P]–adenosine triphosphate. Digested amplicon fragments were separated on denaturing 10% polyacrylamide gels and visualized on phosphor imaging screens (Molecular Dynamics, Sunnyvale, CA) or separated on a WAVE DNA fragment analysis system (Transgenomic, Santa Clara, CA). Some specimen pairs were also analyzed by Southern blotting as previously described.22 Details on the polymorphic loci are listed in Table 1. LOH was assessed by quantification of the area of allele signals with a phosphor imager or WAVE analyzer and scored as LOH if the calculated allele ratio was less than 0.6. In normal tissue specimens, the ratio of signal intensities between two alleles (A1 and A2) is balanced. In tumor specimens, the ratio can deviate from this normal specimen ratio for two reasons, that is, allele loss or allelic imbalance. In case of allele loss, the ratio should be 0.0. However, tumor specimens contain varying amounts of contaminating normal cells, which result in ratios that reflect the proportion of DNA in a tumor specimen derived from normal diploid cells. Alternatively, allele ratios less than 1.0 and greater than 0.0 could result from allelic imbalance in tumor cells, that is, both alleles (A1 and A2) are present, but not at a 1:1 ratio. This can originate within a clonal population of cells; for instance, all cells have two copies of allele A1 and one copy of allele A2 as a result of locus amplification or as a result of aneuploidy. Alternatively, allelic imbalance can result from variations of allele content in different tumor cells (ie, tumor heterogeneity). Aneuploidy and tumor heterogeneity are unlikely mechanisms to account for the observed allele ratios because ratios for different alleles in a narrowly defined chromosomal region should be very similar. As shown in Fig 2, allele ratios were mainly close to 1.0 for one set of alleles and significantly different for other sets of alleles, which strongly favors allele loss (and contamination with normal DNA) as the underlying cause of allelic differences. Locus amplification could also explain the results. In this report, the term LOH is used. We used an allele ratio of 0.6 as a cutoff for LOH because we had previously determined that the fifth, tenth, and twenty-fifth percentiles of signal intensity ratios among normal specimens from different individuals were 0.6, 0.7, and 0.8, respectively.


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Table 1.  Characteristics of Polymorphic Markers
 


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Fig 2. Phosphor images of tumor pairs analyzed for the markers SSA44C/T, D11S4932, RRI9, RR(-)37A/C, and RR(-)524C/T. N indicates DNA from normal tissue and T indicates DNA from tumor tissue. Arrows point to lost alleles.

 
Statistical Analysis
The primary, analytic, statistical method to assess the association between LOH (absent, present, indeterminate) and survival while controlling for potential confounders was a Cox regression analysis. The SPSS Version 10.07 software was used (SPSS, Inc, Chicago, IL, 2000). The confounders in the adjusted model included disease stage (I or II), ECOG performance status (0, 1, or 2), weight loss (present or absent), sex (male or female), age (> or <= the median), and smoking status (never smoker, smokers with > and those with <= the median measured in number of packs smoked per day multiplied by the number of years, ie, pack-years [PY]). Unadjusted Cox regression analyses were performed with each predictor variable entered singly into the model. The proportional hazards assumption was verified in all analyses.


    RESULTS
 TOP
 ABSTRACT
 INTRODUCTION
 PATIENTS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
Characteristics of Lung Cancer Patients
Paired DNA specimens for analysis were available on 193 patients. The study population included 52 women and 141 men. The average age was 63.2 years (median, 64.2 years), with a range of 35.0 to 81.9 years. Fifteen patients were nonsmokers, and 165 were smokers or former smokers (median number of PY, 50; average number of PY, 52.5; range, 1 to 150). Smoking information was not available for 13 patients. Ninety-four patients had adenocarcinoma (including 15 bronchioloalveolar cell carcinomas), 77 had squamous cell carcinoma, nine had large-cell carcinoma, and 13 had adenosquamous carcinoma. The distribution by disease stage was 56 stage IA, 77 stage IB, 12 stage IIA, and 48 stage IIB. For analyses, stage IA and IB and stage IIA and IIB were combined. Table 2 provides an overview of the disease stage by histopathology. The ECOG performance status was 0 in 90 patients, 1 in 76, 2 in 13, and unknown in 14. Weight loss at the time of diagnosis was present in 22 patients, absent in 153, and unknown in 18. Eighty-seven patients were dead and 106 were alive, and survival or follow-up time ranged from less than 1 month to 164.5 months. Four patients, all with stage II disease, died within 30 days of surgery, and they were included in the analysis.


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Table 2.  Histopathology and Pathologic Stage (N = 193)
 
LOH Analysis
The observed heterozygosity rates for the five polymorphic markers ranged from 25.9% to 42.9% (Table 3). LOH for these markers was found in 25.0% (SSA44C/T), 39.6% (D11S4932), 29.3% (RRI9), 27.9% (RR(-)37A/C), and 25.0% (RR(-)524C/T) of patients and is illustrated in Fig 1. Figure 2 depicts five examples of observed LOH patterns and shows that the region with highest frequency of LOH is located in the center of the region including D11S4932 centromeric and RRI9 telomeric. In the 111 cases heterozygous for D11S4932, RRI9, or both, LOH was found in 40 (36.0%). Of the 82 cases that were uninformative for D11S4932 and RRI9, 11 had LOH for at least one of the other three markers (SSA44C/T and/or RR(-)37A/C, or SSA44C/T and/or RR(-)524C/T if RR(-)37A/C was uninformative). In addition, nine cases heterozygous without LOH for either D11S4932 or RRI9 had LOH for one of the other markers. The number of cases with a specific allelic pattern is shown in Fig 3.


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Table 3.  Heterozygosity and LOH for Individual Markers
 


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Fig 3. The patterns of allelic loss for all 193 lung cancer cases is shown. A checkered box symbolizes retained heterozygosity, a solid black box symbolizes LOH, and a solid white box symbolizes homozygosity.

 
Prognostic Significance of LOH at 11p15.5
For the LOH variable (present, absent, or indeterminate), patients were divided into three groups. One group (n = 40) contained patients with LOH for D11S4932, RRI9, or both markers. The second group (n = 71) contained patients without allele loss (ie, retained heterozygosity for these markers). The last group (n = 82) contained patients with unknown LOH status (both markers, D11S4932 and RRI9, were uninformative). Using the {chi}2 test of independence, we did not find a statistically significant association between the categorical variables disease stage, performance status, weight loss, sex, age, smoking status, and LOH.

Table 4 and Fig 4 display the results from the Cox regression analysis. After adjusting for covariates associated with survival, patients with LOH had a significantly shorter survival than patients without LOH (relative risk [RR] = 2.01, P = .021). The survival of patients with indeterminate LOH status was similar to the survival of patients without LOH. Other independent predictors of survival were disease stage (P = .064) and sex (P = .057). The effect of LOH at 11p15.5 on survival of patients by pathologic disease stage was analyzed (see Table 5), and adjusted Cox regression survival curves are present in Fig 5. Patients with stage I and no LOH (n = 50) had a significantly longer survival compared with patients with stage I and LOH (RR = 2.38, P = .038). LOH did not significantly impact on the survival of patients with stage II (n = 14 with LOH and n = 21 without LOH, P = .193). The survival of patients with stage I disease and LOH was not significantly different from that of all patients with stage II disease (P = .701) or with stage II disease without LOH (RR = 1.67, P = .298).


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Table 4.  Cox Proportional Hazards Analysis
 


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Fig 4. Cox regression survival curves for patients with (n = 40), without (n = 71), and with indeterminate (n = 82) LOH status. Survival difference between patients with and without LOH was significant (P = .021) and not significantly different between patients without LOH and indeterminate LOH (P = .819).

 

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Table 5.  Median Survival by LOH Status and Pathologic Tumor Stage
 


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Fig 5. Cox regression survival curves by pathologic disease stage. In stage I, patients with LOH had a relative risk of dying of 2.38 (P = .038) compared with those without LOH, and it was comparable to that of patients with stage II disease without LOH (RR = 1.67, P = .298).

 
We reanalyzed the data after moving the 11 patients with uninformative D11S4932 and RRI9 status but LOH for any of the adjacent markers (SSA44C/T, RR(-)524C/T, and RR(-)37A/C) into the group of patients with LOH (last three allelic patterns shown in Fig 3). The difference in survival between patients with and without LOH adjusted for covariates remained statistically significant (RR = 1.93, P = .029).


    DISCUSSION
 TOP
 ABSTRACT
 INTRODUCTION
 PATIENTS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
Tumor stage has been the most powerful and widely accepted parameter predictive of survival for patients with lung cancer, with P < 0.05 in pairwise comparisons among substages within the broader stages I to IV.28 Many prognostic molecular markers have been described for patients with lung cancer, but none are currently being used in treatment decision making. Most notably, these include mutations of the K-ras oncogene, mutations or protein expression of the p53 tumor suppressor gene, expression of proteins in the epidermal growth factor receptor family, expression of blood group antigen A, expression of proteins involved in the G1 cell cycle checkpoint, expression of extracellular matrix proteinases and inhibitors, and metabolic activity by fluorodeoxyglucose (FDG)-positron emission tomography.

K-ras mutations at codon 12 were initially reported in 19 of 69 adenocarcinomas, and their presence was associated with poor survival (P = .002).8 The majority of patients with K-ras mutations (n = 17) had stage I disease, which suggested that this marker might be particularly useful for stage I patients. Subsequent studies have yielded conflicting results; some confirmed the prognostic utility of K-ras mutations regardless of disease stage,10 whereas others did not find a prognostic significance for K-ras mutations.5,12,30,31 Nuclear staining and gene mutations for p53 were found in 48 of 75 and 38 of 75 NSCLCs, respectively, and nuclear staining was associated with poor survival (P = .05) whereas gene mutations were not (P = .62). In this study, no correlation between nuclear staining and gene mutations was found.9 Multiple other investigators have not found an association between immunohistochemical p53 staining and survival,5,12,31,32 or gene mutations and survival.12,30 HER2/neu (c-erbB-2) overexpression was described in 15 of 55 NSCLCs, and it was associated with poor survival in adenocarcinomas (n = 29, P = .04).33 Subsequent studies reported frequencies of overexpression of 15% and P = 0.94.5,31 Thus, at the present time neither K-ras nor p53 nor HER2/neu are useful prognostic markers for clinical decision making.

Blood group A antigen expression was assessed in 164 NSCLC specimens. Of the 71 patients with blood types A or AB, 28 patients did not express A antigen in tumors, and they had a shorter survival than the 43 patients whose tumors expressed the A antigen (P = .001).34 In an analysis by disease stage, nine of 27 stage I, six of 16 stage II, and 13 of 28 stage III patients lacked A antigen expression in tumors. There was a significant difference in the survival of patients with stage I (P < .001) and stage II (P = .048) by A antigen expression status. For stage III patients, the difference in survival did not reach statistical significance (P = .158). The prognostic significance of absent A antigen expression was confirmed in a study of 90 patients with stage I or II NSCLC positive for blood group A antigen. In this analysis, 36 tumors were negative and 54 positive by immunohistochemistry, and absent staining was predictive of poor survival in a multivariate analysis (P = .01).31 The clinical utility of this promising marker is, however, restricted to the 38% of patients who carry the A antigen.

Brambilla et al studied rb, p16INK4A, and cyclin D1 expression by immunohistochemistry in 168 stage I and II NSCLC and found loss of rb in 20 cases, loss of p16INK4A in 97 cases, and overexpression of cyclin D1 in 72 cases. In a multivariate analysis, expression of p16INK4A was associated with poor survival (P = .01),11 which is in contrast to a previous report where lack of p16INK4A expression was associated with decreased survival.35 Extracellular matrix degradation by enzymes and their inhibitors was investigated in 84 cases of NSCLC, and epithelial expression was associated with lymph node metastases (P = .008).14 Most recently, high values of FDG uptake in NSCLC measured by positron emission tomography was significantly associated with shorter survival (P = .001).4 This study included 46 patients with stage I disease, 19 with stage II disease, and 60 with stage III disease. In a multivariate analysis, which included the variables disease stage, performance status, and tumor type, high FDG uptake values were still significantly correlated with poor survival (P = .01). The future utility of these promising prognostic markers requires confirmation in prospective studies.

Few investigations have shown significant associations between LOH and survival of patients with lung cancer. LOH (four of 40) at chromosome segment 11p13 was predictive of poor outcome in squamous cell carcinomas with P = 0.02,23 and LOH (21 of 66) for the HRAS locus near the telomere of 11p was predictive of poor outcome for all histopathologic subtypes, with P = 0.04.36 However, Sanches-Cespedes et al did not find such an association despite comparable numbers of cases studied and similar frequencies of LOH (12 of 63 for 11p13 and 19 of 61 for the HRAS locus).37 Three regions of LOH on chromosome 3p, namely, 3p14, 3p21, and 3p25-26, have been investigated for associations with survival. In one study of 110 patients with NSCLC, LOH was found in 45 of 98 informative cases, and there was a trend toward poor survival (P = .0631).38 A second study with 35 patients in pathologic stage I showed no trend toward poor survival,30 as did a third study with 103 patients.39 The APC/MCC tumor suppressor gene is located on segment 5q21. LOH was significantly correlated with poor survival (P = .01, LOH in 22 of 75 NSCLCs) in one study40 but not in a second study (P = .33, 14 of 68 NSCLCs).37

These results suggest that LOH per se, as a marker of chromosomal instability resulting from impaired repair of DNA double-strand breaks, does not appear to be prognostically useful. Preliminary data suggest that the RRM1 gene, which is located in the narrowly defined region on chromosome segment 11p15.5 investigated here, suppresses metastasis formation in a syngeneic mouse model and induces cell cycle arrest and apoptosis in vitro.41,42 In addition, inhibition of nude mouse xenograft formation has been reported in genetically modified lung cancer cell lines through transfer of a normal chromosome 11 or radiation-reduced fragments of segment 11p15.5 that contain the LOH11A region.43,44 These results suggest that allele loss in this region on chromosome segment 11p15.5 results in at least a partial loss of function of a gene that impacts on cell proliferation and the ability of transformed cells to establish clonal growth. The data presented in this article suggest that LOH in this region is predictive of survival. The P value was 0.021 in a Cox regression analysis, which included 111 informative patients. Notably, the statistically significant association with survival for stage I disease parallels the finding of LOH on chromosome 18q in stage B (stage II) colon cancer.45 In this disease, patients with stage B and LOH at 18q have a prognosis similar to patients with stage C (stage III). Adjuvant systemic cytotoxic therapy is not routinely used in stage B patients with colon cancer because of marginal benefit. This is in contrast to patients with stage C disease, where adjuvant therapy resulted in a 33% relative reduction and 16% absolute reduction of mortality at 42 months.46 As a result, this molecular marker is often used to guide the decision on adjuvant chemotherapy use in patients with stage B colon cancer. At the present time, adjuvant or neoadjuvant chemotherapy for patients with completely resected stage I or stage II NSCLC is not recommended.47 However, because of the extraordinary high systemic relapse rate and low 5-year survival rate, multiple adjuvant and neoadjuvant phase II and phase III clinical trials are currently being conducted.

Evaluation of patients for LOH in the region on 11p15.5 reported here is technically feasible. Minimal amounts of tumor DNA are required and can be obtained by microdissection of paraffin-embedded tissue. DNA from peripheral-blood mononuclear cells or tumor-free lymph nodes collected during pathologic staging can serve as a source for germline DNA, and it can be used initially to assess whether a patient’s allelotype is suitable for LOH analysis. The information obtained by this analysis is a powerful prognostic discriminator for patients with stage I disease and may be useful for decisions concerning which patients should and should not receive systemic treatment in addition to surgical resection.


    ACKNOWLEDGMENTS
 
Supported by grant nos. 5RO1 CA 70317 and 5P01 CA 72099 from the National Cancer Institute, Bethesda, MD.

We thank Lawrence Leichman, MD, for his advice and critical review of the manuscript.


    REFERENCES
 TOP
 ABSTRACT
 INTRODUCTION
 PATIENTS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
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Submitted February 29, 2000; accepted November 15, 2001.




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