Delineating spatial cell-cell interactions in the solid tumour microenvironment through the lens of highly multiplexed imaging

The growth and metastasis of solid tumours is known to be facilitated by the tumour microenvironment (TME), which is composed of a highly diverse collection of cell types that interact and communicate with one another extensively. Many of these interactions involve the immune cell population within the TME, referred to as the tumour immune microenvironment (TIME). These non-cell autonomous interactions exert substantial influence over cell behaviour and contribute to the reprogramming of immune and stromal cells into numerous pro-tumourigenic phenotypes. The study of some of these interactions, such as the PD-1/PD-L1 axis that induces CD8+ T cell exhaustion, has led to the development of breakthrough therapeutic advances. Yet many common analyses of the TME either do not retain the spatial data necessary to assess cell-cell interactions, or interrogate few (<10) markers, limiting the capacity for cell phenotyping. Recently developed digital pathology technologies, together with sophisticated bioimage analysis programs, now enable the high-resolution, highly-multiplexed analysis of diverse immune and stromal cell markers within the TME of clinical specimens. In this article, we review the tumour-promoting non-cell autonomous interactions in the TME and their impact on tumour behaviour. We additionally survey commonly used image analysis programs and highly-multiplexed spatial imaging technologies, and we discuss their relative advantages and limitations. The spatial organization of the TME varies enormously between patients, and so leveraging these technologies in future studies to further characterize how non-cell autonomous interactions impact tumour behaviour may inform the personalization of cancer treatment.​.

Abstract PO-009: Towards solving overlapping nuclei segmentation: Sequential CNNs for one to many mapping of pixels to objects

Automated cell nucleus segmentation is key to quantifying cell features and functionality to identify the disease state of tissue and its likely biological future development. Despite considerable advances in automated segmentation, it is a challenging task to split overlapping clustered nuclei where pixels can belong to more than one nuclei. To substantially improve upon current cell/nuclei segmentation methods our group has developed a promising nuclear segmentation method using sequential rounds of modified UNet CNNs which we denote SUNet. This sequential application of two separate CNNs is required to allow the reparsing the original image into multiple overlapping sub images which explicitly allows for the SUNet approach to perform a one pixel mapping to many objects that is missing from other CNN based segmentation methods in Digital Pathology. We initially constructed two human annotated 8000 overlapping nuclei training sets one each from lung and prostate tissue sections quantitatively stained for DNA. These were used to train two SUNets. Their performance was evaluated on ~20,000 nuclei from multiple tissues for each tissue type. The average correct visual nuclei segmentation rate was observed to be ~84%. A subset of the training images were hand annotated by multiple observers and the Jaccard similarity coefficient (JSC) was used to quantify the similarity between these annotations. Four human observers have annotated the same 1065 nuclei from 100 nuclei clusters. For the 6 pairwise comparisons of these individuals, the average JSC was found to be 0.69 (range 0.63-0.75). This low number reflects the inability of humans to exactly trace the same boundary by hand and that not all observers recognized the same nuclei within the highly complex clusters. The SUNets JSC was similar to the average JSC and within the range of the human observers. Indicating that for these images the SUNet performs as well as a human at segmenting nuclei within complex clusters of nuclei. Comparing the performance of SUNet with a published mask_RCNN based nuclei segmentation and a recently published nucleAIzer method on a non-complex (not a lot of overlapping nuclei) image; we find the three are almost equivalent. However, the two published methods miss a few overlapping nuclei that are found by SUNet. On images with highly complex overlapping clusters of nuclei SUnet correctly segments more (10-20%, image complexity dependent) nuclei than the other methods in areas of high complexity. In addition, SUNet recognizes and segments large numbers of nuclei completely missed by the other methods. An added benefit of allowing a one to many assignment of pixels, is that it correctly preserves the complete shape of the nuclei as it is able to assign the same pixel(s) in an image to the multiple nuclei involved in the area of their overlap as apposed to assigning it to one of the nuclei involved. In summary, the sequential CNN proposed approach can segment nuclei in complex cluster with an accuracy equivalent to human observers.

Citation Format: Calum E. MacAulay, Kouther Noureddine, Martial Guillaud, Paul Gallagher. Towards solving overlapping nuclei segmentation: Sequential CNNs for one to many mapping of pixels to objects [abstract]. In: Proceedings of the AACR Virtual Special Conference on Artificial Intelligence, Diagnosis, and Imaging; 2021 Jan 13-14. Philadelphia (PA): AACR; Clin Cancer Res 2021;27(5_Suppl):Abstract nr PO-009.

Miniaturized multimodal multiphoton microscope for simultaneous two-photon and three-photon imaging with a dual-wavelength Er-doped fiber laser

A multimodal multiphoton microscopy (MPM) is developed to acquire both two-photon microscopy (2PM) and three-photon microscopy (3PM) signals. A dual-wavelength Er-doped fiber laser is used as the light source, which provides the fundamental pulse at 1580 nm to excite third harmonic generation (THG) and the frequency-doubled pulse at 790 nm to excite intrinsic two-photon excitation fluorescence (TPEF) and second harmonic generation (SHG). Due to their different contrast mechanisms, the TPEF, SHG, and THG images can acquire complementary information about tissues, including cells, collagen fibers, lipids, and interfaces, all label-free. The compact MPM imaging probe is developed using miniature objective lens and a micro-electro-mechanical scanner. Furthermore, the femtosecond laser pulses are delivered by a single mode fiber and the signals are collected by a multimode fiber, which makes the miniaturized MPM directly fiber-coupled, compact, and portable. Design considerations on using the dual excitation wavelengths are discussed. Multimodal and label-free imaging by TPEF, SHG, and THG are demonstrated on biological samples. The miniaturized multimodal MPM is shown to have great potential for label-free imaging of thick and live tissues.

Hyperspectral cell sociology reveals spatial tumor-immune cell interactions associated with lung cancer recurrence

Background

The tumor microenvironment (TME) is a complex mixture of tumor epithelium, stroma and immune cells, and the immune component of the TME is highly prognostic for tumor progression and patient outcome. In lung cancer, anti-PD-1 therapy significantly improves patient survival through activation of T cell cytotoxicity against tumor cells. Direct contact between CD8+ T cells and target cells is necessary for CD8+ T cell activity, indicating that spatial organization of immune cells within the TME reflects a critical process in anti-tumor immunity. Current immunohistochemistry (IHC) imaging techniques identify immune cell numbers and densities, but lack assessment of cell–cell spatial relationships (or “cell sociology”). Immune functionality, however, is often dictated by cell-to-cell contact and cannot be resolved by simple metrics of cell density (for example, number of cells per mm²). To address this issue, we developed a Hyperspectral Cell Sociology technology platform for the analysis of cell–cell interactions in multi-channel IHC-stained tissue.

Methods

Tissue sections of primary tumors from lung adenocarcinoma patients with known clinical outcome were stained using multiplex IHC for CD3, CD8, and CD79a, and hyperspectral image analysis determined the phenotype of all cells. A Voronoi diagram for each cell was used to approximate cell boundaries, and the cell type of all neighboring cells was identified and quantified. Monte Carlo analysis was used to assess whether cell sociology patterns were likely due to random distributions of the cells.

Results

High density of intra-tumoral CD8+ T cells was significantly associated with non-recurrence of tumors. A cell sociology pattern of CD8+ T cells surrounded by tumor cells was more significantly associated with non-recurrence compared to CD8+ T cell density alone. CD3+ CD8- T cells surrounded by tumor cells was also associated with non-recurrence, but at a similar significance as cell density alone. Cell sociology metrics improved recurrence classifications of 12 patients. Monte Carlo re-sampling analysis determined that these cell sociology patterns were non-random.

Conclusion

Hyperspectral Cell Sociology expands our understanding of the complex interplay between tumor cells and immune infiltrate. This technology could improve predictions of responses to immunotherapy and lead to a deeper understanding of anti-tumor immunity.

Electronic supplementary material

The online version of this article (10.1186/s40425-018-0488-6) contains supplementary material, which is available to authorized users.

Abstract PR11: Hyperspectral imaging tools capture the spatial organization of cell subsets within the tumor microenvironment

Immune cells are a major component of the tumor microenvironment (TME). The spatial organization of immune cell subpopulations within the TME is recognized to have biologic significance and clinical relevance. For example, spatial organization of immune cell subsets within the TME is critical for the inhibition of cytotoxic T-cell activity through direct interaction of ligand (PD-L1) with receptor (PD-1)). However, precise spatial deconvolution is limited by the lack of imaging algorithms for in situ multiplex single cell analyses as flow cytometry does not preserve data in the spatial dimension. To this end, we have developed a hyperspectral imaging platform designed for analyzing multichannel immunohistochemical-stained tissue sections for generating cell density data and reconstructing spatial architecture for tumor biology as well as clinical association studies.

Whole-tissue sections from 20 lung adenocarcinomas with at least 5 years’ follow-up were stained for CD3 (pan-T cell), CD8 (cytotoxic T cell), and CD79a (B cell and plasma cell) and counterstained with hematoxylin. Multispectral images were acquired for five fields of view and analyzed to quantify cell types. Regions of Interest (ROIs) were then identified and analyzed in order to quantify cell-cell spatial relationships. Nonrandom patterns of immune cell distributions were identified using the Monte Carlo resampling method (500 iterations). Cell counts, densities, spatial relationships, and significant immune cell distributions were associated with clinical features (Kruskal-Wallis p&lt;0.001).

Our analysis generated 234 image files for analysis, with an average of 16,400 cells per image. The densities of intratumoral CD8+ cytotoxic T cells were significantly higher in nonrecurrent cases, agreeing with literature reports. Similarly, cell sociology deductions identified relationships associated with metastasis: tumor cells in nonmetastatic cases had increased numbers of CD8+ cytotoxic T-cell neighbors. Following Monte Carlo analysis, nonrandom cell~cell spatial proximities emerged that were not identified at a cell density level.

We have developed a hyperspectral imaging platform capable of quantifying cell-cell spatial relationships within tissue sections. This technology can be applied to larger clinical cohorts for the study of therapeutically targetable immune cell subsets with the goal of identifying patterns that correlate with clinical response and patient outcome.

This abstract is also being presented as Poster B16.

Citation Format: Katey S.S. Enfield, Spencer D. Martin, Sonia H.Y. Kung, Paul Gallagher, Calum E. MacAulay, Martial Guillaud, Wan L. Lam. Hyperspectral imaging tools capture the spatial organization of cell subsets within the tumor microenvironment [abstract]. In: Proceedings of the Fifth AACR-IASLC International Joint Conference: Lung Cancer Translational Science from the Bench to the Clinic; Jan 8-11, 2018; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(17_Suppl):Abstract nr PR11.

Abstract A26: Identification of a novel therapeutic target in lung adenocarcinoma

The reactivation of biologic signaling events that occur throughout fetal development has been observed during malignant cell transformation and tumor progression. Transcription factors are typically at the hub of these signaling events, such as NKX2-1 and several ETS transcription factors. ELF3 is an uncharacterized ETS family member that is highly expressed during fetal lung development and could play a biologic role in lung cancer based on its location within the recurrently gained chromosome 1q. We hypothesize that ELF3 is a novel oncogenic transcription factor and a therapeutic target.

Multiple independent datasets encompassing 1,685 clinical samples of lung adenocarcinoma (LUAD), lung squamous cell carcinoma (LUSC), small cell lung cancer, and nonmalignant lung tissues were analyzed to establish the frequency of ELF3 overexpression and underlying genetic mechanisms of selection. ELF3 overexpression was validated by immunohistochemistry. Associations with patient survival were tested using the log-rank method. Isogenic cell lines were established to assess oncogenic phenotypes including tumor growth in a xenograft model. Protein-protein interaction (PPI) networks were constructed around ELF3, and integrated pathway analysis was performed to decipher the signaling network disruptions resulting from ELF3 overexpression.

ELF3 overexpression was frequently observed in LUAD (&gt;2-fold: BCCA 73% TCGA 40%), but was not observed in other lung cancer subtypes. Similarly, high ELF3 expression was significantly associated with poor overall survival of LUAD patients (p&lt;0.0001), but not LUSC patients. These clinical associations prompted further examination of ELF3 in the LUAD subtype of lung cancer. ELF3 knockdown in LUAD cell lines resulted in significantly reduced proliferation, viability, and anchorage-independent growth, demonstrating that ELF3 regulates oncogenic phenotypes. Loss of ELF3 abolished the ability of LUAD cells to establish tumors in xenograft mouse models, demonstrating the requirement of ELF3 expression for tumor growth. ELF3 overexpression is associated with remodeling of 23 direct PPI networks, resulting in loss of interaction with proteins such as NFKB1 and MYC, while forming new interactions with NKX2-1, HOXA5 and ERBB3. Pathway analysis suggests a transcriptional reprogramming from inflammatory and MAPK signallng in nonmalignant and ELF3-low tissues, to adhesion and motility pathways in transformed tissues displaying high ELF3 expression. Core pathways included cell cycle, apoptosis, WNT, and NOTCH signaling, agreeing with our cell models. While mutations in ELF3 were rare, up to 80% of LUAD patients harbored focal amplification, DNA gain, and/or promoter hypomethylation at the ELF3 locus, which resulted in transcript overexpression.

We have deciphered the oncogenic role of ELF3 in LUAD. Its requirement for tumor growth in our model indicates that therapeutic targeting of ELF3 could benefit the 73% of patients who display ELF3 overexpression.

Citation Format: Katey S.S. Enfield, Erin A. Marshall, Christine Anderson, Kevin W. Ng, Sara Rahmati, Zhaolin Xu, Calum E. MacAulay, Stephen Lam, William W. Lockwood, Raj Chari, Aly Karsan, Igor Jurisica, Wan L. Lam. Identification of a novel therapeutic target in lung adenocarcinoma [abstract]. In: Proceedings of the Fifth AACR-IASLC International Joint Conference: Lung Cancer Translational Science from the Bench to the Clinic; Jan 8-11, 2018; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(17_Suppl):Abstract nr A26.

Dual-mode endomicroscopy for detection of epithelial dysplasia in the mouth: a descriptive pilot study

Dual-mode endomicroscopy is a diagnostic tool for early cancer detection. It combines the high-resolution nuclear tissue contrast of fluorescence endomicroscopy with quantified depth-dependent epithelial backscattering as obtained by diffuse optical microscopy. In an in vivo pilot imaging study of 27 oral lesions from 21 patients, we demonstrate the complementary diagnostic value of both modalities and show correlations between grade of epithelial dysplasia and relative depth-dependent shifts in light backscattering. When combined, the two modalities provide diagnostic sensitivity to both moderate and severe epithelial dysplasia in vivo.

Fluorescence confocal endomicroscopy of the cervix: pilot study on the potential and limitations for clinical implementation

Current diagnostic capabilities and limitations of fluorescence endomicroscopy in the cervix are assessed by qualitative and quantitative image analysis. Four cervical tissue types are investigated: normal columnar epithelium, normal and precancerous squamous epithelium, and stromal tissue. This study focuses on the perceived variability within and the subtle differences between the four tissue groups in the context of endomicroscopic in vivo pathology. Conclusions are drawn on the general ability to distinguish and diagnose tissue types, on the need for imaging depth control to enhance differentiation, and on the possible risks for diagnostic misinterpretations.

Fluorescence confocal endomicroscopy of the cervix: pilot study on the potential and limitations for clinical implementation

Current diagnostic capabilities and limitations of fluorescence endomicroscopy in the cervix are assessed by qualitative and quantitative image analysis. Four cervical tissue types are investigated: normal columnar epithelium, normal and precancerous squamous epithelium, and stromal tissue. This study focuses on the perceived variability within and the subtle differences between the four tissue groups in the context of endomicroscopic in vivo pathology. Conclusions are drawn on the general ability to distinguish and diagnose tissue types, on the need for imaging depth control to enhance differentiation, and on the possible risks for diagnostic misinterpretations.

Developmental transcription factor NFIB is a putative target of oncofetal miRNAs and is associated with tumour aggressiveness in lung adenocarcinoma

Genes involved in fetal lung development are thought to play crucial roles in the malignant transformation of adult lung cells. Consequently, the study of lung tumour biology in the context of lung development has the potential to reveal key developmentally relevant genes that play critical roles in lung cancer initiation/progression. Here, we describe for the first time a comprehensive characterization of miRNA expression in human fetal lung tissue, with subsequent identification of 37 miRNAs in non-small cell lung cancer (NSCLC) that recapitulate their fetal expression patterns. Nuclear factor I/B (NFIB), a transcription factor essential for lung development, was identified as a potential frequent target for these 'oncofetal' miRNAs. Concordantly, analysis of NFIB expression in multiple NSCLC independent cohorts revealed its recurrent underexpression (in ∼40-70% of tumours). Interrogation of NFIB copy number, methylation, and mutation status revealed that DNA level disruption of this gene is rare, and further supports the notion that oncofetal miRNAs are likely the primary mechanism responsible for NFIB underexpression in NSCLC. Reflecting its functional role in regulating lung differentiation, low expression of NFIB was significantly associated with biologically more aggressive subtypes and, ultimately, poorer survival in lung adenocarcinoma patients. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Sex and Smoking Status Effects on the Early Detection of Early Lung Cancer in High-Risk Smokers Using an Electronic Nose

OBJECTIVE

Volatile organic compounds (VOCs) in exhaled breath as measured by electronic nose (e-nose) have utility as biomarkers to detect subjects at risk of having lung cancer in a screening setting. We hypothesize that breath analysis using an e-nose chemo-resistive sensor array could be used as a screening tool to discriminate patients diagnosed with lung cancer from high-risk smokers.

METHODS

Breath samples from 191 subjects-25 lung cancer patients and 166 high-risk smoker control subjects without cancer-were analyzed. For clinical relevancy, subjects in both groups were matched for age, sex, and smoking histories. Classification and regression trees and discriminant functions classifiers were used to recognize VOC patterns in e-nose data. Cross-validated results were used to assess classification accuracy. Repeatability and reproducibility of e-nose data were assessed by measuring subject-exhaled breath in parallel across two e-nose devices.

RESULTS

e-Nose measurements could distinguish lung cancer patients from high-risk control subjects, with a better than 80% classification accuracy. Subject sex and smoking status impacted classification as area under the curve results (ex-smoker males 0.846, ex-smoker female 0.816, current smoker male 0.745, and current smoker female 0.725) demonstrated. Two e-nose systems could be calibrated to give equivalent readings across subject-exhaled breath measured in parallel.

CONCLUSIONS

e-Nose technology may have significant utility as a noninvasive screening tool for detecting individuals at increased risk for lung cancer.

SIGNIFICANCE

The results presented further the case that VOC patterns could have real clinical utility to screen for lung cancer in the important growing ex-smoker population.

Targeting of chemoprevention to high-risk potentially malignant oral lesions: challenges and opportunities

Worldwide, oral cancer is responsible for 170,000 deaths per year. Intervention to prevent this disease is a long sought after goal. Chemoprevention studies have focused on clinicopathological features of potentially malignant lesions (PML) in an effort to prevent their progression to cancer. However, prediction of future behavior for such lesions is difficult and remains a major challenge to such intervention. Different approaches to this problem have been tested in the past 20years. Early genetic progression models identified critical regions of allelic imbalance at 3p and 9p, and provided the basis for molecular markers to identify progressing PMLs. Subsequently, technological advances, such as genome-wide high-throughput array platforms, computer imaging, visualization technology and next generation sequencing, have broadened the scope for marker development and have the potential of further improving our ability to identify high-risk lesions in the near future either alone or in combination. In this article, we examine the milestones in the development of markers for PML progression. We emphasize the critical importance of networks among scientists, health professionals and community to facilitate the validation and application of putative markers into clinical practice. With a growing number of new agents to validate, it is necessary to coordinate the design and implementation of strategies for patient recruitment, integration of marker assessment, and the final translation of such approaches into clinical use.

Smoking status impacts microRNA mediated prognosis and lung adenocarcinoma biology

Background

Cigarette smoke is associated with the majority of lung cancers: however, 25% of lung cancer patients are non-smokers, and half of all newly diagnosed lung cancer patients are former smokers. Lung tumors exhibit distinct epidemiological, clinical, pathological, and molecular features depending on smoking status, suggesting divergent mechanisms underlie tumorigenesis in smokers and non-smokers. MicroRNAs (miRNAs) are integral contributors to tumorigenesis and mediate biological responses to smoking. Based on the hypothesis that smoking-specific miRNA differences in lung adenocarcinomas reflect distinct tumorigenic processes selected by different smoking and non-smoking environments, we investigated the contribution of miRNA disruption to lung tumor biology and patient outcome in the context of smoking status.

Methods

We applied a whole transcriptome sequencing based approach to interrogate miRNA levels in 94 patient-matched lung adenocarcinoma and non-malignant lung parenchymal tissue pairs from current, former and never smokers.

Results

We discovered novel and distinct smoking status-specific patterns of miRNA and miRNA-mediated gene networks, and identified miRNAs that were prognostically significant in a smoking dependent manner.

Conclusions

We conclude that miRNAs disrupted in a smoking status-dependent manner affect distinct cellular pathways and differentially influence lung cancer patient prognosis in current, former and never smokers. Our findings may represent promising biologically relevant markers for lung cancer prognosis or therapeutic intervention.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2407-14-778) contains supplementary material, which is available to authorized users.

Evaluation of HPV infection and smoking status impacts on cell proliferation in epithelial layers of cervical neoplasia

Accurate cervical intra-epithelial neoplasia (CIN) lesion grading is needed for effective patient management. We applied computer-assisted scanning and analytic approaches to immuno-stained CIN lesion sections to more accurately delineate disease states and decipher cell proliferation impacts from HPV and smoking within individual epithelial layers. A patient cohort undergoing cervical screening was identified (n = 196) and biopsies of varying disease grades and with intact basement membranes and epithelial layers were obtained (n = 261). Specimens were sectioned, stained (Mib1), and scanned using a high-resolution imaging system. We achieved semi-automated delineation of proliferation status and epithelial cell layers using Otsu segmentation, manual image review, Voronoi tessellation, and immuno-staining. Data were interrogated against known status for HPV infection, smoking, and disease grade. We observed increased cell proliferation and decreased epithelial thickness with increased disease grade (when analyzing the epithelium at full thickness). Analysis within individual cell layers showed a ≥50% increase in cell proliferation for CIN2 vs. CIN1 lesions in higher epithelial layers (with minimal differences seen in basal/parabasal layers). Higher rates of proliferation for HPV-positive vs. -negative cases were seen in epithelial layers beyond the basal/parabasal layers in normal and CIN1 tissues. Comparing smokers vs. non-smokers, we observed increased cell proliferation in parabasal (low and high grade lesions) and basal layers (high grade only). In sum, we report CIN grade-specific differences in cell proliferation within individual epithelial layers. We also show HPV and smoking impacts on cell layer-specific proliferation. Our findings yield insight into CIN progression biology and demonstrate that rigorous, semi-automated imaging of histopathological specimens may be applied to improve disease grading accuracy.

Oral mucosa optical biopsy by a novel handheld fluorescent confocal microscope specifically developed: technologic improvements and future prospects

OBJECTIVE

This pilot study evaluated the baseline effectiveness of a novel handheld fluorescent confocal microscope (FCM) specifically developed for oral mucosa imaging and compared the results with the literature.

STUDY DESIGN

Four different oral sites (covering the mucosa of the lip and of the ventral tongue, the masticatory mucosa of the gingiva, and the specialized mucosa of the dorsal tongue) in 6 healthy nonsmokers were imaged by an FCM made up of a confocal fiberoptic probe ergonomically designed for in vivo oral examination, using light at the wavelength of 457 nm able to excite the fluorophore acriflavine hydrochloride, topically administered. In total, 24 mucosal areas were examined.

RESULTS

The FCM was able to distinctly define epithelial cells, bacterial plaque, and inflammatory cells and to image submucosal structures by detecting their intrinsic fluorescence.

CONCLUSIONS

When compared with other devices, this FCM allowed the user to image each oral site at higher magnification, thus resulting in a clearer view.

DNA methylation is globally disrupted and associated with expression changes in chronic obstructive pulmonary disease small airways

DNA methylation is an epigenetic modification that is highly disrupted in response to cigarette smoke and involved in a wide spectrum of malignant and nonmalignant diseases, but surprisingly not previously assessed in small airways of patients with chronic obstructive pulmonary disease (COPD). Small airways are the primary sites of airflow obstruction in COPD. We sought to determine whether DNA methylation patterns are disrupted in small airway epithelia of patients with COPD, and evaluate whether changes in gene expression are associated with these disruptions. Genome-wide methylation and gene expression analysis were performed on small airway epithelial DNA and RNA obtained from the same patient during bronchoscopy, using Illumina's Infinium HM27 and Affymetrix's Genechip Human Gene 1.0 ST arrays. To control for known effects of cigarette smoking on DNA methylation, methylation and gene expression profiles were compared between former smokers with and without COPD matched for age, pack-years, and years of smoking cessation. Our results indicate that aberrant DNA methylation is (1) a genome-wide phenomenon in small airways of patients with COPD, and (2) associated with altered expression of genes and pathways important to COPD, such as the NF-E2-related factor 2 oxidative response pathway. DNA methylation is likely an important mechanism contributing to modulation of genes important to COPD pathology. Because these methylation events may underlie disease-specific gene expression changes, their characterization is a critical first step toward the development of epigenetic markers and an opportunity for developing novel epigenetic therapeutic interventions for COPD.

EYA4 is inactivated biallelically at a high frequency in sporadic lung cancer and is associated with familial lung cancer risk

In an effort to identify novel biallelically inactivated tumor suppressor genes (TSG) in sporadic invasive and pre-invasive non-small cell lung cancer (NSCLC) genomes, we applied a comprehensive integrated multi-‘omics approach to investigate patient matched, paired NSCLC tumor and non-malignant parenchymal tissues. By surveying lung tumor genomes for genes concomitantly inactivated within individual tumors by multiple mechanisms, and by the frequency of disruption in tumors across multiple cohorts, we have identified a putative lung cancer TSG, Eyes Absent 4 (EYA4). EYA4 is frequently and concomitantly deleted, hypermethylated and underexpressed in multiple independent lung tumor data sets, in both major NSCLC subtypes, and in the earliest stages of lung cancer. We find not only that decreased EYA4 expression is associated with poor survival in sporadic lung cancers, but EYA4 SNPs are associated with increased familial cancer risk, consistent with EYA4’s proximity to the previously reported lung cancer susceptibility locus on 6q. Functionally, we find that EYA4 displays TSG-like properties with a role in modulating apoptosis and DNA repair. Cross examination of EYA4 expression across multiple tumor types suggests a cell type-specific tumorigenic role for EYA4, consistent with a tumor suppressor function in cancers of epithelial origin. This work shows a clear role for EYA4 as a putative TSG in NSCLC.

FV-Guided Surgery Improves Outcome in HGD and Early Oral Cancer

Objective: 1) Become aware of the role of intraoperative fluorescence visualization in assessing subclinical changes at surgical margins in patients presenting with severe dysplasia and carcinoma in situ (HGD) or squamous cell carcinoma (SCC). 2) Understand the effectiveness of FV-guided surgery in reducing locoregional recurrence and improving overall survival.

Method: A retrospective review was conducted from September 1, 2004, to August 31, 2009, identifying 246 patients (SCC 132; HGD 114) presenting to the BCCA. Surgery was done under FV guidance in 149 patients while 97 were treated conventionally. Outcome measures included pathology-proven local recurrence, regional failure, and death.

Results: There was no significant difference between FV and control groups in age, smoking habit, lesion anatomic site, diagnosis, tumor size, and previous cancer history. There were more females in the FV group (51% vs 33%, P = .006). Time to outcome curve was estimated by the Kaplan-Meier method. With an average of 40 months follow-up, the FV group shows significantly lower local recurrence (7% vs 38%), regional failure (6% vs 23%), and death (5% vs 20%), and significant longer time to recurrence ( P < .0001), regional failure ( P = .0007), and death of disease ( P = .004).

Conclusion: The data strongly suggest that use of FV for surgical margin guidance can significantly improve outcomes in early stage oral cancer and HGD. An ongoing 5-year multicenter phase III randomized surgical trial (COOLS), funded by Terry FoResearch Institute, has been established to validate the results of this study.

Divergent genomic and epigenomic landscapes of lung cancer subtypes underscore the selection of different oncogenic pathways during tumor development

For therapeutic purposes, non-small cell lung cancer (NSCLC) has traditionally been regarded as a single disease. However, recent evidence suggest that the two major subtypes of NSCLC, adenocarcinoma (AC) and squamous cell carcinoma (SqCC) respond differently to both molecular targeted and new generation chemotherapies. Therefore, identifying the molecular differences between these tumor types may impact novel treatment strategy. We performed the first large-scale analysis of 261 primary NSCLC tumors (169 AC and 92 SqCC), integrating genome-wide DNA copy number, methylation and gene expression profiles to identify subtype-specific molecular alterations relevant to new agent design and choice of therapy. Comparison of AC and SqCC genomic and epigenomic landscapes revealed 778 altered genes with corresponding expression changes that are selected during tumor development in a subtype-specific manner. Analysis of >200 additional NSCLCs confirmed that these genes are responsible for driving the differential development and resulting phenotypes of AC and SqCC. Importantly, we identified key oncogenic pathways disrupted in each subtype that likely serve as the basis for their differential tumor biology and clinical outcomes. Downregulation of HNF4α target genes was the most common pathway specific to AC, while SqCC demonstrated disruption of numerous histone modifying enzymes as well as the transcription factor E2F1. In silico screening of candidate therapeutic compounds using subtype-specific pathway components identified HDAC and PI3K inhibitors as potential treatments tailored to lung SqCC. Together, our findings suggest that AC and SqCC develop through distinct pathogenetic pathways that have significant implication in our approach to the clinical management of NSCLC.

Abstract 4603: Optically-guided surgical approach using fluorescence visualization can significantly improve locoregional recurrence and overall survival for early stage oral cancer

Recurrence following excision of high-grade dysplasia (HGD, severe dysplasia and carcinoma in situ) or squamous cell carcinoma (SCC) implies that the presence of subclinical changes at the margins is not apparent at surgery, resulting in incomplete excision. Fluorescence visualization (FV) has shown its value in identifying clinically not apparent high-risk oral lesions. The objective of this study is to assess the effectiveness of FV-guided surgery in reducing the loco-regional recurrence and improving overall survival. Method: From September 1st 2004 to August 31, 2009, 264 consecutive patients diagnosed with T1/T2 SCC or HGD were registered at the BC Cancer Agency and treated with surgical excision with intent to cure. Among these, 246 patients (93%; SCC, 132; HGD, 114) had a follow-up period of at least 6 months. Among these patients, 149 had the surgery done under FV guidance (FV group) while the other 97 were treated with conventional surgery procedure (control group). The outcome measurements include pathology-proven local recurrence to severe dysplasia or higher requiring another surgical procedure, regional failure, and death at follow-up. Time to outcome curve was estimated by the Kaplan-Meier method. Results: There is no significant difference between FV and control groups in age, smoking habit, lesion anatomical site, diagnosis, tumor size, and previous cancer history. There were more females in the FV group (51% vs. 33%, P = 0.006). With an average of 40 months follow-up, the FV group shows significantly lower local recurrence (7% vs. 38%), regional failure (6% vs. 23%), and death (5% vs. 20%), and significant longer time to recurrence (P &lt; 0.0001), regional failure (P = 0.0007), and death of disease (P = 0.004). Conclusion: Although they are retrospectively collected from a single centre, the data have strongly demonstrated that the use of FV for surgical margin decision can significantly improve outcomes of the early stage oral cancer. An on-going 5-year multi-centre phase III randomized surgical trial (the COOLS trial), funded by Terry Fox Research Institute, has started to recruit patients and the data will be used to validate the results of this study. (Supported by R01 DE17013 from the National Institute of Dental and Craniofacial Research, CCSRI-20336 from Canadian Cancer Society Research Institute, and TFRI-2009-24 from Terry Fox Research Institute. CFP is currently supported by a Scholar Award from the Michael Smith Foundation for Health Research).

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4603. doi:1538-7445.AM2012-4603

Lung adenocarcinoma of never smokers and smokers harbor differential regions of genetic alteration and exhibit different levels of genomic instability

Recent evidence suggests that the observed clinical distinctions between lung tumors in smokers and never smokers (NS) extend beyond specific gene mutations, such as EGFR, EML4-ALK, and KRAS, some of which have been translated into targeted therapies. However, the molecular alterations identified thus far cannot explain all of the clinical and biological disparities observed in lung tumors of NS and smokers. To this end, we performed an unbiased genome-wide, comparative study to identify novel genomic aberrations that differ between smokers and NS.

High resolution whole genome DNA copy number profiling of 69 lung adenocarcinomas from smokers (n = 39) and NS (n = 30) revealed both global and regional disparities in the tumor genomes of these two groups. We found that NS lung tumors had a greater proportion of their genomes altered than those of smokers. Moreover, copy number gains on chromosomes 5q, 7p, and 16p occurred more frequently in NS. We validated our findings in two independently generated public datasets. Our findings provide a novel line of evidence distinguishing genetic differences between smoker and NS lung tumors, namely, that the extent of segmental genomic alterations is greater in NS tumors. Collectively, our findings provide evidence that these lung tumors are globally and genetically different, which implies they are likely driven by distinct molecular mechanisms.

Abstract A4: An expression map of long noncoding RNAs in human lung and non-small cell lung cancer

Background: Although still largely unexplored, long non-coding RNAs (lncRNAS) are emerging as an integral functional component of the human transcriptome. LncRNAs are mRNA-like transcripts of at least 200 nucleotides (nts) with no protein-coding capacity. Similar to their protein-coding counterparts, lncRNAs are frequently spliced and polyadenylated, but act at the RNA level. The range of functions described for lncRNAs is extensive, and includes key biological roles in chromatin remodeling, alternative splicing and mRNA degradation. Given their biological functions, dysregulation of lncRNAs is rising as an important feature of many disorders, including malignant transformation. However, the extent of the contribution of differential lncRNA expression to normal lung tissue and lung cancer has not been investigated in a comprehensive manner.

Hypothesis: We hypothesized that lncRNAs are expressed in a lung tissue-specific manner and that non-small-cell lung cancer (NSCLC) exhibits aberrant lncRNA expression patterns.

Methods: Serial Analysis of Gene Expression (SAGE) libraries were used to characterize polyadenylated transcripts in lung tissue compared to a panel of 25 different normal human tissues, and to a cohort of 12 NSCLCs. To generate lncRNA expression profiles, we developed a lncRNA discovery pipeline to map-tag-to-lncRNA matches. To identify differentially expressed lncRNAs we used a permutation test based statistical analysis. Expression pattern in lung tumors were compared to profiles from a variety of cancer types in order to identify lncRNA changes prominent in lung cancer.

Results: Here we show that large-scale expression profiling through SAGE, is an effective resource for investigating the expression pattern of polyadenylated lncRNAs. Applying a novel lncRNA discovery pipeline we reveal extensive, tissue-specific lncRNA expression in normal lung compared to a panel of several different normal human tissues. Importantly, our study reveals that NSCLC demonstrate significantly altered lncRNA expression patterns and identify highly dysregulated transcripts associated with this malignancy as oppose to other types of cancer.

Conclusion: Collectively, our findings support an important role for tissue-specific lncRNAs in lung cancer. Characterization of the functional role of these transcripts will have a considerable impact on our understanding of lung cancer development and progression, and may reveal clinically important biomarkers.

Abstract A29: Genomic alteration of E2F/Rb activates EZH2 in small cell lung cancer

Introduction: Small Cell Lung Cancer (SCLC) is a highly aggressive lung tumor with a 5 year survival rate of only 5% for extensive stage disease, which has only modestly improved over the last few decades. Identification of new molecular diagnostic and therapeutic targets is thus imperative. The purpose of this study was to employ genomic profiling of SCLC tumors to identify novel genomic alterations responsible for driving the aggressive biology of SCLC.

Methods: DNA was extracted from a panel of 14 formalin fixed paraffin embedded SCLC tumors and used to perform high resolution array comparative genomic hybridization (aCGH) on a tiling array to identify recurrent copy number alterations. RNA was harvested from a series of SCLC cell lines and used to perform qRT-PCR on candidate genes. Publicly available SCLC tumor microarray data was also analyzed to interrogate the expression of candidate genes.

Results: Through application of integrated genome and transcriptome microarray profiling, and comparison of SCLC to less aggressive non-small cell lung cancers (NSCLC) we have identified novel patterns of genomic alteration mediated pathway disruption specific to SCLC. This includes activation of the cell cycle through deregulation of downstream pathway components, as opposed to upstream deregulation of receptors such as EGFR which is characteristic of NSCLC.

Strikingly we observed direct genomic activation of E2F transcription factors, in addition to the classically described loss of the Rb tumor suppressor. Analysis of targets of the E2F/Rb pathway identified EZH2, a polycomb repressive complex 2 (PRC2) member involved in epigenetic silencing of genes involved in differentiation. EZH2 has been characterized as a target of genomic amplification in prostate and breast cancers, however, no genomic amplifications were detected in our SCLC samples, thus any overexpression is likely regulated by upstream elements of the E2F/Rb pathway. qRT-PCR confirmed EZH2 as being specifically hyper-activated with a mean 42 fold over-expression (range 10 to 74 fold) in SCLC compared to 13 fold in NSCLC. This pattern was verified from an analysis of an independent array study of SCLC. Moreover, shRNA-mediated knockdown demonstrated a significant reduction in cell viability in SCLC cell lines.

Conclusion: We conclude that EZH2 activation through genomic alteration of E2F/Rb contributes to the malignant phenotype of SCLC and may represent a potential therapeutic target.

Long non-coding RNAs are expressed in oral mucosa and altered in oral premalignant lesions

Oral epithelial dysplasias are believed to progress through a series of histopathological stages; from mild to severe dysplasia, to carcinoma in situ, and finally to invasive OSCC. Underlying this change in histopathological grade are gross chromosome alterations and changes in gene expression of both protein-coding genes and non-coding RNAs. Recent papers have described associations of aberrant expression of microRNAs, one class of non-coding RNAs, with oral cancer. However, expression profiling of long non-coding RNAs (lncRNAs) has not been reported. Long non-coding RNAs are a novel class of mRNA-like transcripts with no protein coding capacity, but with a variety of functions including roles in epigenetics and gene regulation. In recent reports, the aberrant expression of lncRNAs has been associated with human cancers, suggesting a critical role in tumorigenesis. Here, we present the first long non-coding RNA expression map for the human oral mucosa. We describe the expression of 325 long non-coding RNAs, suggesting lncRNA expression contributes significantly to the oral transcriptome. Intriguingly, ∼60% of the detected lncRNAs show aberrant expression in oral premalignant lesions. A number of these lncRNAs have been previously associated with other human cancers.

Canadian Optically-guided approach for Oral Lesions Surgical (COOLS) trial: study protocol for a randomized controlled trial

Background

Oral cancer is a major health problem worldwide. The 5-year survival rate ranges from 30-60%, and has remained unchanged in the past few decades. This is mainly due to late diagnosis and high recurrence of the disease. Of the patients who receive treatment, up to one third suffer from a recurrence or a second primary tumor. It is apparent that one major cause of disease recurrence is clinically unrecognized field changes which extend beyond the visible tumor boundary. We have previously developed an approach using fluorescence visualization (FV) technology to improve the recognition of the field at risk surrounding a visible oral cancer that needs to be removed and preliminary results have shown a significant reduction in recurrence rates.

Method/Design

This paper describes the study design of a randomized, multi-centre, double blind, controlled surgical trial, the COOLS trial. Nine institutions across Canada will recruit a total of 400 patients with oral severe dysplasia or carcinoma in situ (N = 160) and invasive squamous cell carcinoma (N = 240). Patients will be stratified by participating institution and histology grade and randomized equally into FV-guided surgery (experimental arm) or white light-guided surgery (control arm). The primary endpoint is a composite of recurrence at or 1 cm within the previous surgery site with 1) the same or higher grade histology compared to the initial diagnosis (i.e., the diagnosis used for randomization); or 2) further treatment due to the presence of severe dysplasia or higher degree of change at follow-up. This is the first randomized, multi-centre trial to validate the effectiveness of the FV-guided surgery.

Discussion

In this paper we described the strategies, novelty, and challenges of this unique trial involving a surgical approach guided by the FV technology. The success of the trial requires training, coordination, and quality assurance across multiple sites within Canada. The COOLS trial, an example of translational research, may result in reduced recurrence rates following surgical treatment of early-stage oral cancer with significant impacts on survival, morbidity, patients' quality of life and the cost to the health care system.

Trial Registration

Clinicaltrials.gov NCT01039298

Abstract A14: DNA alterations to the Cullin-3/Ring box protein-1 E3 ubiquitin ligase complex represent a novel mechanism of NF-κB activation in lung cancer

Background: Nuclear factor kappa B (NF-κB) signaling is essential for lung cancer development, and therefore, may serve as a target for intervention. However, the genetic mechanisms responsible for its activation are not fully understood. Kelch-like ECH-associated protein 1 (KEAP1) binds protein substrates to the Cullin-3 (CUL3)/Ring box protein-1 (RBX1) E3 ubiquitin ligase complex where ubiquitination signals substrates for proteosomal degradation. Recently, inhibitor of nuclear factor kappa-B kinase subunit beta (IKKβ), an activator of NF-κB, was shown to be a substrate of KEAP1, implicating KEAP1's involvement in regulating NF-κB signaling. Loss of function of KEAP1 leads to IKKβ accumulation and NF-κB activation. We hypothesized that DNA deletions of the other E3 complex components (CUL3 and RBX1) are frequent alterations that disrupt complex function and contribute to NF-κB activation in lung cancer.

Methods: We screened DNA copy number profiles of 261 non-small cell lung cancer (NSCLC) tumors for DNA alterations at the KEAP1, CUL3, RBX1, and IKK loci. Profiles were generated by array comparative genomic hybridization on the SMRT array (sub-megabase resolution tiling) platform. We also analyzed mRNA expression of these genes and 9 well annotated NF-κB target genes, using gene expression profiles generated with Agilent gene expression microarrays for a subset (n=48) of the tumors.

Results: Our investigation of genetic disruption to the E3 ubiquitin ligase complex components revealed 54% of tumors harbored DNA copy number loss of at least one complex component (KEAP1, CUL3, or RBX1) or gain of IKKβ. Moreover, at the expression level, 81% of tumors analyzed had aberrant expression of one of these genes (underexpression of complex components or overexpression of IKKβ). Interestingly, the copy number alterations identified appeared to segregate with adenocarcinoma (AC) or squamous cell carcinoma (SCC) histology; KEAP1 loss was more prevalent in AC while CUL3 loss and IKKβ gain were more frequent in SCC. When NF-κB target gene expression was analyzed, we observed higher expression of 5/9 genes in tumors with underexpression of an E3 ubiquitin ligase complex component relative to matched non-malignant tissue from the same individual.

Conclusions: The presence and strikingly high frequency of genetic disruption and aberrant expression of the E3 ubiquitin ligase complex components (KEAP1, CUL3, and RBX1) revealed in this study provides evidence of its importance in lung cancer. These data suggest that DNA level alterations to this complex may represent a novel mechanism of NF-κB activation in lung cancer.

Citation Information: Cancer Prev Res 2010;3(12 Suppl):A14.

A sequence-based approach to identify reference genes for gene expression analysis

BACKGROUND

An important consideration when analyzing both microarray and quantitative PCR expression data is the selection of appropriate genes as endogenous controls or reference genes. This step is especially critical when identifying genes differentially expressed between datasets. Moreover, reference genes suitable in one context (e.g. lung cancer) may not be suitable in another (e.g. breast cancer). Currently, the main approach to identify reference genes involves the mining of expression microarray data for highly expressed and relatively constant transcripts across a sample set. A caveat here is the requirement for transcript normalization prior to analysis, and measurements obtained are relative, not absolute. Alternatively, as sequencing-based technologies provide digital quantitative output, absolute quantification ensues, and reference gene identification becomes more accurate.

METHODS

Serial analysis of gene expression (SAGE) profiles of non-malignant and malignant lung samples were compared using a permutation test to identify the most stably expressed genes across all samples. Subsequently, the specificity of the reference genes was evaluated across multiple tissue types, their constancy of expression was assessed using quantitative RT-PCR (qPCR), and their impact on differential expression analysis of microarray data was evaluated.

RESULTS

We show that (i) conventional references genes such as ACTB and GAPDH are highly variable between cancerous and non-cancerous samples, (ii) reference genes identified for lung cancer do not perform well for other cancer types (breast and brain), (iii) reference genes identified through SAGE show low variability using qPCR in a different cohort of samples, and (iv) normalization of a lung cancer gene expression microarray dataset with or without our reference genes, yields different results for differential gene expression and subsequent analyses. Specifically, key established pathways in lung cancer exhibit higher statistical significance using a dataset normalized with our reference genes relative to normalization without using our reference genes.

CONCLUSIONS

Our analyses found NDUFA1, RPL19, RAB5C, and RPS18 to occupy the top ranking positions among 15 suitable reference genes optimal for normalization of lung tissue expression data. Significantly, the approach used in this study can be applied to data generated using new generation sequencing platforms for the identification of reference genes optimal within diverse contexts.

Integrating the multiple dimensions of genomic and epigenomic landscapes of cancer

Advances in high-throughput, genome-wide profiling technologies have allowed for an unprecedented view of the cancer genome landscape. Specifically, high-density microarrays and sequencing-based strategies have been widely utilized to identify genetic (such as gene dosage, allelic status, and mutations in gene sequence) and epigenetic (such as DNA methylation, histone modification, and microRNA) aberrations in cancer. Although the application of these profiling technologies in unidimensional analyses has been instrumental in cancer gene discovery, genes affected by low-frequency events are often overlooked. The integrative approach of analyzing parallel dimensions has enabled the identification of (a) genes that are often disrupted by multiple mechanisms but at low frequencies by any one mechanism and (b) pathways that are often disrupted at multiple components but at low frequencies at individual components. These benefits of using an integrative approach illustrate the concept that the whole is greater than the sum of its parts. As efforts have now turned toward parallel and integrative multidimensional approaches for studying the cancer genome landscape in hopes of obtaining a more insightful understanding of the key genes and pathways driving cancer cells, this review describes key findings disseminating from such high-throughput, integrative analyses, including contributions to our understanding of causative genetic events in cancer cell biology.

Abstract PR-05: Alterations in tissue autofluorescence using spectroscopy in high-risk oral lesions

High-risk oral lesions can be sometimes difficult to discriminate from reactive oral lesions, which are commonly seen within community settings. New tools need to be developed to aid in screening and early detection of high-risk lesions. The assessment of alteration in tissue autofluorescence using spectroscopy has demonstrated promising results in distinguishing cancerous from normal tissue at many organs and sites; however, there is limited information on its usage to distinguish reactive lesions (as seen by both white-light and autofluoescence imaging) from cancerous/precancerous lesions.

Objectives of this study are: 1) to collect autofluorescence spectra from normal mucosa, mucosa with high-risk histological change and those with chronic inflammation under different excitation wavelengths of light, and 2) to compare the change in tissue autofluorescence in different exciting wavelengths among these oral mucosal lesions.

Methods: Patients with high-risk oral lesions and inflammatory conditions were recruited from the Dysplasia Clinics of the BC Oral Cancer Prevention Program. Spectroscopic measurements were taken using a fiber optic probe of a Remiscope (Remicalm, LLC; Houston, TX). Three excitation wavelengths were used: 436 nm, 405 nm, and 355 nm. Percent loss of peak emission intensity (%PEI) was measured by comparing the PEI of the lesional and contralateral normal areas. Differences in %PEI between groups were compared using unpaired t-test.

Results: From June to September 2009, 102 spectroscopic measurements were recorded from 17 patients (cancer, 5; dysplasia, 6; inflammation, 6). Among these, loss of tissue autofluorescence under 436 nm, 405 nm, and 355 nm was observed in all cases. When comparing the %PEI between cancer and dysplasia groups, increased loss was seen in the cancer group at all three excitation wavelengths, especially under 355 nm and 405 nm excitations (P = 0.023 and 0.045 respectively). When comparing to the inflammation group, there is almost the same degree of loss observed between cancer and inflammation groups in all 3 excitation wavelengths. Interestingly, there is a significant difference in %PEI observed between dysplasia and inflammation group under 436 nm and 355 nm excitations (P = 0.005 and 0.022 respectively) but no statistical difference under 405 nm excitation.

Conclusions: This is the first study to use 3 different excitation wavelengths of light to examine the spectra of oral cancerous, precancerous, and specifically inflammatory oral lesions (as seen by both white-light and autofluoescence imaging). This device has shown its potential to provide an objective, sensitive approach to distinguish precancers from those commonly seen within community settings caused by chronic inflammation. (Supported by grant R01 DE17013 from the National Institute of Dental and Craniofacial Research and grant CCSRI-20336 from Canadian Cancer Society Research Institute. CFP is supported by a Clinician Scientist Award from the Canadian Institutes of Health Research and a Scholar Award from the Michael Smith Foundation for Health Research).

Citation Information: Cancer Prev Res 2010;3(1 Suppl):PR-05.

Reflection-contrast limit of fiber-optic image guides

Fiber-optic image guides in confocal reflectance endomicroscopes introduce background backscatter that limits the achievable contrast in these devices. We show the dominant source of backscatter from the image guide is due to Rayleigh scattering at short wavelengths and terminal reflections of the fibers at long wavelengths. The effective Rayleigh scattering coefficient and the wavelength-independent reflectivity due terminal reflections are measured experimentally in a commercial image guide. The Rayleigh scattering component of backscatter can be accurately predicted using the fractional refractive-index difference and length of the fibers in the image guide. We also presented a simple model that can be used to predict signal-to-background ratio in a fiber-optic confocal reflectance endomicroscope for biologically relevant tissues and contrast agents that cover a wide range of reflectivity.

Simple device for the direct visualization of oral-cavity tissue fluorescence

Early identification of high-risk disease could greatly reduce both mortality and morbidity due to oral cancer. We describe a simple handheld device that facilitates the direct visualization of oral-cavity fluorescence for the detection of high-risk precancerous and early cancerous lesions. Blue excitation light (400 to 460 nm) is employed to excite green-red fluorescence from fluorophores in the oral tissues. Tissue fluorescence is viewed directly along an optical axis collinear with the axis of excitation to reduce inter- and intraoperator variability. This robust, field-of-view device enables the direct visualization of fluorescence in the context of surrounding normal tissue. Results from a pilot study of 44 patients are presented. Using histology as the gold standard, the device achieves a sensitivity of 98% and specificity of 100% when discriminating normal mucosa from severe dysplasia/carcinoma in situ (CIS) or invasive carcinoma. We envisage this device as a suitable adjunct for oral cancer screening, biopsy guidance, and margin delineation.

Nuclear morphometry as a biomarker for bronchial intraepithelial neoplasia: correlation with genetic damage and cancer development

BACKGROUND

Bronchial carcinomas are preceded by epithelial morphologic changes. The variation in interpretation of these grades of intraepithelial neoplasia makes it difficult to determine its natural history and utility of histopathology as a surrogate endpoint biomarker. The objective of this study was to quantitate morphologic changes of intraepitherlial neoplasia and validate its utility through correlation with histopathology, allelic loss, and cancer development.

METHODS

Quantitative nuclear morphometry was performed on 47 normal bronchial biopsies and 28 invasive cancer to generate a morphometry index (MI) that was applied to 1,096 bronchial biopsies from 230 volunteers who were current smokers (> or =25 pack-years) and 30 patients who had cancer. In a subset of 631 biopsies, MI was correlated with frequency of loss of heterozygosity at nine chromosomal regions (14 polymorphic markers).

RESULTS

A significant correlation was found between MI and allelic loss in six of nine chromosomal regions. As part of patient long-term follow-up, 12 sites that progressed to cancer were identified and had significantly increased MIs relative to nonprogressing sites. Significant overlap in the MIs was found between most grades of intraepithelial neoplasia.

CONCLUSIONS

In chemoprevention trials, nuclear morphometry can supplement histopathology as a Surrogate Endpont Biomarker (SEB) because it is quantitative, collelates well with genetic damage, and may predict cancer development.

Nuclear texture features for classifying benign vs. dysplastic or malignant squamous epithelium of the larynx

OBJECTIVE

To search for nuclear features and feature combinations able to assess malignancy and premalignant changes on tissue sections of laryngeal squamous epithelium.

STUDY DESIGN

A total of 139 lesions of benign changes (BC) (n = 44), epithelial dysplasias (ED) (n = 50) and invasive laryngeal cancer (LC) (n = 45) were retrieved from archival pathology specimens. The goal of this study was to identify the best features or feature combinations that discriminate BC from LC and also reflect the degree of ED. In order to verify the results on independent data, the groups were split into two separate subgroups, one for training and one for testing.

RESULTS

On the test set of slides, the overall correct classification of BC vs. LC cases was 82% using only one feature, fractal2_area. This classification rate could be increased to 91% when a discriminant function based on 10 features was used. However, this gain was not significant.

CONCLUSION

Fractal texture features can be used to assess malignancy on tissue sections as an alternative to DNA measurement. In this study feature combinations did not significantly improve classification rates.

New method for detection of heart allograft rejection: validation of sensitivity and reliability in a rat heterotopic allograft model

BACKGROUND

Patients with inflammatory heart muscle diseases would benefit from a safe, convenient, rapidly performed diagnostic technique with real-time results not involving tissue removal. We have performed a detailed evaluation of detection of heart allograft rejection by autofluorescence in a heterotopic abdominal rat heart allograft model ex vivo.

METHODS AND RESULTS

Recipient rats with allograft (Lewis to Fisher 344; n=71) and isograft (Lewis to Lewis; n=33) hearts, treated with cyclosporine or untreated, were killed at days 2, 4, 7, 14, 21, 28, and 56 after transplant. Nontransplant controls with (n=24) or without (n=24) immunosuppressive therapy were also studied. When the rats were killed, autofluorescence spectra were acquired under blue-light excitation from midtransverse ventricular sections of native and transplanted hearts. Corresponding sections were then evaluated pathologically by a modified International Society for Heart and Lung Transplantation (ISHLT) grading schema. The spectral differences between rejecting and nonrejecting hearts were quantified by linear discriminant functions, producing scores that decreased progressively with increasing severity of tissue rejection. Mean+/-SD discriminant function scores were 2.9+/-1.6, 1.8+/-2.2, -0.1+/-2.8, -1.2+/-2.3, and -2.3+/-3.0 for isografts and allograft ISHLT grades 0, I, II, and III, respectively (Spearman rank-order correlation -0.6; P<0.001, test for trend). Cyclosporine had no detectable effect on the spectra.

CONCLUSIONS

The correlation between changes in autofluorescence spectra and ISHLT rejection grade strongly supports the possibility of catheter-based, fluorescence-guided surveillance of rejection.

Image cytometry and chemoprevention in cervical cancer

Of the approximately 60 million Pap smears performed in the United States in 1995, about 8% or 5 million will show cytology that is "not negative" (ASCUS, AGCUS, LSIL, HSIL, etc.). Possibly 15% or about 0.7 million of these cases will have positive follow-up by repeated Pap smears, colposcopy or biopsy. More than 4 million will be false-positive smears based on the reference standard of biopsy or repeated smears. If no treatment or medical intervention was offered to the 0.7 million cytologically and histologically positive cases, perhaps 20,000 (3%) would develop into invasive cancer. Of the original 5 million cytologically "not negative" cases, fewer than 0.5% have the potential to develop into invasive cancer. While considerable attention has been paid to false-negatives in Pap screening, the above considerations indicate that the cytological and histological criteria for assessing the malignant potential of "not negative" samples might benefit from some refinement. Until such refinement occurs, any chemoprevention studies in cervix face a formidable signal-to-noise problem--worse than 1:30. This paper presents data from quantitative image cytometry of cervical smears for assessing the malignant potential of various "not negative" cases. We have approached this in two ways--by analyzing dysplastic cell nuclei and by analyzing the nuclei of cytologically normal cells growing in the vicinity of the neoplastic lesion. In both cases, nuclear features describing the distribution of the DNA in the cell nuclei (especially texture features) are the discriminating factors. Future research into the objective assessment of malignant potential of "not negative" cases is outlined.