Abstract PD5-01: Microenvironment microarrays show that microenvironment mediated resistance mechanisms to lapatinib differ between basal and luminal HER2+ cells

Cell lines represent a valuable model system for the study of breast cancer, as they capture the cellular diversity, mutational spectrum, expression subtypes, and genomic alterations that are observed in clinical specimens. However, like any model system, cell lines are imperfect, particularly when it comes to capturing the effects of the myriad of signals and interactions they encounter in their microenvironment (ME). We are utilizing a technology known as microenvironment microarrays (MEMA) to begin to unravel the consequences of interactions of breast cancer cells with the ME. MEMA consist of thousands of unique combinations of insoluble matrix proteins that are printed to form growth pads with ligands added to the media. Cells are grown on the MEMA spots and the effects of the specific ME that they are exposed to can be read out using immunofluorescent stains of interest. When combined with automated imaging and sophisticated image processing and analysis, the MEMA platform enables the identification of specific ME conditions that alter the phenotypes of cells. We have applied MEMA to understand both baseline responses to the ME as well as how the ME might mediate response to therapeutics. We performed a pilot experiment to investigate the effects of the ME on the response to the HER2-targeted inhibitor lapatinib. We found that HCC1954 cells continued to proliferate robustly in the presence of HGF when treated with 500 nM lapatinib. In contrast, AU565 cells were proliferative in the presence of NRG1 and lapatinib, but not HGF. Focused follow up studies showed that HGF is effective in rescuing only basal HER2+ cells, while NRG1 is effective in rescuing only luminal subtype HER2+cells. Rescue with the relevant growth factor was also observed in 3-d matrigel studies, showing this was not an artifact of the 2-d culture system. We investigated the effects of drug combinations using lapatinib plus drugs that target either MET (Crizotinib) or HER3-HER2 dimers (pertuzumab). These drug combinations were able to overcome the resistance mediated by HGF and NRG1 in basal and luminal cells respectively. We found the effectiveness of pertuzumab particularly interesting, given that lapatinib should still be inhibiting HER2 kinase activity. Parallel studies found that inhibitors targeting other kinase receptors such as IGF1R partially restored sensitivity to HER2 in the presence of NRG1, suggesting a role for such receptors in the resistance. Immunoprecipitation studies showed that IGF1R co-immunoprecipitated with HER2/HER3 when pertuzumab was absent, but that additional of pertuzumab abrogated the binding of IGF1R to HER3, suggesting the formation of HER2-dependent higher order structures that can signal even when HER2 is inhibited. These studies highlight the importance of understanding the effects of the ME on cancer cells, and demonstrate the differences between ME factors that can confer resistance to HER2 targeted inhibitors in basal and luminal HER2+ cells. These findings suggest that both subtype and ME composition may be important in determining response to combinatorial treatments and may be useful to inform clinical decision making.

Citation Format: Korkola JE, Watson S, Smith R, Thompson W, Dame M, Liby T, Bucher E, Sudar D, Nederlof M, Heiser L, Gray JW. Microenvironment microarrays show that microenvironment mediated resistance mechanisms to lapatinib differ between basal and luminal HER2+ cells [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr PD5-01.

Comparative genomic hybridization

Comparative Genomic Hybridization (CGH) is a powerful molecular cytogenetic technique that permits assessment of DNA copy number on a genome-wide scale. Of note, this methodology uses tumor DNA as a probe for fluorescence in situ hybridization (FISH) to normal metaphase chromosomes and does not require dividing cells from the tumor specimen. This unit provides protocols for CGH, for preparation of metaphase chromosomes, tumor and normal DNAs for FISH and for the microscopy and image analysis of CGH experiments.

A large field CCD system for quantitative imaging of microarrays

We describe a charge-coupled device (CCD) imaging system for microarrays capable of acquiring quantitative, high dynamic range images of very large fields. Illumination is supplied by an arc lamp, and filters are used to define excitation and emission bands. The system is linear down to fluorochrome densities ≪1 molecule/µm². The ratios of the illumination intensity distributions for all excitation wavelengths have a maximum deviation ∼±4% over the object field, so that images can be analyzed without computational corrections for the illumination pattern unless higher accuracy is desired. Custom designed detection optics produce achromatic images of the spectral region from ∼ 450 to ∼750 nm. Acquisition of a series of images of multiple fluorochromes from multiple arrays occurs under computer control. The version of the system described in detail provides images of 20 mm square areas using a 27 mm square, 2K × 2K pixel, cooled CCD chip with a well depth of ∼10⁵ electrons, and provides ratio measurements accurate to a few percent over a dynamic range in intensity >1000. Resolution referred to the sample is 10 µm, sufficient for obtaining quantitative multicolor images from >30 000 array elements in an 18 mm × 18 mm square.

Segmentation of confocal microscope images of cell nuclei in thick tissue sections

Segmentation of intact cell nuclei from three-dimensional (3D) images of thick tissue sections is an important basic capability necessary for many biological research studies. However, segmentation is often difficult because of the tight clustering of nuclei in many specimen types. We present a 3D segmentation approach that combines the recognition capabilities of the human visual system with the efficiency of automatic image analysis algorithms. The approach first uses automatic algorithms to separate the 3D image into regions of fluorescence-stained nuclei and unstained background. This includes a novel step, based on the Hough transform and an automatic focusing algorithm to estimate the size of nuclei. Then, using an interactive display, each nuclear region is shown to the analyst, who classifies it as either an individual nucleus, a cluster of multiple nuclei, partial nucleus or debris. Next, automatic image analysis based on morphological reconstruction and the watershed algorithm divides clusters into smaller objects, which are reclassified by the analyst. Once no more clusters remain, the analyst indicates which partial nuclei should be joined to form complete nuclei. The approach was assessed by calculating the fraction of correctly segmented nuclei for a variety of tissue types: Caenorhabditis elegans embryos (839 correct out of a total of 848), normal human skin (343/362), benign human breast tissue (492/525), a human breast cancer cell line grown as a xenograft in mice (425/479) and invasive human breast carcinoma (260/335). Furthermore, due to the analyst's involvement in the segmentation process, it is always known which nuclei in a population are correctly segmented and which not, assuming that the analyst's visual judgement is correct.

High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays

Gene dosage variations occur in many diseases. In cancer, deletions and copy number increases contribute to alterations in the expression of tumour-suppressor genes and oncogenes, respectively. Developmental abnormalities, such as Down, Prader Willi, Angelman and Cri du Chat syndromes, result from gain or loss of one copy of a chromosome or chromosomal region. Thus, detection and mapping of copy number abnormalities provide an approach for associating aberrations with disease phenotype and for localizing critical genes. Comparative genomic hybridization (CGH) was developed for genome-wide analysis of DNA sequence copy number in a single experiment. In CGH, differentially labelled total genomic DNA from a 'test' and a 'reference' cell population are cohybridized to normal metaphase chromosomes, using blocking DNA to suppress signals from repetitive sequences. The resulting ratio of the fluorescence intensities at a location on the 'cytogenetic map', provided by the chromosomes, is approximately proportional to the ratio of the copy numbers of the corresponding DNA sequences in the test and reference genomes. CGH has been broadly applied to human and mouse malignancies. The use of metaphase chromosomes, however, limits detection of events involving small regions (of less than 20 Mb) of the genome, resolution of closely spaced aberrations and linking ratio changes to genomic/genetic markers. Therefore, more laborious locus-by-locus techniques have been required for higher resolution studies. Hybridization to an array of mapped sequences instead of metaphase chromosomes could overcome the limitations of conventional CGH (ref. 6) if adequate performance could be achieved. Copy number would be related to the test/reference fluorescence ratio on the array targets, and genomic resolution could be determined by the map distance between the targets, or by the length of the cloned DNA segments. We describe here our implementation of array CGH. We demonstrate its ability to measure copy number with high precision in the human genome, and to analyse clinical specimens by obtaining new information on chromosome 20 aberrations in breast cancer.

Efficient, interactive, and three-dimensional segmentation of cell nuclei in thick tissue sections

Segmentation of intact cell nuclei in three-dimensional (3D) images of thick tissue sections is an important basic capability necessary for many biological research studies. Because automatic algorithms do not correctly segment all nuclei in tissue sections, interactive algorithms may be preferable for some applications. Existing interactive segmentation algorithms require the analyst to draw a border around the nucleus under consideration in all successive two-dimensional (2D) planes of the 3D image. The present paper describes an algorithm with two main advantages over the existing method. First, the analyst draws borders only in 2D planes that cut approximately through the center of the nucleus under consideration so that the nuclear borders generally are most distinct. Second, the analyst draws only five borders around each nucleus, and then the algorithm interpolates the entire surface. The algorithm results in segmented objects that correspond to individual, visually identifiable nuclei. The segmented surfaces, however, may not exactly represent the true nuclear surface. An optional, automatic surface optimization algorithm can be applied to reduce this error.

Molecular cytometry of cancer

The application of molecular probes to diagnosis and prognosis of malignancies has redefined our perceptions of disease, allowing diagnosis by genotypic rather than phenotypic criteria. DNA analysis is especially useful when applied to pathological material in situ, because this allows the pathologist to combine information from both morphological and molecular observations. DNA in situ hybridization is a useful approach for the molecular pathologist, especially when combined with cytometric analysis. Potential clinical applications for in situ hybridization and the recently described technique of comparative genomic hybridization in tumor diagnosis and prognosis are described.

Computer image analysis of comparative genomic hybridization

We describe and evaluate the image-processing and analysis techniques we have developed for the quantitative analysis of comparative genomic hybridization (CGH; Science 258:818, 1992). In a typical CGH application, two genomic DNA samples are simultaneously hybridized to metaphase chromosomes and detected with different fluorochromes. The primary data in CGH are contained in the intensity ratios of the fluorochromes as a function of position on the chromosomes, which reflect variation in DNA copy number ratio between the two DNA samples. Analysis involves chromosome segmentation, intensity normalization, background corrections, and calculation of the fluorescence intensity profiles and the ratio profile along the chromosome's length. Profiles from several copies of the same chromosome in different metaphases are averaged to reduce the noise. Confidence intervals are calculated and displayed for the mean profiles. The techniques were evaluated by examining the variability found in comparisons of two normal genomic DNAs, where the ratio was expected to be constant, and by measuring the ratios obtained for cell lines with cytogenetically documented copy number changes involving several chromosomal segments. The limits of sensitivity of CGH analysis were investigated by simulation. Guidelines for the interpretation of CGH data and indications of areas for future development of the analytical techniques are also presented.

Semiautomated DNA probe mapping using digital imaging microscopy: II. System performance

This paper describes an evaluation of a semiautomated, multicolor image-analysis system to map cloned probes along metaphase chromosomes. Mapping with this system consists of fluorescence in situ hybridization (FISH) for probe localization, automatic acquisition of multicolor images showing total chromosomal DNA and probe location(s), and automatic determination of the fractional locations of the probes along the chromosomes relative to the short arm telomere (FLpter). The system was evaluated by mapping ten phage and ten cosmid probes previously mapped to chromosome 3 with other procedures. The standard deviations of FLpter measurements averaged 3.4 Mb and 2.6 Mb for phage and cosmid probes, respectively. With this variation, the order of two probes mapped in separate hybridizations could be determined with 95% confidence when their separation was greater than 2.5 Mb. In all cases, the probe locations and order were consistent with previous mapping data. FLpter values were converted to band locations using measurements of the band locations made using digital imaging microscopy. This proved superior to conversions made using ISCN ideograms.

Semiautomated DNA probe mapping using digital imaging microscopy: I. System development

Algorithms have been developed to help automate the mapping of DNA sequences along metaphase chromosomes using fluorescence in situ hybridization (FISH). Custom algorithms computationally define chromosome boundaries and compute chromosomal medial axes. A dynamic regional thresholding (DRT) algorithm is described that allows reliable detection of hybridization domains, even when they differ substantially in size and intensity. Chromosomal locations are calculated by determining the fractional location of each hybridization probe along the medial axis of a metaphase chromosome relative to the short arm (FLpter). These algorithms were tested on simulated data and by analysis of the location of probes that had been previously mapped by other techniques. These algorithms allow probes to be mapped rapidly along human chromosomes with a precision of 2-3 Mb.

Automatic fluorescence metaphase finder speeds translocation scoring in FISH painted chromosomes

A fluorescence metaphase finder was constructed with commercially available hardware and a standard Unix workstation. Its accuracy was measured in terms of the number of false positive and false negative detected metaphases on a variety of different slide preparations. The metaphase finder was used in a translocation scoring experiment in which metaphase preparations of human peripheral blood lymphocytes were hybridized with whole chromosome probes to chromosomes #1, #2, and #4. The automatic finder presented metaphases to the cytogeneticist, centered in the eyepieces at x63. The cytogeneticist's scores of analyzable metaphases and of painted chromosomes involved in rearrangements were recorded. The time for the analysis was recorded and compared to the time to analyze a similar number of cells in a purely visual experiment in which the cytogeneticist scanned for cells and analyzed them, both at x63. The results showed that, neglecting the machine time spent scanning unattended, the amount of time required for the analysis was reduced by a factor of three. Furthermore, in this experiment the metaphase finder found more scorable metaphases than the cytogeneticist found by visual scanning. Machine-assisted scoring had additional, less quantifiable, benefits; notably that digital images of metaphases sometimes assisted the analysis of chromosome rearrangements, that cells could be revisited easily, and that the analysis was much less fatiguing.

Physical mapping of chromosome 17 cosmids by fluorescence in situ hybridization and digital image analysis

We used fluorescence in situ hybridization and digital image analysis to localize cosmids along human chromosome 17. Seventy-one cosmids were selected at random from a chromosome 17 library constructed from a partial Sau3AI digest of flow-sorted chromosomes from a mouse-human hybrid cell line. Sixty-three of these (89%) gave a signal only on chromosome 17. The 40 cosmids producing the most distinct hybridization signals in metaphase and interphase cells were precisely mapped using digital image analysis. An additional 20 cosmids, previously mapped by linkage analysis, were also mapped. The order of these probes determined by metaphase mapping was consistent with the order determined by linkage analysis.

Comparative genomic hybridization: a rapid new method for detecting and mapping DNA amplification in tumors

Recent evidence indicates that many more genes than the currently known oncogenes may undergo amplification in tumors. We have developed a new technique, Comparative Genomic Hybridization (CGH), which allows rapid detection of DNA amplification anywhere in the tumor genome and maps the amplified sequences on normal chromosomes. CGH is based on a competitive in situ hybridization of differentially labeled tumor DNA and normal DNA to a normal human metaphase spread. Regions of gain of DNA sequences are seen as an increased color ratio of two fluorochromes used to detect the labeled DNAs. Over 20 different regions of amplification have been identified using CGH.

Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors

Comparative genomic hybridization produces a map of DNA sequence copy number as a function of chromosomal location throughout the entire genome. Differentially labeled test DNA and normal reference DNA are hybridized simultaneously to normal chromosome spreads. The hybridization is detected with two different fluorochromes. Regions of gain or loss of DNA sequences, such as deletions, duplications, or amplifications, are seen as changes in the ratio of the intensities of the two fluorochromes along the target chromosomes. Analysis of tumor cell lines and primary bladder tumors identified 16 different regions of amplification, many in loci not previously known to be amplified.

Comparison of strategies to detect and quantitate uniquely marked cells in intra- and inter-species hemopoietic chimeras

Evaluation of the outcome of successful bone marrow transplantation and indepth studies of transplantation biology rely increasingly upon detection and enumeration of donor hemopoietic cells in the transplanted recipients. The ability to detect and enumerate low levels of donor engraftment in interphase cell subpopulations in hemopoietic chimeras is particularly important for studies of mixed lineage chimerism, early relapse manifestations, and engraftment of subpopulations present at low frequency. We describe and compare the sensitivity and specificity of DNA-based detection strategies (fluorescence in situ hybridization, in vitro DNA amplification using the polymerase chain reaction) and flow cytometric analysis of cell surface markers to detect cells carrying marker DNA or proteins in syngeneic (mouse-to-mouse) and xenogeneic (mouse-to-human, monkey, sheep) backgrounds. DNA-based detection strategies offer advantages of rapid analysis and enumeration of target cell frequencies with detection sensitivities approximating 10(-4). The sensitivity of immunofluorescence-linked flow cytometric-based detection of nucleated leukocytes approached 10(-3), whereas flow cytometric-based detection of fixed human erythrocytes was feasible at cell frequencies of 10(-5). Data described in this manuscript should facilitate selection of appropriate methodologies for assessment of hemopoietic chimerism following transplantation.

Proposed standard for image cytometry data files

A number of different types of computers running a variety of operating systems are presently used for the collection and analysis of image cytometry data. In order to facilitate the development of sharable data analysis programs, to allow for the transport of image cytometry data from one installation to another, and to provide a uniform and controlled means for including textual information in data files, this document describes a data storage format that is proposed as a standard for use in image cytometry. In this standard, data from an image measurement are stored in a minimum of two files. One file is written in ASCII to include information about the way the image data are written and optionally, information about the sample, experiment, equipment, etc. The image data are written separately into a binary file. This standard is proposed with the intention that it will be used internationally for the storage and handling of biomedical image cytometry data. The method of data storage described in this paper is similar to those methods published in American Association of Physicists in Medicine (AAPM) Report Number 10 and in ACR-NEMA Standards Publication Number 300-1985.