Discrimination between benign and malignant prostate tissue using chromatin texture analysis in 3-D by confocal laser scanning microscopy

Non-coding RNAs and nuclear architecture during epithelial-mesenchymal transition in lung cancer and idiopathic pulmonary fibrosis

Lung cancer (LC) is the leading cause of cancer-related deaths worldwide. On the other hand, idiopathic pulmonary fibrosis (IPF) is the most common interstitial lung disease showing a prevalence of 20 new cases per 100,000 persons per year. Despite differences in cellular origin and pathological phenotypes, LC and IPF are lung diseases that share common features, including hyperproliferation of specific cell types in the lung, involvement of epithelial-mesenchymal transition (EMT) and enhanced activity of signaling pathways, such as tissue growth factor (TGFB), epidermal growth factor (EGF), fibroblast growth factor (FGF), wingless secreted glycoprotein (WNT) signaling, among others. EMT is a process during which epithelial cells lose their cell polarity and cell-cell adhesion, and acquire migratory and invasive properties to become mesenchymal cells. EMT involves numerous morphological hallmarks of hyperproliferative diseases, like cell plasticity, resistance to apoptosis, dedifferentiation and proliferation, thereby playing a central role during organ fibrosis and cancer progression. EMT was considered as an "all-or-none" process. In contrast to these outdated dichotomist interpretations, recent reports suggest that EMT occurs gradually involving different epithelial cell intermediate states with mesenchyme-like characteristics. These cell intermediate states of EMT differ from each other in their cell plasticity, invasiveness and metastatic potential, which in turn are induced by signals from their microenvironment. EMT is regulated by several transcription factors (TFs), which are members of prominent families of master regulators of transcription. In addition, there is increasing evidence for the important contribution of noncoding RNAs (ncRNAs) to EMT. In our review we highlight articles dissecting the function of different ncRNAs subtypes and nuclear architecture in cell intermediate states of EMT, as well as their involvement in LC and IPF.

"Stealth dissemination" of macrophage-tumor cell fusions cultured from blood of patients with pancreatic ductal adenocarcinoma

Here we describe isolation and characterization of macrophage-tumor cell fusions (MTFs) from the blood of pancreatic ductal adenocarcinoma (PDAC) patients. The MTFs were generally aneuploidy, and immunophenotypic characterizations showed that the MTFs express markers characteristic of PDAC and stem cells, as well as M2-polarized macrophages. Single cell RNASeq analyses showed that the MTFs express many transcripts implicated in cancer progression, LINE1 retrotransposons, and very high levels of several long non-coding transcripts involved in metastasis (such as MALAT1). When cultured MTFs were transplanted orthotopically into mouse pancreas, they grew as obvious well-differentiated islands of cells, but they also disseminated widely throughout multiple tissues in "stealth" fashion. They were found distributed throughout multiple organs at 4, 8, or 12 weeks after transplantation (including liver, spleen, lung), occurring as single cells or small groups of cells, without formation of obvious tumors or any apparent progression over the 4 to 12 week period. We suggest that MTFs form continually during PDAC development, and that they disseminate early in cancer progression, forming "niches" at distant sites for subsequent colonization by metastasis-initiating cells.

Nondestructive Techniques to Evaluate the Characteristics and Development of Engineered Cartilage

In this review, methods for evaluating the properties of tissue engineered (TE) cartilage are described. Many of these have been developed for evaluating properties of native and osteoarthritic articular cartilage. However, with the increasing interest in engineering cartilage, specialized methods are needed for nondestructive evaluation of tissue while it is developing and after it is implanted. Such methods are needed, in part, due to the large inter- and intra-donor variability in the performance of the cellular component of the tissue, which remains a barrier to delivering reliable TE cartilage for implantation. Using conventional destructive tests, such variability makes it near-impossible to predict the timing and outcome of the tissue engineering process at the level of a specific piece of engineered tissue and also makes it difficult to assess the impact of changing tissue engineering regimens. While it is clear that the true test of engineered cartilage is its performance after it is implanted, correlation of pre and post implantation properties determined non-destructively in vitro and/or in vivo with performance should lead to predictive methods to improve quality-control and to minimize the chances of implanting inferior tissue.

A versatile pipeline for the multi-scale digital reconstruction and quantitative analysis of 3D tissue architecture

A prerequisite for the systems biology analysis of tissues is an accurate digital three-dimensional reconstruction of tissue structure based on images of markers covering multiple scales. Here, we designed a flexible pipeline for the multi-scale reconstruction and quantitative morphological analysis of tissue architecture from microscopy images. Our pipeline includes newly developed algorithms that address specific challenges of thick dense tissue reconstruction. Our implementation allows for a flexible workflow, scalable to high-throughput analysis and applicable to various mammalian tissues. We applied it to the analysis of liver tissue and extracted quantitative parameters of sinusoids, bile canaliculi and cell shapes, recognizing different liver cell types with high accuracy. Using our platform, we uncovered an unexpected zonation pattern of hepatocytes with different size, nuclei and DNA content, thus revealing new features of liver tissue organization. The pipeline also proved effective to analyse lung and kidney tissue, demonstrating its generality and robustness.

Macrophage-tumor cell fusions from peripheral blood of melanoma patients

Background

While the morbidity and mortality from cancer are largely attributable to its metastatic dissemination, the integral features of the cascade are not well understood. The widely accepted hypothesis is that the primary tumor microenvironment induces the epithelial-to-mesenchymal transition in cancer cells, facilitating their escape into the bloodstream, possibly accompanied by cancer stem cells. An alternative theory for metastasis involves fusion of macrophages with tumor cells (MTFs). Here we culture and characterize apparent MTFs from blood of melanoma patients.

Methods

We isolated enriched CTC populations from peripheral blood samples from melanoma patients, and cultured them. We interrogated these cultured cells for characteristic BRAF mutations, and used confocal microscopy for immunophenotyping, motility, DNA content and chromatin texture analyses, and then conducted xenograft studies using nude mice.

Findings

Morphologically, the cultured MTFs were generally large with many pseudopod extensions and lamellipodia. Ultrastructurally, the cultured MTFs appeared to be macrophages. They were rich in mitochondria and lysosomes, as well as apparent melanosomes. The cultured MTF populations were all heterogeneous with regard to DNA content, containing aneuploid and/or high-ploidy cells, and they typically showed large sheets (and/or clumps) of cytoplasmic chromatin. This cytoplasmic DNA was found within heterogeneously-sized autophagic vacuoles, which prominently contained chromatin and micronuclei. Cultured MTFs uniformly expressed pan-macrophage markers (CD14, CD68) and macrophage markers indicative of M2 polarization (CD163, CD204, CD206). They also expressed melanocyte-specific markers (ALCAM, MLANA), epithelial biomarkers (KRT, EpCAM), as well as the pro-carcinogenic cytokine MIF along with functionally related stem cell markers (CXCR4, CD44). MTF cultures from individual patients (5 of 8) contained melanoma-specific BRAF activating mutations. Chromatin texture analysis of deconvoluted images showed condensed DNA (DAPI-intense) regions similar to focal regions described in stem cell fusions. MTFs were readily apparent in vivo in all human melanomas examined, often exhibiting even higher DNA content than the cultured MTFs. When cultured MTFs were transplanted subcutaneously in nude mice, they disseminated and produced metastatic lesions at distant sites.

Conclusions and Hypothesis

Apparent MTFs are present in peripheral blood of patients with cutaneous melanomas, and they possess the ability to form metastatic lesions when transplanted into mice. We hypothesize that these MTFs arise at the periphery of primary tumors in vivo, that they readily enter the bloodstream and invade distant tissues, secreting cytokines (such as MIF) to prepare “niches” for colonization by metastasis initiating cells.

Nuclear morphometry, epigenetic changes, and clinical relevance in prostate cancer

Nuclear structure alterations in cancer involve global genetic (mutations, amplifications, copy number variations, translocations, etc.) and epigenetic (DNA methylation and histone modifications) events that dramatically and dynamically spatially change chromatin, nuclear body, and chromosome organization. In prostate cancer (CaP) there appears to be early (<50 years) versus late (>60 years) onset clinically significant cancers, and we have yet to clearly understand the hereditary and somatic-based molecular pathways involved. We do know that once cancer is initiated, dedifferentiation of the prostate gland occurs with significant changes in nuclear structure driven by numerous genetic and epigenetic processes. This review focuses upon the nuclear architecture and epigenetic dynamics with potential translational clinically relevant applications to CaP. Further, the review correlates changes in the cancer-driven epigenetic process at the molecular level and correlates these alterations to nuclear morphological quantitative measurements. Finally, we address how we can best utilize this knowledge to improve the efficacy of personalized treatment of cancer.

Three-dimensional solid texture analysis in biomedical imaging: review and opportunities

Three-dimensional computerized characterization of biomedical solid textures is key to large-scale and high-throughput screening of imaging data. Such data increasingly become available in the clinical and research environments with an ever increasing spatial resolution. In this text we exhaustively analyze the state-of-the-art in 3-D biomedical texture analysis to identify the specific needs of the application domains and extract promising trends in image processing algorithms. The geometrical properties of biomedical textures are studied both in their natural space and on digitized lattices. It is found that most of the tissue types have strong multi-scale directional properties, that are well captured by imaging protocols with high resolutions and spherical spatial transfer functions. The information modeled by the various image processing techniques is analyzed and visualized by displaying their 3-D texture primitives. We demonstrate that non-convolutional approaches are expected to provide best results when the size of structures are inferior to five voxels. For larger structures, it is shown that only multi-scale directional convolutional approaches that are non-separable allow for an unbiased modeling of 3-D biomedical textures. With the increase of high-resolution isotropic imaging protocols in clinical routine and research, these models are expected to best leverage the wealth of 3-D biomedical texture analysis in the future. Future research directions and opportunities are proposed to efficiently model personalized image-based phenotypes of normal biomedical tissue and its alterations. The integration of the clinical and genomic context is expected to better explain the intra class variation of healthy biomedical textures. Using texture synthesis, this provides the exciting opportunity to simulate and visualize texture atlases of normal ageing process and disease progression for enhanced treatment planning and clinical care management.

A modified artificial immune system based pattern recognition approach--an application to clinical diagnostics

OBJECTIVE

This paper introduces a modified artificial immune system (AIS)-based pattern recognition method to enhance the recognition ability of the existing conventional AIS-based classification approach and demonstrates the superiority of the proposed new AIS-based method via two case studies of breast cancer diagnosis.

METHODS AND MATERIALS

Conventionally, the AIS approach is often coupled with the k nearest neighbor (k-NN) algorithm to form a classification method called AIS-kNN. In this paper we discuss the basic principle and possible problems of this conventional approach, and propose a new approach where AIS is integrated with the radial basis function--partial least square regression (AIS-RBFPLS). Additionally, both the two AIS-based approaches are compared with two classical and powerful machine learning methods, back-propagation neural network (BPNN) and orthogonal radial basis function network (Ortho-RBF network).

RESULTS

The diagnosis results show that: (1) both the AIS-kNN and the AIS-RBFPLS proved to be a good machine leaning method for clinical diagnosis, but the proposed AIS-RBFPLS generated an even lower misclassification ratio, especially in the cases where the conventional AIS-kNN approach generated poor classification results because of possible improper AIS parameters. For example, based upon the AIS memory cells of "replacement threshold=0.3", the average misclassification ratios of two approaches for study 1 are 3.36% (AIS-RBFPLS) and 9.07% (AIS-kNN), and the misclassification ratios for study 2 are 19.18% (AIS-RBFPLS) and 28.36% (AIS-kNN); (2) the proposed AIS-RBFPLS presented its robustness in terms of the AIS-created memory cells, showing a smaller standard deviation of the results from the multiple trials than AIS-kNN. For example, using the result from the first set of AIS memory cells as an example, the standard deviations of the misclassification ratios for study 1 are 0.45% (AIS-RBFPLS) and 8.71% (AIS-kNN) and those for study 2 are 0.49% (AIS-RBFPLS) and 6.61% (AIS-kNN); and (3) the proposed AIS-RBFPLS classification approaches also yielded better diagnosis results than two classical neural network approaches of BPNN and Ortho-RBF network.

CONCLUSION

In summary, this paper proposed a new machine learning method for complex systems by integrating the AIS system with RBFPLS. This new method demonstrates its satisfactory effect on classification accuracy for clinical diagnosis, and also indicates its wide potential applications to other diagnosis and detection problems.

Quantitative characterization of preneoplastic progression using single-cell computed tomography and three-dimensional karyometry

The development of morphological biosignatures to precisely characterize preneoplastic progression necessitates high-resolution three-dimensional (3D) cell imagery and robust image processing algorithms. We report on the quantitative characterization of nuclear structure alterations associated with preneoplastic progression in human esophageal epithelial cells using single-cell optical tomography and fully automated 3D karyometry. We stained cultured cells with hematoxylin and generated 3D images of individual cells by mathematically reconstructing 500 projection images acquired using optical absorption tomographic imaging. For 3D karyometry, we developed novel, fully automated algorithms to robustly segment the cellular, nuclear, and subnuclear components in the acquired cell images, and computed 41 quantitative morphological descriptors from these segmented volumes. In addition, we developed algorithms to quantify the spatial distribution and texture of the nuclear DNA. We applied our methods to normal, metaplastic, and dysplastic human esophageal epithelial cell lines, analyzing 100 cells per line. The 3D karyometric descriptors elucidated quantitative differences in morphology and enabled robust discrimination between cell lines on the basis of extracted morphological features. The morphometric hallmarks of cancer progression such as increased nuclear size, elevated nuclear content, and anomalous chromatin texture and distribution correlated with this preneoplastic progression model, pointing to the clinical use of our method for early cancer detection.

Hyperacetylation in prostate cancer induces cell cycle aberrations, chromatin reorganization and altered gene expression profiles

Histone acetylation is a fundamental mechanism in the regulation of local chromatin conformation and gene expression. Research has focused on the impact of altered epigenetic environments on the expression of specific genes and their pathways. However, changes in histone acetylation also have a global impact on the cell. In this study we used digital texture analysis to assess global chromatin patterns following treatment with trichostatin A (TSA) and have observed significant alterations in the condensation and distribution of higher-order chromatin, which were associated with altered gene expression profiles in both immortalised normal PNT1A prostate cell line and androgen-dependent prostate cancer cell line LNCaP. Furthermore, the extent of TSA-induced disruption was both cell cycle and cell line dependent. This was illustrated by the identification of sub-populations of prostate cancer cells expressing high levels of H3K9 acetylation in the G(2)/M phase of the cell cycle that were absent in normal cell populations. In addition, the analysis of enriched populations of G(1) cells showed a global decondensation of chromatin exclusively in normal cells.

Valproic acid causes dose- and time-dependent changes in nuclear structure in prostate cancer cells in vitro and in vivo

Histone deacetylase inhibitors such as valproic acid (VPA) are promising anticancer agents that change the acetylation status of histones and loosen the chromatin structure. We assessed nuclear structure changes induced by VPA in prostate cancer LNCaP, CWR22R, DU145, and PC3 cell lines and xenografts and their potential use as a biomarker of treatment. In vitro tissue microarrays consisted of prostate cancer cell lines treated for 3, 7, or 14 days with 0, 0.6, or 1.2 mmol/L VPA. In vivo tissue microarrays consisted of cores from prostate cancer xenografts from nude mice treated for 30 days with 0.2% or 0.4% VPA in drinking water. Digital images of at least 200 Feulgen DNA-stained nuclei were captured using the Nikon CoolScope and nuclear alterations were measured. With a set of seven most frequently significant nuclear alterations (determined by univariate logistic regression analysis), control and VPA treatment nuclei were compared in vitro and in vivo. Depending on the cell line, area under the curve-receiver operating characteristics ranged between 0.6 and 0.9 and were dose- and time-dependent both in vitro and in vivo. Also, VPA treatment caused significant nuclear alterations in normal drug-filtering organs (liver and kidney tissue). In vitro and in vivo VPA treatment of prostate cancer cell lines results in significant dose- and time-dependent changes in nuclear structure. Further, VPA induces nuclear structural changes in normal liver and kidney tissue, which likely reflects a natural physiologic response. Therefore, nuclear structural alterations may serve as a biomarker for histone deacetylase inhibitor treatment.

The cancer nuclear microenvironment: interface between light microscopic cytology and molecular phenotype

A definitive diagnosis of cancer may be rendered by microscopic assessment of only a few cells in an appropriate clinical setting due to the distinctive nuclear structure of most cancer cells in comparison to nuclei of normal human cells. The molecular architecture of non-neoplastic human nuclei--of the nuclear matrix and of matrix-associated proteins and nucleic acids--is being characterized in exquisite molecular detail. What is missing is the application of the findings and tools of molecular biology to understanding the cytological structure of cancer nuclei. This article delves into the basis of nuclear structure at different levels of resolution--light microscopic, electron microscopic, and molecular.

How to measure image quality in tissue-based diagnosis (diagnostic surgical pathology)

Background

Automated image analysis, measurements of virtual slides, and open access electronic measurement user systems require standardized image quality assessment in tissue-based diagnosis.

Aims

To describe the theoretical background and the practical experiences in automated image quality estimation of colour images acquired from histological slides.

Theory, material and measurements

Digital images acquired from histological slides should present with textures and objects that permit automated image information analysis. The quality of digitized images can be estimated by spatial independent and local filter operations that investigate in homogenous brightness, low peak to noise ratio (full range of available grey values), maximum gradients, equalized grey value distribution, and existence of grey value thresholds. Transformation of the red-green-blue (RGB) space into the hue-saturation-intensity (HSI) space permits the detection of colour and intensity maxima/minima. The feature distance of the original image to its standardized counterpart is an appropriate measure to quantify the actual image quality. These measures have been applied to a series of H&E stained, fluorescent (DAPI, Texas Red, FITC), and immunohistochemically stained (PAP, DAB) slides. More than 5,000 slides have been measured and partly analyzed in a time series.

Results

Analysis of H&E stained slides revealed low shading corrections (10%) and moderate grey value standardization (10 – 20%) in the majority of cases. Immunohistochemically stained slides displayed greater shading and grey value correction. Fluorescent stained slides are often revealed to high brightness. Images requiring only low standardization corrections possess at least 5 different statistically significant thresholds, which are useful for object segmentation. Fluorescent images of good quality only posses one singular intensity maximum in contrast to good images obtained from H&E stained slides that present with 2 – 3 intensity maxima.

Conclusion

Evaluation of image quality and creation of formally standardized images should be performed prior to automatic analysis of digital images acquired from histological slides. Spatial dependent and local filter operations as well as analysis of the RGB and HSI spaces are appropriate methods to reproduce evaluated formal image quality.

Fluorescent stains for quantification of DNA by confocal laser scanning microscopy in 3-D

Confocal microscopy requires the use of fluorophores to visualize structures of interest within a specimen. To perform reliable measurements of the intensity of fluorescence, the stain should be specific, penetrate well into tissue sections, and bind stoichiometrically. Furthermore, emission must be linear with respect to DNA content and brightness, and fluorescence should be stable. Confocal microscopy is used to determine DNA ploidy and to analyze texture of nuclei, which is accomplished in three dimensions, because nuclei can be measured within the original tissue context. For this purpose the sample must be stained with a DNA binding fluorophore with the properties described above. Stains with different properties have been developed for different applications. We review here the advantages and disadvantages of these different stains for analyzing DNA ploidy and nuclear texture using three-dimensional microscopy. We conclude that SYBR green I and TO-PRO-3 are the most suitable stains for this purpose at present.

A restaining method to restore faded fluorescence in tissue specimens for quantitative confocal microscopy

The aim of this study was to develop a procedure to remove the TO-PRO-3 fluorescent dye from tissue sections and restain with TO-PRO-3, still allowing calculation of DNA content and distribution by confocal laser scanning microscopy (CLSM). This would allow repeated measurements on the same tissue sections and prevents loss of tissue material from valuable clinical samples. Thick sections (14 microm) were cut from a paraffin block of adrenal tissue and stained using TO-PRO-3. Image stacks were acquired by CLSM. Thereafter, three destaining approaches were tested based on incubation, at different temperatures and durations, in the medium that is normally used to dissolve TO-PRO-3. The same areas were imaged again to measure residual fluorescence and were subsequently restained and imaged again. The intensity of the images acquired after initial staining and restaining were compared. A number of 3-D (texture) features computed after segmentation of nuclei were compared as well. The best destaining result was obtained by incubation of sections at 37 degrees C in preheated medium twice for 20 min. On average, the 3-D feature values were comparable with those after initial staining. With the described protocol it is possible to remove TO-PRO-3 fluorescence from tissue sections that can successfully be restained with minimal influence on fluorescence intensity and nuclear chromatin distribution.