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Within the last decade, the science of molecular testing has evolved from single gene and single protein analysis to broad molecular profiling as a standard of care, quickly transitioning from research to practice. Terms such as genomics, transcriptomics, proteomics, circulating omics, and artificial intelligence are now commonplace, and this rapid evolution has left us with a significant knowledge gap within the medical community. In this paper, we attempt to bridge that gap and prepare the physician in oncology for multiomics, a group of technologies that have gone from looming on the horizon to become a clinical reality. The era of multiomics is here, and we must prepare ourselves for this exciting new age of cancer medicine. [ABSTRACT FROM AUTHOR]

Sentinel lymph nodes are the first nodes draining the lymph from a breast and could reveal early changes in the host immune system upon dissemination of breast cancer cells. To investigate this, we performed single‐cell immune profiling of lymph nodes with and without metastatic cells. Whereas no significant changes were observed for B‐cell and natural killer (NK)‐cell subsets, metastatic lymph nodes had a significantly increased frequency of CD8 T cells and a skewing toward an effector/memory phenotype of CD4 and CD8 T cells, suggesting an ongoing immune response. Additionally, metastatic lymph nodes had an increased frequency of TIGIT (T‐cell immunoreceptor with Ig and ITIM domains)‐positive T cells with suppressed TCR signaling compared with non‐metastatic nodes, indicating exhaustion of effector T cells, and an increased frequency of regulatory T cells (Tregs) with an activated phenotype. T‐cell alterations correlated with the percentage of metastatic tumor cells, reflecting the presence of metastatic tumor cells driving T effector cells toward exhaustion and promoting immunosuppression by recruitment or increased differentiation toward Tregs. These results show that immune suppression occurs already in early stages of tumor progression. [ABSTRACT FROM AUTHOR]

Aims: After local excision of early rectal cancer, definitive lymph node status is not available. An alternative means for accurate assessment of recurrence risk is required to determine the most appropriate subsequent management. Currently used measures are suboptimal. We assess three measures of tumour stromal content to determine their predictive value after local excision in a well‐characterised cohort of rectal cancer patients without prior radiotherapy. Methods and results: A total of 143 patients were included. Haematoxylin and eosin (H&E) sections were scanned for (i) deep neural network (DNN, a machine‐learning algorithm) tumour segmentation into compartments including desmoplastic stroma and inflamed stroma; and (ii) digital assessment of tumour stromal fraction (TSR) and optical DNA ploidy analysis. 3′ mRNA sequencing was performed to obtain gene expression data from which stromal and immune scores were calculated using the ESTIMATE method. Full results were available for 139 samples and compared with disease‐free survival. All three methods were prognostic. Most strongly predictive was a DNN‐determined ratio of desmoplastic to inflamed stroma >5.41 (P < 0.0001). A ratio of ESTIMATE stromal to immune score <1.19 was also predictive of disease‐free survival (P = 0.00051), as was stromal fraction >36.5% (P = 0.037). Conclusions: The DNN‐determined ratio of desmoplastic to inflamed ratio is a novel and powerful predictor of disease recurrence in locally excised early rectal cancer. It can be assessed on a single H&E section, so could be applied in routine clinical practice to improve the prognostic information available to patients and clinicians to inform the decision concerning further management. [ABSTRACT FROM AUTHOR]

The combination of DNA ploidy and automatically estimated stroma fraction has been shown to correlate with recurrence and cancer death in colorectal cancer. We aimed to extend this observation and evaluate the prognostic importance of this combined marker in prostate cancer. DNA ploidy status was determined by image cytometry and the stroma fraction was estimated automatically on hematoxylin and eosin stained sections in three tumor samples from each patient to account for tumor heterogeneity. The optimal threshold for low (≤56%) and high (>56%) stroma fraction was identified in a discovery cohort (n = 253). The combined marker was validated in an independent patient cohort (n = 259) with biochemical recurrence as endpoint. The combined marker predicted biochemical recurrence independently in the validation cohort. Multivariable analysis showed that the highest risk of recurrence was observed for patients with samples that had both non‐diploid ploidy status and a high stroma fraction (hazard ratio: 2.51, 95% confidence interval: 1.18–5.34). In conclusion, we suggest the combination of DNA ploidy and automatically estimated stroma fraction as a prognostic marker for the risk stratification of prostate cancer patients. It may also be a potential generic marker as concurrent results have been described in colorectal cancer. What's new? The stroma that surrounds tumor cells can have significant effects on tumor growth and behavior. Another hallmark of cancer is aneuploidy caused by genomic instability, which offers an important prognostic marker in several cancer types. In this study, the authors found that combining these two markers—stromal fraction and DNA ploidy—provided a significant predictor of biochemical recurrence in prostate cancer. The low cost, high throughput, and accuracy of digital analysis using this combined method thus promise to provide improved prognostic biomarkers in prostate cancer. [ABSTRACT FROM AUTHOR]

Background: The high degree of genomic diversity in cancer represents a challenge for identifying objective prognostic markers. We aimed to examine the extent of tumour heterogeneity and its effect on the evaluation of a selected prognostic marker using prostate cancer as a model.Methods: We assessed Gleason Score (GS), DNA ploidy status and phosphatase and tensin homologue (PTEN) expression in radical prostatectomy specimens (RP) from 304 patients followed for a median of 10 years (interquartile range 6-12). GS was assessed for every tumour-containing block and DNA ploidy for a median of four samples for each RP. In a subgroup of 40 patients we assessed DNA ploidy and PTEN status in every tumour-containing block. In 102 patients assigned to active surveillance (AS), GS and DNA ploidy were studied in needle biopsies.Results: Extensive heterogeneity was observed for GS (89% of the patients) and DNA ploidy (40% of the patients) in the cohort, and DNA ploidy (60% of the patients) and PTEN expression (75% of the patients) in the subgroup. DNA ploidy was a significant prognostic marker when heterogeneity was taken into consideration. In the AS cohort we found heterogeneity in GS (24%) and in DNA ploidy (25%) specimens.Conclusions: Multi-sample analysis should be performed to support clinical treatment decisions. [ABSTRACT FROM AUTHOR]

Background: Pathological evaluations give the best prognostic markers for prostate cancer patients after radical prostatectomy, but the observer variance is substantial. These risk assessments should be supported and supplemented by objective methods for identifying patients at increased risk of recurrence. Markers of epigenetic aberrations have shown promising results in several cancer types and can be assessed by automatic analysis of chromatin organisation in tumour cell nuclei.Methods: A consecutive series of 317 prostate cancer patients treated with radical prostatectomy at a national hospital between 1987 and 2005 were followed for a median of 10 years (interquartile range, 7-14). On average three tumour block samples from each patient were included to account for tumour heterogeneity. We developed a novel marker, termed Nucleotyping, based on automatic assessment of disordered chromatin organisation, and validated its ability to predict recurrence after radical prostatectomy.Results: Nucleotyping predicted recurrence with a hazard ratio (HR) of 3.3 (95% confidence interval (CI), 2.1-5.1). With adjustment for clinical and pathological characteristics, the HR was 2.5 (95% CI, 1.5-4.1). An updated stratification into three risk groups significantly improved the concordance with patient outcome compared with a state-of-the-art risk-stratification tool (P<0.001). The prognostic impact was most evident for the patients who were high-risk by clinical and pathological characteristics and for patients with Gleason score 7.Conclusion: A novel assessment of epigenetic aberrations was capable of improving risk stratification after radical prostatectomy. [ABSTRACT FROM AUTHOR]

Aims Concentric hypertrophy following pressure-overload is linked to preserved systolic function but impaired diastolic function, and is an important substrate for heart failure with preserved ejection fraction. While increased passive stiffness of the myocardium is a suggested mechanism underlying diastolic dysfunction in these hearts, the contribution of active diastolic Ca2+ cycling in cardiomyocytes remains unclear. In this study, we sought to dissect contributions of passive and active mechanisms to diastolic dysfunction in the concentrically hypertrophied heart following pressure-overload. Methods and results Rats were subjected to aortic banding (AB), and experiments were performed 6 weeks after surgery using sham-operated rats as controls. In vivo ejection fraction and fractional shortening were normal, confirming preservation of systolic function. Left ventricular concentric hypertrophy and diastolic dysfunction following AB were indicated by thickening of the ventricular wall, reduced peak early diastolic tissue velocity, and higher E/e' values. Slowed relaxation was also observed in left ventricular muscle strips isolated from AB hearts, during both isometric and isotonic stimulation, and accompanied by increases in passive tension, viscosity, and extracellular collagen. An altered titin phosphorylation profile was observed with hypophosphorylation of the phosphosites S4080 and S3991 sites within the N2Bus, and S12884 within the PEVK region. Increased titin-based stiffness was confirmed by salt-extraction experiments. In contrast, isolated, unloaded cardiomyocytes exhibited accelerated relaxation in AB compared to sham, and less contracture at high pacing frequencies. Parallel enhancement of diastolic Ca2+ handling was observed, with augmented NCX and SERCA2 activity and lowered resting cytosolic [Ca2+]. Conclusion In the hypertrophied heart with preserved systolic function, in vivo diastolic dysfunction develops as cardiac fibrosis and alterations in titin phosphorylation compromise left ventricular compliance, and despite compensatory changes in cardiomyocyte Ca2+ homeostasis. [ABSTRACT FROM AUTHOR]

Nuclear texture analysis measures the spatial arrangement of the pixel gray levels in a digitized microscopic nuclear image and is a promising quantitative tool for prognosis of cancer. The aim of this study was to evaluate the prognostic value of entropy-based adaptive nuclear texture features in a total population of 354 uterine sarcomas. Isolated nuclei (monolayers) were prepared from 50 µm tissue sections and stained with Feulgen-Schiff. Local gray level entropy was measured within small windows of each nuclear image and stored in gray level entropy matrices, and two superior adaptive texture features were calculated from each matrix. The 5-year crude survival was significantly higher ( P < 0.001) for patients with high texture feature values (72%) than for patients with low feature values (36%). When combining DNA ploidy classification (diploid/nondiploid) and texture (high/low feature value), the patients could be stratified into three risk groups with 5-year crude survival of 77, 57, and 34% (Hazard Ratios (HR) of 1, 2.3, and 4.1, P < 0.001). Entropy-based adaptive nuclear texture was an independent prognostic marker for crude survival in multivariate analysis including relevant clinicopathological features (HR = 2.1, P = 0.001), and should therefore be considered as a potential prognostic marker in uterine sarcomas. © The Authors. Published 2014 International Society for Advancement of Cytometry [ABSTRACT FROM AUTHOR]

Previously, we have shown that the phosphoinositidemetabolizing enzymes PIKfyve (phosphoinositide 5-kinase, FYVE finger containing) and MTMR3 (myotubularin-related protein 3), together with their lipid product PtdIns5P, are important for migration of normal human fibroblasts. As these proteins are a kinase and a phosphatase respectively, and thereby considered druggable, we wanted to test their involvement in cancer cell migration and invasion. First, we showed that PIKfyve and MTMR3 are expressed in most cancer cells. Next, we demonstrated that depletion of PIKfyve or MTMR3 resulted in decreased velocity in three different cancer cell lines by using new software for cell tracking. Inhibition of the enzymatic activity of PIKfyve by the inhibitor YM201636 also led to a strong reduction in cell velocity. Mechanistically, we show that PIKfyve and MTMR3 regulate the activation of the Rho family GTPase Rac1. Further experiments also implicated PtdIns5P in the activation of Rac1. The results suggest a model for the activation of Rac1 in cell migration where PIKfyve and MTMR3 produce PtdIns5P on cellular membranes which may then serve to recruit effectors to activate Rac1. Finally, in an invasion assay, we demonstrate that both PIKfyve and MTMR3 are implicated in invasive behaviour of cancer cells. Thus PIKfyve andMTMR3 could represent novel therapeutic targets in metastatic cancer. [ABSTRACT FROM AUTHOR]

Objective. The aims of this study were to establish 15-year postprostatectomy prostate cancer-specific mortality (PCSM), explore the time to prostate-specific antigen (PSA) relapse and identify clinically available prognostic factors. Material and methods. From 1987 to 2004, 309 men (median age 62 years, range 40-74 years) were prostatectomized for localized prostate cancer at a tertiary referral cancer centre. Slightly modified D'Amico risk groups were identified. PSA relapse was defined as PSA ≥ 4 μg/l before 2000, and thereafter as PSA > 0.2 μg/l. Radical prostatectomy (RP) 3-12 months after diagnosis represented 'deferred' RP. PCSM was assessed with competing risk modelling. The level of significance was set at p < 0.05. Results. After a median of 12 years, 41 men were dead from prostate cancer and 68 due to other causes [15-year PCSM 15%, 95% confidence interval (CI) 10-19%], with no significant difference in PCSM between the low- and intermediate-risk groups, and the 'conventional' high-risk group having 24% PCSM (95% CI 16-32%). PCSM was 33% (95% CI 20-46%) for men with two high-risk factors. The median time to PSA relapse ( n = 152) was 5 (range 0-17) years, with a median of 7 (range 0-17) years' survival thereafter. Deferral of RP for up to 1 year had no impact on PCSM for all patients combined. Conclusions. Approximately one in seven men with localized prostate cancer, prostatectomized before the PSA era, will die from the disease within the 15 years post-RP. Men with two high-risk criteria have a particularly poor prognosis. After PSA relapse the median survival is 7 years. The data on deferral of RP need confirmation, taking into account risk group allocation. [ABSTRACT FROM AUTHOR]

TCTP has been implicated in a plethora of important cellular processes related to cell growth, cell cycle progression, malignant transformation and inhibition of apoptosis. In addition to these intracellular functions, TCTP has extracellular functions and plays an important role in immune cells. TCTP expression was previously shown to be deregulated in prostate cancer, but its function in prostate cancer cells is largely unknown. Here we show that TCTP expression is regulated by androgens in LNCaP prostate cancer cells in vitro as well as human prostate cancer xenografts in vivo. Knockdown of TCTP reduced colony formation and increased apoptosis in LNCaP cells, implicating it as an important factor for prostate cancer cell growth. Global gene expression profiling in TCTP knockdown LNCaP cells showed that several interferon regulated genes are regulated by TCTP, suggesting that it may have a role in regulating immune function in prostate cancer. In addition, recombinant TCTP treatment increased colony formation in LNCaP cells suggesting that secreted TCTP may function as a proliferative factor in prostate cancer. These results suggest that TCTP may have a role in prostate cancer development. [ABSTRACT FROM AUTHOR]

Background: Nuclear texture analysis gives information about the spatial arrangement of the pixel gray levels in a digitized microscopic nuclear image, providing texture features that may be used as quantitative tools for prognosis of human cancer. The aim of the study was to evaluate the prognostic value of adaptive nuclear texture features in early stage ovarian cancer. Methods: 246 cases of early stage ovarian cancer were included in the analysis. Isolated nuclei (monolayers) were prepared from 50 μm tissue sections and stained with Feulgen-Schiff. Local gray level entropy was measured within small windows of each nuclear image and stored in gray level entropy matrices. A compact set of adaptive features was computed from these matrices. Results: Univariate Kaplan-Meier analysis showed significantly better relapse-free survival (p < 0.001) for patients with low adaptive feature values compared to patients with high adaptive feature values. The 10-year relapse-free survival was about 78% for patients with low feature values and about 52% for patients with high feature values. Adaptive features were found to be of independent prognostic significance for relapse-free survival in a multivariate analysis. Conclusion: Adaptive nuclear texture features from entropy matrices contain prognostic information and are of independent prognostic significance for relapse-free survival in early stage ovarian cancer. [ABSTRACT FROM AUTHOR]

Digital image analysis of cell nuclei is useful to obtain quantitative information for the diagnosis and prognosis of cancer. However, the lack of a reliable automatic nuclear segmentation is a limiting factor for high-throughput nuclear image analysis. We have developed a method for automatic segmentation of nuclei in Feulgen-stained histological sections of prostate cancer. A local adaptive thresholding with an object perimeter gradient verification step detected the nuclei and was combined with an active contour model that featured an optimized initialization and worked within a restricted region to improve convergence of the segmentation of each nucleus. The method was tested on 30 randomly selected image frames from three cases, comparing the results from the automatic algorithm to a manual delineation of 924 nuclei. The automatic method segmented a few more nuclei compared to the manual method, and about 73% of the manually segmented nuclei were also segmented by the automatic method. For each nucleus segmented both manually and automatically, the accuracy (i.e., agreement with manual delineation) was estimated. The mean segmentation sensitivity/specificity were 95%/96%. The results from the automatic method were not significantly different from the ground truth provided by manual segmentation. This opens the possibility for large-scale nuclear analysis based on automatic segmentation of nuclei in Feulgen-stained histological sections. © 2012 International Society for Advancement of Cytometry [ABSTRACT FROM AUTHOR]

We describe the design, construction and evaluation of a custom-made camera support to gain better access for recording videos of open surgery. [ABSTRACT FROM AUTHOR]

Summary: Giant cell ependymoma, a rare ependymoma subtype, was recently recognized as a separate diagnostic entity with variations both in malignant potential and course of disease. We analyzed the first supratentorial giant cell ependymoma using G-band karyotyping, DNA ploidy analysis, and array comparative genomic hybridization. The tumor was hypodiploid, and the karyotype showed multiple monosomies. This novel cytogenetic pattern seems specific for giant cell ependymoma as the only previous cytogenetic analysis of a giant cell ependymoma found similar monosomies. We were also able to analyze cytogenetically the subsequent recurrent tumor, phenotypically an anaplastic ependymoma, allowing a first insight into the genetic events involved in disease progression. [ABSTRACT FROM AUTHOR]

Background: The clinical outcome for the individual prostate cancer patient is often difficult to predict, due to lack of reliable independent prognostic biomarkers. We tested DNA ploidy as a prognostic factor for clinical outcome in 186 patients treated with radical prostatectomy. Methods: DNA ploidy was measured using an automatic image cytometry system and correlated with preoperative PSA, age at surgery, Mostofi grade, surgical margins and Gleason score. Results: The mean follow up time after operation was 73.3 months (range 2–176 months). Of the 186 prostatectomies, 96 were identified as diploid, 61 as tetraploid and 29 as aneuploid. Twenty-three per cent, 36% and 62% of the diploid, tetraploid and aneuploid cases respectively, suffered from relapse during the observation time. DNA ploidy, Gleason score, Mostofi grading, surgical margins and preoperative PSA were all significant predictors of relapse in a univariate analysis. On multivariate analysis, only Gleason score and DNA ploidy proved to be independently predictors of disease recurrence. Furthermore, among the 68 cases identified with Gleason score 7, DNA ploidy was the only significant predictor of disease recurrence. Conclusions: Our data suggest that DNA ploidy should be included as an important additive prognostic factor for prostate cancer, especially for patients identified with Gleason score 7 tumours. [ABSTRACT FROM AUTHOR]

Background: Nuclear texture analysis is a useful method to obtain quantitative information for use in prognosis of cancer. The first-order gray level statistics of a digitized light microscopic nuclear image may be influenced by variations in the image input conditions. Therefore, we have previously standardized the nuclear gray level mean value and standard deviation. However, there is a clear relation between nuclear DNA content, area, first-order statistics, and texture. For nuclei with approximately the same DNA content, the mean gray level increases with an increasing nuclear area. The aims of the present methodical work were to study: (1) whether the prognostic value of adaptive textural features varies with nuclear area, and (2) the effect of standardizing nuclear first-order statistics. Methods: Nuclei from 134 cases of ovarian cancer were grouped into intervals according to nuclear area. Adaptive features were extracted from two different image sets, i.e., standardized and non-standardized nuclear images. Results: The prognostic value of adaptive textural features varied strongly with nuclear area. A standardization of the first-order statistics significantly reduced this prognostic information. Several single features discriminated the two classes of cancer with a correct classification rate of 70%. Conclusion: Nuclei having an area between 2000–4999 pixels contained most of the class distance information between the good and poor prognosis classes of cancer. By considering the relation between nuclear area and texture, we avoided a loss of information caused by standardizing the first-order statistics and mixing data from cells having different nuclear area. [ABSTRACT FROM AUTHOR]

The aim of this study was to examine any relation between DNA ploidy and previously detected TP53 (p53) or p21[sup WAF1/CIP1] expression in 94 patients with muscle-invasive transitional cell carcinoma of the urinary bladder and to associate these factors with survival. DNA ploidy was determined by image cytometry. In a subgroup of patients, the mutational status of the TP53 gene was assessed by temporal temperature gradient electrophoresis (TTGE) or perpendicular denaturant gradient gel electrophoresis (DGGE) and subsequent sequencing. Significantly more aneuploid than euploid tumours showed TP53 accumulation (p = 0.003). Patients with aneuploid tumours lived longer than patients with euploid tumours (p = 0.003). In the euploid, but not in the aneuploid group, TP53 and p21[sup WAF1/CIP1] were associated with cancer-specific survival (p = 0.002 and 0.02, respectively). Patients with > 50% TP53 expression had the longest survival time. Mutation analyses showed acceptable concordance with TP53 expression. We conclude that DNA aneuploidy may confer increased radiosensitivity in bladder cancer patients and that TP53 accumulation may confer increased radiosensitivity, but its effect is detectable only in euploid tumours. [ABSTRACT FROM AUTHOR]

In order to study the prognostic value of quantifying the chromatin structure of cell nuclei from patients with early ovarian cancer, low dimensionality adaptive fractal and Gray Level Cooccurrence Matrix texture feature vectors were extracted from nuclei images of monolayers and histological sections. Each light microscopy nucleus image was divided into a peripheral and a central part, representing 30% and 70% of the total area of the nucleus, respectively. Textural features were then extracted from the peripheral and central parts of the nuclei images.The adaptive feature extraction was based on Class Difference Matrices and Class Distance Matrices. These matrices were useful to illustrate the difference in chromatin texture between the good and bad prognosis classes of ovarian samples. Class Difference and Distance Matrices also clearly illustrated the difference in texture between the peripheral and central parts of cell nuclei. Both when working with nuclei images from monolayers and from histological sections it seems useful to extract separate features from the peripheral and central parts of the nuclei images. [ABSTRACT FROM AUTHOR]

Simple Summary: Molecular tissue-based prognostic biomarkers are anticipated to complement the current risk stratification systems in prostate cancer, but their manual assessment is subjective and time-consuming. Objective assessment of such biomarkers by machine learning-based methods could advance their adoption in a clinical workflow. PTEN and DNA ploidy status are well-studied biomarkers, which can provide clinically relevant information in prostate cancer at a low cost. Using a cohort of 253 patients who received radical prostatectomy, we developed a novel, fully-automated PTEN scoring in immunohistochemically-stained tissue slides, which could be used to assess PTEN status in a reliable and reproducible manner. In an independent validation cohort of 259 patients, automatically assessed PTEN status was significantly associated with time to biochemical recurrence after radical prostatectomy, and the combination of PTEN and DNA ploidy status further improved risk stratification. These results demonstrate the utility of machine learning in biomarker assessment. Machine learning (ML) is expected to improve biomarker assessment. Using convolution neural networks, we developed a fully-automated method for assessing PTEN protein status in immunohistochemically-stained slides using a radical prostatectomy (RP) cohort (n = 253). It was validated according to a predefined protocol in an independent RP cohort (n = 259), alone and by measuring its prognostic value in combination with DNA ploidy status determined by ML-based image cytometry. In the primary analysis, automatically assessed dichotomized PTEN status was associated with time to biochemical recurrence (TTBCR) (hazard ratio (HR) = 3.32, 95% CI 2.05 to 5.38). Patients with both non-diploid tumors and PTEN-low had an HR of 4.63 (95% CI 2.50 to 8.57), while patients with one of these characteristics had an HR of 1.94 (95% CI 1.15 to 3.30), compared to patients with diploid tumors and PTEN-high, in univariable analysis of TTBCR in the validation cohort. Automatic PTEN scoring was strongly predictive of the PTEN status assessed by human experts (area under the curve 0.987 (95% CI 0.968 to 0.994)). This suggests that PTEN status can be accurately assessed using ML, and that the combined marker of automatically assessed PTEN and DNA ploidy status may provide an objective supplement to the existing risk stratification factors in prostate cancer. [ABSTRACT FROM AUTHOR]

A polygonization-based method is used to estimate the fractal dimension and several new scalar lacunarity features from digitized transmission electron micrographs (TEM) of mouse liver cell nuclei. The fractal features have been estimated in different segments of 1D curves obtained by scanning the 2D cell nuclei in a spiral-like fashion called “peel-off scanning”. This is a venue to separate estimates of fractal features in the center and periphery of a cell nucleus. Our aim was to see if a small set of fractal features could discriminate between samples from normal liver, hyperplastic nodules and hepatocellular carcinomas. The Bhattacharyya distance was used to evaluate the features. Bayesian classification with pooled covariance matrix and equal prior probabilities was used as the rule for classification.Several single fractal features estimated from the periphery of the cell nuclei discriminated samples from the hyperplastic nodules and hepatocellular carcinomas from normal ones. The outer 25–30% of the cell nuclei contained important texture information about the differences between the classes. The polygonization-based method was also used as an analysis tool to relate the differences between the classes to differences in the chromatin structure. [ABSTRACT FROM AUTHOR]

In the majority of colorectal carcinomas, both copies of the tumor suppressor gene TP53 (tumor protein 53) are known to be inactivated. In contrast to a loss of tumor suppressor function, it has been suggested that an increased copy number of the RBI gene is involved in the progression of these tumors. To determine genetic alterations at chromosomes 13 and 17 in colorectal tumors, we have studied several loci on these chromosomes, with special focus on the RBI and TP53 genes at both the level of DNA sequence and the level of gene expression. Restriction fragment length polymorphism analysis was performed after alkaline Southern blotting of the DNA fragments and hybridization (in 7% sodium dodecyl sulfate and 0.5 M NaPO of the nylon membranes with multi-primed, radioactively labeled probes. Total RNA was extracted from tissue biopsy specimens by homogenization of the samples in guanidinium thiocyanate followed by separation in a CsCl gradient. By use of an image-processing system, x-ray film signals were measured densitometrically. Point mutations within the TP53 gene were detected by use of polymerase chain reaction (PCR) in combination with constant denaturant gel electrophoresis. Direct sequencing of PCR products revealed the exact nature of the mutations. Protein expression of TP53 was seen by immuno-staining of sections from paraffin-embedded material using a mouse monoclonal antibody. The two-sided Fisher‘s Exact Test was used for statistical analysis. An increase in allelic copy number at 13q loci was seen in 10 (32% of 31 tumors. In the majority of the cases, this increase probably reflected a change in the diploid status of chromosome 13; in some cases, however, only part of the 13q seemed to be involved. The RBI gene showed an elevated level of RNA compared with the β-actin signal. Four-teen (48%) of 29 tumors showed loss of heterozygosity at loci on 17p, and base mutations within the TP53 gene were seen in 14 (42% of 33 tumors. RNA and protein analyses of TP53 revealed an increased level of expression in the tumors compared with normal mucosa. Allelic variations seen at 13q and 17p were not associated ( = .7). Our results suggest that, in addition to aneuploidy, gain of specific chromosome 13 sequences is involved in the tumorigenesis of the colon and rectum. In addition, they confirm the importance of TP53 mutations for the progression of such tumors and support the view that accumulation of events is more important than the order of events. The genetic changes observed at chromosome arms 13q and 17p seem to be independent of each other. [J Natl Cancer Inst 84:1100–1108, 1992] [ABSTRACT FROM PUBLISHER]

Controversy still exists regarding the validity of parameters commonly used in the evaluation of prognosis of patients with synovial sarcoma (SS). Forty-nine cases of previously untreated primary SS (23 females and 26 males, ranging in age from 7 to 81, with 31 tumors located in the lower extremity, 8 at the upper extremity and 10 at the trunchus), without regional lymph-node or distant metastases were studied. We investigated the relationship between (flow and image) DNA cytometry, proliferation activity, clinicopathologic parameters, and relapse-free and overall survival of the patients. The prognostic value of gender, age, duration of symptoms, location, compartmentalization, size, adequacy of surgical margins, residual tumor, adjuvant therapy, histologic subtype, extent of necrosis, glandular differentiation, calcification, and extent of hemangiopericytic areas, mitotic rate, amount of mast cells, blood vessel invasion, histologic (UICC and NCI) grades, DNA ploidy, percentage of cells in S and S+G2 phases, PCNA and Ki-67 labeling indices (LI), and TNM (UICC) stage of the tumors, were evaluated by univariate and multivariate (Cox hazard model) analyses. Short duration of symptoms (<12 months), biphasic SS, scarcity of mast cells ( [ABSTRACT FROM AUTHOR]

Most attempts to elucidate primary cytogenetic events have been made on the basis of chromosome analysis of cells from the later stages of tumor development. Hence it is difficult to decide which, if any, of the observed chromosomal alterations are causative rather than consequential in neoplastic development. One approach to understand the role of chromosomal changes in neoplasia is to examine the chromosomal constitution of cells at early stages in the process of carcinogenesis. We have developed a method for direct preparation of metaphase plates of cells from preneoplastic liver nodules and we present herein the first report of non-random chromosome changes in solid tumor precursor cells. The results of the cytogenetic analysis demonstrated trisomies/polysomies for chromosome 11 and chromosome 19. A specific increase in the number of chromosome 19 was found in 43% of the 37 plates karyotyped and 25% of the plates demonstrated increase in the number of chromosome 11. The finding shows that gross chromosomal changes such as polysomies may play an important role in the early development of tumors. They further indicate the presence of a gene on chromosome 19 with an essential role either in the initiation or promotion of the neoplastic trans formation of hepatocytes. [ABSTRACT FROM PUBLISHER]

There have been several reports on the distribution of DNA in premalignant and malignant liver cells after carcinogen treatment in rodents. The most striking result so far is that ploidy distributions seems to depend more on experimental protocols and less on carcinogenesis . The present study demonstrates that an evaluation by means of flow cytometry and stereological image analysis yields results showing similar ploidy distributions throughout the known sequence of tissue changes seen during liver cancer development. Furthermore, our results demonstrate inter-individual differences between the lesions in each of the steps in these tissue changes, (foci, nodules and hepatocarcinomas). The present study gives no reason to conclude that changes in ploidy distribution are essential in liver carcinogenesis. [ABSTRACT FROM PUBLISHER]

Simple Summary: Chromatin organisation affects gene expression and contributes to carcinogenesis. Automatic quantification of chromatin heterogeneity can be applied to identify patients with increased risk of cancer recurrence and death in several cancer types. We aimed to investigate the prognostic role of diversity of chromatin compartments in relation to chromatin heterogeneity and as a potential supplement to pathological risk classifications in gynaecological carcinomas. To this end, we computed the entropy of both chromatin compartment sizes and optical densities within compartments. In analysis of two cohorts consisting of 1037 patients with gynaecological carcinoma, we observed a moderately strong correlation between the prognostic value of the entropies and chromatin heterogeneity. The entropies provided an objective marker, which, integrated with pathological risk classifications, might possibly contribute to the selection of high-risk stage I ovarian carcinoma patients for adjuvant chemotherapy and to preoperative identification of low-risk endometrial carcinoma patients who are candidates for less extensive surgery. Statistical texture analysis of cancer cell nuclei stained for DNA has recently been used to develop a pan-cancer prognostic marker of chromatin heterogeneity. In this study, we instead analysed chromatin organisation by automatically quantifying the diversity of chromatin compartments in cancer cell nuclei. The aim was to investigate the prognostic value of such an assessment in relation to chromatin heterogeneity and as a potential supplement to pathological risk classifications in gynaecological carcinomas. The diversity was quantified by calculating the entropy of both chromatin compartment sizes and optical densities within compartments. We analysed a median of 281 nuclei (interquartile range (IQR), 273 to 289) from 246 ovarian carcinoma patients and a median of 997 nuclei (IQR, 502 to 1452) from 791 endometrial carcinoma patients. The prognostic value of the entropies and chromatin heterogeneity was moderately strongly correlated (r ranged from 0.68 to 0.73), but the novel marker was observed to provide additional prognostic information. In multivariable analysis with clinical and pathological markers, the hazard ratio associated with the novel marker was 2.1 (95% CI, 1.3 to 3.5) in ovarian carcinoma and 2.4 (95% CI, 1.5 to 3.9) in endometrial carcinoma. Integration with pathological risk classifications gave three risk groups with distinctly different prognoses. This suggests that the novel marker of diversity of chromatin compartments might possibly contribute to the selection of high-risk stage I ovarian carcinoma patients for adjuvant chemotherapy and low-risk endometrial carcinoma patients for less extensive surgery. [ABSTRACT FROM AUTHOR]

Background: Chromatin organisation affects gene expression and regional mutation frequencies and contributes to carcinogenesis. Aberrant organisation of DNA has been correlated with cancer prognosis in analyses of the chromatin component of tumour cell nuclei using image texture analysis. As yet, the methodology has not been sufficiently validated to permit its clinical application. We aimed to define and validate a novel prognostic biomarker for the automatic detection of heterogeneous chromatin organisation.Methods: Machine learning algorithms analysed the chromatin organisation in 461 000 images of tumour cell nuclei stained for DNA from 390 patients (discovery cohort) treated for stage I or II colorectal cancer at the Aker University Hospital (Oslo, Norway). The resulting marker of chromatin heterogeneity, termed Nucleotyping, was subsequently independently validated in six patient cohorts: 442 patients with stage I or II colorectal cancer in the Gloucester Colorectal Cancer Study (UK); 391 patients with stage II colorectal cancer in the QUASAR 2 trial; 246 patients with stage I ovarian carcinoma; 354 patients with uterine sarcoma; 307 patients with prostate carcinoma; and 791 patients with endometrial carcinoma. The primary outcome was cancer-specific survival.Findings: In all patient cohorts, patients with chromatin heterogeneous tumours had worse cancer-specific survival than patients with chromatin homogeneous tumours (univariable analysis hazard ratio [HR] 1·7, 95% CI 1·2-2·5, in the discovery cohort; 1·8, 1·0-3·0, in the Gloucester validation cohort; 2·2, 1·1-4·5, in the QUASAR 2 validation cohort; 3·1, 1·9-5·0, in the ovarian carcinoma cohort; 2·5, 1·8-3·4, in the uterine sarcoma cohort; 2·3, 1·2-4·6, in the prostate carcinoma cohort; and 4·3, 2·8-6·8, in the endometrial carcinoma cohort). After adjusting for established prognostic patient characteristics in multivariable analyses, Nucleotyping was prognostic in all cohorts except for the prostate carcinoma cohort (HR 1·7, 95% CI 1·1-2·5, in the discovery cohort; 1·9, 1·1-3·2, in the Gloucester validation cohort; 2·6, 1·2-5·6, in the QUASAR 2 cohort; 1·8, 1·1-3·0, for ovarian carcinoma; 1·6, 1·0-2·4, for uterine sarcoma; 1·43, 0·68-2·99, for prostate carcinoma; and 1·9, 1·1-3·1, for endometrial carcinoma). Chromatin heterogeneity was a significant predictor of cancer-specific survival in microsatellite unstable (HR 2·9, 95% CI 1·0-8·4) and microsatellite stable (1·8, 1·2-2·7) stage II colorectal cancer, but microsatellite instability was not a significant predictor of outcome in chromatin homogeneous (1·3, 0·7-2·4) or chromatin heterogeneous (0·8, 0·3-2·0) stage II colorectal cancer.Interpretation: The consistent prognostic prediction of Nucleotyping in different biological and technical circumstances suggests that the marker of chromatin heterogeneity can be reliably assessed in routine clinical practice and could be used to objectively assist decision making in a range of clinical settings. An immediate application would be to identify high-risk patients with stage II colorectal cancer who might have greater absolute benefit from adjuvant chemotherapy. Clinical trials are warranted to evaluate the survival benefit and cost-effectiveness of using Nucleotyping to guide treatment decisions in multiple clinical settings.Funding: The Research Council of Norway, the South-Eastern Norway Regional Health Authority, the National Institute for Health Research, and the Wellcome Trust. [ABSTRACT FROM AUTHOR]

Abstract: Aberrations in the Wnt/β-catenin signalling pathway are suggested as mediators of chromosomal instability and carcinogenesis. β-catenin acts both as a component of the membranous adhesion system, and as a transcription activator in the nucleus. β-Catenin immunoreactivity was evaluated in 353 uterine sarcomas (US) including 231 leiomyosarcomas (LMS), 82 endometrial stromal sarcomas (ESS), 22 adenosarcomas (AS) and 18 undifferentiated uterine sarcomas (UUS). Up-regulated membranous β-catenin was observed in 25% of the LMS (p =0.039), 21% of the ESS (p =0.072) and 39% of the UUS (p =0.025). Cytoplasmic β-catenin was up-regulated in 36% of the LMS (p =0.008) and 33% of the UUS (p =0.028). Nuclear β-catenin expression was observed in 23% of the LMS (p =0.051), 61% of ESS (p =0.628) and in the sarcoma component of 68% of the AS. In patients with LMS, membranous β-catenin was associated with poor crude survival in univariate (p =0.045), but not in multivariate analyses. In patients with ESS, nuclear β-catenin expression was related to spread of tumour (p =0.033), but not to survival. The observation of up-regulated β-catenin expression in US might suggest a so far undocumented role for the Wnt/β-catenin pathway in these malignancies. [Copyright &y& Elsevier]