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Malignancy associated changes in epithelial cells of buccal mucosa: a potential cancer detection test.

OBJECTIVE: To analyze the presence of malignancy associated changes (MACs) in normal buccal mucosa cells of lung and breast cancer patients and their relationship to tumor subtype, stage and size. STUDY DESIGN: Buccal mucosa smears of 107 lung cancer and 100 breast cancer patients and corresponding healthy subjects were collected, stained by the DNA-specific Feulgen-thionin method and scanned using an automated high-resolution cytometer. Nuclear texture features of a minimum of 500 nuclei per slide were calculated, and statistical classifiers using Gaussian models of class-probability distribution were designed, trained and tested in 3 parts: (1) ability to separate cancer patient samples from controls, (2) cross-validation of classifiers for different cancer types, and (3) correlation of MAC expression with tumor subtype, stage and size. RESULTS: Lung and breast cancer induce MACs in normal buccal mucosa cells. The classifiers based on the selected nuclear features correctly recognized >80% of lung and breast cancer cases. The results indicate that MAC detection is not dependent on the tumor subtype, stage or size. CONCLUSION: The presence of MACs in buccal mucosa cells offers the potential for developing a new noninvasive cancer screening test.

Adult↗

Nuclear texture analysis: a new prognostic tool in metastatic prostate cancer.

This report describes the prognostic value of computerized nuclear texture analysis in metastatic prostate cancer. Seventy-seven patients with histologically verified prostate carcinomas and skeletal metastases were selected from a Scandinavian multicenter study (SPCG-2). Thirty-six therapy-resistant patients experienced objective progression and cancer-related death within 2 years after orchiectomy. Thirty patients responded well to orchiectomy, i.e., showed objective disease remission and no signs of progression during 3 years of follow-up. From this data set, 10 randomly chosen therapy-resistant and 10 randomly chosen therapy-sensitive carcinomas were used in our previous study to find the optimal combination of features that can discriminate between the two groups (Yogesan et al.: Cytometry 24:268-276, 1996). In addition to these two groups, 11 patients experienced stable disease or disease remission during the first year and a secondary progression during the second or third year of follow-up, with subsequent cancer-related death. Traditional clinical prognostic factors such as histopathological grading and serum markers could not discriminate between these groups of patients. Therefore, image analysis techniques based on texture analysis have been utilized in this study of prognosis of prostate cancer. Feulgen-stained monolayers of nuclei were prepared from paraffin-embedded material taken from the primary tumor before endocrine ablation. Four different textural features were selected from the training data set to calculate the discriminating function. This function separated the therapy-sensitive and the therapy-resistant patients with 87% accuracy in the independent data set. This study demonstrates that it is possible to predict tumor progression and survival for endocrine-ablated metastatic prostate carcinomas using computerized nuclear texture analysis on light microscopy images from prostate biopsies taken at the time of diagnosis.

Aged↗

Host-specific modulation of the selective constraints driving human immunodeficiency virus type 1 env gene evolution.

To address the evolution of human immunodeficiency virus type 1 (HIV-1) within a single host, we analyzed the HIV-1 C2-V5 env regions of both cell-free genomic-RNA- and proviral-DNA-derived clones. Sequential samples were collected over a period of 3 years from six untreated subjects (three typical progressors [TPs] and three slow progressors [SPs], all with a comparable length of infection except one. The evolutionary analysis of the C2-V5 env sequences performed on 506 molecular clones (253 RNA- and 253 DNA-derived sequences) highlighted a series of differences between TPs and SPs. In particular, (i) clonal sequences from SPs (DNA and RNA) showed lower nucleotide similarity than those from TPs (P = 0. 0001), (ii) DNA clones from SPs showed higher intra- and intersample nucleotide divergence than those from TPs (P < 0.05), (iii) higher host-selective pressure was generally detectable in SPs (DNA and RNA sequences), and (iv) the increase in the genetic distance of DNA and RNA sequences over time was paralleled by an increase in both synonymous (Ks) and nonsynonymous (Ka) substitutions in TPs but only in nonsynonymous substitutions in SPs. Several individual peculiarities of the HIV-1 evolutionary dynamics emerged when the V3, V4, and V5 env regions of both TPs and SPs were evaluated separately. These peculiarities, probably reflecting host-specific features of selective constraints and their continuous modulation, are documented by the dynamics of Ka/Ks ratios of hypervariable env domains.

Base Sequence↗

Cortical inflammation in Alzheimer disease but not dementia with Lewy bodies.

BACKGROUND: There have been no previous studies on the role of inflammation in the brain for the second most common dementing disorder, dementia with Lewy bodies. OBJECTIVE: To investigate the degree of cortical inflammation in dementia with Lewy bodies (DLB) compared with Alzheimer disease (AD) and control brains. DESIGN AND MAIN OUTCOME MEASURES: Post-mortem tissue collection from a brain donor program using standardized diagnostic criteria. Brains collected from January 1, 1993, through December 31, 1996, were screened and selected only for the presence or absence of tau neuritic plaques. Results of immunohistochemistry for HLA-DR were quantified using area fraction counts. Counts were performed by investigators who were unaware of the diagnosis. Results were compared across groups using analysis of variance and posthoc testing. SETTING: A medical research institute in Sydney, Australia. PATIENTS: Eight brains with DLB and without the tau neuritic plaques typical of AD, 10 brains with AD and no Lewy bodies, and 11 nondemented controls without significant neuropathological features were selected from a consecutive sample. RESULTS: Compared with AD, DLB demonstrated significantly less inflammation in the form of HLA-DR-reactive microglia in all cortical regions (P<.001, posthoc). The level of inflammation in DLB was comparable to that seen in controls (P=.54, post hoc). CONCLUSIONS: Inflammation appears related to the tau neuritic plaques of AD. Despite similar clinical presentations, therapeutic anti-inflammatory strategies are not likely to be effective for pure DLB. Arch Neurol. 2000.

Aged↗

Transgenic models of human cancer.

Transgenic animal technology has been useful for the direct demonstration of the tumorigenic potential of oncogenes in vivo. Over the past eight years a wide variety of oncogenes and proto-oncogenes from viral and cellular sources have been inserted into the germline of mice with subsequent development of neoplasia. Many of the published reports describe similarities between morphologic features of the transgenic mice tumors and those occurring naturally in humans. We discuss the morphologic features of selected transgenic models carrying viral genes and review their applicability to investigations directed toward understanding cancer in general and specifically gastric cancer, neurofibromatosis and leukemia. Examples of the impact of nutrition, interaction with growth factors and initiation with chemical carcinogens are presented. In one of the models functional similarities to the mechanism of oncogenesis in human T-cell leukemia virus type-1 (HTLV-1) lymphoma may exist with activation of cytokine production and subsequent autocrine stimulation. The transgenic model of proximal gastric cancer demonstrates features similar to those seen in carcinogen-induced neoplasia. These studies underscore the vast potential of transgenic models for inquiry into the genetic and epigenetic basis of human carcinogenesis. However, many features of transgenic cancer models differ from cancer in humans and the specific criteria for judging the value of transgenic models remain unclarified. For example, although the tumors arising in the HTLV-1 Tax transgenic mice show numerous similarities to human neurofibromatosis including development of lesions of the iris, the similarities do not necessarily extend to the molecular involvement of neurofibromatosis-1 (NF-1), a gene with structural and functional homology to GTPase activating proteins. Transgenic experiments of the future will ask questions beyond whether a particular gene is capable of initiating the neoplastic process. The ability to construct systems in vivo with a defined starting point that facilitate further controlled manipulation of events resulting in cancer provide great opportunities to dissect the various molecular pathways involved in such a process. Therefore, gene knockout experiments and disruption of gene function will further enhance our ability to understand the multi-factorial process of tumor development.(ABSTRACT TRUNCATED AT 400 WORDS)

Adenovirus E1A Proteins↗

Are all high-grade breast cancers with no steroid receptor hormone expression alike? The special case of the medullary phenotype.

BACKGROUND: Medullary carcinoma (MC) of the breast is associated with favorable prognosis compared with other histological types, despite high nuclear grade, fast proliferation and lack of steroid hormone receptor expression. We retrospectively evaluated the clinical relevance of selected immunohistochemical features of tumors in three cohorts of patients with typical medullary (MC), 'atypical' medullary (AMC) or ductal (DC) breast carcinoma. PATIENTS AND METHODS: Evaluation was performed on node-negative tumor specimens from 40 patients who had either MC (12 patients), AMC (nine patients) or DC (19 patients), treated in a single institution. All had no hormonal receptor, Ki-67 > or =30%, G3, expansive pattern of growth and peritumoral lymphocytic infiltration. In addition, p27, p21 and HER2/neu overexpression, p53, cyclin E and E-cadherin expression, presence of apoptotic cells, stromal tenascin (TN), and type of immune cell infiltration (CD3- and CD68-positive cells) were assessed. RESULTS: No difference in expression of HER2/neu, p21, p27, p53, number of apoptotic cells and CD68-positive cells was detected. Lower levels of stromal TN expression were found in MC compared with DC (P=0.0007), but differences between MC and AMC were not significant (P=0.27). A higher proportion of intratumoral CD3-positive cells was seen in MC than in AMC (P=0.046). No differences were seen between MC and DC (P=0.73). With a median follow-up of 67 months, three patients with DC had relapsed in distant sites, while one patient with AMC had a second primary. Two patients with MC had reappearance of DC in the breast. CONCLUSIONS: The three distinct disease types, selected by having similar high proliferation, had similar expression of cell cycle regulators. The lower expression of TN and massive infiltration of T lymphocytes might both indicate a special interaction between tumor cells and microenvironment, important features for conferring improved prognosis through negligible invasive and metastatic potential to MC. In our series, however, patients with a previous MC are not free from the risk of developing a subsequent DC. Finally, defining AMC as a distinct entity from DC is not justified.

Adult↗

Up-date on quantitative grading systems and prognosis.

Several subjective grading systems have been proposed for different premalignant and malignant lesions with varying emphasis on the nuclear component. However, all subjective grading systems are prone to a significant degree of observer error because the subjective evaluation of nuclear features like size and staining density may be inaccurate and not reproducible. Therefore, quantitation-based methods are to be preferred to evaluate accurately the cell and its architectural features and to eliminate the subjective element of microscopy. The problems which have so far been considered and solved in some quantitation-based grading systems are as follows: 1. feature evaluation, selection and combination into indices and grading systems; 2. number of grades to be identified; 3. degree of certainty in the grading systems; 4. quality control and standardisation of the grading systems; 5. routine application of the grading systems and their efficacy in predicting tumour progression and/or regression (also in response to treatment); 6. current and future aims in researching new grading systems and improving the current ones. The solution of these problems has allowed the grading to be accurately evaluated; thus avoiding the poor reproducibility observed when features have been subjectively investigated.

Humans↗

Cognitive impairment and cellular/vascular changes in the cerebral white matter.

A possible relation between cerebral white-matter injury and dementia was intuitively attributed by Alzheimer to changes affecting the small penetrating vessels that supply the cerebral white matter. Several observations support the view that white-matter changes detectable by neuroimaging may contribute to cognitive deficits in the elderly. But many questions concerning this matter remain partially answered. In this communication we review: (1) Selected anatomic features of the blood vessels supplying the white matter; (2) possible pathogenetic mechanisms responsible for the white-matter changes; (3) observations on humans and animals suggesting a causal relationship between ischemia/hypoxemia and white-matter injury; (4) epidemiologic studies linking white-matter abnormalities with cognitive disorders. We conclude that abnormalities in the small vessels caused by aging and arterial hypertension, or other processes (cerebral amyloid angiopathy, CADASIL) together with systemic circulatory disturbances, such as abrupt variations in blood pressure values or cardiac diseases, may be the substrate of selective white-matter injury. The damage is structurally characterized by incomplete infarction or selective cellular injury.

Alzheimer Disease↗

An exact form of the breeder's equation for the evolution of a quantitative trait under natural selection.

Starting with the Price equation, I show that the total evolutionary change in mean phenotype that occurs in the presence of fitness variation can be partitioned exactly into five components representing logically distinct processes. One component is the linear response to selection, as represented by the breeder's equation of quantitative genetics, but with heritability defined as the linear regression coefficient of mean offspring phenotype on parent phenotype. The other components are identified as constitutive transmission bias, two types of induced transmission bias, and a spurious response to selection caused by a covariance between parental fitness and offspring phenotype that cannot be predicted from parental phenotypes. The partitioning can be accomplished in two ways, one with heritability measured before (in the absence of) selection, and the other with heritability measured after (in the presence of) selection. Measuring heritability after selection, though unconventional, yields a representation for the linear response to selection that is most consistent with Darwinian evolution by natural selection because the response to selection is determined by the reproductive features of the selected group, not of the parent population as a whole. The analysis of an explicitly Mendelian model shows that the relative contributions of the five terms to the total evolutionary change depends on the level of organization (gene, individual, or mated pair) at which the parent population is divided into phenotypes, with each frame of reference providing unique insight. It is shown that all five components of phenotypic evolution will generally have nonzero values as a result of various combinations of the normal features of Mendelian populations, including biparental sex, allelic dominance, inbreeding, epistasis, linkage disequilibrium, and environmental covariances between traits. Additive genetic variance can be a poor predictor of the adaptive response to selection in these models. The narrow-sense heritability sigma2A/sigma2P should be viewed as an approximation to the offspring-parent linear regression rather than the other way around.

Biological Evolution↗

Characterization of low-intensity lesions in the peripheral zone of prostate on pre-biopsy endorectal coil MR imaging.

The aim of this study was to determine which morphological features of low-intensity lesions in the peripheral zone of the prostate are predictable of prostate cancer on pre-biopsy T2-weighted integrated endorectal phased-array MR images. The MR examinations were performed in 69 consecutive patients with elevated level of prostate-specific antigen (>4 ng/ml) and/or a positive digital rectal examination before transperineal 12-site biopsy. Two radiologists evaluated presence of lesions, their morphological features, and possibility of malignancy in divided into four sections of the peripheral zone. Imaging analysis findings were compared with biopsy results. Discriminative features were selected by stepwise logistic regression. Descriptive statistics and receiver operating characteristics (ROC) curves were also calculated. Sixty-eight benign lesions and 23 malignant lesions were found. Wedge shape and diffuse extensions without mass effect were significantly associated with benignity ( P=0.0105 and 0.002, respectively). Lesion size was significantly associated with malignancy ( P=0.0001). For evaluating probability of malignancy for lesions, regression model showed a comparable accuracy with the total impression for the readers in ROC analysis (Az 0.9095 vs 0.9266, respectively). Wedge shape, diffuse extension without mass effect, and size are the morphological features of low-intensity lesions in the peripheral zone on pre-biopsy T2-weighted MR images that give the best prediction of malignancy.

Aged↗

Colour visualization as an aid to the comparison of treatment plans for prostatic carcinoma.

The conventional treatment plan is usually presented as a longitudinal set of axial cross-sections showing the patient contour and selected anatomical features, together with a set of isodose lines. It is difficult to interpret the correlation between dose, target and organs at risk, and the comparison of several plans is time-consuming and highly subjective. This procedure has been improved by modifying a treatment planning system to provide 'images of regret', in which regions are shown in appropriate colour if the planned dose distribution is at variance with prescribed conditions defining limits of acceptability. The method has been used for planning treatment for localized prostatic cancer, and found to be useful for the rapid selection of the optimal treatment plan from a set of alternatives.

Adenocarcinoma↗

Classification of mass and normal breast tissue on digital mammograms: multiresolution texture analysis.

We investigated the feasibility of using multiresolution texture analysis for differentiation of masses from normal breast tissue on mammograms. The wavelet transform was used to decompose regions of interest (ROIs) on digitized mammograms into several scales. Multiresolution texture features were calculated from the spatial gray level dependence matrices of (1) the original images at variable distances between the pixel pairs, (2) the wavelet coefficients at different scales, and (3) the wavelet coefficients up to certain scale and then at variable distances between the pixel pairs. In this study, 168 ROIs containing biopsy-proven masses and 504 ROIs containing normal parenchyma were used as the data set. The mass ROIs were randomly and equally divided into training and test groups along with corresponding normal ROIs from the same film. Stepwise linear discriminant analysis was used to select optimal features from the multiresolution texture feature space to maximize the separation of mass and normal tissue for all ROIs. We found that texture features at large pixel distances are important for the classification task. The wavelet transform can effectively condense the image information into its coefficients. With texture features based on the wavelet coefficients and variable distances, the area Az under the receiver operating characteristic curve reached 0.89 and 0.86 for the training and test groups, respectively. The results demonstrate that a linear discriminant classifier using the multiresolution texture features can effectively classify masses from normal tissue on mammograms.

Biopsy↗

Karyometric marker features in fine needle aspirates of follicular adenoma of the thyroid.

Karyometric measurements were performed on fine needle aspirates of clearly identifiable adenomatous areas and adjacent normal-appearing areas in the surgical specimens from ten patients with follicular adenomas of the thyroid. Similar measurements were made on aspirates from nine patients free of thyroid disease. A total of 95 karyometric features were evaluated for each nucleus. Analysis of variance of optical density values did not show a significant difference between the three types of nuclei. Discriminant analysis selected seven karyometric features that produced a statistically highly significant separation of adenoma nuclei from control nuclei. A similar analysis selected six features that produced a statistically highly significant discrimination of normal-appearing nuclei from control nuclei. The validity of these markers for distinguishing control nuclei from adenoma nuclei and normal-appearing nuclei adjacent to adenomas was demonstrated by analysis in further training and test sets. These findings parallel those previously demonstrated for invasive and microinvasive follicular carcinomas of the thyroid.

Adenoma↗

Dynamic heterogeneities in the out-of-equilibrium dynamics of simple spherical spin models.

The response of spherical two-spin interaction models, the spherical ferromagnet (s-FM) and the spherical Sherrington-Kirkpatrick (s-SK) model, is calculated for the protocol of the so-called nonresonant hole burning (NHB) experiment for temperatures below the respective critical temperatures. It is shown that it is possible to select dynamic features in the out-of-equilibrium dynamics of both models, one of the hallmarks of dynamic heterogeneities. The behavior of the s-SK model and the s-FM model in three dimensions is very similar, showing dynamic heterogeneities in the long-time behavior, i.e., in the aging regime. The appearance of dynamic heterogeneities in the s-SK model explicitly demonstrates that these are not necessarily related to spatial heterogeneities. For the s-FM model, it is shown that the nature of the dynamic heterogeneities changes as a function of dimensionality. With the increasing dimension, the frequency selectivity of the NHB diminishes and the dynamics in the mean-field limit of the s-FM model becomes homogeneous.

Journal Article↗

LymphGen-Sig: Integrating Genetic and Transcriptional States to Predict Therapeutic Response in Diffuse Large B-Cell Lymphoma.

PURPOSE: Genetic classification may advance precision medicine in diffuse large B-cell lymphoma (DLBCL), but existing tools like LymphGen (LG) are limited by complexity and incomplete classification and do not incorporate nongenetic features that affect disease biology and therapeutic outcomes. To address these limitations, we developed LG-sig (LGsig), a gene expression-based platform that classifies all DLBCLs and harmonizes both genetic and nongenetic dimensions of the disease. METHODS: LGsig was built on the distinct subtype-specific gene expression signature of each LG class using paired genomic and transcriptomic data (National Cancer Institute/British Columbia Cancer Agency; N = 764). Model development was restricted to DLBCLs classified into MYD88L265P&#xa0;and&#xa0;CD79B&#xa0;mutations (MCD), BCL6&#xa0;translocation and&#xa0;NOTCH2&#xa0;mutations (BN2), EZH2&#xa0;mutations and&#xa0;BCL2&#xa0;translocation (EZB), or SGK1&#xa0;and&#xa0;TET2&#xa0;mutations (ST2). Gene features were selected by differential gene expression, with 294 genes being optimal for classification using a nearest shrunken centroid classifier. LGsig classifications were designated as MCDsig, BN2sig, ST2sig, and EZBsig. The final model was applied to RNAseq from archival samples from the POLARIX trial (N = 678) to assess outcomes after polatuzumab vedotin-R-CHP (pola-R-CHP) or rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP) for each LGsig subtype. RESULTS: LGsig accurately identified LG subtypes using transcriptional data alone and extended assignments to all previously LG-unclassified cases. Importantly, LG-unclassified DLBCLs reassigned by LGsig mirrored the transcriptional and clinical features of their corresponding LG counterparts, supporting their reclassification. In addition, LGsig reassigned LG A53 DLBCLs, characterized by aneuploidy and TP53 alterations, into more biologically and therapeutically relevant LGsig clusters. Finally, LGsig improved the performance of LG as a biomarker in the POLARIX study, by identifying distinct DLBCL subtypes exhibiting a survival benefit with pola-R-CHP over R-CHOP in both LG-classified and LG-unclassified cases. CONCLUSION: LGsig expands molecular classification beyond current genetic classifiers in DLBCL by integrating both genetic and transcriptional dimensions of the disease to better inform subtype-specific therapeutic strategies.

Journal Article↗

MWENA: a novel sample re-weighting-based algorithm for disease classification and data interpretation using extracellular vesicles omics data.

BACKGROUND AND OBJECTIVE: Extracellular vesicles (EVs), considered as a form of liquid biopsy, have gained significant attention in recent years due to their stability and the preservation of disease markers. Research studies underscore the clinical significance of molecules found in EVs, highlighting their role as communicative mediators between cells. However, analyzing this data is challenging due to noisy measurements, having far more variables than samples, and some groups (e.g., disease subtypes or experimental conditions) having much less data than others. We therefore develop an algorithm to address aforementioned challenges for the classification of imbalanced EVs omics data. METHODS AND RESULTS: We propose the EV Meta-Weight Elastic Net Algorithm (MWENA), which utilizes logistic regression with elastic net regularization for the classification and identification of EV signatures, effectively addressing the challenges posed by high-dimensional small sample sizes. To mitigate issues related to class imbalance and high noise levels, MWENA incorporates an automatic sample re-weighting function, which uses a meta-net to adaptively learn generalizable patterns directly from the data itself. We validate the MWENA algorithm on both simulated data and EVs omics data, covering six classification tasks that involve four different types of diseases (pancreatic ductal adenocarcinoma, interstitial lung diseases, colorectal cancer, and ovarian cancer) and three clinical scenarios (disease diagnosis, disease-stage screening, and disease-subtype classification). Compared to other machine learning methods, MWENA demonstrates superiority in identifying small class samples and achieves the highest scores in both sensitivity and G-means. Biological analysis is also performed to further explore the significance of selected signatures as biological markers and their roles in disease mechanisms. CONCLUSIONS: We anticipate that our proposed approach will take a modest step in harnessing EV omics data to discover biomarkers, aiding researchers in gaining a comprehensive understanding of biological processes.

Extracellular Vesicles↗

Factors determining survival of patients with malignant gliomas diagnosed by stereotactic biopsy.

We analyzed the prognostic significance of tumor histology, location, treatment, and selected clinical features at presentation in 91 consecutive patients with malignant gliomas diagnosed by stereotactic biopsy. In 64 patients with glioblastoma multiforme (GBM) the following factors were associated with longer survival: lobar tumor location, adequate radiation therapy (RT) tumor dose 5,000-6,000 cGy, Karnofsky performance rating (KPR) at presentation greater than or equal to 70, and a normal level of consciousness before biopsy. In 27 patients with anaplastic astrocytoma, factors associated with longer survival were lobar tumor location, adequate RT, age less than 40 years at presentation, and a history of seizures. Delayed cytoreductive surgery in lobar GBM extended median survival but did not improve long-term survival. For patients with deep or midline malignant gliomas and for selected patients with lobar tumors, stereotactic biopsy followed by RT may be the most reasonable initial treatment strategy.

Adult↗

Why kin and group selection models may not be enough to explain human other-regarding behaviour.

Models of kin or group selection usually feature only one possible fitness transfer. The phenotypes are either to make this transfer or not to make it and for any given fitness transfer, Hamilton's rule predicts which of the two phenotypes will spread. In this article we allow for the possibility that different individuals or different generations face similar, but not necessarily identical possibilities for fitness transfers. In this setting, phenotypes are preference relations, which concisely specify behaviour for a range of possible fitness transfers (rather than being a specification for only one particular situation an animal or human can be in). For this more general set-up, we find that only preference relations that are linear in fitnesses can be explained using models of kin selection and that the same applies to a large class of group selection models. This provides a new implication of hierarchical selection models that could in principle falsify them, even if relatedness--or a parameter for assortativeness--is unknown. The empirical evidence for humans suggests that hierarchical selection models alone are not enough to explain their other-regarding or altruistic behaviour.

Altruism↗