71 research outputs found
Spatial quantification and classification of skin response following perturbation using organotypic skin cultures
No full textAbstract
Motivation: For a mechanistic understanding of skin and its response to an induced perturbation, systems biology is gaining increasing attention. Unfortunately, quantitative and spatial expression data for skin, like for most other tissues, are almost not available.
Results: Integrating organotypic skin cultures, whole-slide scanning and subsequent image processing provides bioinformatics with a novel source of spatial expression data. We here used this approach to quantitatively describe the effect of treating organotypic skin cultures with sodium dodecyl sulphate in a non-corrosive concentration. We first measured the differentiation-related spatial expression gradient of Heat-Shock-Protein 27 in a time series of up to 24 h. Secondly, a multi-dimensional tissue classifier for predicting skin irritation was developed based on abstract features of these profiles. We obtained a high specificity of 0.94 and a sensitivity of 0.92 compared with manual classification. Our results demonstrate that the integration of tissue cultures, whole-slide scanning and image processing is well suited for both the standardized data acquisition for systems biological tissue models and a highly robust classification of tissue responses.
Contact: [email protected]
Supplementary information: Supplementary data are available at Bioinformatics online.</jats:p
Abstract 4923: Understanding cancer invasion by the systems biological analysis of collective cell migration in 3D tissue models
No full textEstimation of immune cell densities in immune cell conglomerates: an approach for high-throughput quantification.
No full textBackgroundDetermining the correct number of positive immune cells in immunohistological sections of colorectal cancer and other tumor entities is emerging as an important clinical predictor and therapy selector for an individual patient. This task is usually obstructed by cell conglomerates of various sizes. We here show that at least in colorectal cancer the inclusion of immune cell conglomerates is indispensable for estimating reliable patient cell counts. Integrating virtual microscopy and image processing principally allows the high-throughput evaluation of complete tissue slides.Methodology/principal findingsFor such large-scale systems we demonstrate a robust quantitative image processing algorithm for the reproducible quantification of cell conglomerates on CD3 positive T cells in colorectal cancer. While isolated cells (28 to 80 microm(2)) are counted directly, the number of cells contained in a conglomerate is estimated by dividing the area of the conglomerate in thin tissues sections (ConclusionIn summary, we recommend our approach as an objective and robust strategy for quantifying immune cell densities in immunohistological sections which can be directly implemented into automated full slide image processing systems
Wound healing revised: A novel reepithelialization mechanism revealed by in vitro and in silico models
No full textWound healing is a complex process in which a tissue's individual cells have to be orchestrated in an efficient and robust way. We integrated multiplex protein analysis, immunohistochemical analysis, and whole-slide imaging into a novel medium-throughput platform for quantitatively capturing proliferation, differentiation, and migration in large numbers of organotypic skin cultures comprising epidermis and dermis. Using fluorescent time-lag staining, we were able to infer source and final destination of keratinocytes in the healing epidermis. This resulted in a novel extending shield reepithelialization mechanism, which we confirmed by computational multicellular modeling and perturbation of tongue extension. This work provides a consistent experimental and theoretical model for epidermal wound closure in 3D, negating the previously proposed concepts of epidermal tongue extension and highlighting the so far underestimated role of the surrounding tissue. Based on our findings, epidermal wound closure is a process in which cell behavior is orchestrated by a higher level of tissue control that 2D monolayer assays are not able to capture
Book Review: Immersive Media and Books 2020: New Insights About Book Pirates, Libraries and Discovery, Millennials, and Cross-Media Engagement: Before and During COVID
No full textBooks exist within a connected media ecosystem, but few consumer behavior and experience studies capture the relationships between books and other media forms. In Immersive Media & Books 2020, Drs. Rachel Noorda and Kathi Inman Berens from Portland State University explore crossmedia consumer behavior for books, video games, and TV/movies—capturing behaviors both before and during COVID-19. The highlights of the report are highly distributed word-of-mouth discovery, the importance of author brand and genre, avid book engagement of Black and Latinx millennials, context-agnostic book discovery, cross-media engagement and discovery, multidimensional identities and behaviors of book pirates, multitasking as a feature of contemporary book consumption, and libraries as tools of discovery
Quantification of prognostic immune cell markers in colorectal cancer using whole slide imaging tumor maps
No full textTo analyze intratumoral heterogeneity of immune cells and the resulting impact of heterogeneity on the level of individual patient prediction
Molekulare Mechanismen kutaner humaner Papillomviren (HPV) während der Hautkarzinogenese
No full textIn den letzen Jahren gab es durch epidemiologische und molekularbiologische Studien vermehrt Hinweise, dass kutane humane Papillomviren (HPV) ursächlich an der Entstehung nicht-melanozytärer Hauttumore (engl. NMSC) beteiligt sind. Ziel der vorliegenden Arbeit war die Identifizierung molekularer Mechanismen der viralen Proteine E6 und E7 kutaner HPV-Typen. Die E6 oder E7 Gene der verschiedenen HPV-Typen 1, 4, 5, 8, 20, 38 und RTRX7 wurden untersucht. Natürliche Wirtszellen dieser Viren, humane primäre Keratinozyten (HPK) der Haut, wurden mit rekombinanten, für E6 oder E7 kodierenden Retroviren infiziert. Die Analysen erfolgten in Monolayer-Kultur (undifferenzierte Keratinozyten) oder in organotypischen Hautmodellen (Induktion der Keratinozytendifferenzierung). Die Expression von E6 oder E7 führte in Monolayer-HPK zu einer Verlängerung der Lebensspanne und zu einer deutlich erhöhten Verdoppelungsrate. Eine Telomeraseaktivierung, die charakteristisch für immortale Zellen ist, wurde nur in HPV 8 E6 positiven HPK nachgewiesen. In organotypischen Hautmodellen induzierte das E7 Protein von HPV 1, 4 und 38 starke Veränderungen in der Differenzierung sowie eine Zunahme der Proliferation. Weiterhin wurde eine Aufhebung der normalen Zellzykluskontrolle in suprabasalen HPV 5 E7 oder HPV 8 E7 beobachtet. Hinweise auf ein starkes invasives Potential von E7-infizierten HPK wurden für HPV 8 E7 bestätigt und für HPV 4 E7, HPV 38 E7 und RTRX7 E7 erweitert. Molekulare Mechanismen der viralen Gene E6 und E7 kutaner HPV unterscheiden sich von mukosalen Typen. Das Mehrstufenmodell der Karzinogenese beinhaltet eine Reihe fundamentaler Zelltransformationen, die für eine Tumorgenese nötig sind. In dieser Arbeit beschriebene Mechanismen der Modulation der Zelldifferenzierung und Zellproliferation durch die kutanen HPV-Typen 4, 5, 8 und 38 können unter Umständen zur Induktion und Progression früher Stadien von Plattenepithelkarzinomen (SCC) beitragen.In the last years epidemiologic and molecular biological studies accumulated increasing evidence that cutaneous human papillomaviruses are etiologically involved in the formation of non-melanoma skin cancer (NMSC). The presented work aims to identify the underlying molecular mechanisms of the viral proteins E6 and E7 of cutaneous HPV types. The E6 and E7 genes of the different HPV types 1, 4, 5, 8, 20, and RTRX7, which are in vivo associated with cutaneous benign or malignant lesions, were studied. Natural host cells of these viruses, human primary keratinocyts (HPK) of the skin, were infected with recombinant E6 and E7 encoding retroviruses. The following analyses were performed in monolayer culture (non-differentiated keratinocytes) or in organotypic skin culture (induction of keratinocyte differentiation). The expression of E6 and E7 elongated the life span of monolayer HPK and significantly increased the doubling rate. An activation of the telomerase, characteristic for immortalized cells, was only detected in HPV 8 E6 positive cells. In organotypic skin cultures E7 of HPV 1, 4 and 38 induced drastic changes in differentiation and proliferation. Additionally an impairment of the normal cell cycle control in suprabasale HPV 5 E7 and 8 E7 cultures was seen. Hints for a strong invasive potential of E7 infected HPK were proven for HPV 8 E7 and expanded to HPV 4 E7, HPV 38 E7 and RTRX E7. The viral E6 and E7 genes of cutaneous and mucosal HPV types exhibit different molecular mechanisms. The multistep model of carcinogenesis includes a series of fundamental cell transformations necessary for tumorigenesis. Mechanisms for the modulation of cell differentiation and proliferation by cutaneous HPV types 4, 5, 8 and 38 described in this work could potentially contribute to the induction and progression of early stages of squamous cell carcinoma
Quantification of prognostic immune cell markers in colorectal cancer using whole slide imaging tumor maps
No full textTo analyze intratumoral heterogeneity of immune cells and the resulting impact of heterogeneity on the level of individual patient prediction
Robust gridding of TMAs after whole-slide imaging using template matching
No full textTissue microarrays (TMAs) represent an important approach for the high-throughput cellular analysis of large numbers of tissue samples on one single slide in research related to diagnostics and oncology. Whole-slide imaging now enables full scanning and subsequent image analysis of such TMAs. In contrast to automatically spotted RNA microarrays, TMAs are fabricated manually and mechanically by arranging hundreds of tissue cores in a single paraffin block. This procedure frequently results in quality problems severely hampering the later automatic image analysis of TMAs after whole-slide imaging. We therefore set out to (a) determine the extent of these quality issues in exemplary TMAs and (b) to develop a robust gridding method to identify the logical position coordinates of each TMA core on a virtual TMA slide. We present the first robust method identifying these coordinates by shifting a template grid over all cores of the TMA (template matching) and thereby measuring in how far the grid matches a predefined list of cores on the virtual TMA Slide. Analysis of 20 TMAs from Breast Cancer as well as 40 Head-and-Neck Cancer showed that frequent TMA layout issues comprise low staining, debris, core displacement, nonuniform background, missing cores, and rotated subarrays. On this highly demanding test comprising chromogen as well as fluorescence stained TMAs, our template matching method achieved an excellent position analysis. Of 8900 cores, 8864 (99.59%) were assigned properly. In all 60 slides of the test set, no localization error occurred. The automatic grid analysis of TMAs after whole-slide imaging is highly demanding and requires dedicated algorithms. We demonstrate such a method and evaluate its performance. © 2010 International Society for Advancement of Cytometry
Recommended from our members
CSLA 2014
No full textPhotograph of Kathi Macias during the 47th Church and Synagogue Library Association conference, which was held at the Crowne Plaza hotel in Portland, Oregon. She is a guest speaker at the event and is the author of several books. She is standing behind the podium and is holding a microphone in her hand
- …
