Journal: PLoS Genetics

Article Title: Histone Acetyl Transferase 1 Is Essential for Mammalian Development, Genome Stability, and the Processing of Newly Synthesized Histones H3 and H4

doi: 10.1371/journal.pgen.1003518

Figure Lengend Snippet: A) Histologic appearance of lungs from newborn pups obtained from a Hat1 +/−+ and Hat1 −/− mice. Staining was with hematoxylin-eosin; magnification 20×, (inlets ×40). The lungs of Hat1 −/− show less aeration, due to thickened mesenchyme resulting in death due to respiratory failure. B) Hat1 is highly expressed in lungs of Hat1 +/+ but not in Hat1 −/− mice; magnification 20×, (inlets ×40) C) Cleaved Caspase3 stained by IHC showed no difference between lungs of Hat1 ++ and Hat1 −/− mice; magnification 20×, (inlets ×40) D) Ki67 stained by IHC shows significantly higher proliferation rates in lungs of Hat1 −/− mice compared to controls; magnification 20×, (inlets ×40). Quantification was done by HistoQuest software.

Article Snippet: The stainings were quantified with the HistoQuest and TissueQuest software (TissueGnostics GmbH, Vienna, Austria, www.tissuegnostics.com ).

Techniques: Staining, Software

Journal: PLoS ONE

Article Title: B Cells and Ectopic Follicular Structures: Novel Players in Anti-Tumor Programming with Prognostic Power for Patients with Metastatic Colorectal Cancer

doi: 10.1371/journal.pone.0099008

Figure Lengend Snippet: (A) Subpopulation of CD20-positive B cells at metastatic border. Representative examples of the CD45-positive ( a ) ectopic follicle, ( c ) large cell aggregate and ( e ) non-organized cell population and the corresponding areas stained for CD20 are shown ( b , d , f , respectively). Quantitative analysis was done using TissueQuest and HistoQuest software; percentage of positive cells is indicated. Scale bar: 100 µm. (B) Different organisation patterns of CD20-positive cells within the three regions of interest. Representative images (i) at the border: ( a ) single cells, ( b ) cell aggregates; insert: higher power view of CD20-positive cells in contact with the colon tumor epithelial cells, ( c ) ectopic follicular structures; (ii) around the portal veins ( d ) proximate to the border and ( e ) distant to the border as well as (iii) within liver tissue ( f ) are shown. T: tumor; L: liver. Scale bar: 50 µm. (C) Kaplan-Meier estimates for patients stratification based on the CD20-derived values at the border. Kaplan-Meier curves for RFS based on CD20 values for panel I, panel II and panel I+II are shown giving patient stratification into low and high risk groups (higher than median indicates low risk); p value of the log-rank test is indicated. Panel I: median is equal to 2.70, below median n = 5, above median n = 6; panel II: median is equal to 2.11, below median n = 25, above median n = 26; panel I+II: median is equal to 2.22, below median n = 31, above median n = 31. ( d ) Boxplots of CD20 data sets for patients without recurrence (No) versus patients with recurrence (Yes) at the time point of 24 months. The cut off was set according to the latest event occurrence (23.3 month) where no censoring has occurred, giving separation from the censored subjects (≥29.4 months) as visualized on ( b ). Dashed line: the median CD20 value, which was used for patient stratification into low and high risk groups on Kaplan-Meier plot ( b ); p value is shown (t test).

Article Snippet: Quantitative analysis of infiltrating immune cells was performed using TissueQuest or HistoQuest software (TissueGnostics, Vienna, Austria) for immunofluorescent and for immunohistochemical staining, respectively.

Techniques: Staining, Software, Derivative Assay

Journal: Cancers

Article Title: The Immune Phenotype of Isolated Lymphoid Structures in Non-Tumorous Colon Mucosa Encrypts the Information on Pathobiology of Metastatic Colorectal Cancer

doi: 10.3390/cancers12113117

Figure Lengend Snippet: Lymphoid structures at three tissue entities of patients with metastatic colorectal cancer visualized by the digital image cytometry approach. ( A ) Representative images of ILS and ELS within tissue sections stained for the B-cell marker CD20 ( brown color ) and counterstained for nuclei with hematoxylin ( blue color ) are shown for three tissue entities (a, NT (ILS); b, CRC (ELS); c, CRCLM (ELS)). Scale bar: 500 µm. The whole-slide digital images were acquired using the automated microscopy-based TissueFAXS platform (TissueGnostics, Vienna, Austria). ( B ) The quantitative analysis of immune cell populations stained for a specific marker is based on a single cell recognition algorithm (nuclear segmentation) by HistoQuest software (TissueGnostics, Vienna, Austria). Shown are (a) the original image of ELS within CRC upon IHC staining for CD20 (brown color, CD20 staining; blue color, nuclear counterstaining with hematoxylin), (b) software-based recognition of CD20-positive cells (marked in red ) and CD20-negative cells (marked in green ) within the region of interest covering the entire ELS (indicated by a red circle) and (c) the corresponding scatter plot of the HistoQuest-based tissue image cytometry analysis showing the individual cells, represented by dots, detected within the ELS. The cut-off line separates the CD20-positive B cells (upper quadrant, 66.6%) from the CD20-negative cells (lower quadrant, 33.4%). Scale bar: 100 µm. NT, non-tumorous tissue; CRC, colorectal cancer; CRCLM, colorectal cancer liver metastasis; ILS, isolated lymphoid structure; ELS, ectopic lymphoid structure; IHC, immunohistochemical.

Article Snippet: The analysis algorithm is based on a single cell recognition strategy and the quantification of the immune marker-positive cells using HistoQuest (for IHC, versions 3.5.3.0188, 4.0.4.0159 and 6.0.1.125) and TissueQuest (for IF, version 4.0.1.0128) software packages (TissueGnostics, Vienna, Austria).

Techniques: Cytometry, Staining, Marker, Microscopy, Software, Immunohistochemistry, Isolation, Immunohistochemical staining