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Razian SA, Jadidi M. Histology Image Viewer and Converter (HIVC): A High-Speed Freeware Software to View and Convert Whole Slide Histology Images. COMPUTER METHODS IN BIOMECHANICS AND BIOMEDICAL ENGINEERING. IMAGING & VISUALIZATION 2023; 11:1652-1660. [PMID: 37994355 PMCID: PMC10662701 DOI: 10.1080/21681163.2023.2174776] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 01/26/2023] [Indexed: 02/07/2023]
Abstract
Histology images are widely used to assess the microstructure of biological tissues, but scanners often save images in bulky SVS and multi-layered TIFF formats. These formats were designed to archive image blocks and high-resolution textual information and are not compatible with conventional image analysis software. Our goal was to create a freeware Histology Image Viewer and Converter (HIVC) with a graphical user interface that allows viewing and converting whole-slide images in batch. HIVC was developed using C# Language for Windows x64 operating system. HIVC's performance was assessed by converting 20 whole-slide images to a JPG format at 20x and 40x resolution and comparing the results to ImageJ, Cell Profiler, QuPath, Nanoborb, and Aperio ImageScope. HIVC was more than 8-times faster in converting images than other software packages. This software allows high-speed batch conversion of histology images to traditional formats, permitting platform-independent secondary analyses.
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Affiliation(s)
| | - Majid Jadidi
- Department of Biomechanics, University of Nebraska Omaha, Omaha, NE
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2
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Grierson I, Minckler D, Rippy MK, Marshall AJ, Collignon N, Bianco J, Detry B, Johnstone MA. A novel suprachoroidal microinvasive glaucoma implant: in vivo biocompatibility and biointegration. BMC Biomed Eng 2020; 2:10. [PMID: 33073174 PMCID: PMC7556975 DOI: 10.1186/s42490-020-00045-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/22/2020] [Indexed: 12/29/2022] Open
Abstract
Background A major challenge for any glaucoma implant is their ability to provide long-term intraocular pressure lowering efficacy. The formation of a low-permeability fibrous capsule around the device often leads to obstructed drainage channels, which may impair the drainage function of devices. These foreign body-related limitations point to the need to develop biologically inert biomaterials to improve performance in reaching long-term intraocular pressure reduction. The aim of this study was to evaluate in vivo (in rabbits) the ocular biocompatibility and tissue integration of a novel suprachoroidal microinvasive glaucoma implant, MINIject™ (iSTAR Medical, Wavre, Belgium). Results In two rabbit studies, no biocompatibility issue was induced by the suprachoroidal, ab-externo implantation of the MINIject™ device. Clinical evaluation throughout the 6 post-operative months between the sham and test groups were similar, suggesting most reactions were related to the ab-externo surgical technique used for rabbits, rather than the implant material itself. Histological analysis of ocular tissues at post-operative months 1, 3 and 6 revealed that the implant was well-tolerated and induced only minimal fibroplasia and thus minimal encapsulation around the implant. The microporous structure of the device became rapidly colonized by cells, mostly by macrophages through cell migration, which do not, by their nature, impede the flow of aqueous humor through the device. Time-course analysis showed that once established, pore colonization was stable over time. No fibrosis nor dense connective tissue development were observed within any implant at any time point. The presence of pore colonization may be the process by which encapsulation around the implant is minimized, thus preserving the permeability of the surrounding tissues. No degradation nor structural changes of the implant occurred during the course of both studies. Conclusions The novel MINIject™ microinvasive glaucoma implant was well-tolerated in ocular tissues of rabbits, with observance of biointegration, and no biocompatibility issues. Minimal fibrous encapsulation and stable cellular pore colonization provided evidence of preserved drainage properties over time, suggesting that the implant may produce a long-term ability to enhance aqueous outflow.
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Affiliation(s)
- Ian Grierson
- Department of Eye and Vision Science, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
| | - Don Minckler
- University of California, Irvine School of Medicine, Irvine, CA USA
| | | | | | - Nathalie Collignon
- Department of Ophthalmology, Centre Hospitalier Universitaire of Liège, Liège, Belgium
| | | | - Benoit Detry
- iSTAR Medical SA, Avenue Sabin 6, 1300 Wavre, Belgium
| | - Murray A Johnstone
- Department of Ophthalmology, University of Washington, Seattle, Washington USA
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3
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Dussenne M, Gennotte V, Rougeot C, Mélard C, Cornil CA. Consequences of temperature-induced sex reversal on hormones and brain in Nile tilapia (Oreochromis niloticus). Horm Behav 2020; 121:104728. [PMID: 32119880 DOI: 10.1016/j.yhbeh.2020.104728] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 02/17/2020] [Accepted: 02/25/2020] [Indexed: 12/16/2022]
Abstract
Fish present a wide variety of sex determination systems ranging from strict genetic control (genetic sex determination, GSD) to strict environmental control (environmental sex determination, ESD). Temperature is the most frequent environmental factor influencing sex determination. Nile tilapia (Oreochromis niloticus) is characterized by GSD with male heterogamety (XY/XX), which can be overridden by exposure to high masculinizing temperatures. Sex reversed Nile tilapia (XX males; neomales) have been described in the wild and seem undistinguishable from XY males, but little is known about their physiology. The consideration of climate change urges the need to understand the possible physiological and behavioral consequences of such a sex reversal. The present study compared XX females, XY males and XX neomales for testis maturation, circulating sex -steroid concentrations as well as the size and number of neurons expressing arginine-vasotocin [AVT] and gonadotropin releasing hormone [GnRH] which are involved in sociosexual pathways. The results revealed that temperature-induced sex reversal does not affect testis maturation nor circulating sex steroid concentrations. Neomales show dramatically fewer GnRH1-immunoreactive (-ir) neurons than males and females, despite the observed normal testis physiology. Neomales also present fewer AVT-ir neurons in the magnocellular preoptic area than females and bigger AVT-ir neurons in the parvocellular POA (pPOA) compared to both males and females. The absence of consequences of sex reversal on testis development and secretions despite the reduced numbers of GnRH1 neurons suggests the existence of compensatory mechanisms in the hypothalamic-pituitary-gonadal axis, while the larger pPOA AVT neurons might predict a more submissive behavior in neomales.
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Affiliation(s)
- M Dussenne
- Neuroendocrinology Laboratory, GIGA Neurosciences, Avenue Hippocrate, 15 (B36), University of Liège, Liège, Belgium; Aquaculture Research and Education Center (CEFRA), University of Liège, Tihange, Belgium; Laboratory of Functional and Evolutionary Morphology, UR FOCUS, Allée du six Août 11, University of Liège, Liège, Belgium; Behavioural Biology Group, Laboratory of Fish and Amphibian Ethology, Quai Van Beneden 22, University of Liège, Liège, Belgium
| | - V Gennotte
- Aquaculture Research and Education Center (CEFRA), University of Liège, Tihange, Belgium
| | - C Rougeot
- Aquaculture Research and Education Center (CEFRA), University of Liège, Tihange, Belgium
| | - C Mélard
- Aquaculture Research and Education Center (CEFRA), University of Liège, Tihange, Belgium
| | - C A Cornil
- Neuroendocrinology Laboratory, GIGA Neurosciences, Avenue Hippocrate, 15 (B36), University of Liège, Liège, Belgium.
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4
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Quesada-Calvo F, Massot C, Bertrand V, Longuespée R, Blétard N, Somja J, Mazzucchelli G, Smargiasso N, Baiwir D, De Pauw-Gillet MC, Delvenne P, Malaise M, Coimbra Marques C, Polus M, De Pauw E, Meuwis MA, Louis E. OLFM4, KNG1 and Sec24C identified by proteomics and immunohistochemistry as potential markers of early colorectal cancer stages. Clin Proteomics 2017; 14:9. [PMID: 28344541 PMCID: PMC5364649 DOI: 10.1186/s12014-017-9143-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 02/21/2017] [Indexed: 12/17/2022] Open
Abstract
Background Despite recent advances in colorectal cancer (CRC) diagnosis and population screening programs, the identification of patients with preneoplastic lesions or with early CRC stages remains challenging and is important for reducing CRC incidence and increasing patient’s survival.
Methods We analysed 76 colorectal tissue samples originated from early CRC stages, normal or inflamed mucosa by label-free proteomics. The characterisation of three selected biomarker candidates was performed by immunohistochemistry on an independent set of precancerous and cancerous lesions harbouring increasing CRC stages. Results Out of 5258 proteins identified, we obtained 561 proteins with a significant differential distribution among groups of patients and controls. KNG1, OLFM4 and Sec24C distributions were validated in tissues and showed different expression levels especially in the two early CRC stages compared to normal and preneoplastic tissues. Conclusion We highlighted three proteins that require further investigations to better characterise their role in early CRC carcinogenesis and their potential as early CRC markers. Electronic supplementary material The online version of this article (doi:10.1186/s12014-017-9143-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Florence Quesada-Calvo
- Gastroenterology Department, GIGA-R, Liège University Hospital CHU, ULg, GIGA CHU-B34 Avenue de l'Hôpital 11, 4000 Liège, Belgium
| | - Charlotte Massot
- Gastroenterology Department, GIGA-R, Liège University Hospital CHU, ULg, GIGA CHU-B34 Avenue de l'Hôpital 11, 4000 Liège, Belgium
| | - Virginie Bertrand
- Laboratory of Mass Spectrometry, Chemistry Department, GIGA-R, CART, ULg, 4000 Liège, Belgium
| | - Rémi Longuespée
- Laboratory of Mass Spectrometry, Chemistry Department, GIGA-R, CART, ULg, 4000 Liège, Belgium
| | - Noëlla Blétard
- Department of Anatomy and Pathology, GIGA-R, Liège University Hospital CHU, ULg, 4000 Liège, Belgium
| | - Joan Somja
- Department of Anatomy and Pathology, GIGA-R, Liège University Hospital CHU, ULg, 4000 Liège, Belgium
| | - Gabriel Mazzucchelli
- Laboratory of Mass Spectrometry, Chemistry Department, GIGA-R, CART, ULg, 4000 Liège, Belgium
| | - Nicolas Smargiasso
- Laboratory of Mass Spectrometry, Chemistry Department, GIGA-R, CART, ULg, 4000 Liège, Belgium
| | | | - Marie-Claire De Pauw-Gillet
- Mammalian Cell Culture Laboratory, Department of Preclinical and Biomedical Sciences, GIGA-R, ULg, 4000 Liège, Belgium
| | - Philippe Delvenne
- Department of Anatomy and Pathology, GIGA-R, Liège University Hospital CHU, ULg, 4000 Liège, Belgium
| | - Michel Malaise
- Department of Clinical Sciences, Rheumatology, Liège University Hospital CHU, 4000 Liège, Belgium
| | | | - Marc Polus
- Gastroenterology Department, GIGA-R, Liège University Hospital CHU, ULg, GIGA CHU-B34 Avenue de l'Hôpital 11, 4000 Liège, Belgium
| | - Edwin De Pauw
- Laboratory of Mass Spectrometry, Chemistry Department, GIGA-R, CART, ULg, 4000 Liège, Belgium
| | - Marie-Alice Meuwis
- Gastroenterology Department, GIGA-R, Liège University Hospital CHU, ULg, GIGA CHU-B34 Avenue de l'Hôpital 11, 4000 Liège, Belgium
| | - Edouard Louis
- Gastroenterology Department, GIGA-R, Liège University Hospital CHU, ULg, GIGA CHU-B34 Avenue de l'Hôpital 11, 4000 Liège, Belgium
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5
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Leroi N, Sounni NE, Van Overmeire E, Blacher S, Marée R, Van Ginderachter J, Lallemand F, Lenaerts E, Coucke P, Noel A, Martinive P. The timing of surgery after neoadjuvant radiotherapy influences tumor dissemination in a preclinical model. Oncotarget 2017; 6:36825-37. [PMID: 26440148 PMCID: PMC4742213 DOI: 10.18632/oncotarget.5931] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 09/15/2015] [Indexed: 12/18/2022] Open
Abstract
Neoadjuvant radiotherapy (neoRT) used in cancer treatments aims at improving local tumor control and patient overall survival. The neoRT schedule and the timing of the surgical treatment (ST) are empirically based and influenced by the clinician's experience. The current study examines how the sequencing of neoRT and ST affects metastatic dissemination. In a breast carcinoma model, tumors were exposed to different neoRT schedules (2x5Gy or 5x2Gy) followed by surgery at day 4 or 11 post-RT. The impact on the tumor microenvironment and lung metastases was evaluated through immunohistochemical and flow cytometry analyses. After 2x5Gy, early ST (at day 4 post-RT) led to increased size and number of lung metastases as compared to ST performed at day 11. Inversely, after 5x2Gy neoRT, early ST protected the mice against lung metastases. This intriguing relationship between tumor aggressiveness and ST timing could not be explained by differences in classical parameters studied such as hypoxia, vessel density and matrix remodeling. The study of tumor-related inflammation and immunity reveals an increased circulating NK cell percentage following neoRT as compared to non irradiated mice. Then, radiation treatment and surgery were applied to tumor-bearing NOD/SCID mice. In the absence of NK cells, neoRT appears to increase lung metastatic dissemination as compared to non irradiated tumor-bearing mice. Altogether our data demonstrate that the neoRT schedule and the ST timing affect metastasis formation in a pre-clinical model and points out the potential role of NK cells. These findings highlight the importance to cautiously tailor the optimal window for ST following RT.
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Affiliation(s)
- Natacha Leroi
- Laboratory of Tumor and Development Biology, Groupe Interdisciplinaire de Génoprotéomique Appliquée-Cancer (GIGA-Cancer), University of Liège, Belgium.,Department of Radiotherapy-Oncology, Centre Hospitalier Universitaire (CHU) de Liège, Belgium
| | - Nor Eddine Sounni
- Laboratory of Tumor and Development Biology, Groupe Interdisciplinaire de Génoprotéomique Appliquée-Cancer (GIGA-Cancer), University of Liège, Belgium
| | - Eva Van Overmeire
- Laboratory of Myeloid Cell Immunology, VIB, Brussels, Belgium.,Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Silvia Blacher
- Laboratory of Tumor and Development Biology, Groupe Interdisciplinaire de Génoprotéomique Appliquée-Cancer (GIGA-Cancer), University of Liège, Belgium
| | - Raphael Marée
- Systems and Modeling (GIGA-Systems Biology and Chemical Biology), University of Liège, Belgium.,GIGA Bioinformatics Platform, University of Liège, Belgium
| | - Jo Van Ginderachter
- Laboratory of Myeloid Cell Immunology, VIB, Brussels, Belgium.,Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - François Lallemand
- Laboratory of Tumor and Development Biology, Groupe Interdisciplinaire de Génoprotéomique Appliquée-Cancer (GIGA-Cancer), University of Liège, Belgium
| | - Eric Lenaerts
- Department of Radiotherapy-Oncology, Centre Hospitalier Universitaire (CHU) de Liège, Belgium
| | - Philippe Coucke
- Department of Radiotherapy-Oncology, Centre Hospitalier Universitaire (CHU) de Liège, Belgium
| | - Agnès Noel
- Laboratory of Tumor and Development Biology, Groupe Interdisciplinaire de Génoprotéomique Appliquée-Cancer (GIGA-Cancer), University of Liège, Belgium
| | - Philippe Martinive
- Laboratory of Tumor and Development Biology, Groupe Interdisciplinaire de Génoprotéomique Appliquée-Cancer (GIGA-Cancer), University of Liège, Belgium.,Department of Radiotherapy-Oncology, Centre Hospitalier Universitaire (CHU) de Liège, Belgium
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6
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Marée R, Rollus L, Stévens B, Hoyoux R, Louppe G, Vandaele R, Begon JM, Kainz P, Geurts P, Wehenkel L. Collaborative analysis of multi-gigapixel imaging data using Cytomine. Bioinformatics 2016; 32:1395-401. [PMID: 26755625 PMCID: PMC4848407 DOI: 10.1093/bioinformatics/btw013] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 01/04/2016] [Accepted: 01/05/2016] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Collaborative analysis of massive imaging datasets is essential to enable scientific discoveries. RESULTS We developed Cytomine to foster active and distributed collaboration of multidisciplinary teams for large-scale image-based studies. It uses web development methodologies and machine learning in order to readily organize, explore, share and analyze (semantically and quantitatively) multi-gigapixel imaging data over the internet. We illustrate how it has been used in several biomedical applications. AVAILABILITY AND IMPLEMENTATION Cytomine (http://www.cytomine.be/) is freely available under an open-source license from http://github.com/cytomine/ A documentation wiki (http://doc.cytomine.be) and a demo server (http://demo.cytomine.be) are also available. CONTACT info@cytomine.be SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Raphaël Marée
- Systems and Modeling, Department of Electrical Engineering and Computer Science and GIGA-Research, University of Liège, Liège, Belgium Bioimage Analysis Unit, Institut Pasteur, Paris, France
| | - Loïc Rollus
- Systems and Modeling, Department of Electrical Engineering and Computer Science and GIGA-Research, University of Liège, Liège, Belgium
| | - Benjamin Stévens
- Systems and Modeling, Department of Electrical Engineering and Computer Science and GIGA-Research, University of Liège, Liège, Belgium
| | - Renaud Hoyoux
- Systems and Modeling, Department of Electrical Engineering and Computer Science and GIGA-Research, University of Liège, Liège, Belgium
| | - Gilles Louppe
- Systems and Modeling, Department of Electrical Engineering and Computer Science and GIGA-Research, University of Liège, Liège, Belgium
| | - Rémy Vandaele
- Systems and Modeling, Department of Electrical Engineering and Computer Science and GIGA-Research, University of Liège, Liège, Belgium
| | - Jean-Michel Begon
- Systems and Modeling, Department of Electrical Engineering and Computer Science and GIGA-Research, University of Liège, Liège, Belgium
| | - Philipp Kainz
- Institute of Biophysics, Medical University of Graz, Graz, Austria
| | - Pierre Geurts
- Systems and Modeling, Department of Electrical Engineering and Computer Science and GIGA-Research, University of Liège, Liège, Belgium
| | - Louis Wehenkel
- Systems and Modeling, Department of Electrical Engineering and Computer Science and GIGA-Research, University of Liège, Liège, Belgium
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Effects of microgravity simulation on zebrafish transcriptomes and bone physiology-exposure starting at 5 days post fertilization. NPJ Microgravity 2016; 2:16010. [PMID: 28725727 PMCID: PMC5515515 DOI: 10.1038/npjmgrav.2016.10] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Revised: 12/23/2015] [Accepted: 01/21/2016] [Indexed: 12/20/2022] Open
Abstract
Physiological modifications in near weightlessness, as experienced by astronauts during space flight, have been the subject of numerous studies. Various animal models have been used on space missions or in microgravity simulation on ground to understand the effects of gravity on living animals. Here, we used the zebrafish larvae as a model to study the effect of microgravity simulation on bone formation and whole genome gene expression. To simulate microgravity (sim-μg), we used two-dimensional (2D) clinorotation starting at 5 days post fertilization to assess skeletal formation after 5 days of treatment. To assess early, regulatory effects on gene expression, a single day clinorotation was performed. Clinorotation for 5 days caused a significant decrease of bone formation, as shown by staining for cartilage and bone structures. This effect was not due to stress, as assessed by measuring cortisol levels in treated larvae. Gene expression results indicate that 1-day simulated microgravity affected musculoskeletal, cardiovascular, and nuclear receptor systems. With free-swimming model organisms such as zebrafish larvae, the 2D clinorotation setup appears to be a very appropriate approach to sim-μg. We provide evidence for alterations in bone formation and other important biological functions; in addition several affected genes and pathways involved in bone, muscle or cardiovascular development are identified.
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8
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Peng H, Zhou J, Zhou Z, Bria A, Li Y, Kleissas DM, Drenkow NG, Long B, Liu X, Chen H. Bioimage Informatics for Big Data. ADVANCES IN ANATOMY, EMBRYOLOGY, AND CELL BIOLOGY 2016; 219:263-72. [PMID: 27207370 DOI: 10.1007/978-3-319-28549-8_10] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Bioimage informatics is a field wherein high-throughput image informatics methods are used to solve challenging scientific problems related to biology and medicine. When the image datasets become larger and more complicated, many conventional image analysis approaches are no longer applicable. Here, we discuss two critical challenges of large-scale bioimage informatics applications, namely, data accessibility and adaptive data analysis. We highlight case studies to show that these challenges can be tackled based on distributed image computing as well as machine learning of image examples in a multidimensional environment.
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Affiliation(s)
- Hanchuan Peng
- Allen Institute for Brain Science, Seattle, WA, USA.
| | - Jie Zhou
- Department of Computer Science, Northern Illinois University, Dekalb, IL, USA
| | - Zhi Zhou
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Alessandro Bria
- Department of Engineering, University Campus Bio-Medico of Rome, Rome, Italy.,Department of Electrical and Information Engineering, University of Cassino and L.M., Cassino, Italy
| | - Yujie Li
- Allen Institute for Brain Science, Seattle, WA, USA.,Department of Computer Science, University of Georgia, Athens, GA, USA
| | | | - Nathan G Drenkow
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD, USA
| | - Brian Long
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Xiaoxiao Liu
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Hanbo Chen
- Allen Institute for Brain Science, Seattle, WA, USA.,Department of Computer Science, University of Georgia, Athens, GA, USA
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9
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Longuespée R, Alberts D, Pottier C, Smargiasso N, Mazzucchelli G, Baiwir D, Kriegsmann M, Herfs M, Kriegsmann J, Delvenne P, De Pauw E. A laser microdissection-based workflow for FFPE tissue microproteomics: Important considerations for small sample processing. Methods 2015; 104:154-62. [PMID: 26690073 DOI: 10.1016/j.ymeth.2015.12.008] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 12/09/2015] [Accepted: 12/12/2015] [Indexed: 11/29/2022] Open
Abstract
Proteomic methods are today widely applied to formalin-fixed paraffin-embedded (FFPE) tissue samples for several applications in research, especially in molecular pathology. To date, there is an unmet need for the analysis of small tissue samples, such as for early cancerous lesions. Indeed, no method has yet been proposed for the reproducible processing of small FFPE tissue samples to allow biomarker discovery. In this work, we tested several procedures to process laser microdissected tissue pieces bearing less than 3000 cells. Combined with appropriate settings for liquid chromatography mass spectrometry-mass spectrometry (LC-MS/MS) analysis, a citric acid antigen retrieval (CAAR)-based procedure was established, allowing to identify more than 1400 proteins from a single microdissected breast cancer tissue biopsy. This work demonstrates important considerations concerning the handling and processing of laser microdissected tissue samples of extremely limited size, in the process opening new perspectives in molecular pathology. A proof of the proposed method for biomarker discovery, with respect to these specific handling considerations, is illustrated using the differential proteomic analysis of invasive breast carcinoma of no special type and invasive lobular triple-negative breast cancer tissues. This work will be of utmost importance for early biomarker discovery or in support of matrix-assisted laser desorption/ionization (MALDI) imaging for microproteomics from small regions of interest.
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Affiliation(s)
- Rémi Longuespée
- Mass Spectrometry Laboratory, Systems Biology and Chemical Biology, GIGA-Research, University of Liège, Liège, Belgium; Proteopath GmbH, Trier, Germany.
| | - Deborah Alberts
- Mass Spectrometry Laboratory, Systems Biology and Chemical Biology, GIGA-Research, University of Liège, Liège, Belgium
| | - Charles Pottier
- Department of Pathology, University of Liège Hospital, Liege, Belgium; GIGA Cancer, University of Liège, Liège, Belgium
| | - Nicolas Smargiasso
- Mass Spectrometry Laboratory, Systems Biology and Chemical Biology, GIGA-Research, University of Liège, Liège, Belgium
| | - Gabriel Mazzucchelli
- Mass Spectrometry Laboratory, Systems Biology and Chemical Biology, GIGA-Research, University of Liège, Liège, Belgium
| | | | - Mark Kriegsmann
- Institute of Pathology, University of Heidelberg, Heidelberg, Germany
| | - Michael Herfs
- Department of Pathology, University of Liège Hospital, Liege, Belgium; GIGA Cancer, University of Liège, Liège, Belgium
| | - Jörg Kriegsmann
- Proteopath GmbH, Trier, Germany; MVZ for Histology, Cytology and Molecular Diagnostics Trier, Trier, Germany
| | - Philippe Delvenne
- Department of Pathology, University of Liège Hospital, Liege, Belgium; GIGA Cancer, University of Liège, Liège, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, Systems Biology and Chemical Biology, GIGA-Research, University of Liège, Liège, Belgium
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10
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Evaluation of BRCA1-related molecular features and microRNAs as prognostic factors for triple negative breast cancers. BMC Cancer 2015; 15:755. [PMID: 26490435 PMCID: PMC4618357 DOI: 10.1186/s12885-015-1740-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 10/08/2015] [Indexed: 01/03/2023] Open
Abstract
Background The BRCA1 gene plays a key role in triple negative breast cancers (TNBCs), in which its expression can be lost by multiple mechanisms: germinal mutation followed by deletion of the second allele; negative regulation by promoter methylation; or miRNA-mediated silencing. This study aimed to establish a correlation among the BRCA1-related molecular parameters, tumor characteristics and clinical follow-up of patients to find new prognostic factors. Methods BRCA1 protein and mRNA expression was quantified in situ in the TNBCs of 69 patients. BRCA1 promoter methylation status was checked, as well as cytokeratin 5/6 expression. Maintenance of expressed BRCA1 protein interaction with BARD1 was quantified, as a marker of BRCA1 functionality, and the tumor expression profiles of 27 microRNAs were determined. Results miR-548c-5p was emphasized as a new independent prognostic factor in TNBC. A combination of the tumoral expression of miR-548c and three other known prognostic parameters (tumor size, lymph node invasion and CK 5/6 expression status) allowed for relapse prediction by logistic regression with an area under the curve (AUC) = 0.96. BRCA1 mRNA and protein in situ expression, as well as the amount of BRCA1 ligated to BARD1 in the tumor, lacked any associations with patient outcomes, likely due to high intratumoral heterogeneity, and thus could not be used for clinical purposes. Conclusions In situ BRCA1-related expression parameters could be used for clinical purposes at the time of diagnosis. In contrast, miR-548c-5p showed a promising potential as a prognostic factor in TNBC. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1740-9) contains supplementary material, which is available to authorized users.
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Abstract
Background Histology images comprise one of the important sources of knowledge for phenotyping studies in systems biology. However, the annotation and analyses of histological data have remained a manual, subjective and relatively low-throughput process. Results We introduce Graph based Histology Image Explorer (GRAPHIE)-a visual analytics tool to explore, annotate and discover potential relationships in histology image collections within a biologically relevant context. The design of GRAPHIE is guided by domain experts' requirements and well-known InfoVis mantras. By representing each image with informative features and then subsequently visualizing the image collection with a graph, GRAPHIE allows users to effectively explore the image collection. The features were designed to capture localized morphological properties in the given tissue specimen. More importantly, users can perform feature selection in an interactive way to improve the visualization of the image collection and the overall annotation process. Finally, the annotation allows for a better prospective examination of datasets as demonstrated in the users study. Thus, our design of GRAPHIE allows for the users to navigate and explore large collections of histology image datasets. Conclusions We demonstrated the usefulness of our visual analytics approach through two case studies. Both of the cases showed efficient annotation and analysis of histology image collection.
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Aceto J, Nourizadeh-Lillabadi R, Marée R, Dardenne N, Jeanray N, Wehenkel L, Aleström P, van Loon JJWA, Muller M. Zebrafish Bone and General Physiology Are Differently Affected by Hormones or Changes in Gravity. PLoS One 2015; 10:e0126928. [PMID: 26061167 PMCID: PMC4465622 DOI: 10.1371/journal.pone.0126928] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 04/09/2015] [Indexed: 11/18/2022] Open
Abstract
Teleost fish such as zebrafish (Danio rerio) are increasingly used for physiological, genetic and developmental studies. Our understanding of the physiological consequences of altered gravity in an entire organism is still incomplete. We used altered gravity and drug treatment experiments to evaluate their effects specifically on bone formation and more generally on whole genome gene expression. By combining morphometric tools with an objective scoring system for the state of development for each element in the head skeleton and specific gene expression analysis, we confirmed and characterized in detail the decrease or increase of bone formation caused by a 5 day treatment (from 5dpf to 10 dpf) of, respectively parathyroid hormone (PTH) or vitamin D3 (VitD3). Microarray transcriptome analysis after 24 hours treatment reveals a general effect on physiology upon VitD3 treatment, while PTH causes more specifically developmental effects. Hypergravity (3g from 5dpf to 9 dpf) exposure results in a significantly larger head and a significant increase in bone formation for a subset of the cranial bones. Gene expression analysis after 24 hrs at 3g revealed differential expression of genes involved in the development and function of the skeletal, muscular, nervous, endocrine and cardiovascular systems. Finally, we propose a novel type of experimental approach, the "Reduced Gravity Paradigm", by keeping the developing larvae at 3g hypergravity for the first 5 days before returning them to 1g for one additional day. 5 days exposure to 3g during these early stages also caused increased bone formation, while gene expression analysis revealed a central network of regulatory genes (hes5, sox10, lgals3bp, egr1, edn1, fos, fosb, klf2, gadd45ba and socs3a) whose expression was consistently affected by the transition from hyper- to normal gravity.
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Affiliation(s)
- Jessica Aceto
- Laboratory for Organogenesis and Regeneration, GIGA- Research, University of Liège, B-4000, Liège, Sart-Tilman, Belgium
| | | | - Raphael Marée
- GIGA & Department of Electrical Engineering and Computer Science, University of Liège, Liège, Belgium
| | - Nadia Dardenne
- Unité de soutien méth. en Biostatistique et Epidémiologie, University of Liège, B23, Sart Tilman, Liège, Belgium
| | - Nathalie Jeanray
- Laboratory for Organogenesis and Regeneration, GIGA- Research, University of Liège, B-4000, Liège, Sart-Tilman, Belgium
| | - Louis Wehenkel
- GIGA & Department of Electrical Engineering and Computer Science, University of Liège, Liège, Belgium
| | - Peter Aleström
- BasAM, Norwegian University of Life Sciences, Vetbio, 0033 Dep, Oslo, Norway
| | - Jack J. W. A. van Loon
- DESC (Dutch Experiment Support Center), Department of Oral and Maxillofacial Surgery / Oral Pathology, VU University Medical Center & Academic Centre for Dentistry Amsterdam (ACTA), Amsterdam, The Netherlands
- ESA-ESTEC, TEC-MMG, NL-2200 AG, Noordwijk, The Netherlands
| | - Marc Muller
- Laboratory for Organogenesis and Regeneration, GIGA- Research, University of Liège, B-4000, Liège, Sart-Tilman, Belgium
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