A Java tool for dynamic web-based 3D visualization of anatomy and overlapping gene or protein expression patterns

Abstract Background Epstein-Barr virus-associated gastric cancer (EBVaGC) is the most common EBV-related malignancy. A comprehensive research for the protein expression patterns in EBVaGC established by high-throughput assay remains lacking. In the present study, the protein profile in EBVaGC tissue was explored and related functional analysis was performed. Methods Epstein-Barr virus-encoded RNA (EBER) in situ hybridization (ISH) was applied to EBV detection in GC cases. Data-independent acquisition (DIA) mass spectrometry (MS) was performed for proteomics assay of EBVaGC. Functional analysis of identified proteins was conducted with bioinformatics methods. Immunohistochemistry (IHC) staining was employed to detect protein expression in tissue. Results The proteomics study for EBVaGC was conducted with 7 pairs of GC cases. A total of 137 differentially expressed proteins in EBV-positive GC group were identified compared with EBV-negative GC group. A PPI network was constructed for all of them, and several proteins with relatively high interaction degrees could be the hub genes in EBVaGC. Gene enrichment analysis showed they might be involved in the biological pathways related to energy and biochemical metabolism. Combined with GEO datasets, a highly associated protein (GBP5) with EBVaGC was screened out and validated with IHC staining. Further analyses demonstrated that GBP5 protein might be associated with clinicopathological parameters and EBV infection in GC. Conclusions The newly identified proteins with significant differences and potential central roles could be applied as diagnostic markers of EBVaGC. Our study would provide research clues for EBVaGC pathogenesis as well as novel targets for the molecular-targeted therapy of EBVaGC.

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Dynamic gene and protein expression patterns of the autism-associated met receptor tyrosine kinase in the developing mouse forebrain

The Journal of Comparative Neurology ◽

10.1002/cne.21969 ◽

2009 ◽

Vol 513 (5) ◽

pp. 511-531 ◽

Cited By ~ 47

Author(s):

Matthew C. Judson ◽

Mica Y. Bergman ◽

Daniel B. Campbell ◽

Kathie L. Eagleson ◽

Pat Levitt

Keyword(s):

Protein Expression ◽

Tyrosine Kinase ◽

Receptor Tyrosine Kinase ◽

Expression Patterns ◽

Met Receptor ◽

Met Receptor Tyrosine Kinase ◽

Gene And Protein Expression

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Immunohistochemical Analysis of GDNF and Its Cognate Receptor GFRα-1 Protein Expression in Vitiliginous Skin Lesions

Journal of Cutaneous Medicine and Surgery ◽

10.1177/1203475415601828 ◽

2015 ◽

Vol 20 (2) ◽

pp. 130-134 ◽

Cited By ~ 1

Author(s):

Mohamed A. Adly ◽

Hanan A. Assaf ◽

Shaima’a F. Abdel-Rady ◽

Nagwa Sayed Ahmed ◽

Mahmoud Rezk Abdelwahed Hussein

Keyword(s):

Protein Expression ◽

Basal Cell ◽

Cell Layer ◽

Expression Patterns ◽

Granular Cell ◽

Epidermal Keratinocytes ◽

Healthy Skin ◽

Granular Cell Layer ◽

Cognate Receptor ◽

Spinous Layer

Background: Vitiligo is an idiopathic skin disease, characterized by circumscribed white macules or patches on the skin due to loss of the functional melanocytes. Glial cell line–derived neurotrophic factor (GDNF) and its cognate receptor (GFRα-1) are distal members of the transforming growth factor-β superfamily. GDNF, produced by the basal cell keratinocytes, is involved in the migration and differentiation of the melanocytes from the neural crest to the epidermis. This study examines the hypothesis that expression of GDNF protein and its cognate receptor GFRα-1 protein is altered in vitiliginous skin. Patients and Methods: To test our hypothesis, we examined the expression patterns of these proteins in vitiliginous and corresponding healthy (control) skin biopsies (20 specimens each) using immunoperoxidase staining techniques. Results: We found variations between the vitiliginous skin and healthy skin. In healthy skin, the expression of GDNF and GFRα-1 proteins was strong (basal cell keratinocytes and melanocytes), moderate (spinous layer), and weak (granular cell layer). In contrast, weak expression of GDNF protein was observed in all epidermal layers of vitiliginous skin. GFRα-1 protein expression was strong (basal cell keratinocytes and melanocytes), moderate (spinous layer), and weak (granular cell layer). In both healthy skin and vitiliginous skin, the expression of GDNF and GFRα-1 proteins was strong in the adnexal structures. Conclusions: We report, for the first time, decreased expression of GDNF proteins in the epidermal keratinocytes of vitiliginous skin. Our findings suggest possible pathogenetic roles for these proteins in the development of vitiligo. The clinical ramifications of these observations mandate further investigations.

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Protein expression patterns of identified neurons and of sprouting cells from the leech central nervous system

Journal of Neurobiology ◽

10.1002/1097-4695(20000905)44:3<320::aid-neu3>3.0.co;2-4 ◽

2000 ◽

Vol 44 (3) ◽

pp. 320-332 ◽

Cited By ~ 7

Author(s):

Xueqing Wu ◽

Barbara Ritter ◽

Jan Henrik Schlattjan ◽

Volkmar Lessmann ◽

Rolf Heumann ◽

...

Keyword(s):

Central Nervous System ◽

Nervous System ◽

Protein Expression ◽

Expression Patterns ◽

Identified Neurons

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Tissue ischemia time affects gene and protein expression patterns within minutes following surgical tumor excision

BioTechniques ◽

10.2144/04366rr04 ◽

2004 ◽

Vol 36 (6) ◽

pp. 1030-1037 ◽

Cited By ~ 167

Author(s):

Annika Spruessel ◽

Garnet Steimann ◽

Mira Jung ◽

Sung A. Lee ◽

Theresa Carr ◽

...

Keyword(s):

Protein Expression ◽

Expression Patterns ◽

Tumor Excision ◽

Ischemia Time ◽

Tissue Ischemia ◽

Gene And Protein Expression

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IMP3 Protein Overexpression Is Linked to Unfavorable Outcome in Laryngeal Squamous Cell Carcinoma

Cancers ◽

10.3390/cancers13174306 ◽

2021 ◽

Vol 13 (17) ◽

pp. 4306

Author(s):

Diana Maržić ◽

Blažen Marijić ◽

Tamara Braut ◽

Stefan Janik ◽

Manuela Avirović ◽

...

Keyword(s):

Squamous Cell Carcinoma ◽

Protein Expression ◽

Cell Carcinoma ◽

Cyclin D1 ◽

Squamous Cell ◽

Expression Patterns ◽

Low Grade ◽

Benign Lesions ◽

Ki 67 ◽

Neck Node

Background: The aim of this study was to (i) determine IMP3 protein expression in benign and malignant laryngeal lesions, (ii) compare its expression to Ki-67, p53, cyclin D1, and (iii) finally, to examine the prognostic power of IMP3 in squamous cell carcinomas of the larynx (LSSC). Methods: IMP3 protein expression was evaluated in 145 patients, including 62 LSCC, 45 dysplasia (25 with low and 20 with high-grade dysplasia), and 38 benign lesions (vocal cord polyps and nodules). Results: IMP3 was significantly higher expressed in LSCC compared to dysplasia and benign lesions (p < 0.001; p < 0.001, respectively). Similarly, higher expression patterns were observed for Ki-67 and p53, whereas cyclin D1 was equally distributed in all three lesions. IMP3 (p = 0.04) and Ki-67 (p = 0.02) expressions were significantly linked to neck node positivity, and IMP3 overexpression to worse disease-specific survival (p = 0.027). Conclusion: Since IMP3 showed significantly higher expression in laryngeal carcinomas, but not in high- or low-grade dysplasia, it serves as a useful marker to differentiate between invasive and noninvasive lesions. Higher IMP3 expression represented a significantly worse prognosticator for clinical outcomes of patients with squamous cell carcinoma of the larynx.

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Cell signaling pathways in human mutant PAX6 corneal cells: an in vitro model for aniridia-related keratopathy

10.1101/2021.03.19.436143 ◽

2021 ◽

Author(s):

Marta Słoniecka ◽

André Vicente ◽

Berit Byström ◽

Fátima Pedrosa Domellöf

Keyword(s):

Protein Expression ◽

Signaling Pathways ◽

Cell Fate ◽

Expression Patterns ◽

Pax6 Gene ◽

Cas9 Nuclease ◽

Extracellular Matrix Components ◽

Gene And Protein Expression ◽

Human Keratocytes

ABSTRACTPURPOSETo establish an in vitro model of aniridia-related keratopathy (ARK) using CRISPR/Cas9 engineered human keratocytes with mutations in the PAX6 gene, and to study the Notch Homolog 1, Translocation-Associated (Notch1), sonic hedgehog (SHH), mammalian target of rapamycin (mTOR), and Wnt/β-catenin signaling pathways in the PAX6 mutant keratocytes.METHODSPrimary human keratocytes were isolated from healthy corneas. Keratocytes were transduced with Cas9 lentiviral particles in order to create cells stably expressing Cas9 nuclease. Lentiviral particles carrying PAX6 sgRNA were transduced into the Cas9 keratocytes creating mutants. Analysis of signaling pathways was assessed by RT-qPCR for gene expression and western blot for protein expression.RESULTSHuman keratocytes stably expressing Cas9 nuclease were created. Keratocytes carrying PAX6 gene mutation were successfully generated. PAX6 mutant keratocytes showed modified expression patterns of extracellular matrix components such as collagens and fibrotic markers. Analysis of the Notch1, SHH, mTOR, and Wnt/β-catenin signaling pathways in the PAX6 mutant keratocytes revealed altered gene and protein expression of the key players involved in these pathways.CONCLUSIONSA properly functioning PAX6 gene in keratocytes is crucial for the regulation of signaling pathways important for cell fate determination, proliferation, and inflammation. Pax6 mutation in the in vitro settings leads to changes in these pathways which resemble those found in corneas of patients with ARK.

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