scholarly journals Identification of Differentially Expressed Genes in Metastatic and Non-Metastatic Nasopharyngeal Carcinoma Cells by Suppression Subtractive Hybridization

2005 ◽  
Vol 27 (4) ◽  
pp. 215-223
Author(s):  
Xu-Yu Yang ◽  
Cai-Ping Ren ◽  
Lei Wang ◽  
Hui Li ◽  
Chun-Jie Jiang ◽  
...  
Keyword(s):  
Nasopharyngeal Carcinoma ◽  
Ribosomal Proteins ◽  
Southern China ◽  
Early Stage ◽  
Subtractive Hybridization ◽  
Northern Blotting ◽  
Differentially Expressed ◽  
Treatment Modalities ◽  
Damage Repair ◽  
Reverse Northern

Background & Objective: Nasopharyngeal carcinoma (NPC) is an epithelial neoplasm with high occurrence rates in southern China. The disease often metastasizes to regional lymphnodes at a very early stage. Local recurrences and metastasis occur frequently in patients with NPC and are a leading cause of death, despite improvements on treatment modalities. The molecular mechanism underlying the metastasis of nasopharyngeal carcinoma remains poorly understood, however, and requires additional elucidation. The aim of this study was to explore possible NPC gene candidates that may play key roles in NPC metastasis. Methods: Subtractive suppression hybridization (SSH) was performed to isolate differentially expressed clones between the metastatic 5-8F and non-metastatic 6-10B nasopharyngeal carcinoma cell lines. Differentially expressed clones were screened and confirmed by reverse Northern blotting. The sequences of cDNA fragments were subsequently analyzed and compared to known sequences in Genbank. Results & Discussion: The SSH library contained thousands of positive clones. Random analysis of 300 clones by PCR demonstrated that 269 clones contained inserted fragments. Reverse Northern blot confirmed that 20 out of 192 clones examined were significantly up-regulated in the 5-8F cell line. Among these 20 clones, 16 were previously identified genes (flotilin-2, ezrin, pim-3, fli-1, mel, neugrin, znf216, ASB1, raly, UBE2A, keratin6A, TMED7, EIF3S9, FTL, two ribosomal proteins RPL21 and RPL16), two were predicted genes (c9orf74 and MDS006), and two sequences shared no homology with known genes listed in GenBank and may represent novel genes. The proposed functions of the genes identified in this study include cell signal transduction, cell survival, transcription regulation, cell mobility, protein synthesis, and DNA damage repair. Flotillin-2, fli-1, pim-3 and ezrin have previously been reported to be associated with tumor metastasis and progression. The remaining up-regulated genes identified in this study have not been reported to be markers of metastasis and may represent new candidates of NPC metastasis-related genes. The Results of this study may provide novel points of therapeutic intervention for NPC.

scholarly journals Cloning of a Gene Encoding an Alt a 1 Isoallergen Differentially Expressed by the Necrotrophic Fungus Alternaria brassicicola during Arabidopsis Infection

2003 ◽  
Vol 69 (4) ◽  
pp. 2361-2364 ◽  
Author(s):  
Robert A. Cramer ◽  
Christopher B. Lawrence
Keyword(s):  
Suppression Subtractive Hybridization ◽  
Subtractive Hybridization ◽  
Northern Blotting ◽  
Infection Process ◽  
Differentially Expressed ◽  
Alternaria Brassicicola ◽  
Phytopathogenic Fungus ◽  
Northern Blots ◽  
Gene Encoding ◽  
Reading Frame

ABSTRACT Alternaria species are considered some of the most important fungi responsible for allergenic morbidity in humans. The Alternaria protein that elicits the most intense allergic reaction in humans is Alt a 1, yet no biological function has been identified for this protein. In this study, suppression subtractive hybridization and virtual Northern blots were used to identify and characterize an Alt a 1 homolog in the phytopathogenic fungus Alternaria brassicicola. RNA was extracted from A. brassicicola spores germinated in water and on leaf surfaces of the Arabidopsis ecotype Landsberg for 24 h and used to create cDNA by PCR. Double-stranded cDNA was then used in suppression subtractive hybridization to identify differentially expressed genes. mRNA transcript levels were assessed by virtual Northern blotting. A sequence with significant homology (90% amino acid, 92% cDNA) to the Alt a 1 subunit from Alternaria alternata was identified. Virtual Northern blots demonstrated that this homolog, designated Alt b 1 precursor, was highly up-regulated during the infection process of A. brassicicola on Arabidopsis. The full-length cDNA sequence of Alt b 1 was 815 bp, with an open reading frame of 477 bp. In this preliminary study, we identified a homolog of the major Alternaria allergen precursor, Alt a 1, in A. brassicicola, designated Alt b 1. This isoallergen is differentially expressed during fungal pathogenesis on Arabidopsis, suggesting a possible biological role in pathogenesis.

Transcriptomic approach to the study of osmoregulation in the European eelAnguilla anguilla

2007 ◽  
Vol 31 (3) ◽  
pp. 385-401 ◽  
Author(s):  
Svetlana Kalujnaia ◽  
Iain S. McWilliam ◽  
Vitalii A. Zaguinaiko ◽  
Anja L. Feilen ◽  
John Nicholson ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Sea Water ◽  
Subtractive Hybridization ◽  
Northern Blotting ◽  
Differentially Expressed ◽  
Suppressive Subtractive Hybridization ◽  
European Eel ◽  
Sargasso Sea ◽  
Functional Roles ◽  
Physiological Adaptations

In euryhaline teleosts, osmoregulation is a fundamental and dynamic process that is essential for the maintenance of ion and water balance, especially when fish migrate between fresh water (FW) and sea water (SW) environments. The European eel has proved to be an excellent model species to study the molecular and physiological adaptations associated with this osmoregulatory plasticity. The life cycle of the European eel includes two migratory periods, the second being the migration of FW eels back to the Sargasso Sea for reproduction. Various anatomical and physiological changes allow the successful transition to SW. The aim of this study was to use a microarray approach to screen the osmoregulatory tissues of the eel for changes in gene expression following acclimation to SW. Tissues were sampled from fish at selected intervals over a 5-mo period following FW/SW transfer, and RNA was isolated. Suppressive subtractive hybridization was used for enrichment of differentially expressed genes. Microarrays comprising 6,144 cDNAs from brain, gill, intestine, and kidney libraries were hybridized with appropriate targets and analyzed; 229 differentially expressed clones with unique sequences were identified. These clones represented the sequences for 95 known genes, with the remaining sequences (59%) being unknown. The results of the microarray analysis were validated by quantification of 28 differentially expressed genes by Northern blotting. A number of the differentially expressed genes were already known to be involved in osmoregulation, but the functional roles of many others, not normally associated with ion or water transport, remain to be characterized.

scholarly journals Host gene expression at an early stage of virus resistance induction

2017 ◽  
Vol 38 (SI 2 - 6th Conf EFPP 2002) ◽  
pp. 502-503
Author(s):  
E. Gammelgård ◽  
M.L. Mohan ◽  
R.A. Andersson ◽  
J.P.T. Valkonen
Keyword(s):  
Gene Expression ◽  
Virus Resistance ◽  
Early Stage ◽  
Blot Hybridization ◽  
Systemic Infection ◽  
Subtractive Hybridization ◽  
Differentially Expressed ◽  
Host Gene Expression ◽  
Resistance Induction ◽  
Potato Virus A

Suppression subtractive hybridization (SSH) was carried out to detect genes differentially expressed in plants expressing resistance to systemic infection with Potato virus A (PVA), genus Potyvirus. Differential screening has up to now revealed 19 putative differentially expressed genes. Nothern blot hybridization has confirmed the differential expression of seven genes. Three of them were only induced by the virus, but four genes were also wound-induced.

scholarly journals Alteration of protein expression and spliceosome pathway activity during Barrett’s carcinogenesis

2021 ◽  
Author(s):  
Christoph Stingl ◽  
Angela Bureo Gonzalez ◽  
Coşkun Güzel ◽  
Kai Yi Nadine Phoa ◽  
Michail Doukas ◽  
...  
Keyword(s):  
Micro Rna ◽  
Differentially Expressed ◽  
Epithelial Tissue ◽  
Label Free ◽  
Tissue Samples ◽  
Damage Repair ◽  
Inter Observer Variability ◽  
Stromal Tissue ◽  
The Face ◽  
Abundance And Diversity

Abstract Background Barrett’s esophagus (BE) is a known precursor lesion and the strongest risk factor for esophageal adenocarcinoma (EAC), a common and lethal type of cancer. Prediction of risk, the basis for efficient intervention, is commonly solely based on histologic examination. This approach is challenged by problems such as inter-observer variability in the face of the high heterogeneity of dysplastic tissue. Molecular markers might offer an additional way to understand the carcinogenesis and improve the diagnosis—and eventually treatment. In this study, we probed significant proteomic changes during dysplastic progression from BE into EAC. Methods During endoscopic mucosa resection, epithelial and stromal tissue samples were collected by laser capture microdissection from 10 patients with normal BE and 13 patients with high-grade dysplastic/EAC. Samples were analyzed by mass spectrometry-based proteomic analysis. Expressed proteins were determined by label-free quantitation, and gene set enrichment was used to find differentially expressed pathways. The results were validated by immunohistochemistry for two selected key proteins (MSH6 and XPO5). Results Comparing dysplastic/EAC to non-dysplastic BE, we found in equal volumes of epithelial tissue an overall up-regulation in terms of protein abundance and diversity, and determined a set of 226 differentially expressed proteins. Significantly higher expressions of MSH6 and XPO5 were validated orthogonally and confirmed by immunohistochemistry. Conclusions Our results demonstrate that disease-related proteomic alterations can be determined by analyzing minute amounts of cell-type-specific collected tissue. Further analysis indicated that alterations of certain pathways associated with carcinogenesis, such as micro-RNA trafficking, DNA damage repair, and spliceosome activity, exist in dysplastic/EAC.

scholarly journals Current Status and Future Perspectives about Molecular Biomarkers of Nasopharyngeal Carcinoma

Cancers ◽  
2021 ◽  
Vol 13 (14) ◽  
pp. 3490
Author(s):  
Pui Yan Siak ◽  
Alan Soo-Beng Khoo ◽  
Chee Onn Leong ◽  
Boon-Peng Hoh ◽  
Shiau-Chuen Cheah
Keyword(s):  
Nasopharyngeal Carcinoma ◽  
Biomarker Discovery ◽  
Southern China ◽  
Disease Diagnosis ◽  
Late Presentation ◽  
Dietary Factors ◽  
Current Status ◽  
Complex Nature ◽  
Epstein Barr Virus Infection ◽  
Potential Biomarker

Nasopharyngeal carcinoma (NPC) is an epithelial malignancy that shows a remarkable ethnic and geographical distribution. It is one of the major public health problems in some countries, especially Southern China and Southeast Asia, but rare in most Western countries. Multifactorial interactions such as Epstein–Barr virus infection, individual’s genetic susceptibility, as well as environmental and dietary factors may facilitate the pathogenesis of this malignancy. Late presentation and the complex nature of the disease have led it to become a major cause of mortality. Therefore, an effective, sensitive, and specific molecular biomarker is urgently needed for early disease diagnosis, prognosis, and prediction of metastasis and recurrence after treatment. In this review, we discuss the recent research status of potential biomarker discovery and the problems that need to be explored further for better NPC management. By studying the aberrant pattern of these candidate biomarkers that promote NPC development and progression, we are able to understand the complexity of this malignancy better, hence positing our stands better towards strategies that may provide a way forward to the discovery of more reliable and specific biomarkers for diagnosis and targeted therapeutic development.

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