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Expression Profiling of Cassava Storage Roots Reveals an Active Process of Glycolysis/Gluconeogenesis

Journal of Integrative Plant Biology 2011年第3期53卷 193-211页

作者： Jun Yang Dong An Peng Zhang Shanghai Center for Cassava Biotechnology National Laboratory of Plant Molecular Genetics Institute of Plant Physiology & Ecology Shanghai Institutes for Biological Sciences the Chinese Academy of Sciences Shanghai 200032 China Key Laboratory of Synthetic Biology Institute of Plant Physiology & Ecology Shanghai Institutes for Biological Sciences the Chinese Academy of Sciences Shanghai 200032 China Shanghai Chenshan Plant Science Research Center the Chinese Academy of Sciences Chenshan Botanical Garden Shanghai 201602 China

Mechanisms related to the development of cassava storage roots and starch accumulation remain largely unknown. To evaluate genome-wide expression patterns during tuberization, a 60 mer oligonucleotide microarray representing 20 840 cassawl genes was designed to identify differentially expressed transcripts in fibrous roots, developing storage roots and mature storage roots. Using a random variance model and the traditional twofold change method for statistical analysis, 912 and 3 386 upregulated and downregulated genes related to the three developmental phases were identified. Among 25 significantly changed pathways identified, glycolysis/gluconeogenesis was the most evident one. Rate-limiting enzymes were identified from each individual pathway, for example, enolase, L-lactate dehydrogenase and aldehyde dehydrogenase for glycolysis/gluconeogenesis, and ADP-glucose pyrophosphorylase, starch branching enzyme and glucan phosphorylase for sucrose and starch metabolism. This study revealed that dynamic changes in at least 16% of the total transcripts, including transcription fac- tors, oxidoreductases/transferases/hydrolases, hormone-related genes, and effectors of homeostasis. The reliability of these differentially expressed genes was verified by quantitative real-time reverse transcription-polymerase chain reaction. Tlhese studies should facilitate our understanding of the storage root formation and cassava improvement.

关键词： CASSAVA ROOTS (Botany) -- Formation GLYCOLYSIS GLUCONEOGENESIS LACTATE dehydrogenase REVERSE transcriptase polymerase chain reaction PLANT gene expression oligonucleotide arrays

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Identification of osteopontin as the most consistently over-expressed gene in intrahepatic cholangiocarcinoma: Detection by oligonucleotide microarray and real-time PCR analysis

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World Journal of Gastroenterology 2008年第16期14卷 2501-2510页

作者： Holger G Hass Oliver Nehls Juergen Jobst Andrea Frilling Ulrich Vogel Stephan Kaiser Department of Oncology Hematology and Palliative Care Marien Hospital Stuttgart Department of Hematology Oncology and Rheumatology University of Tuebingen Matrigene GmbH Company Reutlingen Department of Abdominal and Transplant Surgery University of Essen Department of Pathology University of Tuebingen Department of Gastroenterology Hepatology and Infectious Diseases University of Tuebingen

AIM: To investigate the molecular pathways involved in human cholangiocarcinogenesis by gene expression profiling. METHODS: oligonucleotide arrays (Affymetrix U133A) were used to establish a specific gene expression profile of intrahepatic CCC in comparison to corresponding non- malignant liver tissue. To validate the expression values of the most overexpressed genes, RT-PCR experiments were performed. RESULTS: Five hundred and fifty-two statistically differentially expressed genes/ESTs (221 probes significantly up-regulated, 331 probes down-regulated; P 2; ≥ 70%) were identified. Using these data and two-dimensional cluster analysis,a specific gene expression profile was obtained allowing fast and reproducible differentiation of CCC, which was confirmed by supervised neuronal network modelling. The most consistently overexpressed gene (median fold change 33.5, significantly overexpressed in 100%) encoded osteopontin. Furthermore, an association of various genes with the histopathological grading could be demonstrated. CONCLUSION: A highly specific gene expression profile for intrahepatic CCC was identified, allowing for its fast and reproducible discrimination against non- malignant liver tissue and other liver masses. The most overexpressed gene in intrahepatic CCC was the gene encoding osteopontin. These data may lead to a better understanding of human cholangiocarcinogenesis.

关键词： Cholangiocarcinoma oligonucleotide arrays Osteopontin Cell cycle regulation Gene expression

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