Transcriptome-based gene expression profiling identifies differentially expressed genes critical for salt stress response in radish (Raphanus sativus L.)

2015 ◽  
Vol 35 (2) ◽  
pp. 329-346 ◽  
Author(s):  
Xiaochuan Sun ◽  
Liang Xu ◽  
Yan Wang ◽  
Xiaobo Luo ◽  
Xianwen Zhu ◽  
...  
2018 ◽  
Vol 2018 ◽  
pp. 1-10 ◽  
Author(s):  
Nan Liu ◽  
Yunyao Jiang ◽  
Min Xing ◽  
Baixiao Zhao ◽  
Jincai Hou ◽  
...  

Aging is closely connected with death, progressive physiological decline, and increased risk of diseases, such as cancer, arteriosclerosis, heart disease, hypertension, and neurodegenerative diseases. It is reported that moxibustion can treat more than 300 kinds of diseases including aging related problems and can improve immune function and physiological functions. The digital gene expression profiling of aged mice with or without moxibustion treatment was investigated and the mechanisms of moxibustion in aged mice were speculated by gene ontology and pathway analysis in the study. Almost 145 million raw reads were obtained by digital gene expression analysis and about 140 million (96.55%) were clean reads. Five differentially expressed genes with an adjusted P value < 0.05 and |log⁡2(fold  change)| > 1 were identified between the control and moxibustion groups. They were Gm6563, Gm8116, Rps26-ps1, Nat8f4, and Igkv3-12. Gene ontology analysis was carried out by the GOseq R package and functional annotations of the differentially expressed genes related to translation, mRNA export from nucleus, mRNA transport, nuclear body, acetyltransferase activity, and so on. Kyoto Encyclopedia of Genes and Genomes database was used for pathway analysis and ribosome was the most significantly enriched pathway term.


Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 5201-5201
Author(s):  
Chieh Lee Wong ◽  
Baoshan Ma ◽  
Gareth Gerrard ◽  
Martyna Adamowicz-Brice ◽  
Zainul Abidin Norziha ◽  
...  

Abstract Background The past decade has witnessed a significant progress in the understanding of the molecular pathogenesis of myeloproliferative neoplasms (MPN). A large number of genes have now been implicated in the pathogenesis of MPN but their relative importance, the mechanisms by which they cause different cell types to predominate and their implications for prognosis remain unknown. We hypothesized that there are other genes which may contribute to the pathogenesis of the different disease subtypes detectable only by cell-type specific analysis. Aim The aim of this study was to perform gene expression profiling on different cell types from patients with MPN in order to identify novel variants and driver mutations, to elucidate the pathogenesis and to identify predictors of survival in patients with MPN in a multiracial country. Methods We performed gene expression profiling on normal controls (NC) and patients with MPN from 3 different races (Malay, Chinese and Indian) in Malaysia who were diagnosed with essential thrombocythemia (ET), polycythemia vera (PV) and primary myelofibrosis (PMF) according to the 2008 WHO diagnostic criteria for MPN. Two cohorts of patients, the patient and validation cohorts, from 3 tertiary-level hospitals were recruited prospectively over 3 years and informed consents were obtained. Peripheral blood samples were taken and sorted into polymorphonuclear cells (PMNs), mononuclear cells (MNCs) and T cells. RNA was extracted from each cell population. Gene expression profiling was performed using the Illumina HumanHT-12 Expression Beadchip for microarray and the Illumina Nextera XT DNA Sample Preparation Kit for next generation sequencing on the patient and validation cohorts respectively. Results Twenty-eight patients (10 ET, 11 PV and 7 PMF) and 11 NC were recruited into the patient cohort. Twelve patients (4 ET, 4 PV and 4 PMF) and 4 NC were recruited into the validation cohort. Gene expression levels for each cell type in each disease were compared with NC. In the patient cohort, the number of differentially expressed genes in ET, PV and PMF was 0, 141 and 15 respectively for PMNs (p < 0.05 after multiple testing correction) and 5, 170 and 562 respectively for MNCs (p < 0.05). No differentially expressed genes were identified for T cells in any of the three disease groups. RNA-seq analysis of samples from the validation cohort was used to corroborate these findings. After combination, we were able to confirm differential expression of 0, 14 and 7 genes in ET, PV and PMF respectively for PMNs (p < 0.05) and 51 genes in only PMF for MNCs (p < 0.05). The validated differentially expressed genes for PMNs and MNCs were mutually exclusive except for one gene. The differentially expressed genes in PV and PMF for PMNs were involved in cellular processes and metabolic pathways whereas the differentially expressed genes for PMF in MNCs were involved in regulation of cytoskeleton, focal adhesion and cell signaling pathways. Conclusion This is the first study to use microarray and next generation sequencing techniques to compare cell type-specific expression of genes between different subtypes of MPN. The lack of differential expression in T cells validates the techniques used and indicates that they are not part of the neoplastic clone. Differential expression of genes for MNCs was seen only in PMF which may be related to their more severe phenotype. Interestingly, there were fewer differentially expressed genes in PMF compared to PV for PMNs. The lack of differential expression in ET may either reflect the relatively milder phenotype of the disease or that differential expression is limited to megakaryocytes-platelets which were not studied. The lists of mutually exclusive cell type-specific differentially expressed genes for PMNs and MNCs provide further insight into the pathogenesis of MPN and into the differences between its different forms. The identified genes also indicate further routes for investigation of pathogenesis and possible disease-specific targets for therapy. Disclosures Aitman: Illumina: Honoraria.


Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 2938-2938
Author(s):  
Frank Dicker ◽  
Susanne Schnittger ◽  
Claudia Schoch ◽  
Alexander Kohlmann ◽  
Wei-Min Liu ◽  
...  

Abstract The lack of somatic mutations of the immunoglobulin variable heavy chain (IgVH) gene has been established as poor prognostic marker for chronic lymphocytic leukemia (CLL) patients at early stage disease. Expression of the non receptor tyrosine kinase zeta chain associated protein (ZAP-70) was proposed as a surrogate marker for an unmutated IgVH, however, up to 30% discordant samples have been reported depending on the respective study. B cell receptor (BCR) mediated signaling is enhanced by ZAP-70 expression in CLL cells in vitro and ZAP-70 expression also tends to decrease the time from diagnosis to treatment irrespective of the IgVH status. Therefore, we wanted to identify differentially expressed genes between the ZAP-70 positive and negative CLLs by gene expression profiling of peripheral blood mononuclear cells (PBMCs) using Affymetrix microarrays (HG-U133 Plus 2.0). ZAP-70 expression was analyzed by quantitative real time PCR of CD19 purified (purity &gt; 99%) PBMCs (n=62) using a LightCycler instrument. Expression of ZAP-70 mRNA was normalized against the housekeeping gene ABL and a relative quantitation against Jurkat T cells as a calibrator was performed. Results are expressed as normalized ratio and a cut-off of 0.5 normalized ratio gave the best correlation to the IgVH status with 77% concordant samples between ZAP-70 expression and the IgVH status. The discordant samples consisted of 5 unmutated IgVHs in the ZAP-70 negative group and 9 mutated in the ZAP-70 positive group. In a second step PBMCs of the same samples were analyzed by gene expression profiling and differentially expressed genes were identified by t-test. Among the two best genes that could be used in a classification algorithm (SVM) to distinguish between the 2 subsets with 92% accuracy were ZAP-70 and B cell scaffold protein with ankyrin repeats (BANK1). The expression of BANK1 was increased 3–4-fold in the ZAP-70 negative compared to the ZAP-70 positive CLL subset (P = 0,001). In the literature, BANK1 has been identified in human BCR expressing B cells and seems to be B cell restricted. In B cells the scaffolding protein BANK1 enhances BCR-mediated Ca2+-signaling, a signaling pathway that is also enhanced by ZAP-70 expression in CLL B cells. Based on these data we show that increased BANK1 expression correlates with a ZAP-70 negative status in CLL B cells. The functional consequences of BANK1 expression in the ZAP-70 negative subset of CLL B cells, which are usually associated with a more favorable prognosis, still need to be established further.


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