Bacterial blight is caused by the pathogen Xanthomonas oryzae pv. oryzae (Xoo). Genome scale integrative analysis on the interaction of high and low temperatures on the molecular response signature ...in rice during the Xoo infection has not been conducted yet. We have analysed a unique RNA-Seq dataset generated on the susceptible rice variety IR24 under combined exposure of Xoo with low 29/21 °C (day/night) and high 35/31 °C (day/night) temperatures. Differentially regulated key genes and pathways in rice plants during both the stress conditions were identified. Differential dynamics of the regulatory network topology showed that WRKY and ERF families of transcription factors play a crucial role during signal crosstalk events in rice plants while responding to combined exposure of Xoo with low temperature vs. Xoo with high temperatures. Our study suggests that upon onset of high temperature, rice plants tend to switch its focus from defence response towards growth and reproduction.
•Differential regulation of the rice transcriptome to Xoo pathogen under normal vs. high temperature was prominent.•Specific genes and pathways in rice regulated by normal and high temperature during Xoo infection were identified.•Upon exposure to high temperature, rice plant shows to shift its focus from defence response towards growth and reproduction.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Biotic and abiotic stresses limit agricultural yields, and plants are often simultaneously exposed to multiple stresses. Combinations of stresses such as heat and drought or cold and high light ...intensity have profound effects on crop performance and yields. Thus, delineation of the regulatory networks and metabolic pathways responding to single and multiple concurrent stresses is required for breeding and engineering crop stress tolerance. Many studies have described transcriptome changes in response to single stresses. However, exposure of plants to a combination of stress factors may require agonistic or antagonistic responses or responses potentially unrelated to responses to the corresponding single stresses. To analyze such responses, we initially compared transcriptome changes in 10 Arabidopsis (Arabidopsis thaliana) ecotypes using cold, heat, high-light, salt, and flagellin treatments as single stress factors as well as their double combinations. This revealed that some 61% of the transcriptome changes in response to double stresses were not predictable from the responses to single stress treatments. It also showed that plants prioritized between potentially antagonistic responses for only 5% to 10% of the responding transcripts. This indicates that plants have evolved to cope with combinations of stresses and, therefore, may be bred to endure them. In addition, using a subset of this data from the Columbia and Landsberg erecta ecotypes, we have delineated coexpression network modules responding to single and combined stresses.
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BFBNIB, NMLJ, NUK, PNG, SAZU, UL, UM, UPUK
We studied how intratumoral genetic heterogeneity shapes tumor growth and therapy response for isocitrate dehydrogenase (IDH)-wild-type glioblastoma, a rapidly regrowing tumor. We inferred the ...evolutionary trajectories of matched pairs of primary and relapsed tumors based on deep whole-genome-sequencing data. This analysis suggests both a distant origin of de novo glioblastoma, up to 7 years before diagnosis, and a common path of early tumorigenesis, with one or more of chromosome 7 gain, 9p loss, or 10 loss, at tumor initiation. TERT promoter mutations often occurred later as a prerequisite for rapid growth. In contrast to this common early path, relapsed tumors acquired no stereotypical pattern of mutations and typically regrew from oligoclonal origins, suggesting sparse selective pressure by therapeutic measures.
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•We inferred evolutionary trajectories of pairs of primary/relapsed glioblastomas•Chromosome 7 gain, 9p loss, or 10 loss commonly occurred at tumor initiation•TERT promoter mutations often occurred later as a prerequisite for rapid growth•Relapsed tumors typically regrew from oligoclonal origins
By analyzing 21 paired primary and locally relapsed IDH-wild-type glioblastomas (GBM), Körber et al. show that most GBM initiate by gains and losses of specific chromosomes; TERT promoter mutations often occur later as a prerequisite for rapid growth, and relapsed GBM acquire few stereotypical mutations.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Gallbladder cancer (GBC) is one of the most fatal malignancies of the biliary tract system and is ranked sixth among the neoplasms of the gastrointestinal tract. Gallstone disease (GSD) is considered ...the major risk factor for GBC. However, the underlying molecular mechanism of GBC pathogenesis from different stages of GSD is not yet clearly understood. We analyzed transcriptomic datasets of GBC with reference to GSD of three different follow-up periods, i.e., GBC vs. GSD3 (1–3 years), GBC vs. GSD5 (5–10 years), and GBC vs. GSD10 (more than 10 years). We identified overlapping and specific molecular signatures in GBC compared with GSD at three different follow-up periods. Using integrative network biology approaches, such as protein–protein interaction network analysis, transcriptional regulatory network analysis, and miRNA–target gene network analysis, we have identified a few hub genes. The hub genes identified from GBC vs. GSD3, GBC vs. GSD5, and GBC vs. GSD10 were directly or indirectly associated with cancer progression and initiation from GSD. Functional enrichment analysis indicated significant correlation between GSD and GBC pathogenesis. The identified hub genes can be used for future targeted validation to develop potential diagnostic, prognostic, or therapeutic biomarkers in GBC.
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DOBA, EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, IZUM, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UILJ, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Glioblastoma multiforme (GBM) is one of the most lethal malignancies of the central nervous system characterized by high mortality rate. The complexity of GBM pathogenesis, progression, and prognosis ...is not fully understood yet. GBM-derived extracellular vesicles (EVs) carry several oncogenic elements that facilitate GBM progression. The purpose of this study was to identify systems level molecular signatures from GBM-derived EVs using integrative analysis of publicly available transcriptomic data generated from plasma and serum samples. The dataset contained 19 samples in total, of which 15 samples were from plasma (11 GBM patients and 4 healthy samples) and 4 samples were from serum (2 GBM and 2 healthy samples). We carried out statistical analysis to identify differentially expressed genes (DEGs), functional enrichment analysis of the DEGs, protein–protein interaction networks, module analysis, transcription factors and target gene regulatory networks analysis, and identification of hub genes. The differential expression of the identified hub genes were validated with the independent TCGA-GBM dataset. We have identified a few crucial genes and pathways associated with GBM prognosis and therapy resistance. The DEGs identified from plasma were associated with inflammatory processes and viral infection. On the other hand, the hub genes identified from the serum samples were significantly associated with protein ubiquitinylation processes and cytokine signaling regulation. The findings indicate that GBM-derived plasma and serum DEGs may be associated with distinct cellular processes and pathways which facilitate GBM progression. The findings will provide better understanding of the molecular mechanisms of GBM pathogenesis and progression. These results can further be utilized for developing and validating minimally invasive diagnostic and therapeutic molecular biomarkers for GBM.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Under the threat of global climatic change and food shortages, it is essential to take the initiative to obtain a comprehensive understanding of common and specific defence mechanisms existing in ...plant systems for protection against different types of biotic invaders. We have implemented an integrated approach to analyse the overall transcriptomic reprogramming and systems-level defence responses in the model plant species Arabidopsis thaliana (A. thaliana henceforth) during insect Brevicoryne brassicae (B. brassicae henceforth) and bacterial Pseudomonas syringae pv. tomato strain DC3000 (P. syringae henceforth) attacks. The main aim of this study was to identify the attacker-specific and general defence response signatures in A. thaliana when attacked by phloem-feeding aphids or pathogenic bacteria.
The obtained annotated networks of differentially expressed transcripts indicated that members of transcription factor families, such as WRKY, MYB, ERF, BHLH and bZIP, could be crucial for stress-specific defence regulation in Arabidopsis during aphid and P. syringae attack. The defence response pathways, signalling pathways and metabolic processes associated with aphid attack and P. syringae infection partially overlapped. Components of several important biosynthesis and signalling pathways, such as salicylic acid (SA), jasmonic acid (JA), ethylene (ET) and glucosinolates, were differentially affected during the two the treatments. Several stress-regulated transcription factors were known to be associated with stress-inducible microRNAs. The differentially regulated gene sets included many signature transcription factors, and our co-expression analysis showed that they were also strongly co-expressed during 69 other biotic stress experiments.
Defence responses and functional networks that were unique and specific to aphid or P. syringae stresses were identified. Furthermore, our analysis revealed a probable link between biotic stress and microRNAs in Arabidopsis and, thus gives indicates a new direction for conducting large-scale targeted experiments to explore the detailed regulatory links between them. The presented results provide a comparative understanding of Arabidopsis - B. brassicae and Arabidopsis - P. syringae interactions at the transcriptomic level.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Besides short-term non-genomic effects, the G-protein coupled estrogen receptor (GPER) also mediates long-term genomic effects of estrogen. The genomic effects of GPER activation are not completely ...understood. G1 is a selective GPER agonist, which is popularly used for addressing the effects of GPER activation. Here, we present transcriptomic (RNA-seq) data on MCF-7 cells treated with 100 nM, or 1 µM G1 for a period of 48 h. The data are available from GEO (accession number GSE188706).
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Diseases by protozoan pathogens pose a significant public health concern, particularly in tropical and subtropical countries, where these are responsible for significant morbidity and mortality. ...Protozoan pathogens tend to establish chronic infections underscoring their competence at subversion of host immune processes, an important component of disease pathogenesis and of their virulence. Modulation of cytokine and chemokine levels, their crosstalks and downstream signaling pathways, and thereby influencing recruitment and activation of immune cells is crucial to immune evasion and subversion. Many protozoans are now known to secrete effector molecules that actively modulate host immune transcriptome and bring about alterations in host epigenome to alter cytokine levels and signaling. The complexity of multi-dimensional events during interaction of hosts and protozoan parasites ranges from microscopic molecular levels to macroscopic ecological and epidemiological levels that includes disrupting metabolic pathways, cell cycle (
and
sp.), respiratory burst, and antigen presentation (
spp.) to manipulation of signaling hubs. This requires an integrative systems biology approach to combine the knowledge from all these levels to identify the complex mechanisms of protozoan evolution
immune escape during host-parasite coevolution. Considering the diversity of protozoan parasites, in this review, we have focused on
and
infections. Along with the biological understanding, we further elucidate the current efforts in generating, integrating, and modeling of multi-dimensional data to explain the modulation of cytokine networks by these two protozoan parasites to achieve their persistence in host
immune escape during host-parasite coevolution.
Gallbladder cancer (GBC) has a lower incidence rate among the population relative to other cancer types but is a major contributor to the total number of biliary tract system cancer cases. GBC is ...distinguished from other malignancies by its high mortality, marked geographical variation and poor prognosis. To date no systemic targeted therapy is available for GBC. The main objective of this study is to determine the molecular signatures correlated with GBC development using integrative systems level approaches. We performed analysis of publicly available transcriptomic data to identify differentially regulated genes and pathways. Differential co-expression network analysis and transcriptional regulatory network analysis was performed to identify hub genes and hub transcription factors (TFs) associated with GBC pathogenesis and progression. Subsequently, we assessed the epithelial-mesenchymal transition (EMT) status of the hub genes using a combination of three scoring methods. The identified hub genes including, CDC6, MAPK15, CCNB2, BIRC7, L3MBTL1 were found to be regulators of cell cycle components which suggested their potential role in GBC pathogenesis and progression.
Esophageal Squamous Cell Carcinoma (ESCC) is considered as a deadly disease especially in the North-East, India. A series of differentially expressed genes (DEGs) are suspected to be involved in the ...progression of ESCC. To search the DEGs a good number of tools are available. To remove the biasness of resulting DEGs given by all such tools, a consensus function is necessary on which user can rely on the output generated by differential expression analysis methods applied on multiple sources of data. In this study, we have considered two microarrays (of 34 and 106 samples, respectively) and one RNA-seq data (of 29 samples) to conduct an unbiased integrative analysis towards the identification of critical genes for ESCC. Initially, independent downstream analysis on each type of data using six differentially expressed gene identification tools followed by an integrative analysis supported by an effective consensus function is conducted to identify an unbiased set of differently expressed genes. The identified gene set includes common genes obtained (for P-value cut-off < 0.01) from the tools as well as some uncommon top-ranked genes (for P-value cut-off < 0.001). Next, further preservation analysis is performed and identified a set of low preserved modules. Finally, hub genes are identified from the selected low preserved modules and validated both topologically and biologically. A set of hub genes are identified such as SOX11, COL27A1, TOP3A, BAG6, CDC6, EZH2, COL7A1, G6PD, and AKR1C2 which have been established to be critical for ESCC.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
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