Host plant adaptation in the polyphagous whitefly, Trialeurodes vaporariorum, is associated with transcriptional plasticity and altered sensitivity to insecticides

Abstract Background The glasshouse whitefly, Trialeurodes vaporariorum, is a damaging crop pest and an invasive generalist capable of feeding on a broad range of host plants. As such this species has evolved mechanisms to circumvent the wide spectrum of anti-herbivore allelochemicals produced by its host range. T. vaporariorum has also demonstrated a remarkable ability to evolve resistance to many of the synthetic insecticides used for control. Results To gain insight into the molecular mechanisms that underpin the polyphagy of T. vaporariorum and its resistance to natural and synthetic xenobiotics, we sequenced and assembled a reference genome for this species. Curation of genes putatively involved in the detoxification of natural and synthetic xenobiotics revealed a marked reduction in specific gene families between this species and another generalist whitefly, Bemisia tabaci. Transcriptome profiling of T. vaporariorum upon transfer to a range of different host plants revealed profound differences in the transcriptional response to more or less challenging hosts. Large scale changes in gene expression (> 20% of genes) were observed during adaptation to challenging hosts with a range of genes involved in gene regulation, signalling, and detoxification differentially expressed. Remarkably, these changes in gene expression were associated with significant shifts in the tolerance of host-adapted T. vaporariorum lines to natural and synthetic insecticides. Conclusions Our findings provide further insights into the ability of polyphagous insects to extensively reprogram gene expression during host adaptation and illustrate the potential implications of this on their sensitivity to synthetic insecticides.

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Identification and validation of hub genes of synovial tissue for patients with osteoarthritis and rheumatoid arthritis

10.21203/rs.3.rs-564869/v1 ◽

2021 ◽

Author(s):

Yanzhi Ge ◽

Zuxiang Chen ◽

Yanbin Fu ◽

Li Zhou ◽

Haipeng Xu ◽

...

Keyword(s):

Rheumatoid Arthritis ◽

Gene Expression ◽

Differentially Expressed Genes ◽

Large Scale ◽

Molecular Mechanisms ◽

Immune Cell ◽

Interaction Network ◽

Differentially Expressed ◽

Specific Gene ◽

Hub Genes

Abstract Osteoarthritis (OA) and rheumatoid arthritis (RA) were two major joint diseases with partially common phenotypes and genotypes. This study aimed to determine the mechanistic similarities and differences between osteoarthritis and rheumatoid arthritis by analyzing the differentially expressed genes and signaling pathways. Microarray data of osteoarthritis and rheumatoid arthritis were obtained from the Gene Expression Omnibus. By integrating multiple gene data sets, specific differentially expressed genes (DEGs) were identified in synovial membrane samples from patients and healthy donations. Then, the Gene ontology significant functions annotation, Kyoto Encyclopedia of Genes and Genomes pathways and protein-protein interaction network analysis were conducted. Moreover, CIBERSORT was used to further distinguish OA and RA in immune infiltration. Finally, animal experimentation was conducted and the establishment of model, which was verified using PCR in the mouse. As an overlapping process, we identified 1116 DEGs between OA and RA. It was indicated that specific gene signatures differed significantly between OA and RA connected with the distinct pathways. Of identified DEGs, 9 immune cell types among 22 were identified to distinguish from each other. The qRT-PCR result showed that the eight-tenths expression levels of the hub genes were significantly increased in OA samples (P < 0.05). This large-scale gene expression study provided new insights for disease-associated genes and molecular mechanisms as well as their associated function in osteoarthritis and rheumatoid arthritis, which simultaneously offer a new direction for biomarker development and the distinguishment of gene-level mechanisms between osteoarthritis and rheumatoid arthritis.

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The combined detection of Amphiregulin, Cyclin A1 and DDX20/Gemin3 expression predicts aggressive forms of oral squamous cell carcinoma

British Journal of Cancer ◽

10.1038/s41416-021-01491-x ◽

2021 ◽

Author(s):

Ekaterina Bourova-Flin ◽

Samira Derakhshan ◽

Afsaneh Goudarzi ◽

Tao Wang ◽

Anne-Laure Vitte ◽

...

Keyword(s):

Gene Expression ◽

Squamous Cell ◽

Large Scale ◽

Biomarker Discovery ◽

Gene Expression Signature ◽

Predictive Biomarkers ◽

Specific Gene ◽

Specific Expression ◽

Intrinsic Nature ◽

Independent Cohort

Abstract Background Large-scale genetic and epigenetic deregulations enable cancer cells to ectopically activate tissue-specific expression programmes. A specifically designed strategy was applied to oral squamous cell carcinomas (OSCC) in order to detect ectopic gene activations and develop a prognostic stratification test. Methods A dedicated original prognosis biomarker discovery approach was implemented using genome-wide transcriptomic data of OSCC, including training and validation cohorts. Abnormal expressions of silent genes were systematically detected, correlated with survival probabilities and evaluated as predictive biomarkers. The resulting stratification test was confirmed in an independent cohort using immunohistochemistry. Results A specific gene expression signature, including a combination of three genes, AREG, CCNA1 and DDX20, was found associated with high-risk OSCC in univariate and multivariate analyses. It was translated into an immunohistochemistry-based test, which successfully stratified patients of our own independent cohort. Discussion The exploration of the whole gene expression profile characterising aggressive OSCC tumours highlights their enhanced proliferative and poorly differentiated intrinsic nature. Experimental targeting of CCNA1 in OSCC cells is associated with a shift of transcriptomic signature towards the less aggressive form of OSCC, suggesting that CCNA1 could be a good target for therapeutic approaches.

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Serial analysis of gene expression (SAGE) during porcine embryo development

Reproduction Fertility and Development ◽

10.1071/rd03081 ◽

2004 ◽

Vol 16 (2) ◽

pp. 87 ◽

Cited By ~ 12

Author(s):

Le Ann Blomberg ◽

Kurt A. Zuelke

Keyword(s):

Gene Expression ◽

Functional Genomics ◽

Embryo Development ◽

Molecular Mechanisms ◽

Physiological Role ◽

Transgenic Animals ◽

Specific Gene ◽

Research Strategies

Functional genomics provides a powerful means for delving into the molecular mechanisms involved in pre-implantation development of porcine embryos. High rates of embryonic mortality (30%), following either natural mating or artificial insemination, emphasise the need to improve the efficiency of reproduction in the pig. The poor success rate of live offspring from in vitro-manipulated pig embryos also hampers efforts to generate transgenic animals for biotechnology applications. Previous analysis of differential gene expression has demonstrated stage-specific gene expression for in vivo-derived embryos and altered gene expression for in vitro-derived embryos. However, the methods used to date examine relatively few genes simultaneously and, thus, provide an incomplete glimpse of the physiological role of these genes during embryogenesis. The present review will focus on two aspects of applying functional genomics research strategies for analysing the expression of genes during elongation of pig embryos between gestational day (D) 11 and D12. First, we compare and contrast current methodologies that are being used for gene discovery and expression analysis during pig embryo development. Second, we establish a paradigm for applying serial analysis of gene expression as a functional genomics tool to obtain preliminary information essential for discovering the physiological mechanisms by which distinct embryonic phenotypes are derived.

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Transcriptome profiling of immune tissues reveals habitat‐specific gene expression between lake and river sticklebacks

Molecular Ecology ◽

10.1111/mec.13520 ◽

2016 ◽

Vol 25 (4) ◽

pp. 943-958 ◽

Cited By ~ 33

Author(s):

Yun Huang ◽

Frédéric J. J. Chain ◽

Mahesh Panchal ◽

Christophe Eizaguirre ◽

Martin Kalbe ◽

...

Keyword(s):

Gene Expression ◽

Transcriptome Profiling ◽

Specific Gene ◽

Specific Gene Expression ◽

Immune Tissues

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Identification of biological pathways and genes associated with neurogenic heterotopic ossification by text mining

PeerJ ◽

10.7717/peerj.8276 ◽

2020 ◽

Vol 8 ◽

pp. e8276 ◽

Cited By ~ 1

Author(s):

Yichong Zhang ◽

Yuanbo Zhan ◽

Yuhui Kou ◽

Xiaofeng Yin ◽

Yanhua Wang ◽

...

Keyword(s):

Gene Expression ◽

Text Mining ◽

Heterotopic Ossification ◽

Signaling Pathway ◽

Molecular Mechanisms ◽

Egf Receptor ◽

Enrichment Analysis ◽

Biological Pathways ◽

Specific Gene ◽

Cord Injury

Background Neurogenic heterotopic ossification is a disorder of aberrant bone formation affecting one in five patients sustaining a spinal cord injury or traumatic brain injury (SCI-TBI-HO). However, the underlying mechanisms of SCI-TBI-HO have proven difficult to elucidate. The aim of the present study is to identify the most promising candidate genes and biological pathways for SCI-TBI-HO. Methods In this study, we used text mining to generate potential explanations for SCI-TBI-HO. Moreover, we employed several additional datasets, including gene expression profile data, drug data and tissue-specific gene expression data, to explore promising genes that associated with SCI-TBI-HO. Results We identified four SCI-TBI-HO-associated genes, including GDF15, LDLR, CCL2, and CLU. Finally, using enrichment analysis, we identified several pathways, including integrin signaling, insulin pathway, internalization of ErbB1, urokinase-type plasminogen activator and uPAR-mediated signaling, PDGFR-beta signaling pathway, EGF receptor (ErbB1) signaling pathway, and class I PI3K signaling events, which may be associated with SCI-TBI-HO. Conclusions These results enhance our understanding of the molecular mechanisms of SCI-TBI-HO and offer new leads for researchers and innovative therapeutic strategies.

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Genome Assemblies of the Warthog and Kenyan Domestic Pig Provide Insights into Suidae Evolution and Candidate Genes for African Swine Fever Tolerance

10.1101/2021.12.17.473133 ◽

2021 ◽

Author(s):

Wen Feng ◽

Lei Zhou ◽

Pengju Zhao ◽

Heng Du ◽

Chenguang Diao ◽

...

Keyword(s):

Large Scale ◽

Genetic Resistance ◽

African Swine Fever ◽

Gene Families ◽

Specific Gene ◽

Chromosome 2 ◽

Sequencing Data ◽

Domestic Pig ◽

Phacochoerus Africanus ◽

Contraction And Expansion

As warthog (Phacochoerus africanus) has innate immunity against African swine fever (ASF), it is critical to understanding the evolutionary novelty of warthog to explain its specific ASF resistance. Here, we present two completed new genomes of one warthog and one Kenyan domestic pig, as the fundamental genomic references to decode the genetic mechanism on ASF tolerance. Our results indicated, multiple genomic variations, including gene losses, independent contraction and expansion of specific gene families, likely moulded warthog's genome to adapt the environment. Importantly, the analysis of presence and absence of genomic sequences revealed that, the warthog genome had a DNA sequence absence of the lactate dehydrogenase B (LDHB) gene on chromosome 2 compared to the reference genome. The overexpression and siRNA of LDHB indicated that its inhibition on the replication of ASFV. The Combining with large scale sequencing data of 123 pigs from all over world, contraction and expansion of TRIM genes families revealed that TRIM family genes in the warthog genome were potentially responsible for its tolerance to ASF. Our results will help further improve the understanding of genetic resistance ASF in pigs.

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Convergent evolution of venom gland transcriptomes across Metazoa

10.1101/2021.07.04.451048 ◽

2021 ◽

Author(s):

Giulia Zancolli ◽

Maarten Reijnders ◽

Robert Waterhouse ◽

Marc Robinson-Rechavi

Keyword(s):

Gene Expression ◽

Regulatory Networks ◽

Molecular Mechanisms ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Venom Gland ◽

Bioactive Molecules ◽

Specific Gene ◽

Animal Kingdom ◽

Venom Glands

Animals have repeatedly evolved specialized organs and anatomical structures to produce and deliver a cocktail of potent bioactive molecules to subdue prey or predators: venom. This makes it one of the most widespread convergent functions in the animal kingdom. Whether animals have adopted the same genetic toolkit to evolved venom systems is a fascinating question that still eludes us. Here, we performed the first comparative analysis of venom gland transcriptomes from 20 venomous species spanning the main Metazoan lineages, to test whether different animals have independently adopted similar molecular mechanisms to perform the same function. We found a strong convergence in gene expression profiles, with venom glands being more similar to each other than to any other tissue from the same species, and their differences closely mirroring the species phylogeny. Although venom glands secrete some of the fastest evolving molecules (toxins), their gene expression does not evolve faster than evolutionarily older tissues. We found 15 venom gland specific gene modules enriched in endoplasmic reticulum stress and unfolded protein response pathways, indicating that animals have independently adopted stress response mechanisms to cope with mass production of toxins. This, in turns, activates regulatory networks for epithelial development, cell turnover and maintenance which seem composed of both convergent and lineage-specific factors, possibly reflecting the different developmental origins of venom glands. This study represents the first step towards an understanding of the molecular mechanisms underlying the repeated evolution of one of the most successful adaptive traits in the animal kingdom.

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Transcriptome profiling reveals phase-specific gene expression in the developing barley inflorescence

The Crop Journal ◽

10.1016/j.cj.2019.04.005 ◽

2020 ◽

Vol 8 (1) ◽

pp. 71-86 ◽

Cited By ~ 3

Author(s):

Huiran Liu ◽

Gang Li ◽

Xiujuan Yang ◽

Hendrik N.J. Kuijer ◽

Wanqi Liang ◽

...

Keyword(s):

Gene Expression ◽

Transcriptome Profiling ◽

Specific Gene ◽

Specific Gene Expression

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Transcriptome Profiling of Adipose Tissue Reveals Depot-Specific Metabolic Alterations Among Patients with Colorectal Cancer

The Journal of Clinical Endocrinology & Metabolism ◽

10.1210/jc.2019-00461 ◽

2019 ◽

Vol 104 (11) ◽

pp. 5225-5237 ◽

Cited By ~ 3

Author(s):

Mariam Haffa ◽

Andreana N Holowatyj ◽

Mario Kratz ◽

Reka Toth ◽

Axel Benner ◽

...

Keyword(s):

Gene Expression ◽

Colorectal Cancer ◽

Adipose Tissue ◽

Large Scale ◽

Expression Profiles ◽

Expression Patterns ◽

Human Study ◽

Subcutaneous Fat ◽

Specific Gene ◽

Adipose Tissue Depots

Abstract Context Adipose tissue inflammation and dysregulated energy homeostasis are key mechanisms linking obesity and cancer. Distinct adipose tissue depots strongly differ in their metabolic profiles; however, comprehensive studies of depot-specific perturbations among patients with cancer are lacking. Objective We compared transcriptome profiles of visceral adipose tissue (VAT) and subcutaneous adipose tissue (SAT) from patients with colorectal cancer and assessed the associations of different anthropometric measures with depot-specific gene expression. Design Whole transcriptomes of VAT and SAT were measured in 233 patients from the ColoCare Study, and visceral and subcutaneous fat area were quantified via CT. Results VAT compared with SAT showed elevated gene expression of cytokines, cell adhesion molecules, and key regulators of metabolic homeostasis. Increased fat area was associated with downregulated lipid and small molecule metabolism and upregulated inflammatory pathways in both compartments. Comparing these patterns between depots proved specific and more pronounced gene expression alterations in SAT and identified unique associations of integrins and lipid metabolism–related enzymes. VAT gene expression patterns that were associated with visceral fat area poorly overlapped with patterns associated with self-reported body mass index (BMI). However, subcutaneous fat area and BMI showed similar associations with SAT gene expression. Conclusions This large-scale human study demonstrates pronounced disparities between distinct adipose tissue depots and reveals that BMI poorly correlates with fat mass–associated changes in VAT. Taken together, these results provide crucial evidence for the necessity to differentiate between distinct adipose tissue depots for a correct characterization of gene expression profiles that may affect metabolic health of patients with colorectal cancer.

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Molecular Mechanisms, Diagnostic Aspects and Therapeutic Opportunities of Micro Ribonucleic Acids in Atrial Fibrillation

International Journal of Molecular Sciences ◽

10.3390/ijms21082742 ◽

2020 ◽

Vol 21 (8) ◽

pp. 2742 ◽

Cited By ~ 1

Author(s):

Allan Böhm ◽

Marianna Vachalcova ◽

Peter Snopek ◽

Ljuba Bacharova ◽

Dominika Komarova ◽

...

Keyword(s):

Gene Expression ◽

Atrial Fibrillation ◽

Molecular Mechanisms ◽

Wide Spectrum ◽

Regulation Of Gene Expression ◽

Review Article ◽

Ribonucleic Acids ◽

Rna Molecules ◽

Diagnostic Aspects ◽

Non Coding Rna

Micro ribonucleic acids (miRNAs) are short non-coding RNA molecules responsible for regulation of gene expression. They are involved in many pathophysiological processes of a wide spectrum of diseases. Recent studies showed their involvement in atrial fibrillation. They seem to become potential screening biomarkers for atrial fibrillation and even treatment targets for this arrhythmia. The aim of this review article was to summarize the latest knowledge about miRNA and their molecular relation to the pathophysiology, diagnosis and treatment of atrial fibrillation.

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