Global gene expression profiling using heterologous DNA microarrays to analyze alterations in the transcriptome of Mus spretus mice living in a heavily polluted environment

Ruiz-Laguna, Julia; Vélez, José M.; Pueyo, Carmen; Abril, Nieves

doi:10.1007/s11356-015-5824-5

Cited by 14 publications

(10 citation statements)

References 79 publications

(99 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…agricultural runoff) sources, in turn generating spatial variation in immunity. For example, tree swallows breeding in mercury‐contaminated habitats exhibited weaker immune responses to phytohaemagglutinin challenge than birds in reference habitats (Hawley, Hallinger, & Cristol, ), and Algerian mice Mus spretus sampled from a polluted site showed distinct immune gene expression relative to mice from uncontaminated habitats (Ruiz‐Laguna, Vélez, Pueyo, & Abril, ).…”

Section: Spatial Factors Driving Immune Variationmentioning

confidence: 99%

Macroimmunology: The drivers and consequences of spatial patterns in wildlife immune defence

Becker

Albery

Kessler

et al. 2020

Journal of Animal Ecology

100

122

View full text Add to dashboard Cite

The prevalence and intensity of parasites in wild hosts varies across space and is a key determinant of infection risk in humans, domestic animals and threatened wildlife. Because the immune system serves as the primary barrier to infection, replication and transmission following exposure, we here consider the environmental drivers of immunity. Spatial variation in parasite pressure, abiotic and biotic conditions, and anthropogenic factors can all shape immunity across spatial scales. Identifying the most important spatial drivers of immunity could help pre‐empt infectious disease risks, especially in the context of how large‐scale factors such as urbanization affect defence by changing environmental conditions. We provide a synthesis of how to apply macroecological approaches to the study of ecoimmunology (i.e. macroimmunology). We first review spatial factors that could generate spatial variation in defence, highlighting the need for large‐scale studies that can differentiate competing environmental predictors of immunity and detailing contexts where this approach might be favoured over small‐scale experimental studies. We next conduct a systematic review of the literature to assess the frequency of spatial studies and to classify them according to taxa, immune measures, spatial replication and extent, and statistical methods. We review 210 ecoimmunology studies sampling multiple host populations. We show that whereas spatial approaches are relatively common, spatial replication is generally low and unlikely to provide sufficient environmental variation or power to differentiate competing spatial hypotheses. We also highlight statistical biases in macroimmunology, in that few studies characterize and account for spatial dependence statistically, potentially affecting inferences for the relationships between environmental conditions and immune defence. We use these findings to describe tools from geostatistics and spatial modelling that can improve inference about the associations between environmental and immunological variation. In particular, we emphasize exploratory tools that can guide spatial sampling and highlight the need for greater use of mixed‐effects models that account for spatial variability while also allowing researchers to account for both individual‐ and habitat‐level covariates. We finally discuss future research priorities for macroimmunology, including focusing on latitudinal gradients, range expansions and urbanization as being especially amenable to large‐scale spatial approaches. Methodologically, we highlight critical opportunities posed by assessing spatial variation in host tolerance, using metagenomics to quantify spatial variation in parasite pressure, coupling large‐scale field studies with small‐scale field experiments and longitudinal approaches, and applying statistical tools from macroecology and meta‐analysis to identify generalizable spatial patterns. Such work will facilitate scaling ecoimmunology from individual‐ to habitat‐level insights about the drivers of immu...

show abstract

Section: Spatial Factors Driving Immune Variationmentioning

confidence: 99%

Macroimmunology: The drivers and consequences of spatial patterns in wildlife immune defence

Becker

Albery

Kessler

et al. 2020

Journal of Animal Ecology

100

122

View full text Add to dashboard Cite

show abstract

“…The results showed the hybridization of 19,539 genes with the lower AgNP concentration (6 µg/L), and 19,472 genes with the higher concentration (36 µg/L), out of 20,000 genes contained in the C. elegans microarray ( Figure 1 , Supplementary Materials ). We used heterologous microarray hybridization (instead of New Generation Sequencing (NGS)-based technologies such as RNA-Seq) because it represented an interesting and inexpensive strategy; the microarray for C. elegans was available, and this species is phylogenetically related to the target species [ 36 , 37 , 38 ]. This approach provided sufficient information to determine the main mechanisms of action of AgNPs in monogenean parasites.…”

Section: Resultsmentioning

confidence: 99%

“…Specifically, the lin-9 gene was highly up-regulated (4.67 z-score). In C. elegans , lin-9 is necessary for the development of the hermaphrodite gonads and the male reproductive system, spicule, rays, and gonads [ 37 , 139 ]. Similarly, syp-3 regulates synapses along chromosomes, contributing to meiotic progression in early prophase during reproduction [ 41 ].…”

Section: Discussionmentioning

confidence: 99%

Molecular Effects of Silver Nanoparticles on Monogenean Parasites: Lessons from Caenorhabditis elegans

Pimentel-Acosta

Ramírez-Salcedo

Morales-Serna

et al. 2020

IJMS

View full text Add to dashboard Cite

The mechanisms of action of silver nanoparticles (AgNPs) in monogenean parasites of the genus Cichlidogyrus were investigated through a microarray hybridization approach using genomic information from the nematode Caenorhabditis elegans. The effects of two concentrations of AgNPs were explored, low (6 µg/L Ag) and high (36 µg/L Ag). Microarray analysis revealed that both concentrations of AgNPs activated similar biological processes, although by different mechanisms. Expression profiles included genes involved in detoxification, neurotoxicity, modulation of cell signaling, reproduction, embryonic development, and tegument organization as the main biological processes dysregulated by AgNPs. Two important processes (DNA damage and cell death) were mostly activated in parasites exposed to the lower concentration of AgNPs. To our knowledge, this is the first study providing information on the sub-cellular and molecular effects of exposure to AgNPs in metazoan parasites of fish.

show abstract

“…902499; Applied Biosystems, Foster City, CA, USA). Briefly, equal amounts of total RNA from three biological replicates of an assay point were pooled to get a minimum of 500 ng total RNA ( Ruiz-Laguna et al, 2016 ). The RNA was then reverse transcribed to synthesize complementary RNA (cRNA) using GeneChip™ WT Plus kit (Catalogue No.…”

Section: Methodsmentioning

confidence: 99%

Microarray gene expression profiling in colorectal (HCT116) and hepatocellular (HepG2) carcinoma cell lines treated withMelicope ptelefolialeaf extract reveals transcriptome profiles exhibiting anticancer activity

Kabir

Ali

Hashim

2018

PeerJ

View full text Add to dashboard Cite

BackgroundWe have previously reported anticancer activities of Melicope ptelefolia (MP) leaf extracts on four different cancer cell lines. However, the underlying mechanisms of actions have yet to be deciphered. In the present study, the anticancer activity of MP hexane extract (MP-HX) on colorectal (HCT116) and hepatocellular carcinoma (HepG2) cell lines was characterized through microarray gene expression profiling.MethodsHCT116 and HepG2 cells were treated with MP-HX for 24 hr. Total RNA was extracted from the cells and used for transcriptome profiling using Applied Biosystem GeneChip™ Human Gene 2.0 ST Array. Gene expression data was analysed using an Applied Biosystems Expression Console and Transcriptome Analysis Console software. Pathway enrichment analyses was performed using Ingenuity Pathway Analysis (IPA) software. The microarray data was validated by profiling the expression of 17 genes through quantitative reverse transcription PCR (RT-qPCR).ResultsMP-HX induced differential expression of 1,290 and 1,325 genes in HCT116 and HepG2 cells, respectively (microarray data fold change, MA_FC ≥ ±2.0). The direction of gene expression change for the 17 genes assayed through RT-qPCR agree with the microarray data. In both cell lines, MP-HX modulated the expression of many genes in directions that support antiproliferative activity. IPA software analyses revealed MP-HX modulated canonical pathways, networks and biological processes that are associated with cell cycle, DNA replication, cellular growth and cell proliferation. In both cell lines, upregulation of genes which promote apoptosis, cell cycle arrest and growth inhibition were observed, while genes that are typically overexpressed in diverse human cancers or those that promoted cell cycle progression, DNA replication and cellular proliferation were downregulated. Some of the genes upregulated by MP-HX include pro-apoptotic genes (DDIT3, BBC3, JUN), cell cycle arresting (CDKN1A, CDKN2B), growth arrest/repair (TP53, GADD45A) and metastasis suppression (NDRG1). MP-HX downregulated the expression of genes that could promote anti-apoptotic effect, cell cycle progression, tumor development and progression, which include BIRC5, CCNA2, CCNB1, CCNB2, CCNE2, CDK1/2/6, GINS2, HELLS, MCM2/10 PLK1, RRM2 and SKP2. It is interesting to note that all six top-ranked genes proposed to be cancer-associated (PLK1, MCM2, MCM3, MCM7, MCM10 and SKP2) were downregulated by MP-HX in both cell lines.DiscussionThe present study showed that the anticancer activities of MP-HX are exerted through its actions on genes regulating apoptosis, cell proliferation, DNA replication and cell cycle progression. These findings further project the potential use of MP as a nutraceutical agent for cancer therapeutics.

show abstract

Global gene expression profiling using heterologous DNA microarrays to analyze alterations in the transcriptome of Mus spretus mice living in a heavily polluted environment

Cited by 14 publications

References 79 publications

Macroimmunology: The drivers and consequences of spatial patterns in wildlife immune defence

Macroimmunology: The drivers and consequences of spatial patterns in wildlife immune defence

Molecular Effects of Silver Nanoparticles on Monogenean Parasites: Lessons from Caenorhabditis elegans

Microarray gene expression profiling in colorectal (HCT116) and hepatocellular (HepG2) carcinoma cell lines treated withMelicope ptelefolialeaf extract reveals transcriptome profiles exhibiting anticancer activity

Contact Info

Product

Resources

About