Differential immune gene expression associated with contemporary range expansion of two invasive rodents in Senegal

BackgroundBiological invasions are major anthropogenic changes associated with threats to biodiversity and health. What determines the successful establishment of introduced populations still remains unsolved. Here we explore the appealing assertion that invasion success relies on immune phenotypic traits that would be advantageous in recently invaded sites.ResultsWe compared gene expression profiles between anciently and recently established populations of two major invading species, the house mouse Mus musculus domesticus and the black rat Rattus rattus, in Senegal. Transcriptome analyses revealed respectively 364 and 83 differentially expressed genes along the mouse and rat invasion routes. Among them, 20.0% and 10.6% were annotated with functions related to immunity. All immune-related genes detected along the mouse invasion route were over-expressed in recently invaded sites. Genes of the complement activation pathway were over-represented. Results were less straightforward when considering the black rat as no particular immunological process was over-represented.ConclusionsWe revealed changes in transcriptome profiles along invasion routes. Patterns differed between both invasive species. These changes potentially be driven by increased infection risks in recently invaded sites for the house mouse and stochastic events associated with colonization history for the black rat. These results provide a first step in identifying the immune ecoevolutionary processes potentially involved in invasion success.

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Differential immune gene expression associated with contemporary range expansion in two invasive rodents in Senegal

Scientific Reports ◽

10.1038/s41598-020-75060-2 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Nathalie Charbonnel ◽

Maxime Galan ◽

Caroline Tatard ◽

Anne Loiseau ◽

Christophe Diagne ◽

...

Keyword(s):

Gene Expression ◽

Differential Expression ◽

House Mouse ◽

Expression Profiles ◽

Rattus Rattus ◽

Gene Expression Profiles ◽

Invasion Success ◽

Immune Gene ◽

Mus Musculus Domesticus ◽

Black Rat

Abstract Biological invasions are major anthropogenic changes associated with threats to biodiversity and health. However, what determines the successful establishment and spread of introduced populations remains unclear. Here, we explore several hypotheses linking invasion success and immune phenotype traits, including those based on the evolution of increased competitive ability concept. We compared gene expression profiles between anciently and recently established populations of two major invading species, the house mouse Mus musculus domesticus and the black rat Rattus rattus, in Senegal (West Africa). Transcriptome analyses identified differential expression between anciently and recently established populations for 364 mouse genes and 83 rat genes. All immune-related genes displaying differential expression along the mouse invasion route were overexpressed at three of the four recently invaded sites studied. Complement activation pathway genes were overrepresented among these genes. By contrast, no particular immunological process was found to be overrepresented among the differentially expressed genes of black rat. Changes in transcriptome profiles were thus observed along invasion routes, but with different specific patterns between the two invasive species. These changes may be driven by increases in infection risks at sites recently invaded by the house mouse, and by stochastic events associated with colonization history for the black rat. These results constitute a first step toward the identification of immune eco-evolutionary processes potentially involved in the invasion success of these two rodent species.

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Same Invasion, Different Routes: Helminth Assemblages May Favor the Invasion Success of the House Mouse in Senegal

Frontiers in Veterinary Science ◽

10.3389/fvets.2021.740617 ◽

2021 ◽

Vol 8 ◽

Author(s):

Christophe Diagne ◽

Laurent Granjon ◽

Caroline Tatard ◽

Alexis Ribas ◽

Arame Ndiaye ◽

...

Keyword(s):

House Mouse ◽

Native Species ◽

Invasion Success ◽

Enemy Release ◽

Mus Musculus Domesticus ◽

Invasion Pathways ◽

Invasion Fronts ◽

Invasion Routes ◽

Rodent Communities

Previous field-based studies have evidenced patterns in gastrointestinal helminth (GIH) assemblages of rodent communities that are consistent with “enemy release” and “spill-back” hypotheses, suggesting a role of parasites in the ongoing invasion success of the exotic house mouse (Mus musculus domesticus) in Senegal (West Africa). However, these findings came from a single invasion route, thus preventing to ascertain that they did not result from stochastic and/or selective processes that could differ across invasion pathways. In the present study, we investigated the distribution of rodent communities and their GIH assemblages in three distinct zones of Northern Senegal, which corresponded to independent house mouse invasion fronts. Our findings first showed an unexpectedly rapid spread of the house mouse, which reached even remote areas where native species would have been expected to dominate the rodent communities. They also strengthened previous insights suggesting a role of helminths in the invasion success of the house mouse, such as: (i) low infestation rates of invading mice by the exotic nematode Aspiculuris tetraptera at invasion fronts—except in a single zone where the establishment of the house mouse could be older than initially thought, which was consistent with the “enemy release” hypothesis; and (ii) higher infection rates by the local cestode Mathevotaenia symmetrica in native rodents with long co-existence history with invasive mice, bringing support to the “spill-back” hypothesis. Therefore, “enemy release” and “spill-back” mechanisms should be seriously considered when explaining the invasion success of the house mouse—provided further experimental works demonstrate that involved GIHs affect rodent fitness or exert selective pressures. Next steps should also include evolutionary, immunological, and behavioral perspectives to fully capture the complexity, causes and consequences of GIH variations along these invasion routes.

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Immune Profile of the Nasal Mucosa in Patients with Cutaneous Leishmaniasis

Infection and Immunity ◽

10.1128/iai.00881-19 ◽

2020 ◽

Vol 88 (5) ◽

Author(s):

María J. Gómez-Zafra ◽

Adriana Navas ◽

Jimena Jojoa ◽

Julieth Murillo ◽

Camila González ◽

...

Keyword(s):

Gene Expression ◽

Cutaneous Leishmaniasis ◽

Nasal Mucosa ◽

Expression Profiles ◽

Clinical Signs ◽

Molecular Evidence ◽

Immune Gene ◽

Mucosal Disease ◽

Mucosal Tissues ◽

Anti Inflammatory

ABSTRACT Localized skin lesions are characteristic of cutaneous leishmaniasis (CL); however, Leishmania (Viannia) species, which are responsible for most CL cases in the Americas, can spread systemically, sometimes resulting in mucosal disease. Detection of Leishmania has been documented in healthy mucosal tissues (conjunctiva, tonsils, and nasal mucosa) and healthy skin of CL patients and in individuals with asymptomatic infection in areas of endemicity of L. (V.) panamensis and L. (V.) braziliensis transmission. However, the conditions and mechanisms that favor parasite persistence in healthy mucosal tissues are unknown. In this descriptive study, we compared the cell populations of the nasal mucosa (NM) of healthy donors and patients with active CL and explored the immune gene expression signatures related to molecular detection of Leishmania in this tissue in the absence of clinical signs or symptoms of mucosal disease. The cellular composition and gene expression profiles of NM samples from active CL patients were similar to those of healthy volunteers, with a predominance of epithelial over immune cells, and within the CD45+ cell population, a higher frequency of CD66b+ followed by CD14+ and CD3+ cells. In CL patients with molecular evidence of Leishmania persistence in the NM, genes characteristic of an anti-inflammatory and tissue repair responses (IL4R, IL5RA, POSTN, and SATB1) were overexpressed relative to NM samples from CL patients in which Leishmania was not detected. Here, we report the first immunological description of subclinically infected NM tissues of CL patients and provide evidence of a local anti-inflammatory environment favoring parasite persistence in the NM.

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Innate and adaptive immune gene expression profiles as biomarkers in human type 1 diabetes

Clinical & Experimental Immunology ◽

10.1111/j.1365-2249.2012.04650.x ◽

2012 ◽

Vol 170 (2) ◽

pp. 131-138 ◽

Cited By ~ 8

Author(s):

D. Han ◽

X. Cai ◽

J. Wen ◽

D. Matheson ◽

J. S. Skyler ◽

...

Keyword(s):

Gene Expression ◽

Type 1 Diabetes ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Immune Gene ◽

Adaptive Immune ◽

Human Type ◽

Immune Gene Expression ◽

Human Type 1 Diabetes

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A survey of zoonotic pathogens carried by house mouse and black rat populations in Yucatan, Mexico

Epidemiology and Infection ◽

10.1017/s0950268817001352 ◽

2017 ◽

Vol 145 (11) ◽

pp. 2287-2295 ◽

Cited By ~ 13

Author(s):

J. A. PANTI-MAY ◽

R. R. C. DE ANDRADE ◽

Y. GURUBEL-GONZÁLEZ ◽

E. PALOMO-ARJONA ◽

L. SODÁ-TAMAYO ◽

...

Keyword(s):

House Mouse ◽

Neglected Tropical Diseases ◽

Rat Kidney ◽

Rattus Rattus ◽

Hymenolepis Diminuta ◽

House Mice ◽

Residential Areas ◽

Zoonotic Pathogens ◽

Black Rat ◽

Black Rats

SUMMARYThe house mouse (Mus musculus) and the black rat (Rattus rattus) are reservoir hosts for zoonotic pathogens, several of which cause neglected tropical diseases (NTDs). Studies of the prevalence of these NTD-causing zoonotic pathogens, in house mice and black rats from tropical residential areas are scarce. Three hundred and two house mice and 161 black rats were trapped in 2013 from two urban neighbourhoods and a rural village in Yucatan, Mexico, and subsequently tested forTrypanosoma cruzi,Hymenolepis diminutaandLeptospira interrogans. Using the polymerase chain reaction we detectedT. cruziDNA in the hearts of 4·9% (8/165) and 6·2% (7/113) of house mice and black rats, respectively. We applied the sedimentation technique to detect eggs ofH. diminutain 0·5% (1/182) and 14·2% (15/106) of house mice and black rats, respectively. Through the immunofluorescent imprint method,L. interroganswas identified in 0·9% (1/106) of rat kidney impressions. Our results suggest that the black rat could be an important reservoir forT. cruziandH. diminutain the studied sites. Further studies examining seasonal and geographical patterns could increase our knowledge on the epidemiology of these pathogens in Mexico and the risk to public health posed by rodents.

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Biological invasions in rodent communities: from ecological interactions to zoonotic bacterial infection issues

10.1101/108423 ◽

2017 ◽

Author(s):

Christophe Diagne ◽

M. Galan ◽

Lucie Tamisier ◽

Jonathan d’Ambrosio ◽

Ambroise Dalecky ◽

...

Keyword(s):

Disease Risk ◽

Rattus Rattus ◽

Experimental Studies ◽

Amplicon Sequencing ◽

Invasion Success ◽

Enemy Release ◽

Ecological Interactions ◽

Invasion Process ◽

Mus Musculus Domesticus ◽

Zoonotic Bacteria

AbstractSeveral hypotheses (such as ‘enemy release’, ‘novel weapon’, ‘spillback’ and ‘dilution/density effect’) suggest changes in host-parasite ecological interactions during biological invasion events. Such changes can impact both invasion process outcome and the dynamics of exotic and/or endemic zoonotic diseases. To evaluate these predictions, we investigated the ongoing invasions of the house mouse Mus musculus domesticus, and the black rat, Rattus rattus, in Senegal (West Africa). We focused on zoonotic bacterial communities depicted using 16S rRNA amplicon sequencing approach in both invasive and native rodents sampled along two well-defined invasion routes. Overall, this study provided new ecological evidence connecting parasitism and rodent invasion process, with diverse potential roles of zoonotic bacteria in the invasion success. Our results also highlighted the main factors that lie behind bacterial community structure in commensal rodents. Further experimental studies as well as comparative spatio-temporal surveys are necessary to decipher the actual role of zoonotic bacteria in these invasions. Our data also gave new support for the difficulty to predict the direction in which the relationship between biodiversity changes and disease risk could go. These results should be used as a basis for public health prevention services to design reservoir monitoring strategies based on multiple pathogen surveillance.

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An embedded gene selection method using knockoffs optimizing neural network

BMC Bioinformatics ◽

10.1186/s12859-020-03717-w ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Juncheng Guo ◽

Min Jin ◽

Yuanyuan Chen ◽

Jianxiao Liu

Keyword(s):

Neural Network ◽

Gene Expression ◽

Gene Selection ◽

Expression Profiles ◽

Research Work ◽

Selection Method ◽

Small Subset ◽

Phenotypic Traits ◽

Breast Cancer Dataset ◽

Gene Selection Method

Abstract Background Gene selection refers to find a small subset of discriminant genes from the gene expression profiles. How to select genes that affect specific phenotypic traits effectively is an important research work in the field of biology. The neural network has better fitting ability when dealing with nonlinear data, and it can capture features automatically and flexibly. In this work, we propose an embedded gene selection method using neural network. The important genes can be obtained by calculating the weight coefficient after the training is completed. In order to solve the problem of black box of neural network and further make the training results interpretable in neural network, we use the idea of knockoffs to construct the knockoff feature genes of the original feature genes. This method not only make each feature gene to compete with each other, but also make each feature gene compete with its knockoff feature gene. This approach can help to select the key genes that affect the decision-making of neural networks. Results We use maize carotenoids, tocopherol methyltransferase, raffinose family oligosaccharides and human breast cancer dataset to do verification and analysis. Conclusions The experiment results demonstrate that the knockoffs optimizing neural network method has better detection effect than the other existing algorithms, and specially for processing the nonlinear gene expression and phenotype data.

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