Comparative Transcriptomic Analysis of Antimony Resistant and Susceptible Leishmania Infantum Lines

Abstract Background: One of the major challenges for leishmaniasis treatment is the emergence of parasites resistant to antimony. In order to study differentially expressed genes associated with drug resistance we performed a comparative transcriptomic analysis between wild-type and potassium antimonyl tartrate (SbIII)-resistant Leishmania infantum lines using high-throughput RNA sequencing.Methods: All the cDNA libraries were constructed from promastigote forms of each line, sequenced and analyzed using STAR for mapping the reads against the reference genome (L. infantum JPCM5) and DESeq2 for differential expression statistical analyses. All the genes were functionally annotated using sequence similarity search.Results: The analytical pipeline considering an adjusted p-value lower than 0.05 and fold change greater than 2.0 identified 933 transcripts differentially expressed (DE) between wild-type and SbIII-resistant L. infantum lines. Out of 933 DE transcripts, 504 presented functional annotation and 429 were assigned as hypothetical proteins. A total of 837 transcripts were upregulated and 96 were downregulated in the SbIII-resistant L. infantum line. Using this DE dataset, the proteins were further grouped in functional classes according to Gene Ontology database. The functional enrichment analysis for biological process showed that the upregulated transcripts in the SbIII-resistant line are associated with protein phosphorylation, microtubule-based movement, ubiquitination, host-parasite interaction, cellular process and other categories. The downregulated transcripts in the SbIII-resistant line are assigned in the GO categories: ribonucleoprotein complex, ribosome biogenesis, rRNA processing, nucleosome assembly and translation.Conclusions: The transcriptomic profile of L. infantum showed a robust set of genes from different metabolic pathways associated with antimony resistance phenotype in this parasite. Our results address the complex and multifactorial antimony resistance mechanism of Leishmania, identifying several potential genes for resistance markers and drug targets against leishmaniasis.

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Comparative transcriptomic analysis of antimony resistant and susceptible Leishmania infantum lines

10.21203/rs.3.rs-55997/v2 ◽

2020 ◽

Author(s):

Juvana Moreira Andrade ◽

Leilane Oliveira Gonçalves ◽

Daniel Barbosa Liarte ◽

Davi Alvarenga Lima ◽

Frederico Gonçalves Guimarães ◽

...

Keyword(s):

Ribosome Biogenesis ◽

Transcriptomic Analysis ◽

Functional Enrichment ◽

Differentially Expressed ◽

Cdna Libraries ◽

P Value ◽

Resistant Line ◽

Wild Type ◽

Antimony Resistance ◽

Comparative Transcriptomic Analysis

Abstract Background: One of the major challenges for leishmaniasis treatment is the emergence of parasites resistant to antimony. In order to study differentially expressed genes associated with drug resistance we performed a comparative transcriptomic analysis between wild-type and potassium antimonyl tartrate (SbIII)-resistant Leishmania infantum lines using high-throughput RNA sequencing.Methods: All the cDNA libraries were constructed from promastigote forms of each line, sequenced and analyzed using STAR for mapping the reads against the reference genome (L. infantum JPCM5) and DESeq2 for differential expression statistical analyses. All the genes were functionally annotated using sequence similarity search.Results: The analytical pipeline considering an adjusted p-value lower than 0.05 and fold change greater than 2.0 identified 933 transcripts differentially expressed (DE) between wild-type and SbIII-resistant L. infantum lines. Out of 933 DE transcripts, 504 presented functional annotation and 429 were assigned as hypothetical proteins. A total of 837 transcripts were upregulated and 96 were downregulated in the SbIII-resistant L. infantum line. Using this DE dataset, the proteins were further grouped in functional classes according to the Gene Ontology database. The functional enrichment analysis for biological processes showed that the upregulated transcripts in the SbIII-resistant line are associated with protein phosphorylation, microtubule-based movement, ubiquitination, host-parasite interaction, cellular process and other categories. The downregulated transcripts in the SbIII-resistant line are assigned in the GO categories: ribonucleoprotein complex, ribosome biogenesis, rRNA processing, nucleosome assembly and translation.Conclusions: The transcriptomic profile of L. infantum showed a robust set of genes from different metabolic pathways associated with antimony resistance phenotype in this parasite. Our results address the complex and multifactorial antimony resistance mechanisms in Leishmania, identifying several candidate genes that may be further evaluated as molecular targets for chemotherapy of leishmaniasis.

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Comparative transcriptomic analysis of antimony resistant and susceptible Leishmania infantum lines

10.21203/rs.3.rs-55997/v3 ◽

2020 ◽

Author(s):

Juvana Moreira Andrade ◽

Leilane Oliveira Gonçalves ◽

Daniel Barbosa Liarte ◽

Davi Alvarenga Lima ◽

Frederico Gonçalves Guimarães ◽

...

Keyword(s):

Ribosome Biogenesis ◽

Transcriptomic Analysis ◽

Functional Enrichment ◽

Differentially Expressed ◽

Cdna Libraries ◽

P Value ◽

Resistant Line ◽

Wild Type ◽

Antimony Resistance ◽

Comparative Transcriptomic Analysis

Abstract Background: One of the major challenges for leishmaniasis treatment is the emergence of parasites resistant to antimony. In order to study differentially expressed genes associated with drug resistance we performed a comparative transcriptomic analysis between wild-type and potassium antimonyl tartrate (SbIII)-resistant Leishmania infantum lines using high-throughput RNA sequencing.Methods: All the cDNA libraries were constructed from promastigote forms of each line, sequenced and analyzed using STAR for mapping the reads against the reference genome (L. infantum JPCM5) and DESeq2 for differential expression statistical analyses. All the genes were functionally annotated using sequence similarity search.Results: The analytical pipeline considering an adjusted p-value lower than 0.05 and fold change greater than 2.0 identified 933 transcripts differentially expressed (DE) between wild-type and SbIII-resistant L. infantum lines. Out of 933 DE transcripts, 504 presented functional annotation and 429 were assigned as hypothetical proteins. A total of 837 transcripts were upregulated and 96 were downregulated in the SbIII-resistant L. infantum line. Using this DE dataset, the proteins were further grouped in functional classes according to the Gene Ontology database. The functional enrichment analysis for biological processes showed that the upregulated transcripts in the SbIII-resistant line are associated with protein phosphorylation, microtubule-based movement, ubiquitination, host-parasite interaction, cellular process and other categories. The downregulated transcripts in the SbIII-resistant line are assigned in the GO categories: ribonucleoprotein complex, ribosome biogenesis, rRNA processing, nucleosome assembly and translation.Conclusions: The transcriptomic profile of L. infantum showed a robust set of genes from different metabolic pathways associated with antimony resistance phenotype in this parasite. Our results address the complex and multifactorial antimony resistance mechanisms in Leishmania, identifying several candidate genes that may be further evaluated as molecular targets for chemotherapy of leishmaniasis.

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Comparative transcriptomic analysis of antimony resistant and susceptible Leishmania infantum lines

Parasites & Vectors ◽

10.1186/s13071-020-04486-4 ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

Juvana Moreira Andrade ◽

Leilane Oliveira Gonçalves ◽

Daniel Barbosa Liarte ◽

Davi Alvarenga Lima ◽

Frederico Gonçalves Guimarães ◽

...

Keyword(s):

Leishmania Infantum ◽

Ribosome Biogenesis ◽

Transcriptomic Analysis ◽

Functional Enrichment ◽

Differentially Expressed ◽

Cdna Libraries ◽

Resistant Line ◽

Wild Type ◽

Antimony Resistance ◽

Comparative Transcriptomic Analysis

Abstract Background One of the major challenges to leishmaniasis treatment is the emergence of parasites resistant to antimony. To study differentially expressed genes associated with drug resistance, we performed a comparative transcriptomic analysis between wild-type and potassium antimonyl tartrate (SbIII)-resistant Leishmania infantum lines using high-throughput RNA sequencing. Methods All the cDNA libraries were constructed from promastigote forms of each line, sequenced and analyzed using STAR for mapping the reads against the reference genome (L. infantum JPCM5) and DESeq2 for differential expression statistical analyses. All the genes were functionally annotated using sequence similarity search. Results The analytical pipeline considering an adjusted p-value < 0.05 and fold change > 2.0 identified 933 transcripts differentially expressed (DE) between wild-type and SbIII-resistant L. infantum lines. Out of 933 DE transcripts, 504 presented functional annotation and 429 were assigned as hypothetical proteins. A total of 837 transcripts were upregulated and 96 were downregulated in the SbIII-resistant L. infantum line. Using this DE dataset, the proteins were further grouped in functional classes according to the gene ontology database. The functional enrichment analysis for biological processes showed that the upregulated transcripts in the SbIII-resistant line are associated with protein phosphorylation, microtubule-based movement, ubiquitination, host–parasite interaction, cellular process and other categories. The downregulated transcripts in the SbIII-resistant line are assigned in the GO categories: ribonucleoprotein complex, ribosome biogenesis, rRNA processing, nucleosome assembly and translation. Conclusions The transcriptomic profile of L. infantum showed a robust set of genes from different metabolic pathways associated with the antimony resistance phenotype in this parasite. Our results address the complex and multifactorial antimony resistance mechanisms in Leishmania, identifying several candidate genes that may be further evaluated as molecular targets for chemotherapy of leishmaniasis.

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Identification of Differentially Expressed MicroRNAs and Their Potential Target Genes in Adipose Tissue from Pigs with Highly Divergent Backfat Thickness

Animals ◽

10.3390/ani10040624 ◽

2020 ◽

Vol 10 (4) ◽

pp. 624

Author(s):

Kai Xing ◽

Xitong Zhao ◽

Yibing Liu ◽

Fengxia Zhang ◽

Zhen Tan ◽

...

Keyword(s):

Target Genes ◽

Expression Patterns ◽

Fat Deposition ◽

Functional Enrichment ◽

Differentially Expressed ◽

Backfat Thickness ◽

P Value ◽

Sibling Pairs ◽

Differentially Expressed Mirnas

Fatty traits are very important in pig production. However, the role of microRNAs (miRNAs) in fat deposition is not clearly understood. In this study, we compared adipose miRNAs from three full-sibling pairs of female Landrace pigs, with high and low backfat thickness, to investigate the associated regulatory network. We obtained an average of 17.29 million raw reads from six libraries, 62.27% of which mapped to the pig reference genome. A total of 318 pig miRNAs were detected among the samples. Among them, 18 miRNAs were differentially expressed (p-value < 0.05, |log2fold change| ≥ 1) between the high and low backfat groups; 6 were up-regulated and 12 were down-regulated. Functional enrichment of the predicted target genes of the differentially expressed miRNAs, indicated that these miRNAs were involved mainly in lipid and carbohydrate metabolism, and glycan biosynthesis and metabolism. Comprehensive analysis of the mRNA and miRNA transcriptomes revealed possible regulatory relationships for fat deposition. Negatively correlated mRNA–miRNA pairs included miR-137–PPARGC1A, miR-141–FASN, and miR-122-5p–PKM, indicating these interactions may be key regulators of fat deposition. Our findings provide important insights into miRNA expression patterns in the backfat tissue of pig and new insights into the regulatory mechanisms of fat deposition in pig.

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Comparative transcriptomic analysis identified differentially expressed genes and pathways involved in the interaction between Tremella fuciformis and Annulohypoxylon stygium

Antonie van Leeuwenhoek ◽

10.1007/s10482-019-01294-4 ◽

2019 ◽

Vol 112 (11) ◽

pp. 1675-1689

Author(s):

Dongmei Liu ◽

Dwi Pujiana ◽

Yuanyuan Wang ◽

Zhaosong Zhang ◽

Liesheng Zheng ◽

...

Keyword(s):

Differentially Expressed Genes ◽

Transcriptomic Analysis ◽

Differentially Expressed ◽

Tremella Fuciformis ◽

Annulohypoxylon Stygium ◽

Comparative Transcriptomic Analysis

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Transcriptomic analysis of differentially expressed genes in an orange-pericarp mutant and wild type in pummelo (Citrus grandis)

BMC Plant Biology ◽

10.1186/s12870-015-0435-3 ◽

2015 ◽

Vol 15 (1) ◽

pp. 44 ◽

Cited By ~ 23

Author(s):

Fei Guo ◽

Huiwen Yu ◽

Qiang Xu ◽

Xiuxin Deng

Keyword(s):

Differentially Expressed Genes ◽

Transcriptomic Analysis ◽

Differentially Expressed ◽

Wild Type

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Transcriptomic analysis of PPARα-dependent alterations during cardiac hypertrophy

Physiological Genomics ◽

10.1152/physiolgenomics.90296.2008 ◽

2008 ◽

Vol 36 (1) ◽

pp. 15-23 ◽

Cited By ~ 26

Author(s):

Pascal J. H. Smeets ◽

Heleen M. de Vogel-van den Bosch ◽

Peter H. M. Willemsen ◽

Alphons P. Stassen ◽

Torik Ayoubi ◽

...

Keyword(s):

Gene Expression ◽

Immune Response ◽

Lipid Metabolism ◽

Cardiac Hypertrophy ◽

Signaling Pathways ◽

Differentially Expressed Genes ◽

Left Ventricular ◽

Transcriptomic Analysis ◽

Differentially Expressed ◽

Wild Type

Peroxisome proliferator-activated receptor (PPAR)α regulates lipid metabolism at the transcriptional level and modulates the expression of genes involved in inflammation, cell proliferation, and differentiation. Although PPARα has been shown to mitigate cardiac hypertrophy, knowledge about underlying mechanisms and the nature of signaling pathways involved is fragmentary and incomplete. The aim of this study was to identify the processes and signaling pathways regulated by PPARα in hearts challenged by a chronic pressure overload by means of whole genome transcriptomic analysis. PPARα−/− and wild-type mice were subjected to transverse aortic constriction (TAC) for 28 days, and left ventricular gene expression profile was determined with Affymetrix GeneChip Mouse Genome 430 2.0 arrays containing >45,000 probe sets. In unchallenged hearts, the mere lack of PPARα resulted in 821 differentially expressed genes, many of which are related to lipid metabolism and immune response. TAC resulted in a more pronounced cardiac hypertrophy and more extensive changes in gene expression (1,910 and 312 differentially expressed genes, respectively) in PPARα−/− mice than in wild-type mice. Many of the hypertrophy-related genes were related to development, signal transduction, actin filament organization, and collagen synthesis. Compared with wild-type hypertrophied hearts, PPARα−/− hypertrophied hearts revealed enrichment of gene clusters related to extracellular matrix remodeling, immune response, oxidative stress, and inflammatory signaling pathways. The present study therefore demonstrates that, in addition to lipid metabolism, PPARα is an important modulator of immune and inflammatory response in cardiac muscle.

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