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RNA-seq data from two metronidazole resistant and one revertant line derived from Giardia intestinalis line WB

ABSTRACT: In this study we compare the baseline transcriptomic changes two resistant lines show without drug in the media compared to both the line they are derived from as well as a revertant.

ORGANISM(S): Giardia duodenalis

PROVIDER: GSE139624 | GEO | 2022/01/26

REPOSITORIES: GEO

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RNA-seq data from two metronidazole resistant and one revertant line derived from Giardia intestinalis line WB

Project description:RNA-seq data from two metronidazole resistant and one revertant line derived from Giardia intestinalis line WB

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Comparative LC-MS analysis of two metronidazole resistant (M1,M2) and one revertant (M1NR) Giardia intestinalis strains with their parental strain (WB-C6)

Project description:I this study we analyzed three lines, two of which were created by UV- directed mutagenesis and showed increased levels of metronidazole tolerance (M1 and M2) and the third being a line that reverted spontanously to sensitive after several passages (M1NR) of M1 without metronidazole in the media. On the physiological side we analyzed the ability of these lines to reists metronidazole exposure and to encyst as well as their respective doublings times. At the same time we conducted a trasncriptomics and proteomics analysis to understand which exact changes lead to M1 and M2 being resistant while M1NR shows wildtype levels of metrondiazole sensitivty. We than compared these datasets to already existing datasets of other metrondiazole resistant lines and managed to identify a few core changes which are shared between all lines. In all lines proteins that are activating the drug are downregulated while proteins that are part of the oxidative stress response are found in higher abundance. On the other side these core changes are accompanied by a line specific set of changes, showing that there is more than one way for Giardia intestinalis to become resistant to metronidazole.

2022-01-26 | PXD027813 | Pride

A chromosome-scale reference genome for Giardia intestinalis WB.

Project description:Giardia intestinalis is a protist causing diarrhea in humans. The first G. intestinalis genome, from the WB isolate, was published more than ten years ago, and has been widely used as the reference genome for Giardia research. However, the genome is fragmented, thus hindering research at the chromosomal level. We re-sequenced the Giardia genome with Pacbio long-read sequencing technology and obtained a new reference genome, which was assembled into near-complete chromosomes with only four internal gaps at long repeats. This new genome is not only more complete but also better annotated at both structural and functional levels, providing more details about gene families, gene organizations and chromosomal structure. This near-complete reference genome will be a valuable resource for the Giardia community and protist research. It also showcases how a fragmented genome can be improved with long-read sequencing technology completed with optical maps.

| S-EPMC7000408 | biostudies-literature

Characterization of Metronidazole-Resistant <i>Giardia intestinalis</i> Lines by Comparative Transcriptomics and Proteomics.

Project description:Metronidazole (MTZ) is a clinically important antimicrobial agent that is active against both bacterial and protozoan organisms. MTZ has been used extensively for more than 60 years and until now resistance has been rare. However, a recent and dramatic increase in the number of MTZ resistant bacteria and protozoa is of great concern since there are few alternative drugs with a similarly broad activity spectrum. To identify key factors and mechanisms underlying MTZ resistance, we utilized the protozoan parasite Giardia intestinalis, which is commonly treated with MTZ. We characterized two in vitro selected, metronidazole resistant parasite lines, as well as one revertant, by analyzing fitness aspects associated with increased drug resistance and transcriptomes and proteomes. We also conducted a meta-analysis using already existing data from additional resistant G. intestinalis isolates. The combined data suggest that in vitro generated MTZ resistance has a substantial fitness cost to the parasite, which may partly explain why resistance is not widespread despite decades of heavy use. Mechanistically, MTZ resistance in Giardia is multifactorial and associated with complex changes, yet a core set of pathways involving oxidoreductases, oxidative stress responses and DNA repair proteins, is central to MTZ resistance in both bacteria and protozoa.

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Comprehensive analysis of flavohemoprotein copy number variation in Giardia intestinalis: exploring links to metronidazole resistance.

Project description:BackgroundGiardiasis, caused by the protozoan parasite Giardia intestinalis, often presents a treatment challenge, particularly in terms of resistance to metronidazole. Despite extensive research, markers for metronidazole resistance have not yet been identified.MethodsThis study analysed 28 clinical samples of G. intestinalis from sub-assemblage AII, characterised by varying responses to metronidazole treatment. We focussed on copy number variation (CNV) of the multi-copy flavohemoprotein gene, analysed using digital polymerase chain reaction (dPCR) and next generation sequencing (NGS). Additionally, chromosomal ploidy was tested in 18 of these samples. Flavohemoprotein CNV was also assessed in 17 samples from other sub-assemblages.ResultsAnalyses revealed variable CNVs of the flavohemoprotein gene among the isolates, with no correlation to clinical metronidazole resistance. Discrepancies in CNVs detected from NGS data were attributed to biases linked to the whole genome amplification. However, dPCR helped to clarify these discrepancies by providing more consistent CNV data. Significant differences in flavohemoprotein CNVs were observed across different G. intestinalis sub-assemblages. Notably, Giardia exhibits a propensity for aneuploidy, contributing to genomic variability within and between sub-assemblages.ConclusionsThe complexity of the clinical metronidazole resistance in Giardia is influenced by multiple genetic factors, including CNVs and aneuploidy. No significant differences in the CNV of the flavohemoprotein gene between isolates from metronidazole-resistant and metronidazole-sensitive cases of giardiasis were found, underscoring the need for further research to identify reliable genetic markers for resistance. We demonstrate that dPCR and NGS are robust methods for analysing CNVs and provide cross-validating results, highlighting their utility in the genetic analyses of this parasite.

| S-EPMC11316999 | biostudies-literature

RNA-seq data from Giardia intestinalis WB trohozoites infecting human Caco-2 cells

Project description:RNA-seq data from Giardia intestinalis WB trohozoites infecting human Caco-2 cells

2020-02-20 | GSE144004 | GEO

RNA-seq data from Giardia intestinalis WB trohozoites 7h into encysting Giardia cells infecting human Caco-2 cells

Project description:RNA-seq data from Giardia intestinalis WB trohozoites 7h into encysting Giardia cells infecting human Caco-2 cells

2022-01-31 | GSE144001 | GEO

Treatment with cultured epidermal autograft from revertant skin for epidermolytic ichthyosis

Project description:We performed clinical trial of treatment with cultured epidermal autograft (CEA) produced from patients’ own revertant epidermal keratinocytes as a proof-of-concept study. We successfully produced CEAs from genetically confirmed revertant skin of the three EI patients and genetically confirmed that CEAs mainly consist of revertant wild-type cells by amplicon sequencing and droplet digital PCR analysis. Single-cell RNA sequencing analysis confirmed normal proliferation and safety profiling of CEAs.

2024-05-22 | GSE245859 | GEO

Detection of revertant mosaicism in epidermolysis bullosa through Cas9-targeted long read sequencing

Project description:Revertant mosaicism (RM) is a phenomenon in which inherited mutations are spontaneously corrected in somatic cells. RM occurs in some congenital skin diseases, although genetic validation of RM in clinically revertant skin has been challenging, especially when homologous recombination (HR) is responsible for RM. We introduced Nanopore Cas9-targeted sequencing (nCATS) for identifying HR in clinically revertant skin.

2022-01-13 | GSE186002 | GEO

Gene expression microarray of: 1) Cbx1 null versus revertant (single allele expression), and 2) Jarid2 null versus revertant, mutant mouse ES cells.

Project description:Gene expression as measured by microarray, in order to determine the cohort of differentially expressed genes, in each of two different mutant ES cell lines (Cbx1 and Jarid2), each comparing the respective null mutant ES cells to revertant (single allele expression) mutant ES cells. Hybridization was performed concurrently. Experiments are: 1) Cbx1 null mutant (Cbx1^tm1a(EUCOMM)Wtsi/Cbx1^tm1Wcs) compared to revertant mutant (Cbx1^tm1c(EUCOMM)Wtsi/Cbx1^tm1Wcs) ES cell lines (n=6 per genotype). 2) Jarid2 null mutant (Jarid2^tm1a(KOMP)Wtsi/Jarid2tm1Wcs) compared to revertant mutant (Jarid2^tm1c(KOMP)Wtsi/Jarid2tm1Wcs) ES cell lines (n=3 per genotype). Biological replicates (individual ES clones) were used. Parental ES cell lines are from the International Knockout Mouse Consortium (IKMC - EUCOMM and KOMP-CSD programmes) and were modified to generate null ES cells using bi-allelic gene targeting with a targeted trapping vector generated by re-purposing Intermediate Vectors from the IKMC resource. Revertant ES cell lines were generated by using Flp recombinase to revert the IKMC tm1a null allele to the conditional tm1c allele, in order to reinstate gene expression from one allele. The tm1Wcs allele is constitutive null.

2017-09-12 | E-MTAB-5930 | biostudies-arrayexpress

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