PXD053404

PXD053404 is an original dataset announced via ProteomeXchange.

Title	Analysis of changes in liver protein expression and quantification regarding to sex, treatment and genotype in C57BL/6J Wild-type and KO AhR mice: Unraveling the influence of AhR and Indoxyl sulfate in coagulation and liver metabolism
Description	Chronic kidney disease (CKD), defined as a glomerular filtration rate <60 mL/min/1.73 m2 for at least 3 months, is a major public health concern with high prevalence in developed countries. CKD patients present dysregulations in their coagulation system, with higher levels of factor VII, factor VIII, thrombin, and tissue factor (main initiator of blood coagulation in vivo). Paradoxically, these patients present both an increased risk of thrombotic events and a higher bleeding rate compared to healthy subjects. Traditional cardiovascular risk factors are insufficient to explain the elevated rates of CVD, since it is the leading cause of death among CKD patients, rising uremic toxins as a possible link. Uremic toxins are compounds eliminated by the kidneys in physiological conditions. They tend to accumulate in the blood and tissues of patients with CKD due to its inadequate renal clearance. Uremia could influence biotransformation and transport across cellular membranes, disturbing drug tissue distribution. Therefore, CKD not only alters the elimination of drugs excreted by the kidneys, but it also impacts the metabolism of drugs subject to non-renal clearance, which involves mainly the liver and the gut. The liver is a highly specialized tissue, involved in the synthesis of plasma proteins and production of clotting factors, it has a major role in drug metabolization. The liver is also the main producer of thrombopoietin (hormone that regulates the production of platelets). All these processes are thought to be highly disturbed in CKD patients. Hepatocytes express high levels of AhR, ligand-inducible transcription factor activated by by xeno- and endobiotics, that mediate the induction of various liver cytochrome P450 enzymes. Hence, liver AhR regulates both nutrient metabolism and xenobiotic detoxification. Tryptophan derived uremic toxins (TDUT), induce tissue factor expression via the aryl hydrocarbon receptor (AhR) pathway, explaining the connection between CKD uremic toxin accumulation and hemostatic disbalances. Indoxyl sulfate (IS) is the main TDUT involved in uremic syndrome and acts as an AhR agonist in human primary hepatocytes. Tryptophan is metabolize to indole in the gut, absorbed into blood circulation and further process by the liver creating IS. In patients with CKD, IS tends to accumulate since it is poorly removed via dialysis. IS induces vascular endothelium and hemostatic dysfunction impacting cardiovascular morbidity and mortality during CKD. IS being a nephrotoxic, prothrombotic, pro-oxidative and pro-inflammatory molecule is proposed as the responsible for thrombotic events and metabolic changes in CKD patients. To further investigate the role of AhR and IS in metabolism and coagulation we want to analyse 60 C57BL/6J mice liver samples. These samples come from 8 different experimental groups: 4 groups of male mice and 4 groups of female mice. Each subset consists of a wildtype group treated with KCl (control), a KO AhR group treated with KCl (control), a wildtype group treated with 0,1% IS and a KO AhR group treated with 0,1% IS. The number of animals per group ranges from 6 to 8. Mice were fed ad libitum during the whole animal trial which started at 10 weeks of life. Both KCl and IS where solubilized in 5% sucrose water and administer in the drinking water of the mice for 1 week, after which mice were sacrificed at 11 weeks of age. KCl was used as control substance since IS is used under its potassium salt form. Although in many studies the variable gender is not considered, since we though that there could be a difference in basal expression as well as a hormonal bias that could influence the results, we decided to create separate experimental groups for both male and females. Hence, the large number of samples that needed to be analysed. The liver samples collected, were snap frozen and have been stored at −80 °C until further analyses.
HostingRepository	PRIDE
AnnounceDate	2025-05-07
AnnouncementXML	Submission_2025-05-06_23:45:55.974.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Václav Pustka
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	acetylated residue; monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2024-06-25 13:13:10	ID requested
⏵ 1	2025-05-06 23:45:56	announced

10.1038/s41598-025-90405-5;

Pina-Beltran B, Dimitrov D, McKay N, Giot M, Zdr, á, hal Z, Pot, ě, š, il D, Pustka V, Peinado-Izaguerri J, Saez-Rodriguez J, Poitevin S, Burtey S, Unveiling the role of sex in the metabolism of indoxyl sulfate and apixaban. Sci Rep, 15(1):6075(2025) [pubmed]

submitter keyword: AhR, liver, Sex,Mice, Indoxyl Sulfate

Zbynek Zdrahal
contact affiliation	Proteomics Core Facility and Research Group Proteomics, CEITEC-MU, Masaryk University, Brno, Czech Republic
contact email	zdrahal@sci.muni.cz
lab head
Václav Pustka
contact affiliation	Proteomics Core Facility and Research Group Proteomics CEITEC-MU Masaryk University Brno, Czech Republic
contact email	vaclav.pustka@ceitec.muni.cz
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD053404
     1. Label: PRIDE project
     2. Name: Analysis of changes in liver protein expression and quantification regarding to sex, treatment and genotype in C57BL/6J Wild-type and KO AhR mice: Unraveling the influence of AhR and Indoxyl sulfate in coagulation and liver metabolism