Housekeeping Genes for Parkinson’s Disease in Humans and Mice

Abstract

A critical aspect of real-time PCR is the presence of housekeeping genes (HKGs) as an internal control for the normalization of expression data for genes of interest. It is necessary to select correct HKGs in the investigation of various pathologies. Thereby, we analyzed the stability of expression of the HKGs in Parkinson’s disease (PD). The work was carried out in the peripheral blood of patients with PD and in the brain tissues and peripheral blood of mice with MPTP-induced PD. As a result, Aars was the most stably expressed HKG in the mouse brain as a whole. However, different genes were more stably expressed in different parts of the brain. Polr2f was the most stably expressed in the cortex, Psmd6 was the most stably expressed in the cerebellum, and Psmd7 was the most stably expressed in the striatum and substantia nigra. HKGs were different in similar tissues of the studied organisms. Polr2f was the most stably expressed HKG in the peripheral blood of mice, whereas PSMD6 was the most stably expressed gene in humans. Thus, there is no universal HKG both for different brain tissues of one organism and for similar tissues of different organisms. Furthermore, the identified most stably expressed HKGs can be considered as such only under conditions in PD.

Application of OpenArray Technology to Assess Changes in the Expression of Functionally Significant Genes in the Substantia Nigra of Mice in a Model of Parkinson’s Disease

“…Based on previous experience using RG in RT-qPCR [36,37,[46][47][48][49][50], we selected 11 HKGs: X-prolyl aminopeptidase (aminopeptidase P) 1 (Xpnpep1), alanyl-tRNA synthetase (Aars), GTPase activating protein and VPS9 domains 1 (Gapvd1), oxysterol binding protein (Osbp), glyceraldehyde-3-phosphate dehydrogenase (Gapdh), succinate dehydrogenase complex, subunit A (Sdha), 40S ribosomal protein S27a (Rps27a), ubiquitin-conjugating enzyme E2D2 (Ube2d2), cytochrome C1 (Cyc1), ribosomal protein L13 (Rpl13), and hypoxanthine guanine phosphoribosyl transferase (Hprt). The stability of the expressions of some genes was previously shown in patients with PD and in animal models of PD [36,37,49]. Concentrations of DA metabolites, including 3,4-dihydroxyphenylacetic acid (DOPAC), 3-methoxytyramine (3-MT), and homovanillic acid (HVA), decreased in the striatum of MPTP-treated mice by 85%, 66%, and 59%, respectively (Figure 1B).…”

“…The expressions of reference genes should not reliably change in pathology, for example, during neurodegeneration in PD. They are called housekeeping genes (HKGs) [36,37], which are expressed in all cells of the body, and the proteins they encode are necessary for the normal functioning of the cell. However, the expressions of some HKGs may still change during neurodegeneration [38], which requires preliminary testing of the stability of HKG expression in each specific pathology.…”

“…However, the expressions of some HKGs may still change during neurodegeneration [38], which requires preliminary testing of the stability of HKG expression in each specific pathology. In addition, it should be taken into account that the most stable HKGs may differ in various brain regions in patients with PD and in mice models of PD [37]. In this regard, the choice of HKGs that will be used for comparison with the expressions of genes of interest is crucial for the correct interpretation of the RT-qPCR data [36].…”

Identification of stable reference genes in peripheral blood mononuclear cells from type 2 diabetes mellitus patients

“…In this backdrop, the aim of this study was to evaluate stability of expression of 4 widely used reference genes: Beta-actin ( ACTB ), Peptidylprolyl Isomerase B ( PPIB ), Tyrosine 3-Monooxygenase/Tryptophan 5-Monooxygenase Activation Protein Zeta ( YWHAZ ), and GAPDH in PBMCs from T2DM patients and healthy control subjects. The primary reason for the selection of these 4 genes in the study was that they have been widely used as reference genes in gene-expression studies on human PBMCs— GAPDH 11 , 25 , ACTB 11 , 29 , PPIB 29 , YWHAZ 30 , 31 . Further, the 4 genes chosen for this study have different physiological and cellular roles: cytoskeleton ( ACTB ) 32 , carbohydrate metabolism ( GAPDH ) 33 , protein folding ( PPIB ) 34 , an adapter protein in signaling pathways ( YWHAZ ) 35 .…”

Ubigen: Interactive Ranking and Enrichment Test for Ubiquitously Expressed Genes

“…In some studies, the terms housekeeping or ubiquity are used in the context of a limited coverage that only considers a specific set of tissues and/or conditions (like, e.g., cancer 10 or Parkinson’s disease 11 ), to describe genes that are characteristic for that situation and highly expressed. Depending on the kind of analysis, the selection of ubiquitous genes can be positive as just shown for cancer or negative, when searching for specific explicitly non-ubiquitous marker proteins 12 .…”