Alterations of housekeeping proteins in human aged and diseased hearts

Expressions of commonly used housekeeping proteins are altered in asthmatic mouse lungs

Housekeeping protein expression in tissue samples is often used to normalize immunoblotting data. However, utilizing common loading control proteins in pathological conditions without validation can be problematic. Here, we describe the alteration of commonly used loading control protein expressions in asthmatic lung samples and present a simpler and more reliable loading control for western blot analysis. Lung samples from control and asthmatic mice groups were used to assess the expression levels of three commonly used housekeeping proteins (beta-actin, alpha-tubulin, and glyceraldehyde-3-phosphate dehydrogenase). Ponceau S staining data was also obtained to assess the consistency of protein loading. Housekeeping protein expressions varied dramatically in asthmatic groups, ranging from 26 to 278 % compared to the control group (p < 0.05). On the other hand, no significant differences in Ponceau S staining were observed among the groups. There were no differences in protein extraction from lung samples among the groups, but significant differences were observed in bronchoalveolar lavage leukocyte populations (p < 0.05). Our data suggest that lung resident immune cells were dramatically altered in asthma groups, and protein expression of commonly used loading control proteins are unreliable for western blot analysis of asthmatic lungs. We recommend Ponceau S staining as a more reliable loading control for asthmatic lung samples to normalize western blot data.

Western blotting (immunoblotting): history, theory, uses, protocol and problems

Western blotting (immunoblotting) is a powerful and commonly used technique that is capable of detecting or semiquantifying an individual protein from complex mixtures of proteins extracted from cells or tissues. The history surrounding the origin of western blotting, the theory behind the western blotting technique, a comprehensive protocol and the uses of western blotting are presented. Lesser known and significant problems in the western blotting field and troubleshooting of common problems are highlighted and discussed. This work is a comprehensive primer and guide for new western blotting researchers and those interested in a better understanding of the technique or getting better results.

Swiss Vascular Biobank: Evaluation of Optimal Extraction Method and Admission Solution for Preserving RNA from Human Vascular Tissue

Proper biobanking is essential for obtaining reliable data, particularly for next-generation sequencing approaches. Diseased vascular tissues, having extended atherosclerotic pathologies, represent a particular challenge due to low RNA quality. In order to address this issue, we isolated RNA from vascular samples collected in our Swiss Vascular Biobank (SVB); these included abdominal aortic aneurysm (AAA), peripheral arterial disease (PAD), healthy aorta (HA), and muscle samples. We used different methods, investigated various admission solutions, determined RNA integrity numbers (RINs), and performed expression analyses of housekeeping genes (ACTB, GAPDH), ribosomal genes (18S, 28S), and long non-coding RNAs (MALAT1, H19). Our results show that RINs from diseased vascular tissue are low (2-4). If the isolation of primary cells is intended, as in our SVB, a cryoprotective solution is a better option for tissue preservation than RNAlater. Because RNA degradation proceeds randomly, controls with similar RINs are recommended. Otherwise, the data might convey differences in RNA degradation rather than the expressions of the corresponding genes. Moreover, since the 18S and 28S genes in the diseased vascular samples were degraded and corresponded with the low RINs, we believe that DV200, which represents the total RNA's disintegration state, is a better decision-making aid in choosing samples for omics analyses.

Research on the oncogenic role of the house-keeping gene GAPDH in human tumors

BACKGROUND

As an internal reference gene, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) plays an important role in glycolysis. While increasing evidence suggests that GAPDH plays a crucial role in tumorigenesis of some cancers, no systematic analysis of GAPDH has been conducted. Here, we sought to analyze the expression of GAPDH and its oncogenic processes in pan-cancer.

METHODS

GAPDH was investigated in The Cancer Genome Atlas (TCGA) tumor types using several bioinformatic tools including Tumor IMmune Estimation Resource (TIMER), Gene Expression Profiling Interactive Analysis (GEPIA), University of ALabama at Birmingham CANcer (UALCAN), cBio Cancer Genomics Portal (cBioPortal), and Search Tool for Recurring Instances of Neighbouring Genes (STRING) for the expression and relationships with prognosis and immune infiltration separately.

RESULTS

Through our analysis, we measured the higher expression of GAPDH across the majority of TCGA tumors. GAPDH overexpression predicts poor survival in patients with tumors expressing a high level of GAPDH. Moreover, the genetic changes in GAPDH contributed to an increased mRNA expression. Additionally, GAPDH expression was negatively correlated with immune infiltration involving cancer-associated fibroblasts, neutrophil cell and endothelial.

CONCLUSIONS

The house-keeping gene GAPDH might be a promising biomarker for pan-cancer prognosis. And GAPDH is not suitable as an internal reference gene for most cancer research, whether RNA or protein analyses.

Diet-Induced Hypercholesterolemia Leads to Cardiac Dysfunction and Alterations in the Myocardial Proteome

Elevated blood cholesterol is a major risk factor for coronary heart disease. Moreover, direct effects on the myocardium also contribute to the adverse effects of hypercholesterolemia. Here, we investigated the effect of hypercholesterolemia on the cardiac proteome. Male Wistar rats were fed with a laboratory rodent chow supplemented with 2% cholesterol for 8 weeks to induce hypercholesterolemia. The protein expression data obtained from the proteomic characterization of left ventricular samples from normo- and hypercholesterolemic animals were subjected to gene ontology (GO) and protein interaction analyses. Elevated circulating cholesterol levels were accompanied by diastolic dysfunction in cholesterol-fed rats. The proteomic characterization of left ventricular samples revealed altered expression of 45 proteins due to hypercholesterolemia. Based on the Gene Ontology analysis, hypercholesterolemia was associated with disturbed expression of cytoskeletal and contractile proteins. Beta-actin was downregulated in the hypercholesterolemic myocardium, and established a prominent hub of the protein interaction network. Analysis of the unfiltered dataset revealed concordant downregulated expression patterns in proteins associated with the arrangement of the contractile system (e.g., cardiac-specific troponins and myosin complex), and in subunits of the mitochondrial respiratory chain. We conclude that the observed changes in the cardiac proteome may contribute to the development of diastolic dysfunction in hypercholesterolemia.

Reversing mitochondrial defects in aged hearts: role of mitochondrial calpain activation

Aging chronically increases endoplasmic reticulum (ER) stress that contributes to mitochondrial dysfunction. Activation of calpain 1 (CPN1) impairs mitochondrial function during acute ER stress. We proposed that aging-induced ER stress led to mitochondrial dysfunction by activating CPN1. We posit that attenuation of the ER stress or direct inhibition of CPN1 in aged hearts can decrease cardiac injury during ischemia-reperfusion by improving mitochondrial function. Male young (3 mo) and aged mice (24 mo) were used in the present study, and 4-phenylbutyrate (4-PBA) was used to decrease the ER stress in aged mice. Subsarcolemmal (SSM) and interfibrillar mitochondria (IFM) were isolated. Chronic 4-PBA treatment for 2 wk decreased CPN1 activation as shown by the decreased cleavage of spectrin in cytosol and apoptosis inducing factor (AIF) and the α1 subunit of pyruvate dehydrogenase (PDH) in mitochondria. Treatment improved oxidative phosphorylation in 24-mo-old SSM and IFM at baseline compared with vehicle. When 4-PBA-treated 24-mo-old hearts were subjected to ischemia-reperfusion, infarct size was decreased. These results support that attenuation of the ER stress decreased cardiac injury in aged hearts by improving mitochondrial function before ischemia. To challenge the role of CPN1 as an effector of the ER stress, aged mice were treated with MDL-28170 (MDL, an inhibitor of calpain 1). MDL treatment improved mitochondrial function in aged SSM and IFM. MDL-treated 24-mo-old hearts sustained less cardiac injury following ischemia-reperfusion. These results support that age-induced ER stress augments cardiac injury during ischemia-reperfusion by impairing mitochondrial function through activation of CPN1.

The function and regulation of calsequestrin-2: implications in calcium-mediated arrhythmias

Cardiac arrhythmias are life-threatening events in which the heart develops an irregular rhythm. Mishandling of Ca²⁺ within the myocytes of the heart has been widely demonstrated to be an underlying mechanism of arrhythmogenesis. This includes altered function of the ryanodine receptor (RyR2)-the primary Ca²⁺ release channel located to the sarcoplasmic reticulum (SR). The spontaneous leak of SR Ca²⁺ via RyR2 is a well-established contributor in the development of arrhythmic contractions. This leak is associated with increased channel activity in response to changes in SR Ca²⁺ load. RyR2 activity can be regulated through several avenues, including interactions with numerous accessory proteins. One such protein is calsequestrin-2 (CSQ2), which is the primary Ca²⁺-buffering protein within the SR. The capacity of CSQ2 to buffer Ca²⁺ is tightly associated with the ability of the protein to polymerise in response to changing Ca²⁺ levels. CSQ2 can itself be regulated through phosphorylation and glycosylation modifications, which impact protein polymerisation and trafficking. Changes in CSQ2 modifications are implicated in cardiac pathologies, while mutations in CSQ2 have been identified in arrhythmic patients. Here, we review the role of CSQ2 in arrhythmogenesis including evidence for the indirect and direct regulation of RyR2 by CSQ2, and the consequences of a loss of functional CSQ2 in Ca²⁺ homeostasis and Ca²⁺-mediated arrhythmias.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12551-021-00914-6.