Reverse Phase Protein Array Reveals Correlation of Retinoic Acid Metabolism With Cardiomyopathy in Friedreich's Ataxia

Autor: Lauren A. Hauser, Marek Napierala, Amanda Clark, Jennifer M. Farmer, Kimal Rajapakshe, David A. Lynch, Peining Xu, Clementina Mesaros, Dean P. Edwards, Yu-Yun Chen, Ian A. Blair, Shixia Huang, Cristian Coarfa, Jill S. Napierala
Jazyk: angličtina
Rok vydání: 2021
Předmět:
Male
Proteomics
Retinoic acid
Biochemistry
Analytical Chemistry
chemistry.chemical_compound
reverse phase protein array
Iron-Binding Proteins
Gene expression
RA
retinoic acid
Cells
Cultured
ROL
retinol
0303 health sciences
frataxin
biology
LDH
lactate dehydrogenase
030302 biochemistry & molecular biology
PDT
population doubling time
Reverse phase protein lysate microarray
Middle Aged
DE
differentially expressed
Aldehyde Oxidoreductases
H2O2
hydrogen peroxide
CTRL
control
Biomarker (medicine)
biomarker
Female
medicine.symptom
Cardiomyopathies
Adult
IRB
Institutional Review Board
Ataxia
Adolescent
retinoid metabolism
ALDH1A3
aldehyde dehydrogenase family 1 member A3
Protein Array Analysis
UAB
University of Alabama at Birmingham
GAA
guanine–adenine–adenine
CHOP
Children's Hospital of Philadelphia
03 medical and health sciences
Retinoids
Young Adult
FRDA
Friedreich's ataxia
medicine
Humans
RAL
retinal
Molecular Biology
030304 developmental biology
AOX1
aldehyde oxidase 1
Aged
RPPA
reverse phase protein array
HL
hearing loss
Research
Friedreich's ataxia
FARS
Functional Assessment Rating Scale
FC
fold change
Fibroblasts
Molecular biology
Fold change
CMP
cardiomyopathy
FXN
frataxin
chemistry
ISTD
internal standard
Friedreich Ataxia
BCM
Baylor College of Medicine
Frataxin
biology.protein
integrins
Biomarkers
Zdroj: Molecular & Cellular Proteomics : MCP
ISSN: 1535-9484
1535-9476
Popis: Identifying biomarkers is important for assessment of disease progression, prediction of symptom development, and determination of treatment effectiveness. While unbiased analyses of differential gene expression using next-generation sequencing methods are now routinely conducted, proteomics studies are more challenging because of traditional methods predominantly being low throughput and offering a limited dynamic range for simultaneous detection of hundreds of proteins that drastically differ in their intracellular abundance. We utilized a sensitive and high-throughput proteomic technique, reverse phase protein array (RPPA), to attain protein expression profiles of primary fibroblasts obtained from patients with Friedreich's ataxia (FRDA) and unaffected controls (CTRLs). The RPPA was designed to detect 217 proteins or phosphorylated proteins by individual antibody, and the specificity of each antibody was validated prior to the experiment. Among 62 fibroblast samples (44 FRDA and 18 CTRLs) analyzed, 30 proteins/phosphoproteins were significantly changed in FRDA fibroblasts compared with CTRL cells (p < 0.05), mostly representing signaling molecules and metabolic enzymes. As expected, frataxin was significantly downregulated in FRDA samples, thus serving as an internal CTRL for assay integrity. Extensive bioinformatics analyses were conducted to correlate differentially expressed proteins with critical disease parameters (e.g., selected symptoms, age of onset, guanine–adenine–adenine sizes, frataxin levels, and Functional Assessment Rating Scale scores). Members of the integrin family of proteins specifically associated with hearing loss in FRDA. Also, RPPA data, combined with results of transcriptome profiling, uncovered defects in the retinoic acid metabolism pathway in FRDA samples. Moreover, expression of aldehyde dehydrogenase family 1 member A3 differed significantly between cardiomyopathy-positive and cardiomyopathy-negative FRDA cohorts, demonstrating that metabolites such as retinol, retinal, or retinoic acid could become potential predictive biomarkers of cardiac presentation in FRDA.
Graphical abstract
Highlights • RPPA analyzing Friedreich's ataxia cells reveals changed expression of 30 proteins. • Integrin expression correlates with hearing loss in Friedreich's ataxia samples. • Retinol levels are lower in serum of patients with Friedreich's ataxia than controls.
In Brief We conducted a sensitive and high-throughput reverse phase protein array to attain protein expression profiles of primary fibroblasts from patients with Friedreich's ataxia (FRDA) and unaffected controls using a pool of 217 validated antibodies. Our extensive bioinformatics analyses correlated differentially expressed (DE) proteins with critical disease parameters. Expression levels of several integrin proteins specifically associated with hearing loss in FRDA. Also, reverse phase protein array data integrated with transcriptome data uncovered defects in retinoic acid metabolism in FRDA samples.
Databáze: OpenAIRE
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