Using Olink PEA technology and RNA-Seq to study disease pathology

Clinical research , Proteomics
Monday 22 February 2021
Read time: 4 minutes

The following study illustrates how transcriptomics and proteomics complement one another to clarify the pathology of a complex, and little understood disease. Atopic dermatitis (AD) is the most common chronic skin condition affecting up to 20% of children and 7-10% of adults, depending on the population.

The disease is incredibly complex and heterogenous, so finding an effective treatment has proven to be quite difficult. Moreover, the use of the skin biopsy as a method of sample collection is incredibly invasive and can cause scarring. Therefore, Rojahn et al. (2020) sought to test a less invasive and painful method known as skin blistering, which, unlike skin biopsies, would allow both transcriptomic analysis from skin cells, and proteomic analysis of the interstitial fluid from the blister.

Proteomics complementing transcriptomics

Olink Neurology, Inflammation, and Immune panels were used to analyze 368 proteins from 8 AD samples and 8 healthy controls and coupled with single-cell RNA transcriptomics (scRNA-seq). Transcriptomic data revealed key inflammatory pathways that had also been found using skin biopsies, but at a higher resolution. By complementing the scRNA-seq data with proteomic data, the researchers found that 67% of the proteins that overlapped between the two were mutually up-or downregulated in AD samples compared to healthy control samples.

A further several protein were identified with proteomics that had not been detected using scRNA-seq alone. Specifically, myeloid dendritic cells and proteins were the most expanded immune population in AD samples. Pathway enrichment analysis also detected cytokine to cytokine receptor interaction proteins and other proteins that act as mediators in antigen processing and presentation and remodeling of the extracellular matrix. Overall, results revealed a far clearer picture of the inflammatory molecules that make up the cellular and proteomic microenvironment of AD.

mRNA abundance doesn’t accurately reflect that of proteins

The study concluded that the skin blister method had certain advantages to the use of skin biopsies to monitor AD, primarily because transcriptomic analysis of skin cells could be combined with proteomic analysis of blister fluid. This is especially beneficial as mRNA abundance doesn’t accurately reflect that of proteins. The skin blistering method also resulted in better transcriptomic resolution of skin cells than skin biopsies, which gave a far clearer picture of AD pathology than has been previously understood. With a disease that is so heterogeneous amongst infected individuals, clarity is paramount.

Here, proteomics complemented transcriptomics to result in a deeper understanding of a little-understood skin condition. What could proteomics do for your research?

Rojahn et al. (2020), Single-cell transcriptomics combined with interstitial fluid proteomics defines cell type–specific immune regulation in atopic dermatitis, Journal of Allergy and Clinical Immunology.

Read the article on ScienceDirect

How the proteome behaves in healthy individuals

Clinical research, Multiomics
To achieve the goal of precision medicine, not only do different molecular profiles need to be understood in disease populations, but they must also be understood in the context of healthy populations.

Key proteomics publications from 2020

Proteomics
Welcome to the first post of the all-new weekly Olink to Science! Our customer survey revealed that you would like to know more about the many publications, research, and other science happening at Olink, therefore this blog aims to do just that: keep you informed on the exciting science taking place with our technology.

Protein biomarkers are crucial in early detection of cancer

Clinical research, Oncology, Protein biomarkers
A central premise of precision medicine is to identify biomarkers indicative of disease transitions early on. This is especially important in cancer where early treatment intervention could increase a patient’s chance of survival and reduce the probability of cancer recurrence.

Using PEA and RNA-Seq to study disease pathology

Clinical research, Proteomics
The following study illustrates how transcriptomics and proteomics complement one another to clarify the pathology of a complex, and little understood disease. Atopic dermatitis (AD) is the most common chronic skin condition affecting up to 20% of children and 7-10% of adults, depending on the population.

Olink protein biomarker panel indicates fermented foods fight inflammation

Inflammation, Proteomics
Could food be used to fight chronic disease?

Study identifies proteins involved in immunotherapy response

Oncology, Proteomics
'Ultimately, it is all about understanding and treating patients better in the future.'

Proteins diagnostic of lung cancer up to 5 years before disease onset

Oncology
An earlier Olink to Science blog post covered some amazing research that found that certain blood protein biomarkers have the potential to predict cancer up to 3 years before diagnosis. This may also be the case for lung cancer, as detailed in a recent study by Dagnino and her colleagues, where elevated levels of CDCP1 were detected in participants of a cohort who later developed the disease.

Utilizing proteogenomics technology for novel drug target discovery

Drug discovery & development
High-throughput multiplexed proteomic technology is leading the way to the latest developments in pre-clinical disease analysis in drug discovery. The pharmaceutical industry is now increasing its efforts in the discovery of novel drug targets by using protein quantitative trait loci (pQTLs), which allows for a more confident inference of disease causality and associated protein regulation.

Developing a high-performance biomarker panel for Alzheimer’s disease

Clinical research, Neurology, Protein biomarkers
A simple search of the term ‘scourge of Alzheimer’s Disease’ brings up over half a million website hits. A major disease, about 15% of us that reach the age of 67 to 74, and 44% of those 75 to 84 will develop AD.

How proteomics helped diabetic kidney disease research advance

Clinical research, Proteomics
Dr. Krolewski and his team at the Harvard Medical School found 56 proteins to be significant in diabetic kidney disease patients. Potentially, these could serve as prognostic biomarkers for disease progression and treatment response. This is how adding proteomics to the methodologies elevated their research.

2947

Biomarker assays

~881 million

Protein data points generated

1182

Publications listed on website