Sharing of omics research ideas based on clinical FFPE samples & micro puncture samples

Clinical FFPE and puncture samples are still important sample sources in the current medical field and disease diagnosis, and can provide accurate and effective pathological information for medical and drug research

Let's take a look at related classic research cases

Case 1 (IF = 38.

FFPE proteome reveals that melanoma's response to immunotherapy is mitochondrial

Researchers used proteomics to study FFPE samples of 116 patients with advanced (stage IV) melanoma who received tumor-infiltrating lymphocytes (TIL) or anti-programmed death (PD1) immunotherapy, and found the immunotherapy Differential protein between responding and non-responsive patients

The study found that the oxidative phosphorylation and lipid metabolism of the response group were higher than those of the non-response group

Proteomics of Melanoma Response to Immunotherapy Reveals Mitochondrial Dependence.

Case 2

The combination of protein markers obtained based on a large sample of FFPE protein profile can distinguish benign and malignant thyroid nodules

The Guo Tiannan/Li Ziqing team of West Lake University performed systematic protein analysis on 931 thyroid nodule tissue samples (including the discovery cohort FFPE sample n=579, retrospective test array FFPE sample n=288 and prospective prediction array puncture sample n=64).

Finally, the protein marker model tested and verified by machine learning contains 14 proteins and has good diagnostic capabilities.

Protein Classifier for Thyroid Nodules Learned from Rapidly Acquired Proteotypes.

Case 3 (IF = 4.

FFPE proteomics study reveals a conservative MSI-H colorectal cancer immune feature

The research team of Hebrew University Medical Center in Israel conducted a proteomic study on 19 microsatellite unstable (MSI-H) and microsatellite stable (MSS) colorectal cancer FFPE samples

Studies have found that proteins overexpressed in MSI-H but not MSS are enriched in immune-related pathways, especially antigen processing and presentation

Novel Proteome Extraction Method Illustrates a Conserved Immunological Signature of MSI-H Colorectal Tumors.

Case 4 (IF = 8.

Using skin puncture samples to study the characteristics of extracellular matrix proteins in recurrent spontaneous carotid artery dissection

The research team from the University of Innsbruck in Australia obtained results from patients with spontaneous carotid artery dissection (n=6), patients with single-vessel carotid artery dissection (n=19), patients with multi-vessel carotid artery dissection (n=13) and healthy controls (n=13).

Proteomics analysis showed that there was no difference in protein between patients with single-vessel carotid artery dissection or patients with multi-vessel carotid artery dissection, or compared with healthy controls.

This study revealed the characteristics of extracellular matrix proteins in recurrent spontaneous carotid artery dissection
.
In the long term, the authors’ findings may help identify patients at risk of recurring spontaneous carotid dissection and guide treatment
.

Extracellular matrix protein signature of recurrent spontaneous cervical artery dissection.
Neurology.
2020 https://doi.
org/10.
1212/WNL.
0000000000010710

Case 5 (IF = 4.
87)

Proteomics of human heart biopsy reveals remodeling protein profile of dilated left atrium without atrial fibrillation

Researchers at New York University in the United States obtained precious heart biopsy samples from seven mitral valve prolapse (MVP) patients undergoing valve replacement operations, including samples of the right atrium, left atrium, and left ventricle
.
The left atrium of these patients was dilated, but there was no history of atrial fibrillation
.

After proteomic testing of all samples, more than 7000 proteins were obtained, and specific molecular characteristics of different heart tissue regions were discovered, which reflect the special functions of different heart regions
.
At the same time, the authors made it clear that quantitative proteomic analysis from freshly collected biopsy tissue is superior to autopsy samples because there is more non-specific protein degradation in the latter
.
At the same time, the authors also found that the increased protein abundance associated with persistent atrial fibrillation is not a sufficient condition for the disease state
.
The difference in protein abundance between atria and ventricles is mainly due to the level of gene regulation, which reflects a functional requirement
.

Quantitative proteomics of human heart samples collected in vivo reveal the remodeled protein landscape of dilated left atrium without atrial fibrillation.
Molecular & Cellular Proteomics.
2020.
https://doi.
org/10.
1074/mcp.
RA119.
001878

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