Scientists from ICCVS publish in Nature Methods

dr Javier Alfaro

A recently published article in Nature Methods entitled „The emerging landscape of single-molecule protein sequencing technologies” jointly led by researchers including dr Javier Alfaro from the ICCVS, University of Gdansk and dr Adam Pomorski from the University of Wrocław, was developed in cooperation with scientists from around the world including significant contributions by dr Umesh Kalathiya, MSc Georges Bedran and prof. David Goodlett from ICCVS. Its aim is to describe the technologies developed for studying proteins at the level of a single molecule, which would enable the determination of the proteome at the level of one cell.

Single-cell sequencing methods are a new technology that allows us to study individual cells within a tissue. In cancer this is helping us to understand why tumours sometimes cannot be treated. While genomes (DNA) and transcriptomes (RNA) can be explored at the single-cell level, single-cell profiling of proteomes (proteins) has been very difficult. Since proteins carry out many of the most important activities in the cell, this gap in technology is greatly limiting our understanding of tissue biology.  

“Proteomics is currently dominated by mass-spectrometry technologies” – says dr Javier Alfaro from the International Center for Cancer Vaccine Science in Gdansk. These technologies are expensive and sequence proteins poorly in complex mixtures. "We do not sequence every amino-acid in the sequence as we do in DNA in these complex mixtures" – says dr Javier Alfaro. The field is really waiting for a transformative wave of technologies similar to what hit the DNA sequencing world - but applied to proteins. "The problem is that unlike DNA, there is no way to amplify proteins - and this poses a big challenge to the sensitivity of current instrumentation" – adds dr Javier Alfaro.  

 

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These up and coming sequencing techniques could one day sequence the proteomes of single cells, or lead to new highly sensitive diagnostics. Generally, the techniques involve protein extraction, followed by some sample preparation specific to a diversity of technologies. Each technologies identifies a protein in a different way as described in the figure.  

Proteomics awaits a similar transformative wave of protein-sequencing techniques that will allow for the examination of proteins at the single-cell and ultimately single-molecule levels, even with low-abundant proteins. Such techniques would allow routine proteome profiling, like today’s single-cell RNA sequencing studies, creating opportunities for single-cell proteomics and potentially permitting real-time testing for on-site medical diagnostics and disease screening.

"These new technologies depend on new chemistries and biological reporters that allow us to fluorescently detect not only specific amino acids in proteins, but also their modifications" – dr Adam Pomorski from the University of Wrocław.

During the writing of the work, a blossoming world of biophysicists, technologists, clinicians and computational researchers was invited to share their perspectives as equal contributors.  “In this day and age, we are all masters of our own specific fields. Bringing people together as equals so that their full energy and diverse perspectives can be combined is essential to break barriers and bring about scientific insight” – says dr Javier Alfaro 

 

Link to the article: https://www.nature.com/articles/s41592-021-01143-1

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