Open-ST: un nuovo metodo per creare mappe accurate dei tessuti in 3D

Open-ST: a new method for creating accurate 3D tissue maps

An international study carried out by researchers of Sapienza University of Rome in collaboration with the MDC Institute in Berlin and the University of Milan, funded by the MUR from PNRR funds through the Centro Nazionale per la terapia genica e farmaci RNA, has developed 'Open-ST', a new method for generating a three-dimensional map of the cells of a tissue and for identifying molecular interactions. The results of the study, published in the journal Cell, will improve understanding of tissue physiology and bring new information to support precision medicine

The ability to map tissue by distinguishing individual cells in three dimensions is a goal of much clinical research in pathology and physiology. To achieve this, systems for analysing and mapping biological specimens and their components must be perfected to be increasingly accurate, efficient and cost-effective.

This is the aim of the new "Open Spatial Transcriptomics (Open-ST)" system, developed by a scientific collaboration between researchers at Sapienza University of Rome, the Institute for Medical Systems Biology in Berlin and the University of Milan-Istituto Fondazione Oncologia Molecolare, thanks also to funding from the Ministry for Universities and Research within the framework of the National Centre ' Sviluppo di terapia genica e farmaci con tecnologia a RNA" on Next Generation EU - National Plan for Recovery and Resilience (PNRR) funds.

This new approach allows the three-dimensional analysis of transcripts, i.e. the RNA molecules that transmit information contained in genes within the cell

Until a few years ago, it was not possible to carry out detailed molecular analyses because the techniques used only allowed average values to be obtained for a large number of molecules. Since the last decade, however, it has been possible to study the aspects of each cell and thus their specific molecular contribution within a sample using "single-cell omics" tools. These analyses have greatly increased the information that can be obtained but do not allow the spatial localisation of each cell within a tissue to be defined.

For this reason, further technologies have more recently been developed to also consider the spatial arrangement of cells. Such transcript analysis technologies characterise molecules transcribed from each gene while preserving their location but have limitations due to their high cost and limited resolution in terms of sensitivity in defining molecules in each individual cell.

In this context, the new Open-ST system was developed, which allows the three-dimensional study of cellular components through a precise sequence of experimental steps, including the analysis of molecular markers, the division of the cell into subunits to be analysed separately, and finally the editing and digital visualisation of the data using specially developed software.

To demonstrate the quality and efficiency of their method, the scientists tested the system on different types of tissue. In particular, they successfully analysed tissue from a human carcinoma, which is characterised by high variability in the genetic code, and from a lymphoma, for which the Open-ST approach could be used to identify biomarkers useful for characterising the tumour tissue itself.

"The study", states Elisabetta Ferretti of the Department of Experimental Medicine, "is the result of a collaboration with Giuseppe Macino, Emeritus of Sapienza University and President of the Forge Foundation in Udine, with Nikolaus Rajewsky, Director of the Laboratory of Systems Biology of Gene Regulatory Elements at the Berlin Institute for Medical Systems Biology of the Max Delbrück Centre (MDC-BIMSB) and with Massimiliano Pagani of the University of Milan and Director of the Laboratory of Molecular Oncology and Immunology at IFOM".

"RNA transcripts", says Elena Splendiani of Sapienza University of Rome and first author of the study, "are fundamental molecules for the transmission of the information contained in each gene. Measuring their quantity with the new Open-ST technology makes it possible not only to define them accurately but also to know their distribution in 3D space down to the intracellular level in each cell, making it possible to obtain new information on positioning and communication between cells. Specifically, in addition to the fine-tuning of the new technology, the first samples of both healthy and tumour tissue were analysed".

"The high definition of the technique on a tumour sample showed that there are 10 different types of tumour cells in a single tumour, defining details of tumour heterogeneity never previously described", added Giuseppe Macino.

"These results", Elisabetta Ferretti and Giuseppe Macino conclude, "lay the foundations for the knowledge of new RNA molecules, useful for the development of gene therapy and the definition of biomarkers for patient diagnosis and management in the field of precision medicine".