Spatial transcriptomics and proteomics provide additional information that has changed our understanding of complex biological processes. However, the experimental integration of these modalities is limited.

A new method called Spatial Protein and Transcriptome Sequencing (SPOTS) can illuminate the identity and activities of cells in an organ or a tumor with unprecedented resolution. Developed by researchers at Weill Cornell Medicine, NewYork-Presbyterian and the New York Genome Center, SPOTS can illuminate the identities and activities of cells in an organ or tumor with unprecedented resolution.

The technique preserves information about the precise locations of the cells while recording patterns of gene activity and the presence of essential proteins in cells in tissue samples. This makes it possible to create intricate, data-rich “maps” of organs, including organs that are diseased and tumours, which can be very useful in both basic and clinical research.

Study co-senior author Dr. Dan Landau, an associate professor of medicine in the Department of Hematology and Medical Oncology and a member of the Sandra and Edward Meyer Cancer Center at Weill Cornell Medicine and a core faculty member at the New York Genome Center, said, “This technology is exciting because it allows us to map the spatial organization of tissues, including cell types, cell activities and cell-to-cell interactions, like never before.”

The new approach is part of a larger initiative by scientists and engineers to create more effective means of “seeing” how organs and tissues function at the microscopic level. Significant advances in research have been made in recent years, particularly in methods for profiling gene activity and other layers of data in single cells or small groups of cells. However, the information regarding the original placement of the profiled cells in the tissues needs to be recovered, as these approaches often call for the breakdown of tissues and the separation of cells from their neighbours. The new technique also records this spatial data and does so with excellent resolution.

The method is partly based on existing 10x Genomics technology. It uses slides suitable for imaging tissue samples with common microscope-based pathology methods, but is also coated with thousands of specific probe molecules.

The chemical “bar code” of each probe molecule identifies its two-dimensional location on the slide. The probe molecules on the slide grab the messenger RNAs (mRNAs), essentially the transcripts of activated genes, from neighboring cells. When a thinly sliced ​​sample of tissue is placed on the slide, the cells are permeabilized. Designer antibodies are used in the procedure and they attach to the unique probe molecules and proteins of interest in the tissue.

Researchers can quickly and automatically identify the collected mRNAs and chosen proteins and accurately map them to their original locations in the tissue sample. The maps produced can be considered independently or in comparison to the routine pathology imaging of the sample.

On tissue from a healthy mouse spleen, the team used SPOTS to show the organ’s intricate functional architecture, including clusters of different cell types, their functional states, and how those states changed depending on the placement of the cells.

The researchers also used SPOTS to map the cellular structure of a mammary tumor in mice, highlighting its potential for use in cancer research. The map generated showed macrophages and immune cells in two different states, each indicated by a different protein marker: one condition was active and fought against tumors, while the other was immunosuppressive and erected a barrier to shield the tumor.

Dr. Landau, an oncologist at NewYork-Presbyterian/Weill Cornell Medical Center, said: “We could see that these two subsets of macrophages are found in different parts of the tumor and interact with different cells — and that difference in the microenvironment is likely what drives their different states of activity.”

“Such details of the tumor’s immune environment — details that often cannot be resolved due to the paucity of immune cells in tumors — could help explain why some patients respond to immune stimulant therapy and others do not, and thus inform design.” of future immunotherapies.”

“This first version of SPOTS has a spatial resolution so that each “pixel” of the resulting dataset sums up gene activity information for at least several cells. However, the researchers hope to soon limit this resolution to single cells while adding other layers of important cellular information. to add.”

Magazine reference:

  1. Ben-Chetrit, N., Niu, X., Swett, A. D. et al. Integrating whole transcriptome spatial profiling with protein markers. Nat Biotechnology (2023). DOI: 10.1038/s41587-022-01536-3