A new method accurately identifies the activity of genes and proteins across tissues

A new method accurately identifies the activity of genes and proteins across tissues

Image of human breast cancer cells showing a) immunosuppressive macrophages near the connective tissue of the tumor, and b) immunosuppressive macrophages near tumor nests. Credit: Nir Ben Sheetrit.

A new method can shed light on the identities and activities of cells throughout an organ or tumor with unprecedented precision, according to a study co-led by researchers at Weill Cornell Medicine, New York-Presbyterian and New York Genome Center.

The method, described on January 2 in a paper in Nature Biotechnologyrecords the activity patterns of genes and the presence of key proteins in cells next to tissue samples, while retaining information about the exact locations of cells. This enables the creation of complex, data-rich ‘maps’ of organs, including diseased organs and tumours, which can be broadly useful in basics and oncology. Clinical research.

said senior study author Dr. Dan Landau, associate professor of medicine in the division 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.

Another co-author was Dr. Marlon Stoikios of 10x Genomics, a California-based biotechnology company that makes lab equipment for profiling cells within tissue samples. The first three co-authors are Dr. Nir Ben-Shetrit, Chiang Niu, and Ariel Sweet, respectively, a postdoctoral researcher, graduate student, and research technician in Landau’s lab during the study.

The new method is part of a broader effort by scientists and engineers to develop better ways to “see” on a microscale how organs and tissues are working. In recent years, researchers have made significant advances, particularly in techniques for identifying gene activity and other layers of information in individual cells or small groups of cells. However, these techniques typically require tissue dissociation and separation of cells from their neighbours, so that information about the original locations of specific cells within the tissue is lost. The new method captures that Spatial information Well, and in high resolution.

The method, called Spatial Protein and Transcriptome Sequence (SPOTS), is based in part on existing 10x Genomics technology. It uses glass slides suitable for imaging tissue samples using normal microscope-based pathology methods, but is also coated with thousands of special probe particles. Each probe molecule contains a molecular “barcode” indicating its two-dimensional position on the chip. When a sample of thinly sliced ​​tissue is placed on the slide and its cells become permeable, probe molecules on the slide capture neighboring cells’ messenger RNAs (mRNAs), which are essentially transcripts of active genes. The method involves using designed antibodies that bind to proteins of interest in tissues – as well as bind to special probe molecules. Through rapid automated techniques, researchers can identify captured mRNAs and selected proteins, and precisely map them to their original locations across the tissue sample. The resulting maps can be viewed on their own, or compared to standard imaging of the sample’s pathology.

SHOW THE SPOTS TEAM ON tissue of a normal mouse spleen, revealing the complex functional architecture of this organ including different combinations Cell typestheir functional states, and how those states differ at different cell sites.

HIGHLIGHT THE POTENTIAL OF SPOTS IN cancer research, investigators have also used it to map the cellular organization of a mouse breast tumor. The resulting map is photographed immune cells Macrophages are termed in two distinct states as indicated by protein markers—one that is active and tumor-fighting, and the other that is immunosuppressive and forms a tumor-protective barrier.

“We can see that these two subsets of macrophages are in different regions of the tumor and interact with different cells — and this difference in the microenvironment likely drives their distinct activity states,” said Dr. Landau, also a New York-based oncologist. Presbyterian/Weill Cornell Medical Center.

“Such details of the tumor’s immune milieu—details that often cannot be resolved due to the scattering of immune cells within tumors—may help explain why some patients respond to immune-boosting therapy and others do not, and thus could aid the design of immunotherapies in the future.”

This preliminary version of SPOTS has a file spatial accuracy So that each “pixel” of the resulting data set collects information on the genetic activity of at least several cells. However, researchers soon hope to narrow this decision down to single cells, while adding other layers of key cellular information,” said Dr. Landau.

more information:
Marlon Stoikios, Integration of Full Transcriptome Spatial Profiling with Protein Markers, Nature Biotechnology (2023). DOI: 10.1038/s41587-022-01536-3. www.nature.com/articles/s41587-022-01536-3

the quote: New Method Precisely Determines Gene and Protein Activity Across Tissue (2023, January 2) Retrieved January 2, 2023 from https://phys.org/news/2023-01-method-precisely-gene-proteins-tissues.html

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