New method precisely localizes gene activity and proteins in tissue – Zoo House News
A new method can shed light on the identities and activities of cells in an organ or tumor with unprecedented resolution, according to a study co-led by researchers from Weill Cornell Medicine, New York-Presbyterian and the New York Genome Center.
The method, described in a Jan. 2 article in Nature Biotechnology, maps patterns of gene activity and the presence of key proteins in cells across tissue samples, while storing information about the exact locations of the cells. This enables the creation of complex, data-rich “maps” of organs, including diseased organs and tumors, which could be of great use in basic and clinical research.
“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,” said Dr. Dan Landau, co-senior author of the study, associate professor of medicine in the division of hematology and medical oncology and Sandra and Edward Meyer Cancer Center member at Weill Cornell Medicine and core faculty member at the New York Genome Center.
The other co-senior author was Dr. Marlon Stoeckius of 10x Genomics, a California-based biotechnology company that makes laboratory equipment for profiling cells in tissue samples. The three co-first authors were Dr. Nir Ben-Chetrit, Xiang Niu, and Ariel Swett, respectively postdoctoral fellows, graduate students, and research technicians at the Landau lab during the study.
The new method is part of a broader effort by scientists and engineers to develop better ways to ‘see’ how organs and tissues function on a micro scale. Researchers have made great strides in recent years, particularly in techniques for profiling gene activity and other layers of information in individual cells or small groups of cells. However, these techniques typically require the dissolution of tissues and the separation of cells from their neighbors such that information about the original locations of the profiled cells within the tissue is lost. The new method also captures this spatial information and in high resolution.
The method, called Spatial PrOtein and Transcriptome Sequencing (SPOTS), is based in part on existing 10x Genomics technology. It uses glass slides that are suitable for imaging tissue samples using standard microscope-based pathology methods, but are also coated with thousands of special probe molecules. Each of the probe molecules contains a molecular “barcode” that indicates its two-dimensional position on the slide. When a thinly sectioned tissue sample is placed on the slide and its cells perfused, the probe molecules on the slide grab the messenger RNAs (mRNAs) of neighboring cells, which are essentially the transcripts of active genes. The procedure involves the use of designer antibodies that bind to proteins of interest in the tissue — and also bind to the special probe molecules. Using rapid, automated techniques, researchers can identify the captured mRNAs and selected proteins and accurately image them to their original locations in the tissue sample. The resulting maps can be viewed alone or compared to standard pathological imaging of the sample.
The team demonstrated SPOTS on tissue from a normal mouse spleen, revealing the complex functional architecture of this organ, including clusters of different cell types, their functional states and how these states varied with cell locations.
Highlighting the potential of SPOTS in cancer research, the researchers also used it to map the cellular organization of a mouse mammary tumor. The resulting map showed immune cells, called macrophages, in two different states, identified by protein markers – one state active and tumour-fighting, the other immunosuppressive and forming a barrier to protect the tumour.
“We could see that these two macrophage subsets are found in different areas of the tumor and interact with different cells – and that the difference in microenvironment likely drives their different states of activity,” said Dr. Landau, who is also an oncologist in New York – Presbyterian/Weill Cornell Medical Center.
Such details of the tumor’s immune environment – details that often cannot be resolved due to the small number of immune cells in tumors – could help explain why some patients respond to immune-enhancing therapy and others do not, and thus could inform the design of future immunotherapies, he added.
This first version of SPOTS has such a spatial resolution that each “pixel” of the resulting dataset sums the gene activity information for at least several cells. However, researchers hope to soon narrow this resolution down to single cells while adding more layers of important cellular information, said Dr. Landau.
Many of Weill Cornell Medicine’s physicians and scientists maintain relationships and collaborate with outside organizations to promote scientific innovation and provide expert advice. The institution makes these disclosures public to ensure transparency. For this information see profile of Dr. Landau.