A new method can pinpoint gene activity and proteins with unprecedented resolution

A study co-led by researchers at Weill Cornell Medical College, New York-Presbyterian Hospital and the New York Genome Center has shown that a new approach can elucidate the identity and activity
of cells in an entire organ or tumor with unprecedented resolution.

The approach, described in a paper published Jan.
2 in the journal Nature Biotechnology, records patterns of gene activity in tissue samples and the presence of key proteins in cells, while retaining information about the precise location of
cells.
This makes it possible to create complex, data-rich "maps" of organs, including diseased organs and tumors, which could be widely used
in basic and clinical research.

"This technique is exciting because it allows us to map the spatial organization of tissues, including cell types, cellular activities, and cell-to-cell interactions, which is unprecedented.
"

A co-corresponding author is Dr.
Marlon Stoeckius of 10x Genomics, a California-based biotechnology company that manufactures lab equipment
for the analysis of cells in tissue samples.
The three co-first authors are Nir Ben-Chetrit, PhD, Xiang Niu, and Ariel Swett, who are postdoctoral researchers, graduate students, and research technicians in the lab
, respectively.

This new approach came from the joint efforts of scientists and engineers who are developing better ways to "see" how organs and tissues work
at the microscopic scale.
In recent years, researchers have made significant advances, particularly in
techniques for analyzing gene activity and other layers of information in single cells or small cell populations.
However, these techniques often require dissolving the tissue and separating the cells from neighboring cells, so information about the original location of the cells being tested in the tissue is lost
.
This new method can also capture spatial information at high resolution
.

The method, called spatial protein and transcriptome sequencing (SPOTS), is based in part on existing 10x genomics techniques
.
It uses glass slides and is suitable for imaging tissue samples with common microscopy-based pathological methods, which are also coated with thousands of special probe molecules
.
Each probe molecule contains a molecular "barcode" that indicates its two-dimensional position
on the slide.
When a thin tissue sample is placed on a glass slide and makes its cells permeable, probe molecules on the slide capture messenger RNAs (mRNAs) of neighboring cells, which are essentially transcripts of active genes
.
The method includes the use of designed antibodies that bind to proteins of interest in the tissue, or to specialized probe molecules
.
With fast, automated techniques, researchers can identify captured mRNA and selected proteins and map them precisely to their original locations
in tissue samples.
The resulting plot can be considered individually or compared
with standard pathological imaging of the sample.

The team showed SPOTS on spleen tissue in normal mice, revealing the organ's complex functional structure, including clusters of different cell types, their functional states, and how these states change
with cell location.

To highlight the potential of SPOTS in cancer research, the researchers also used it to map the cellular tissue
of mouse breast tumors.
The resulting atlas depicts protein markers in two different states, of immune cells known as macrophages — one that is active and anti-tumor, and the other that is immunosuppressive and forms a barrier
that protects tumors.

"We can see that these two macrophage subsets exist in different regions of the tumor and interact with different cells – differences in the microenvironment may have contributed to their different states of activity.
"

The authors add that these details of the tumor immune environment — details that often can't be resolved due to the thinning of immune cells within tumors — may help explain why some patients respond to immune-boosting therapies and others do not, and therefore inform the design of future immunotherapies
.

The initial version of SPOTS had spatial resolution, so that each "pixel" of the resulting dataset could aggregate information about gene activity in at least a few cells
.
However, the authors say the researchers hope to soon narrow this resolution to individual cells, while adding key cellular information
to other layers.

Journal Reference:

1. Nir Ben-Chetrit, Xiang Niu, Ariel D.
   Swett, Jesus Sotelo, Maria S.
   Jiao, Caitlin M.
   Stewart, Catherine Potenski, Paulius Mielinis, Patrick Roelli, Marlon Stoeckius, Dan A.
   Landau.
   Integration of whole transcriptome spatial profiling with protein markers.
   Nature Biotechnology, 2023; DOI: 10.
   1038/s41587-022-01536-3