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Gene & Protein in Disease Insights from In situ spatial profiling

Spatial profiling requires meticulous attention to detail. has been linked to disease states and their progression.
The quality of the tissue is paramount, especially when However, there has been a notable gap in understanding
dealing with precious or limited samples. Every step of the spatial organization, differentiation, and localization
sample preparation can be challenging, from obtaining the at the genomic and transcriptomic levels both within
right tissue sections to library preparation and sequencing. individual cells and across tissues. Traditional tools have
It involves a delicate balance between preserving the cell been limited in their ability to capture this data effectively,
outline and visualizing its internal structural elements. resulting in the loss of several critical insights into cellular
Many decisions in spatial profiling experiments are mechanisms.
influenced by the type of sample and the specific biological Spatial genomics and spatial transcriptomics are rapidly
question being addressed. However, success also hinges advancing fields aimed at addressing this knowledge gap.
on experience, careful planning, optimization, and a Recent technological breakthroughs have made it possible
willingness to stay flexible and creative. to achieve single-cell resolution. In recent years, the field
5,6
Single-cell spatial profiling technologies are becoming has experienced significant growth with the introduction
the de facto standard for studying complex biological of multiplexed, high-throughput systems capable of
and clinical samples, resulting in a multi-billion-dollar analyzing tens of thousands of genes within a small tissue
market. Leading companies – including 10× Genomics, section. Examples of technologies that employ such an
1-4
NanoString Technologies, and Vizgen – have gained approach include NanoString Technologies’ GeoMx Digital
widespread adoption of these technologies by offering Spatial Profiler and 10x Genomics’ Visium platform – both
robust assays, reliable technical support, and standardized marking significant milestones in sequencing-based spatial
data processing workflows. These innovative approaches are omics methods. Spatial genomics has also seen substantial
reshaping research paradigms – shifting the focus to fewer progress thanks to improvements in techniques, such as
cells analyzed with deeper molecular coverage to better fluorescence in situ hybridization, live DNA imaging using
explore the underlying dysregulated pathways. Similarly, microscopy, genome perturbation tools, massively parallel
in situ spatial profiling technologies are undergoing a sequencing, and several other biochemical methods. This
pivotal shift – once constrained by resolution, they now technological revolution enables researchers to dissect the
emphasize multiplexing capabilities. Several groups are biological architecture of both normal and diseased tissues
pioneering novel methods, including hardware-free single- while preserving the spatial relationships between cells.
cell systems, which may complement existing platforms in This approach provides valuable insights not only at the
the future. individual cell level but also at the tissue level. Researchers
can now map whole-transcriptome spatial gene expression
The aim of this review is to track the translation of across multiple cells in complex tissue samples. This highly
these technologies from academic laboratories to the sensitive technique allows for the simultaneous analysis of
commercial market, creating a valuable resource for the hundreds of thousands of cells in a tissue section through
bioscience community. This includes two key objectives: total messenger RNA (mRNA) spatial gene expression
(i) empowering potential adopters with clear, comparative analysis (Figure 1). 7
insights into available tools, and (ii) accelerating the
integration of cutting-edge academic discoveries into 2.1. Small details reveal the big picture
industrial workflows. The pace of advancement is striking Despite being a new frontier in the genomics field, spatial
– so rapid, in fact, that even dedicated researchers struggle genomics has demonstrated a broad range of impactful
to stay abreast of new technologies while balancing other applications. This technology is agnostic to both tissue
scientific priorities.
type and species, making it applicable to numerous
2. An in-depth analysis of spatial genomics studies involving both healthy and diseased tissues. It has
and transcriptomics been widely used to examine tumor heterogeneity, tissue
morphology, mechanisms of tissue development, and
The multicellular layout of tissues has been meticulously responses to therapeutic interventions. Variations in the
explored through the use of microscopy, imaging, and a spatial organization of the genome have been leveraged
range of visualization techniques. Similarly, the intricate as diagnostic biomarkers for identifying specific disease
structure and configuration of genetic elements – such as conditions. Recent research highlights the effectiveness of
DNA, RNA, and the chromatin network – within cells have spatial technology in examining tumor-associated tertiary
been thoroughly examined. This wealth of information lymphoid structures – highly organized emergent immune
has been crucial for evaluating gene expression changes, compartments – to characterize molecular patterns
cellular functions, and maintaining homeostasis, and it associated with responses to checkpoint inhibitors in

Volume 4 Issue 3 (2025) 2 doi: 10.36922/GPD025050007