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Gene & Protein in Disease Insights from In situ spatial profiling

Figure 1. An illustrative example of spatial transcriptomic profiling performed on a lung cancer formalin-fixed paraffin-embedded sample to localize
and quantify tumor cells coexpressing KRAS and PCNA genes. Image created by the authors.

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advanced melanoma. Understanding the interaction spatial changes in RNA transcription in both fresh and
between the immune system and tumor biology is central FFPE tissues. 11
to comprehending disease progression and therapeutic
responses to immuno-oncology agents. These studies 2.2. Spatial perspectives
are enhancing our understanding of patients’ immune Although spatial genomics and transcriptomics offer
responses to checkpoint therapies and aiding in the promising applications, there are still a few challenges that
development of biomarkers. remain. Current advancements in spatial genomics and
Spatial technologies have been utilized to gain a better transcriptomics face several critical challenges – including
understanding of the immune response on dementia validating disease-specific biomarkers, integrating
disorders. Neuroscientists are using single-cell genomics multiomics sequencing with spatial imaging, resolving
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and transcriptomics to study neural tissue architecture. tissue phenotypes, and mapping cellular states within their
The National Institutes of Health has launched the Brain microenvironmental niches. While these challenges persist,
Research through Advancing Innovative Neurotechnologies efforts to address them are actively underway. To support
Initiative to leverage spatial transcriptomics for disease the field’s rapid expansion, researchers must develop
diagnosis. Recently, researchers have applied spatial scalable, cost-effective assays and analytical pipelines that
technologies to investigate the mechanisms by which the minimize bias while enhancing throughput. In addition,
SARS-CoV-2 virus infects patients and the subsequent there is an urgent need to push technical boundaries by
immune responses in lung, brain, and cardiac tissues. 10 improving spatial resolution, expanding multiplexing
capacity, and diversifying measurable molecular features.
In situ sequencing (ISS) enables the sequencing of Widespread adoption will depend on standardized,
hundreds of genes directly within tissue samples while reproducible protocols that ensure data consistency across
preserving spatial information. This process involves laboratories, enabling robust cross-study comparisons and
generating and sequencing clonally amplified barcode accelerating translation into clinical and research settings.
sequences, which are introduced by ligating gene-specific
probes at their original tissue locations. The newly Next-generation spatial technologies will significantly
developed in situ technology allows researchers to analyze advance clinical translational research by identifying gene
fresh, fixed-frozen, or FFPE samples and rapidly generate signatures crucial for biomarker discovery, evaluating target
single-cell gene expression maps for hundreds of genes antigen expression for engineered immune cell therapies,
(Figure 2). The ability to access high-plex information from and enhancing stratification for companion diagnostics
FFPE tissue is particularly significant, as it provides access and clinical trials. Moreover, single-cell spatial analysis
to millions of samples stored in biobanks worldwide and stands as one of the most vital technologies for deepening
associated with clinical outcomes data. The introduction of our biological understanding of the complexities within
the Cancer Transcriptome Atlas and Whole Transcriptome the approximately 40 trillion dynamic cells that make up
Atlas will offer researchers an unbiased approach to assess the human body.

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