Tracing the Spatial Transcriptomics Timeline

1) The Beginning of Spatial In Situ Insights

Scientists first reported a method to locate RNA within tissue samples in the late 1960s, using in situ hybridization (ISH) to fix cells within their spatial context, label specific RNA molecules with complementary oligonucleotide probes, and detect targets via microscopy.¹ Today, many herald ISH as the foundation for spatial biology, and modern iterations such as single molecule fluorescent in situ hybridization (smFISH) and multiplexed error-robust fluorescence in situ hybridization (MERFISH) are among the most widely used imaging-based spatial transcriptomic methods.

2) Spatial Transcriptomic Sequencing Comes of Age

From ISH to next-generation sequencing (NGS), RNA detection methods have rapidly progressed from low-throughput, single-target assays to spatial transcriptomics analyses.¹ Researchers generally categorize spatial transcriptomics approaches as imaging-based or sequencing-based.¹ In contrast to ISH-related methods that rely on microscopy to see a target’s position in space, in situ barcoding array-based capture methods—introduced in 2016—use positionally-distinct probes to detect and convert mRNA into cDNA for sequencing.² Array methods such as Slide-seq have various advantages and disadvantages; they often profile larger tissue sections than ISH and in situ sequencing (ISS), but typically provide lower spatial resolution and mRNA recovery rates.²

3) Make Way for More Spatial Methods

Although technologies for transcriptional profiling in tissues have existed for decades, sequencing-enabled profiling and other high-throughput spatial biology techniques such as mass spectrometry imaging bolstered the field as a whole. Spatial transcriptomics was named the 2020 Method of the Year by Nature Methods, followed by spatial proteomics not long after, in 2024.^2,3 Spatial genomic and epigenomic measurements are also increasingly performed using techniques such as ISS, seqFISH+, MERFISH, microfluidic barcoding, Slide-seq, Cut&Tag, and assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq).⁴

4) The Future Is Multiomic

Although current technologies mostly permit scientists to spatially profile only one or two molecular groups at a time, spatial multiomic technologies that combine several omic insights while preserving positional context are on the rise.⁴ For instance, researchers have recently begun integrating spatial barcoding with single-cell methods such as ATAC-seq and RNA-seq, capturing epigenetic, transcriptomic, and genomic data alongside spatial information from complex tissues such as healthy and wound-healing skin and melanoma samples.^4,5