Spatial biology has transformed the way researchers view tissues, revealing that cells are defined not only by their molecular identities but also by their precise locations and interactions. Yet the field still faces a stubborn technical problem: the most informative experiments often demand more sensitivity, more molecular targets and more than one type of biological measurement at the same time. A new method called protein and nucleic acid serial tyramide amplification, or PASTA, aims to close that gap by combining highly sensitive protein detection with RNA visualization in the same tissue section. The approach, reported by Michel, McCallum, Wu and colleagues in Nature Methods, could help move sophisticated spatial discoveries toward practical clinical assays.
Spatial proteomics typically relies on antibodies to identify proteins within preserved tissue. In principle, this allows researchers to map cellular states and signaling pathways while retaining the architecture of tumors, organs or diseased tissue. In practice, however, conventional fluorescence-based detection can be constrained by weak signals, overlapping emission spectra and the limited number of markers that can be measured simultaneously. These restrictions become especially important in formalin-fixed, paraffin-embedded samples, or FFPE tissue, which are widely used in pathology archives and routine clinical diagnostics but can contain damaged or chemically modified biomolecules.
PASTA addresses the sensitivity problem through tyramide amplification, a strategy built around the enzyme horseradish peroxidase. When an antibody-linked or probe-associated HRP molecule encounters the appropriate chemical substrate, it generates highly reactive tyramide intermediates. These intermediates form covalent bonds with nearby proteins in the tissue, depositing a dense layer of signal close to the original target. Because many reporter molecules can accumulate around a single binding event, the resulting signal can be substantially stronger than that produced by a conventional fluorescent antibody alone. The method therefore converts a relatively faint molecular recognition event into a bright, spatially confined mark.
The distinctive feature of PASTA is that the deposited signal is not limited to a conventional fluorescent dye. Instead, the system uses oligonucleotides—short synthetic DNA sequences—as amplifiable molecular labels. These oligonucleotide tags can be detected during repeated imaging cycles, allowing researchers to identify numerous targets sequentially rather than attempting to distinguish every marker in a single image. In a cyclical imaging workflow, one group of labels is visualized, recorded and chemically removed or inactivated before the next cycle begins. The same tissue section can then be interrogated again, expanding the number of measurable features while preserving the spatial relationships among cells.
This design also creates a route to multimodal analysis. PASTA is described as compatible with conjugated antibodies for protein detection and with in situ hybridization, a family of techniques used to locate specific RNA molecules directly within cells. The combination means that protein abundance and gene activity can be examined together, rather than inferred from separate tissue sections or parallel experiments. Such co-detection is particularly valuable because proteins and RNAs do not always change in lockstep. A transcript may be present before its protein product accumulates, while a stable protein may remain after its corresponding RNA has declined. Measuring both signals in their original cellular context can provide a more nuanced view of cell states and tissue behavior.
The method’s relevance extends beyond technical novelty because FFPE samples are central to clinical medicine. Hospitals and biobanks routinely preserve biopsy and surgical material in this format, creating extensive archives of tissue linked to diagnoses, treatment histories and patient outcomes. Many cutting-edge spatial methods, however, are optimized for fresh or specially preserved material, limiting their direct applicability to routine pathology specimens. By supporting multimodal spatial profiling in FFPE sections, PASTA could make it easier to test research discoveries against real-world clinical cohorts. Researchers may be able to revisit archived material and ask whether a spatial pattern identified in an experimental study also appears across larger collections of patient samples.
The approach could be especially useful in cancer research, where the biological meaning of a marker often depends on its neighborhood. A tumor cell expressing an immune-regulatory protein may have very different implications depending on whether it is surrounded by cytotoxic lymphocytes, suppressive myeloid cells or regions of oxygen deprivation. Protein measurements can describe the signaling machinery present, while RNA measurements can indicate active transcriptional programs and cell identity. With serial amplification and imaging, investigators can build increasingly detailed maps of these interactions. The resulting data may help connect molecular features to tissue architecture, treatment response and disease progression without sacrificing the physical context that bulk sequencing removes.
PASTA also speaks to a broader challenge in biomedical research: the distance between discovery platforms and assays that can realistically be adopted in clinical laboratories. Highly multiplexed technologies can generate remarkable datasets but may require expensive instruments, specialized reagents or workflows that are difficult to scale. The developers present PASTA as a cost-effective bridge, using enzyme-mediated deposition, oligonucleotide labeling and repeated imaging rather than relying exclusively on large, complex instrumentation. Its practical value will depend on factors such as reproducibility, signal carryover between cycles, antibody and probe performance, image-registration accuracy and the ability to interpret large multimodal datasets. Even so, a platform that works with established antibodies, in situ hybridization and FFPE tissue could lower barriers to validation.
The significance of PASTA ultimately lies in its attempt to make spatial biology more comprehensive without forcing researchers to choose between sensitivity, multiplexing and molecular breadth. By translating HRP activity into localized oligonucleotide deposition, the method links enzymatic signal amplification with digital, cycle-based imaging. By supporting proteins and RNA in the same section, it brings two complementary layers of biology into a shared coordinate system. The technology does not eliminate the challenges of spatial measurement, but it offers a strategy for tackling them together. If validated across diverse tissues and clinical applications, PASTA could help turn increasingly sophisticated molecular maps into practical tools for understanding disease and guiding diagnosis.
Subject of Research: Protein and nucleic acid serial tyramide amplification for multimodal spatial profiling of proteins and RNA in tissue samples.
Article Title: PASTA: versatile tyramide-oligonucleotide amplification for multimodal spatial biology
Article References: Michel, H.A., McCallum, P., Wu, W. et al. PASTA: versatile tyramide-oligonucleotide amplification for multimodal spatial biology. Nature Methods (2026). https://doi.org/10.1038/s41592-026-03200-z
Image Credits: AI Generated
DOI: https://doi.org/10.1038/s41592-026-03200-z
Keywords: spatial proteomics, spatial biology, PASTA, tyramide amplification, oligonucleotide deposition, multimodal imaging, RNA detection, protein detection, in situ hybridization, FFPE tissue, multiplexing, clinical pathology
Tags: advanced tissue visualization methodsclinical applications of spatial biologyformalin-fixed paraffin-embedded tissue imaginghigh-sensitivity tissue imaging techniquesmultimodal spatial biologymultiplexed tissue analysisovercoming fluorescence detection limitationsPASTA spatial detection methodprotein and RNA co-detection in tissuesspatial proteomics and transcriptomics integrationtissue architecture preservation in spatial biologytyramide-oligonucleotide amplification
