Calcified Artery Preparation and Processing with Preserved Morphology and RNA for Digital Spatial Profiling

Hong Niu; Keisuke Kamada; Emily Beirne; Gale L. Tang

doi:10.3791/69159

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Method Article

Calcified Artery Preparation and Processing with Preserved Morphology and RNA for Digital Spatial Profiling

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DOI:

10.3791/69159

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January 23rd, 2026

Hong Niu^*¹ , Keisuke Kamada^*¹ , Emily Beirne² , Gale L. Tang¹^,³

¹Division of Vascular Surgery, Department of Surgery, University of Washington, ²Department of Laboratory Medicine and Pathology, University of Washington, ³Division of Vascular Surgery, VA Puget Sound Health Care System

^* These authors contributed equally

Summary

This protocol includes a step-by-step workflow for calcified vascular specimens: tissue handling, decalcification, RNA validation, calcification level detection, and region-of-interest selection strategies on the Nanostring GeoMx Digital Spatial Profiler (DSP). The goal is to present a comprehensive method for preserving vascular tissue morphology and RNA for reliable spatial transcriptomic analysis.

Abstract

Spatial transcriptomics maps whole-transcriptome profiles directly onto tissue sections, correlating between cellular neighborhoods and gene expression and how these activities drive health and disease. Although the approach has transformed oncology, neuroscience, immunology, developmental sciences, and many fields, it has been less widely used in vascular biology, even though vascular disease remains a leading cause of death worldwide. Two obstacles stand out: arteries and veins offer little flat surface for sectioning, and diseased specimens, often atherosclerotic, thrombosed, plaque-laden, or calcified, require harsh treatments such as decalcification that jeopardize morphology and RNA integrity. Yet these same vessels, with their concentric intima, media, and adventitia layered structures, are ideal for spatial analysis because each layer hosts distinct cell types and gene programs that interact across the wall.

Few detailed protocols address how to prepare vascular tissues for spatial transcriptomics. This shortage limits researchers' ability to exploit the technique's full potential. To bridge the gap, we present a step-by-step workflow optimized for human tibial arteries with advanced lesions. The protocol covers tissue handling, fixation, and proper decalcification that preserve structure and RNA quality, followed by histological staining to grade calcification severity. We also describe the construction of tissue microarray (TMA) to curb batch effects and region of interest (ROI) selection strategies on the NanoString GeoMx Digital Spatial Profiler (DSP).

By lowering technical barriers, this protocol enables vascular researchers to generate reliable spatial transcriptomic data and study layer-specific transcriptional activities in healthy and diseased vessels. We anticipate that it will accelerate the discovery of mechanisms underlying calcification, inflammation, intimal atherosclerosis, and other vascular pathologies and foster broader adoption of spatial transcriptomics in vascular biology.

Introduction

Over the past decade, next-generation sequencing and high-resolution imaging have converged to advance spatial transcriptomics, a method of whole transcriptome quantification while preserving each transcript's precise location in tissue sections¹^,². When paired with the rapidly maturing single-cell RNA-sequencing (scRNA-seq) field, spatial approaches provide an efficient route to link gene signatures with specific cell types, states, and niches within a tissue or organ, greatly enriching our understanding of disease mechanisms³^,⁴^,