Microarray integrated spatial transcriptomics (MIST) for affordable and robust digital pathology

Juwayria; Priyansh Shrivastava; Kaustar Yadav; Sourabh Das; Shubham Mittal; Sunil Kumar; Deepali Jain; Prabhat Singh Malik; Ishaan Gupta

doi:10.1038/s41540-024-00462-1

npj Systems Biology and Applications (Nov 2024)

Microarray integrated spatial transcriptomics (MIST) for affordable and robust digital pathology

Juwayria,
Priyansh Shrivastava,
Kaustar Yadav,
Sourabh Das,
Shubham Mittal,
Sunil Kumar,
Deepali Jain,
Prabhat Singh Malik,
Ishaan Gupta

Affiliations

Juwayria: Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology
Priyansh Shrivastava: Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology
Kaustar Yadav: Department of Pathology, All India Institute of Medical Sciences
Sourabh Das: Department of Mechanical Engineering, Indian Institute of Technology
Shubham Mittal: Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology
Sunil Kumar: Department of Surgical Oncology, All India Institute of Medical Sciences
Deepali Jain: Department of Pathology, All India Institute of Medical Sciences
Prabhat Singh Malik: Department of Medical Oncology, All India Institute of Medical Sciences
Ishaan Gupta: Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology

DOI: https://doi.org/10.1038/s41540-024-00462-1
Journal volume & issue: Vol. 10, no. 1
pp. 1 – 10

Abstract

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Abstract 10X Visium, a popular Spatial transcriptomics (ST) method, faces limited adoption due to its high cost and restricted sample usage per slide. To address these issues, we propose Microarray Integrated Spatial Transcriptomics (MIST), combining conventional tissue microarray (TMA) with Visium, using laser-cutting and 3D printing to enhance slide throughput. Our design facilitates independent replication and customization in individual labs to suit specific experimental needs. We provide a step-by-step guide from designing TMAs to the library preparation step. We demonstrate MIST’s cost-effectiveness and technical benefits over Visium and GeoMx Nanostring. We also introduce ‘AnnotateMap’, a novel computational tool for efficient analysis of multiple ROIs processed through MIST.

Published in npj Systems Biology and Applications

ISSN: 2056-7189 (Online)
Publisher: Nature Portfolio
Country of publisher: United Kingdom
LCC subjects: Science: Biology (General)
Website: https://www.nature.com/npjsba/

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