# 3D Cellular and Molecular Mapping within Skeletal Tissue

> **NIH NIH U54** · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · 2021 · $100,000

## Abstract

The goal of the HuBMAP program is to build high resolution 3-D molecular maps of tissues at
the subcellular level including spatial gene expression analysis of transcriptional activity. To date the
representative tissues have not included the mineralized skeletal system due to technical issues that
preclude the requirements of the HuBMAP program. We have solved those issues with a protocol that
is capable of performing multimodal histology that include methods for advanced and repetitive in situ
hybridization for both RNA and protein targets, known as MERFISH and CODEX, respectively. In this
pilot project, we will develop this technology for the bone and cartilage structures of the knee. There
are three divisions of effort led by separate directors. The Coordination Component will acquire de-
identified human distal femur samples from the National Disease Research Interchange. A series of
core biopsies will be extracted from the articular and enthenic cartilage, oriented to its source location,
imaged by µCT to capture its mineral structure and processed into a histological stack to create a 3D
representation of the tissue. Using the histological stack, the Mineralized Tissue Component will
perform both MERFISH in situ hybridization and immunohistology using bar coded antibodies to
identify multiple cell types. The Data Analysis Component will translate the image files generated by
these techniques into 3D cellular maps of the target tissue of each cell type. From those data files, our
contextual molecular mapping program, TOPAS, will identify the 3D relationship of cells within the
cartilage, osteoblast and osteoclast lineages.
 Essential to the objectives underlined above, we need to assemble and implement a high
throughput microscope system capable of performing MERFISH or CODEX types of experiments in
which a computer automation script coordinates cycles of hybridization and washes with a microscope
which scans, images and tiles specific regions of tissue. This supplement request funds to cover cost
of this instrumentation. Our long-term goal, once the pilot program affirms the validity of our
experimental platform for the knee, is to expand its use to a broad range of skeletal tissues and more
complex cellular targets as a new investigatory resource to interrogate the major genetic and
therapeutic challenges affecting skeletal health.

## Key facts

- **NIH application ID:** 10355748
- **Project number:** 3U54AR078664-02S1
- **Recipient organization:** UNIVERSITY OF CONNECTICUT SCH OF MED/DNT
- **Principal Investigator:** PETER MAYE
- **Activity code:** U54 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $100,000
- **Award type:** 3
- **Project period:** 2020-09-21 → 2023-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10355748

## Citation

> US National Institutes of Health, RePORTER application 10355748, 3D Cellular and Molecular Mapping within Skeletal Tissue (3U54AR078664-02S1). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/10355748. Licensed CC0.

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