# High-resolution 3D in situ Spatial Gene Expression Profiling Technology for Human Brain Specimens

> **NIH NIH R43** · EXPANSION TECHNOLOGIES, INC. · 2022 · $500,000

## Abstract

Project Title: High-resolution 3D in situ Spatial Gene Expression Profiling Technology for
Human Brain Specimens
Project Description
 The overall aim of this Phase I project is to apply Expansion Sequencing, a
genome-wide in situ transcriptomics profiling technology with unprecedented spatial resolution
in 3D, to human brain tissues to empower brain disease research and therapeutic development.
Neurodegenerative diseases, such as Alzheimer’s disease affects over 11% of the population
aged above 65, causing ⅓ of death in seniors, and costs hundreds of billions of dollars a year.
Yet, no disease modifying therapeutics have been approved for marketing. The ability to obtain
data and validate discoveries directly in human samples is paramount to our ability to
characterize and understand brain disorders. Spatially resolved transcriptomics, helps
scientists understand how the different cells are organized, using fluorescence microscopy
imaging has shown unmatched promise in characterizing different cell types in native tissue,
change during development and aging, and how they influence behavior and disease.
 However, many of existing spatial technologies are limited to thin animal brain sections.
They are bound by optical diffraction-limited resolution, restraining the ability to precisely define
a large variety of cell types organized in 3D. Tissues from humans and those with
neurodegenerative disease have high degree of autofluorescence caused by protein aggregates
(such as Amyloid plaques), lipofuscin granules and dense vessels. Recently published in
Science, Expansion Sequencing (ExSeq) is the first in situ genome-wide 3D spatial gene
expression profiling technology. It provides unprecedented imaging resolution in 3D using thick
mouse brain sections. This allows for clear definition of synapse junctions and mapping gene
transcripts with single- and sub-cellular precision, which had not been possible with
conventional fluorescence confocal microscopes used by most researchers. In order to make
ExSeq suitable for human studies and commercially available, we identified and tested a new
set of methods that will allow us to optimise ExSeq for human specimens, and improve
sensitivity and specificity. We are building a set of analytical tools to help visualize, debug and
improve the robustness of the analytics pipeline. We have also obtained access to a wide
variety of precious human brain tissues, to help us test different sample preparation conditions
and validate our methods.
 For this Phase I project, we will develop ExSeq protocol for human brain tissue
characterisation with a proof-of-concept gene panel, and create a robust image processing and
analytical pipeline that can accommodate images generated from different experimental and
laboratory settings. Finally, we will process and analyse a set of human normal and
Alzheimer’s diseased brain tissues, and validate results against published data and prior
research. Building upon a strong scientific f...

## Key facts

- **NIH application ID:** 10385072
- **Project number:** 1R43AG076178-01
- **Recipient organization:** EXPANSION TECHNOLOGIES, INC.
- **Principal Investigator:** Mahender Babu Dewal
- **Activity code:** R43 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $500,000
- **Award type:** 1
- **Project period:** 2022-09-01 → 2024-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10385072

## Citation

> US National Institutes of Health, RePORTER application 10385072, High-resolution 3D in situ Spatial Gene Expression Profiling Technology for Human Brain Specimens (1R43AG076178-01). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10385072. Licensed CC0.

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