# A 3D Tissue Map of the Human Lymphatic System

> **NIH NIH U54** · UNIVERSITY OF FLORIDA · 2020 · $1,775,000

## Abstract

The lymphatic system serves five primary roles: 1) removal of excess body fluids; 2) absorption and transport
of fatty acids/chyle to the circulatory system; 3) blood filtration; 4) mounting the primary defense against
infections and cancer through immune cell production and activation; and 5) generation and activation of
regulatory immune cells that protect against autoimmune/autoinflammatory disease. Given these key
physiological functions, we deem it important to develop a three-dimensional (3D) tissue map for three major
lymphoid organs of the human immune system: spleen, thymus and lymph nodes (Organ Specific Projects 1-
3, respectively). As one of our primary strengths, we have over 10 years of experience in the procurement of
transplant-quality organs for research, including those of the lymphatic system. As part of this 24/7/365 effort,
we have well-established relationships with the U.S. Organ Procurement Organizations (OPO), having referrals
from 56/58 over the last decade. Our standard operating procedures (SOPs), both published and web-based,
include assessment of normality, quality control assays, and systematic anatomical dissection/storage. We
also participate in National QA/QC programs to evaluate tissue processing/banking procedures. Our approach
to developing assay pipelines towards the common goal of a 3D tissue map will initially involve acquiring a
macro image of the intact tissue and addressing tissue morphology, using our strengths in magnetic resonance
imaging (MRI). The proposed optical microscopy pipeline will address microanatomical features using formalin
fixed paraffin embedded (FFPE) and optimal cutting temperature (OCT) compound embedded sections as well
as tissue optical clearing and expansion. These specimens will be studied from nm to mm resolution using
stochastic optical reconstruction microscopy (STORM), confocal, multiphoton and light sheet fluorescence
microscopies (LSFM), with all pipelines sharing a common file format for simplified 3D reconstruction. Based
on the unique role for lymphatic organs in production and trafficking of immune cells, fluorescence activated
cell sorting (FACS) of cells from blood and each lymphatic organ will provide a comparison of the patient-
specific immune cell repertoire and serve in subsequent single cell RNA-seq analyses. To co-register
biomolecules to their cognate cells, we will employ imaging mass cytometry (IMC), multiplex single molecule
fluorescence in situ hybridization (smFISH) and multiplexed error-robust FISH (MERFISH) to map cellular
protein and mRNA expression, ultimately on each 3D tissue atlas. Our experience in organ procurement, the
availability of the National High Magnetic Field Laboratory (NHML) Advanced Magnetic Resonance Imaging
and Spectroscopy (AMRIS) Facility at UF, multiphoton/confocal microscopy, LSFM, state of the art FACS, 10X
GENOMICS Chromium controller, and high throughput cDNA library sequencing for RNA-Seq at the University
of Florida, as we...

## Key facts

- **NIH application ID:** 9970184
- **Project number:** 5U54AI142766-03
- **Recipient organization:** UNIVERSITY OF FLORIDA
- **Principal Investigator:** MARK A. ATKINSON
- **Activity code:** U54 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $1,775,000
- **Award type:** 5
- **Project period:** 2018-09-14 → 2022-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9970184

## Citation

> US National Institutes of Health, RePORTER application 9970184, A 3D Tissue Map of the Human Lymphatic System (5U54AI142766-03). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/9970184. Licensed CC0.

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