# Spatial Data Analysis Demo Report

## GeoMx® Demo Report: Diabetic Kidney Disease

NanoString Technologies, Inc. 1

2024-05-15

# 1 Introduction

We present here a data analysis report for GeoMx® Whole Transcriptome Atlas (WTA) data collected from diseased and healthy kidney samples. In particular, glomeruli and tubule structures were spatially profiled from the tissues. We explore biological differences as a function of disease status and structure at gene, cell type, and pathway levels.

## 1.1 Slides and Profiling Strategy

The dataset of interest includes 4 diabetic kidney disease (DKD) and 3 healthy kidney tissue samples. Regions of interest (ROI) were spatially profiled to focus on two different kidney structures: tubules or glomeruli. One glomerular ROI segment contains the entirety of a single glomerulus. Each tubular ROI contains multiple tubules that were further subdivided into distinct distal (PanCK+) and proximal (PanCK-) tubule area of illumination (AOI) segments.

We can look at a representative tissue section below. ROIs are shown as white geometric outlines. AOI segments are shown as transparent overlays within the ROIs.

Example Kidney ROI Layout.

## 1.2 Experimental Questions

This analysis report focuses on two key experimental comparisons:

Question 1: What are the differences between glomeruli and tubules across all samples?

Question 2: What are the differences in glomeruli from healthy versus diseased (DKD) kidneys?

For each comparison above, we look for differentially expressed genes, quantify differences in cell type abundances using spatial deconvolution, and examine pathway differences using single sample Gene Set Enrichment Analysis (ssGSEA).

Additionally, we tracked WFDC2, PODXL, and PLA2R1 genes of interest and the INTRAFLAGELLAR_TRANSPORT pathway of interest throughout the analysis.

## 1.3 Results Overview

Below is an executive summary of the analysis generated from the report.

### 1.3.1 Overview of report analysis

- 7 of 7 tissue slides were analyzed.
- 221 of the 235 ROI/AOI segments were analyzed.
- 10,131 genes, 29 cell types, and 1,467 pathways were explored in depth.
- The following were noted as differences between Glomeruli vs Tubules with FDR<0.05:
  - 3,048 genes were differentially expressed.
  - 13 cell types were differentially observed.
  - 625 pathways were differentially enriched.
- The following were noted as differences between Normal vs Diseased (DKD) Glomeruli with FDR<0.05:
  - 107 genes were differentially expressed.
  - 0 cell types were differentially observed.
  - 10 pathways were differentially enriched.

Below are the most significant results for each analysis, as well as the genes and pathways of interest mentioned above.

### 1.3.2 Glomeruli vs Tubules

### 1.3.3 Normal vs Diseased (DKD) Glomeruli

1. NanoString Technologies, Inc.↩︎