Computational Reconstruction of Pancreatic Islets as a Tool for Structural and Functional Analysis

Summary

In this protocol, the pancreatic islets are reconstructed and analyzed using computational algorithms implemented in a dedicated multiplatform application.

Abstract

Structural properties of pancreatic islets are key for the functional response of insulin, glucagon, and somatostatin-secreting cells, due to their implications in intraislet communication via electric, paracrine, and autocrine signaling. In this protocol, the three-dimensional architecture of a pancreatic islet is firstly reconstructed from experimental data using a novel computational algorithm. Next, the morphological and connectivity properties of the reconstructed islet, such as the number and percentages of the different type of cells, cellular volume, and cell-to-cell contacts, are obtained. Then, network theory is used to describe the connectivity properties of the islet through network-derived metrics such as average degree, clustering coefficient, density, diameter, and efficiency. Finally, all these properties are functionally evaluated through computational simulations using a model of coupled oscillators. Overall, here we describe a step-by-step workflow, implemented in IsletLab, a multiplatform application developed specifically for the study and simulation of pancreatic islets, to apply a novel computational methodology to characterize and analyze pancreatic islets as a complement to the experimental work.

Introduction

The pancreas is divided into regions referred to as head, neck, body, and tail, each having different structures, functions, and anatomical position^1,2. From a functional viewpoint, the pancreas can be divided into endocrine and exocrine systems with the former responsible for the secretion of hormones critically involved in the regulation of glucose homeostasis, while the latter contributes to food digestion via the secretion of enzymes into the duodenum¹. Pancreatic islets constitute the endocrine tissue of the pancreas and are responsible for the secretion of glucagon, insul....

Protocol

NOTE: A schematic diagram of the protocol is shown in Figure 1. A step-by-step description is given is as follows (see Supplementary File 1 for details about the control panels used at every step of the protocol).

Figure 1: Flow diagram. A flow diagram describing the seque....

Results

 The reconstruction of pancreatic islets using the methodology proposed by Félix-Martínez et al.¹⁹ is highly dependent on the parameters given to the optimization algorithm (defined in the reconstruction settings). An example of this is shown visually in Figure 3 where reconstructed islets obtained using different sets of parameters are shown. First, in Figure 3A, a reconstruction that included 86.6% of the cells included in the initial d.......

Discussion

The above protocol outlines a practical approach to reconstruct and analyze pancreatic islet architectures using novel computational algorithms. The main objective of this work is to enable the islet research community to derive quantitative metrics to characterize the morphological and connectivity properties of pancreatic islet architectures and to evaluate the possible functional implications of such properties via computational simulations.

While the algorithms adopted in this pro.......

Materials

List of materials used in this article

Name	Company	Catalog Number	Comments
CUDA-capable NVIDIA graphics card			Required for the functional simulations
IsletLab			https://github.com/gjfelix/IsletLab (Follow the instructions to download and install the application.)