Methods for Extracellular Matrix Research in Development, Health, and Disease

TOPICAL COLLECTIONS

Guest Editor

Alexandra Naba

Department of Physiology and Biophysics, University of Illinois Chicago

<p>Alexandra Naba is an associate professor in the Department of Physiology and Biophysics at the University of Illinois Chicago and a member of the University of Illinois Cancer Center. Alexandra received her PhD from the Curie Institute in Paris, France, where she studied the role of the membrane-cytoskeleton linker, ezrin, in normal and tumor cell adhesion in the laboratory of Pr. Daniel Louvard under the supervision of Dr. Monique Arpin. For her postdoctoral training, Alexandra joined the laboratory of Dr. Richard Hynes at MIT, where she developed the first proteomic and bioinformatic pipelines to comprehensively characterize the extracellular matrix composition of tissues, thereby defining the concept of “matrisome” and pioneering the field of ECM proteomics, also known as “matrisomics.” </p>

Collection Overview

The extracellular matrix (ECM) is a complex meshwork of proteins and glycans that provides structural support to cells and organizes them into tissues. The biochemical composition of the ECM and its physical and mechanical properties are organ-specific. In addition to its architectural role, the ECM conveys signals to cells that regulate key cellular functions, such as proliferation, adhesion, migration, stemness, and differentiation. Consequently, alterations in ECM composition or structure can disrupt tissue homeostasis and contribute to the development of disease.

This Topical Collection aims to highlight and facilitate the dissemination of the latest techniques in ECM research and their application across diverse fields of research, including development, cancer, fibrosis, skeletal disorders, tissue engineering, wound healing, and aging.

The collection will cover, but is not limited to:

Techniques to profile the global composition of the ECM (e.g., proteomic, mass spectrometry imaging, multiplexed IHC)
Techniques to image and quantify the physical and mechanical properties of the ECM from in-vitro cell culture systems or in- or ex-vivo samples across model organisms
Techniques to characterize the mechanisms of ECM assembly and remodeling
Techniques to probe cell-ECM and ECM protein-protein interactions
Techniques to engineer in-vitro ECMs and ECM mimics with applications to cancer research, wound healing, or tissue regeneration
Computational approaches to mine -omic datasets to gain insights into genetic, transcriptional, translational, and post-translational regulations of the matrisome across systems

Articles

Generation of Polyacrylamide and Silicone Extracellular Matrix Substrates with Defined Stiffness for Cell Biology Applications

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2026

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Aisha Almsoud^1,2, Upama Nyaupane^1,2, Kashish Jain³, Ghmkin Hassan³, Johnathan N. Lakins³, Valerie M. Weaver^4,5,6, FuiBoon Kai^1,2

¹Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, ²Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, ³Department of Surgery, University of California, San Francisco, ⁴Center for Bioengineering and Tissue Regeneration, University of California, San Francisco, ⁵UCSF Helen Diller Comprehensive Cancer, University of California, San Francisco, ⁶Department of Bioengineering and Therapeutic Sciences, Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco

Abstracts

OptoRheo for matrix biology: a custom microscope for live 3D imaging and micro-mechanical characterisation.

Amanda Wright^*1,

Jennifer Ashworth ^*2,

Tania Mendonca^*2,

Cathy Merry ²,

Samantha Mitchell ²,

Victoria James ²,

Supisara Jearranaiprepame ²,

Cameron Alexander²,

Ruman Rahman ²,

Lydia Blacklock ²,

Bapan Pramanik²,

Amir Ghaemmaghami ²,

Alvaro Mata ²,

Gordon Moran ²

¹University of Nottingham,

²University of Nottingham

Anatomically Diverse Fibroblast-Derived Extracellular Matrices for Cell Motility Assays

Haylee Wagner¹

¹Tufts University

Spatial Matrisome Profiling of Human Lung Fibrosis using MatriSpace

Ayomide Oshinjo^*1,

Petar Petrov²,

Valerio Izzi^*2

¹Faculty of Biochemistry and Molecular Medicine, University of Oulu,

²Faculty of Biochemistry and Molecular Medicine, University of Oulu; Infotech Institute, University of Oulu

Visualization and Quantification of Elastin Staining in Histological Sections

Elizabeth Rush¹,

Timothy Mead^*1

¹Case Western Reserve University

Quantitative Evaluation of Imaging Approaches for Characterizing Fibrillar Collagen Organization

Kevin Eliceiri^*1

¹University of Wisconsin-Madison

QuTools: An ECM Visualization and Analysis toolkit for QuPath

Conner Quinlan¹,

Sonali Karnik¹,

Piper Wilburn¹,

Connor Gulbronson¹,

Melissa Kacena¹,

Milos Marinkovic^*1

¹Indiana University School of Medicine

Using Electron Microscopy to investigate extracellular cellular matrix dynamics

Joan Chang^*1,

Aleksandr Mironov ^*1,

Ashvatti Durai¹,

Emily Barot¹,

David Holmes¹

¹University of Manchester