Surreal illustration of 3D organoids floating in space, representing stem cell research.

Stem Cell Breakthroughs: How 3D Organoids Are Revolutionizing Disease Research

Avery Sinclair in Science & Nature December 2025 • 4 min read.

"Explore the cutting-edge advancements in stem cell research, from 3D organoids to cancer therapies, and how they're shaping the future of regenerative medicine."

In May 2017, Münster, Germany, hosted the 9th International Meeting of the Stem Cell Network North Rhine Westphalia, spotlighting groundbreaking research in stem cell differentiation, regenerative medicine, and disease modeling. This prestigious event, hosted by Martin Götte and Hans Schöler, drew over 600 participants and featured over 160 posters, creating a vibrant platform for interdisciplinary discussions and collaborations. The meeting underscored the rapid advancements in stem cell technology and its potential to revolutionize medical treatments.

The conference highlighted several key areas, including the use of three-dimensional (3D) organoids, induced pluripotent stem cells (iPSCs), cancer stem cells, and the crucial role of epigenetics. These topics reflect the evolving landscape of stem cell research, which is increasingly focused on creating more accurate models of human tissues and diseases. By fostering collaboration and knowledge sharing, the meeting aimed to accelerate the translation of these discoveries into clinical applications.

This report focuses on the most compelling presentations from the conference, providing a comprehensive overview of the challenges and innovative approaches driving stem cell research. From understanding the 3D dynamics of the genome to exploring the ethical implications of germline modification, this meeting showcased the breadth and depth of the field.

Unlocking the 3D Genome: How Enhancers Regulate Gene Expression

Surreal illustration of 3D organoids floating in space, representing stem cell research.

Frank Grosveld from Erasmus University Rotterdam presented insights into the three-dimensional structures of genomes in hematopoietic development. Enhancers, which regulate gene expression by interacting with the promoter regions of target genes over vast distances, are central to this process. The mammalian genome comprises topologically associating domains (TADs), formed by the binding of transcription factors (TFs) like CTCF and cohesin.

These TADs organize the genome into a series of rosettes connected by linker chromatin, within which enhancer-promoter interactions create functional loops in transcriptional factories. Grosveld’s research, using the developing hematopoietic system, explored how new enhancers are activated during differentiation. The GATA1/TAL1/LDB1 TF complex and co-TF EVIL are vital for differentiating between hematopoietic and cardiac lineages. Later, the co-TF RUNX1 leads to new enhancer usage, followed by co-TF KLF1 for erythroid differentiation.

Enhancers and Gene Expression: Enhancers regulate gene expression by interacting with promoter regions, acting over large distances.
Topologically Associating Domains (TADs): The genome is organized into TADs via transcription factors like CTCF and cohesin.
Functional Loops: Enhancer-promoter interactions form functional loops within TADs in transcriptional factories.
Hematopoietic Development: The study used the hematopoietic system to explore the 3D dynamics of the genome.
Key Transcription Factors: GATA1/TAL1/LDB1, EVIL, RUNX1, and KLF1 are crucial for cell differentiation.

In summary, Grosveld’s presentation underscored the cooperative role of transcription factors in regulating transcription within the hematopoietic system. This 3D organization is crucial for understanding how genes are turned on and off during development and disease.

Looking Ahead: The Future of Stem Cell Research

The 9th International Meeting of the Stem Cell Network North Rhine Westphalia showcased the dynamic and evolving field of stem cell research. By bringing together leading researchers and industry partners, the conference facilitated critical discussions and new collaborations. These interactions are essential for translating basic research into practical applications that can improve human health.

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This article is based on research published under:

DOI-LINK: 10.1089/cell.2017.0037, Alternate LINK

Title: From Stem Cell Research To Three-Dimensional Organoids And Their Applications In Cancer Research: Meeting Report On The 9Th International Meeting Of The Stem Cell Network North Rhine Westphalia

Subject: Cell Biology

Journal: Cellular Reprogramming

Publisher: Mary Ann Liebert Inc

Authors: Samantha Langer, Peter A. Horn, Stefan Heinrichs

Published: 2017-10-01

Everything You Need To Know

What was the main focus of the 9th International Meeting of the Stem Cell Network North Rhine Westphalia?

The 9th International Meeting of the Stem Cell Network North Rhine Westphalia showcased the rapid advancements in the field of stem cell research. Over 600 participants and over 160 posters were present, providing a platform for interdisciplinary discussions and collaborations. This kind of environment facilitates the translation of basic research into clinical applications.

What are 3D organoids, and why are they significant in stem cell research?

3D organoids are three-dimensional structures that mimic the complexity of human tissues. They are used in disease modeling to create more accurate models of human tissues and diseases, offering a significant improvement over traditional methods. They allow researchers to study how diseases develop and test potential treatments in a more realistic environment, leading to faster and more effective drug discovery and regenerative medicine applications.

Can you explain the role of enhancers, TADs, and transcription factors in gene regulation?

The process discussed involves the study of three-dimensional structures of genomes in hematopoietic development. Enhancers, which regulate gene expression, interact with the promoter regions of target genes. The mammalian genome organizes itself into Topologically Associating Domains (TADs), formed by the binding of transcription factors like CTCF and cohesin. Within these TADs, enhancer-promoter interactions create functional loops, playing a crucial role in how genes are turned on and off during development and disease. Key Transcription Factors like GATA1/TAL1/LDB1, EVIL, RUNX1, and KLF1 are crucial for cell differentiation.

What are induced pluripotent stem cells (iPSCs), and why are they important?

Induced pluripotent stem cells (iPSCs) are a type of stem cell that can be created from adult cells and reprogrammed to behave like embryonic stem cells. This allows researchers to generate patient-specific cells for research and therapeutic applications. iPSCs are crucial because they offer a way to study diseases and develop personalized treatments without the ethical concerns associated with embryonic stem cells.

How does epigenetics relate to stem cell research and regenerative medicine?

Epigenetics is the study of changes in gene expression that are not due to alterations in the DNA sequence itself. It focuses on how factors like DNA methylation and histone modifications influence gene activity. In stem cell research, understanding epigenetics is vital because it helps explain how stem cells differentiate into various cell types. This knowledge is crucial for regenerative medicine and disease modeling as it can be used to control and direct the differentiation of stem cells to create specific tissues or repair damaged ones.