Understanding Disease with Tabula Muris – The Open Source Database via Chan Zuckerberg Biohub

In this new Open Science article, we have explored an Open Source Database called Tabula Muris and how can it significantly contribute in the process of understanding disease for its prevention or cure.

But before we do that, we’d like to introduce in brief the Chan Zuckerberg Initiative by Priscilla Chan and her husband Mark Zuckerberg, who we already know as the founder and CEO of Facebook.

The initiative was founded on December 1, 2015, with a focus on supporting Science through basic biomedical research and education through personalized learning. It has an endowment of 99% of Facebook shares, pledged at $45 billion.

The following video describes its journey so far:

The Chan Zuckerberg Biohub, trademarked as “CZ Biohub”, is a part of this initiative which operates separately. Researchers from Stanford University, Chan Zuckerberg Biohub, VA Palo Alto Healthcare System and the University of California formed a team together and created quite a comprehensive Open Source database of mouse cells and named it Tabula Muris, which means ‘Mouse Atlas’.

The Biohub conducts research by following these simple ideals:

  • Helping solve big health problems by finding and supporting the best and brightest biologists, scientists, engineers and technologists.
  • A culture that emphasizes intellectual freedom and collaboration.
  • Providing their team with the best scientific tools.
  • Inventing the right scientific tools when they aren’t available at hand.

Why is this new Open Source database so significant for understanding disease?

Behind every preventive measure or cure, lies how well a disease is understood in order to treat or handle it.

Before we know the contents of this database, it is important to know what is a mouse model. A mouse model is extremely useful because genetically and genomically, the human and the mouse are very similar, with many of the disease-related genes being nearly identical. So if you discover a cure to a mouse ailment, a new path opens and there is a high chance that you can work on the same method to treat a similar human condition.

Hence it is clear why an Open Source database like Tabula Muris can greatly contribute to effectively using and strengthening this mouse model.

DOI: 10.1038/s41586-018-0590-4

The database consists of ~15 GB of Open Source Datasets available on Figshare, which is an open platform for sharing research data. Code and annotations are available on GitHub.

This ‘Mouse Atlas’ consists of single-cell transcriptomic data from the model organism Mus musculus (the scientific name for mouse) comprises of more than 100,000 cells from 20 organs and tissues.

The Tabula Muris, though not exhaustive at its current stage, has but laid down a solid foundation for future studies across diverse physiological disciplines.

If we briefly look into some conclusions of past research which are based on mouse models to combat disease, it would be easier for us to understand why the database can be so helpful in studying all of them.

Research on Diseases based on Mouse Model

Alzheimer’s Disease

The paper concluded that there are several mouse models being used in preclinical studies and although they constitute a valuable tool for both the testing of new drugs and deciphering the pathophysiology of Alzheimer’s Disease, they must be improved to allow a better extrapolation of the generated results into the clinic.

DOI: 10.3233/jad-170045

Diabetes

In its final paragraph, the paper concluded its discussion about effective mouse models to understand diabetes and obesity-related kidney disease and develop new diagnostic and treatment strategies. Diabetes, obesity and kidney diseases are all inter-linked.

DOI: 10.1371/journal.pone.0162131

Heart Failure

 The conclusion of this paper stresses that relatively simple modifications in the experimental design of animal models of heart failure have the potential to allow increased understanding of the complexity of the clinical heart failure syndrome that may lead to clinical advances using currently available technologies.

DOI: 10.1242/dmm.005017

Cancer

This last paper shows the significance of an Open Science Initiative like Biohub. It talks about about multi-skilled team comprising of tumour biologists,pathologists and clinicians, as well as experts in tissue engineering& regenerative medicine, systems biology, biomaterials,biomedical imaging, pharmacology, engineering, physics, materials sciences and bioinformatics joining forces to improve preclinical mouse model design, which is very similar to the vision behind how Tabula Muris was made.

DOI: 10.1016/j.tibtech.2017.12.001

Going through all of these conclusions and referring to the database on Figshare, one can relate to its significance as a new platform for students and researchers to build upon improving the mouse model.

Summary

So in this article, we briefly discussed Tabula Muris and also tried to understand its significance by relating it to research work on diseases that are driven by the mouse model.

Please share with us in the comments section below if you have any feedback or thoughts onthis newly available ‘Mouse Atlas’.

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