FEB 22, 2017 5:23 PM PST

Algorithm can Predict Stem Cell Fate

WRITTEN BY: Carmen Leitch

Stem cells are still not well understood, but there is a lot of interest in knowing more about them for many reasons; they have tremendous therapeutic potential, they are critical players in development, and they have many unique characteristics. Scientists have now applied machine learning to hematopoietic stem cells to learn more about the decisions that lead to their fate as a more specialized blood cell. The researchers are featured in this video below explaining the work, which was published in Nature Methods.

"A hematopoietic stem cell's decision to become a certain cell type cannot be observed. At this time, it is only possible to verify the decision retrospectively with cell surface markers," explained Dr. Carsten Marr, head of the Quantitative Single Cell Dynamics Research Group at the Helmholtz Zentrum München's Institute of Computational Biology (ICB).

Using deep learning, which simulates human learning in a computational framework, Marr's team have created an algorithm that predicts stem cell fate decisions. "Deep Neural Networks play a major role in our method," said Marr. "Our algorithm classifies light microscopic images and videos of individual cells by comparing these data with past experience from the development of such cells. In this way, the algorithm 'learns' how certain cells behave."

A collaborator, Timm Schroeder at ETH Zurich, worked to film stem cells. With the data that was gathered on appearance and speed, the software could track and remember behavioral patterns, which led to the ability to make predictions. "Compared to conventional methods, such as fluorescent antibodies against certain surface proteins, we know how the cells will decide three cell generations earlier," said ICB scientist Dr. Felix Buggenthin, who was co-first author of the work, along with Dr. Florian Büttner.

Marr explained the potential applications and benefits of the work; "Since we now know which cells will develop in which way, we can isolate them earlier than before and examine how they differ at a molecular level. We want to use this information to understand how the choices are made for particular developmental traits."

The scientists are not limiting themselves to hematopoietic stem cells. "We are using Deep Learning for very different problems with sufficiently large data records," said Prof. Dr. Dr. Fabian Theis, ICB director and holder of the Mathematical Modeling of Biological Systems Chair at the TUM, who was study leader with Carsten Marr. "For example, we use very similar algorithms to analyze disease-associated patterns in the genome and identify biomarkers in clinical cell screens."

 

Sources: AAAS/Eurekalert! via Helmholtz Zentrum München, Nature Methods

About the Author
  • Experienced research scientist and technical expert with authorships on over 30 peer-reviewed publications, traveler to over 70 countries, published photographer and internationally-exhibited painter, volunteer trained in disaster-response, CPR and DV counseling.
You May Also Like
SEP 11, 2020
Cancer
Targeting Senescence in the Peripheral Nervous System to Fight Toxicity
SEP 11, 2020
Targeting Senescence in the Peripheral Nervous System to Fight Toxicity
Chemotherapy is a life-saving discovery for cancer patients. One of its biggest drawbacks is the toxicity that comes wit ...
SEP 07, 2020
Immunology
CRISPR Pumps the Brakes on the Immune System to Support Gene Therapies
SEP 07, 2020
CRISPR Pumps the Brakes on the Immune System to Support Gene Therapies
The ability to edit the human genome using CRISPR has been heralded as a revolution in medicine. However, one of the big ...
OCT 04, 2020
Genetics & Genomics
The Intriguing Genome of Mitochondria
OCT 04, 2020
The Intriguing Genome of Mitochondria
Our cells carry special structures called organelles, with each different organelle performing various specialized, crit ...
OCT 14, 2020
Genetics & Genomics
Robots Are Moving Developmental Biology Forward
OCT 14, 2020
Robots Are Moving Developmental Biology Forward
Researchers have created a robot that can analyze the effects of mutations that occur in portions of the genome that hel ...
OCT 14, 2020
Neuroscience
Researchers Pinpoint Neurons Affected by Epilepsy
OCT 14, 2020
Researchers Pinpoint Neurons Affected by Epilepsy
Video: Explains in more detail the different receptors affected by epilepsy. Researchers at the University of Copenhagen ...
NOV 14, 2020
Cell & Molecular Biology
Towards a Better Characterization of Neurons
NOV 14, 2020
Towards a Better Characterization of Neurons
The human body is made up of a wide array of different types of cells, and if we want to understand human diseases and t ...
Loading Comments...