A New Method for Studying the DNA You Only Inherit from Your Mom, and What It Reveals About Disease and Aging

The Context: Mitochondria are structures in our cells that carry their own DNA inherited only from our mothers and provide energy to help our bodies function. Mutations in mitochondrial DNA (mtDNA) can cause deadly diseases that primarily affect children. The unique way that mtDNA is inherited means these harmful mutations have complicated effects on our cells and organs, and until now, it has been very challenging to study these effects in a thorough manner.

The Study: A new study in Nature Biotechnology by NYSCF – Robertson Stem Cell Investigator Vijay Sankaran, MD, PhD, of Boston Children’s Hospital develops a method for profiling mtDNA in thousands of individual cells at a time, allowing researchers to examine how pathogenic mutations vary across different tissues and track cell ancestry. A collaboration between Dr. Sankaran and Massachusetts General Hospital’s Vamsi K. Mootha, MD, leveraged the new technique to study one of the most common mitochondrial diseases, MELAS, illuminating which cell populations are most affected in patients. This work appears in The New England Journal of Medicine.

The Importance: The new method provides a clearer window into mitochondrial diseases and allows detailed studies of how they impact different cells and tissues in the body.

Inside each one of your cells is a structure called the mitochondria which provides the cell with all the energy it needs to keep your body functioning. Each mitochondria also comes with its own set of DNA (mtDNA), inherited only from your mother. If mutations in this DNA (either inherited or acquired) start to accumulate above a certain threshold, then mitochondria can malfunction, cells can get tired, and diseases can arise. 

A new study in Nature Biotechnology by NYSCF – Robertson Stem Cell Investigator Vijay Sankaran, MD, PhD, of Boston Children’s Hospital develops a method for profiling mtDNA across large numbers of individual cells, giving scientists a better understanding of how mutations accumulate in disease. In a collaboration between Dr. Sankaran and Massachusetts General Hospital’s Vamsi K. Mootha, MD, scientists leveraged the new technique to examine mtDNA in cells from patients with one of the most common mitochondrial diseases, MELAS, showing which cell types are prone to carrying the disease-causing mutations. This work appears in The New England Journal of Medicine.

Mitochondrial DNA: A Blueprint for Cell Ancestry

Our cells carry two types of DNA: DNA in the nucleus (the cell’s ‘command center’) and DNA in the mitochondria (the cell’s ‘power generators’). Nuclear DNA is inherited from both our parents, but mtDNA is only inherited from our mothers, and because of the unique way it is passed on and how quickly it accumulates mutations compared to nuclear DNA, tracing it can help researchers determine which cells are related to each other.

However, while researchers can examine mtDNA at the level of single cells, they haven’t been able to do it for very many cells at a time. Thanks to Dr. Sankaran’s method, scientists can now sequence mtDNA across thousands of individual cells in more detail, helping them to better track features of this genome in different tissues and understand how accumulated mutations drive mitochondrial diseases.

Accumulated Mutations Tip the Scale to Drive Mitochondrial Diseases

Patients with mitochondrial diseases carry mutations in their mtDNA inherited from their mothers. In 2012, NYSCF scientists pioneered a technique called mitochondrial replacement therapy that prevents transmission of these diseases from mother to child by removing mutant mitochondria in the mothers’ egg cells. This technique is currently used in clinics across the United Kingdom.

A unique feature of mitochondrial diseases is that patients’ cells contain a mixture of mutant and non-mutant DNA (referred to as ‘heteroplasmy’). For a patient to experience a mitochondrial disease, the proportion of mutated DNA must hit a certain threshold, and symptoms can range depending on which parts of the body carry mutated cells.

Dr. Mootha teamed up with Dr. Sankaran to apply the new method to examine which cell types were affected (and how badly they were affected) in patients with a mitochondrial disease called MELAS, characterized by brain dysfunction and stroke-like episodes that can vary in intensity across patients.

“It is generally accepted that the fraction of mutant heteroplasmy is what determines whether or not a tissue will exhibit disease. To better understand heteroplasmic dynamics, we applied a brand new genomics technology — with single cell resolution — in which we could simultaneously determine the cell type and the fraction of mutant heteroplasmy in thousands of individual blood cells,” said Dr. Mootha in a press release.

The results showed ranges of heteroplasmy across different cell types, with significantly lower levels in immune cells, a finding which could be leveraged for development of new therapies.

“What makes this study unique is that it is, to our knowledge, the first time anyone has been able to quantify the percentage of disease-causing mitochondrial DNA mutations in thousands of individual cells of different types from the same patient, as well as in multiple patients with inherited mitochondrial disease,” said first author Melissa A. Walker, MD, PhD, an investigator in the Department of Neurology at Massachusetts General Hospital.

Why it Matters

With a better way to study and trace mtDNA in thousands of cells at a time, scientists can now deepen their understanding of mitochondrial diseases by analyzing which cell populations are most affected, and to what degree. They can also use the new tool to explore the aging process, as mutations in mtDNA are known to spontaneously occur as we get older.

Journal Articles:

Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling
Caleb A. Lareau, Leif S. Ludwig, Christoph Muus, Satyen H. Gohil, Tongtong Zhao, Zachary Chiang, Karin Pelka, Jeffrey M. Verboon, Wendy Luo, Elena Christian, Daniel Rosebrock, Gad Getz, Genevieve M. Boland, Fei Chen, Jason D. Buenrostro, Nir Hacohen, Catherine J. Wu, Martin J. Aryee, Aviv Regev & Vijay G. Sankaran. 2020. Nature Biotechnology. DOI: https://doi.org/10.1038/s41587-020-0645-6

Purifying Selection against Pathogenic Mitochondrial DNA in Human T Cells
Melissa A. Walker, Caleb A. Lareau, Leif S. Ludwig, Amel Karaa, Vijay G. Sankaran, Aviv Regev, and Vamsi K. Mootha. The New England Journal of Medicine. 2020. DOI: 10.1056/NEJMoa2001265