Islands of Mutated Neurons Dot the Brain. Are They Bad for Us?

The genomes we inherit from our parents are not set in stone. After sperm meets egg, and mitosis is on its merry way, mutations occur in our DNA. They give rise to populations of cells harboring unique genomes and indeed, researchers suspect that cliques of brain cells bearing variants could trigger neurodegeneration. But how common are such somatic mutations? According to a study in the October 15 Nature Communications, everyone’s brain is chock-full of them.

Islands in the Brain. The distribution of somatic variants across the 54 brains. Large circles represent the number of sequenced DNA molecules in each region; smaller circles reflect the occurrence of a given single (green) or multiple (purple) region variant. [Courtesy of Keogh et al., 2018, Nature Communications.]

Researchers led by Patrick Chinnery at the University of Cambridge, U.K., deep-sequenced genes related to neurodegenerative disorders from several regions of 54 postmortem brains from people with Alzheimer’s, Parkinson’s disease, or controls. They found 39 unique somatic variants lurking in those samples, which collectively represent a minuscule fraction of the human brain. Extrapolating their findings to the entire brain, the scientists predicted that people have between 100,000 and 1 million cells carrying somatic mutations in genes related to neurodegenerative disease. These variants are spread out into hundreds of small islands and occasional large ones. The number of brains in the study was too small to definitively tie such mutations to neurodegenerative disease, but the predictions imply a potential role.

“In a very thorough and carefully planned study, Chinnery’s team have significantly advanced our knowledge of brain somatic mutations, and possible relevance to neurodegenerative diseases,” wrote Christos Proukakis of University College London. “They demonstrate that ‘islands’ of neurons with somatic mutations may occur frequently in the human brain, and larger studies will be needed to show if there is a clear relationship with neurodegenerative disease.”

Researchers have long suspected that the brain contains a genomic patchwork of cells harboring mutations that arose at different stages of development. These variants have even been tied to a handful of sporadic cases of neurodegenerative disease (see Sept 2017 newsBeck et al., 2004Nicolas et al., 2018).

However, due to the localized nature of these mutations throughout the brain, tracking them down, let alone investigating their involvement in disease, requires cutting-edge sequencing, cell isolation, and computational techniques. Using single-cell sequencing, a recent study estimated that each cell in the brain harbors 200–400 somatic mutations that arose during brain development, while another study reported around 1,500 per post-mitotic neurons (Bae et al., 2018Lodato et al., 2015). The mutation rate of human neurons also reportedly ramps up with age (Lodato et al., 2018). Yet the cumulative impact of these mutations, and how many cells harbor each one, remains uncertain.

To address these questions, first author Michael Keogh and colleagues employed ultra-deep sequencing of select genes in different regions from postmortem brain samples. The scientists resequenced each sample more than 1,000 times, allowing them to detect variants with high specificity and sensitivity, even for genes that are typically extremely difficult to sequence. Then, using a computational model of brain development, they used their findings to estimate the burden of somatic variation in the entire brain. The researchers sequenced the exons of 56 genes linked to neurodegenerative disease, including APP, PS1/2, TREM2, ApoE, LRRK2, and Parkin, as well as 46 cancer-related genes expressed at low levels in the brain as controls. They sequenced these genes in DNA extracted from 173 frozen brain samples, which came from the frontal cortices, entorhinal cortices, cingulate cortices, cerebella, or medullas of 54 brains. Twenty of the brains came from donors with AD, 20 from people with Lewy body disorders, and 14 from age-matched controls. The researchers extracted the bulk DNA from a section of each region, so could not discern if a variant they found came from neurons, glia, or vascular cells. In addition, they sequenced blood samples that were available from six of the donors.

In all, the researchers found 39 somatic variants among 44 of the 173 brain samples (see image above). Eight were in neurodegenerative disease genes: EIF4G1, LRRK2, NOTCH3, SETX, SORL1, TAF15, UCHL1, and VPS35. Twenty-seven of the 54 brains in the cohort had at least one variant. Of the 39, 18 appeared only in a single region of one brain, and four were detected in a single blood sample. These single-region mutations (SRMs) were similarly common in any of the tested brain regions, in neurodegenerative disease versus control genes, or in people with or without neurodegenerative disease. That’s not to say these variants are not linked to neurodegeneration. The authors estimated they would need to analyze 190 cases and 190 controls to detect a twofold difference in variant incidence between groups.

Somatic Variation. Among people with AD (brown bars), Lewy body disease (purple), and controls (green), each of 39 mutations occurred at different rates across four brain regions and blood. [Courtesy of Keogh et al., 2018, Nature Communications.]

Seventeen of the 39 variants occurred in more than one brain region, or in paired blood/brain samples. Unlike the SRMs, these multiple-region mutations (MRMs) overwhelmingly were in cancer-related genes. Only one MRM was detected in a neurodegenerative disease-related gene—TAF15—and it was detected in three brain regions of one healthy control. Fifteen of the remaining 16 MRMs resided within genes related to myeloproliferative blood disorders, and blood samples had a higher frequency of the mutant alleles than did brain samples from the same donor (see image below). This suggested circulating immune cells were the source of the somatic mutant alleles.

The two most common MRMs occurred in the genes for TET2 and DNMT3A, which play a role in DNA methylation and have been implicated in hematopoietic disorders. In a blood sample from one AD patient, two TET2 variants cropped up in almost 20 percent of sequences (see image above). Forty percent of brains from people with Lewy body disorders had one of these mutations, compared with just 7 percent of brains from healthy controls. The researchers speculated that this could explain previously reported observations that people with PD have altered DNA methylation in the blood and brain. Circulating cells carrying these variants might infiltrate the brain and wreak havoc, they proposed. In support of this, the occurrence of these TET2 and DNMT3A variants was highest in brain regions harboring Lewy body pathology.

The researchers next sought to extrapolate their findings to estimate the burden of variants in neurodegenerative disease-related genes across the entire brain. Using a cellular barcoding technique, they estimated they had sequenced DNA from around 611,000 cells. They were also able to estimate the proportion of cells in any given region that carried a somatic mutation in a neurodegenerative disease-related gene.

They fed this data into a statistical algorithm that simulated brain development to predict the total number and distribution of mutated cells among the estimated 86 billion in each brain. The answer: 100,000 to 1 million cells carry a somatic mutation in a disease-related gene. Incorporating information about how cells divide, differentiate, and mutate during development, the algorithm also foretold that each person likely had one large island of 10,000 to 100,000 cells that grew from one original mutation in a disease gene, while 10 percent of people had at least one island of more than 200,000 such cells. In addition, each brain contained 75 to 481 smaller islands, each consisting of just more than 100 descendants of a cell carrying a pathological variant.

The researchers speculated that these islands of somatic variants trigger sporadic neurodegenerative disease, which reportedly affects roughly 10 percent of the human population.

“Even if only one island of 10,000 to 100,000 cells carried a mutation related to Alzheimer’s disease, it could hypothetically serve as a hotspot for amyloid or tau seed formation and could in turn have an effect that spreads beyond their own cell population,” commented Huntington Potter of the University of Colorado in Denver. However, he noted that the data do not yet conclusively link such mutations and disease. In AD patients, the authors found no variants in the entorhinal cortex, a region affected early in the disease process.

While Chinnery and colleagues speculated that larger numbers of mutated cells would be more likely to cause disease, they did not exclude the possibility that a small number would be sufficient to instigate the slow spread throughout the brain of toxic protein, such as Aβ, α-synuclein, tau, and others that can propagate by templated misfolding.

Gaël Nicolas of Radboud University Medical Center in Nijmegen, The Netherlands, called the study a significant contribution to the field of somatic mutations in the brain, but cautioned that it fell short of linking specific somatic variants to aberrant protein aggregation or neurodegeneration, as did several other recent reports, including his own.

Alexander Hoischen, also at Radboud, had similar impressions. “The study shows how the latest sequencing technology combined with smart analysis can detect somatic mutations much more accurately,” he wrote. “This paper provides further leads about fascinating human biology, but elucidating the exact involvement of somatic mutations in brain disease, and neurodegeneration in particular, requires a lot of work.”

Featured Paper

Keogh MJ, Wei W, Aryaman J, Walker L, van den Ameele J, Coxhead J, Wilson I, Bashton M, Beck J, West J, Chen R, Haudenschild C, Bartha G, Luo S, Morris CM, Jones NS, Attems J, Chinnery PF. High prevalence of focal and multi-focal somatic genetic variants in the human brain. Nat Commun. 2018 Oct 15;9(1):4257. PubMed.

References

Beck JA, Poulter M, Campbell TA, Uphill JB, Adamson G, Geddes JF, Revesz T, Davis MB, Wood NW, Collinge J, Tabrizi SJ. Somatic and germline mosaicism in sporadic early-onset Alzheimer’s disease. Hum Mol Genet. 2004 Jun 15;13(12):1219-24. Epub 2004 Apr 28 PubMed.

Nicolas G, Acuña-Hidalgo R, Keogh MJ, Quenez O, Steehouwer M, Lelieveld S, Rousseau S, Richard AC, Oud MS, Marguet F, Laquerrière A, Morris CM, Attems J, Smith C, Ansorge O, Al Sarraj S, Frebourg T, Campion D, Hannequin D, Wallon D, Gilissen C, Chinnery PF, Veltman JA, Hoischen A. Somatic variants in autosomal dominant genes are a rare cause of sporadic Alzheimer’s disease. Alzheimers Dement. 2018 Aug 13; PubMed.

Bae T, Tomasini L, Mariani J, Zhou B, Roychowdhury T, Franjic D, Pletikos M, Pattni R, Chen BJ, Venturini E, Riley-Gillis B, Sestan N, Urban AE, Abyzov A, Vaccarino FM. Different mutational rates and mechanisms in human cells at pregastrulation and neurogenesis. Science. 2018 Feb 2;359(6375):550-555. Epub 2017 Dec 7 PubMed.

Lodato MA, Woodworth MB, Lee S, Evrony GD, Mehta BK, Karger A, Lee S, Chittenden TW, D’Gama AM, Cai X, Luquette LJ, Lee E, Park PJ, Walsh CA. Somatic mutation in single human neurons tracks developmental and transcriptional history. Science. 2015 Oct 2;350(6256):94-98. PubMed.

Lodato MA, Rodin RE, Bohrson CL, Coulter ME, Barton AR, Kwon M, Sherman MA, Vitzthum CM, Luquette LJ, Yandava CN, Yang P, Chittenden TW, Hatem NE, Ryu SC, Woodworth MB, Park PJ, Walsh CA. Aging and neurodegeneration are associated with increased mutations in single human neurons. Science. 2018 Feb 2;359(6375):555-559. Epub 2017 Dec 7 PubMed.

Further Reading

Leija-Salazar M, Piette C, Proukakis C. Review: Somatic mutations in neurodegeneration. Neuropathol Appl Neurobiol. 2018 Apr;44(3):267-285. PubMed.

Chestnut BA, Chang Q, Price A, Lesuisse C, Wong M, Martin LJ. Epigenetic regulation of motor neuron cell death through DNA methylation. J Neurosci. 2011 Nov 16;31(46):16619-36. PubMed.

Ziller MJ, Ortega JA, Quinlan KA, Santos DP, Gu H, Martin EJ, Galonska C, Pop R, Maidl S, Di Pardo A, Huang M, Meltzer HY, Gnirke A, Heckman CJ, Meissner A, Kiskinis E. Dissecting the Functional Consequences of De Novo DNA Methylation Dynamics in Human Motor Neuron Differentiation and Physiology. Cell Stem Cell. 2018 Apr 5;22(4):559-574.e9. PubMed.


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