inheritance of mtDNA heteroplasmy

Each human cell contains hundreds of mitochondria and thousands of mtDNAs. When an mtDNA mutation occurs in a cell, a mixture of wild type and mutant mtDNAs is produced—a condition called heteroplasmy. If the mutant mtDNA causes mitochondrial dysfunction, then the level of heteroplasmy in an individual determines the severity of dysfunction. Therefore, the inheritance of mtDNA heteroplasmy plays an important role in the inheritance of dysfunctions or diseases caused by mtDNA mutations.

Maternal inheritance of mtDNA is the rule in most animals, but the reasons for this pattern remain unclear. To investigate the consequence of overriding uniparental inheritance, we generated mice containing an admixture (heteroplasmy) of of two normal yet different mtDNAs in the presence of a congenic nuclear background. Analysis of the segregation of the two mtDNAs across subsequent maternal generations revealed that proportion of one of them was preferentially reduced. Ultimately, the segregation process produced heteroplasmic mice as well as their homoplasmic counterparts. Phenotypic comparison of these three mtDNA lines demonstrated that the heteroplasmic mice, but neither homoplasmic counterpart, had reduced activity, food intake, respiratory exchange ratio; accentuated stress response; and cognitive impairment. Therefore, admixture of two normal but different mouse mtDNAs can be genetically unstable and can produce adverse physiological effects, factors that may explain the advantage of uniparental inheritance of mtDNA.

Regarding its inheritance both selection and random genetic drift have been indicated as putative mechanisms for mtDNA heteroplasmy. Whether selection or random genetic drift is the driving force behind the inheritance of mtDNA heteroplasmy is still an open question. Wonnapinij et al., based on Motoo Kimura’s probability density functions for gene frequencies under pure random genetic drift (Kimura 1955), developed a tool that tests the selection hypothesis for heteroplasmy experimental data. We evaluated this tool by utilizing two recently published large datasets on mouse heteroplasmy (Sharpley et al., 2012, Freyer et al., 2012). We measured the heteroplasmy distribution in groups of offspring from single mothers or from mothers with similar heteroplasmy levels pooled. Our results suggest that the Wonnapinij et al, tool shows strong statistical evidence for segregation when the percentage of the minority mtDNA is low. However, it fails to detect the even more robust evidence for directional segregation when the percentage of the two mtDNAs is equal. Additionally, when the offspring mutation levels are binned into groups on the basis of the mothers’ heteroplasmy levels the results differ with the bin size. Such inconsistences point to a fault in the Wonnapinij et al, tool. We think that the fault lies in the underlying assumptions on which the tool is based, as well as on the nature of the Kolmogorov-Smirnov test that is used to compare the experimental data for mtDNA heteroplasmy distributions to the Kimura probability distributions. For more details see Wallace and Chalkia, 2013.

mtDNA & adaptation: high altitute

Multiple studies suggest that physiological changes observed in high-altitude adapted populations (Tibetans, Peruvian Andean Native Americans, and India subcontinent populations) may be the result of changes in mitochondrial physiology. We hypothesize that the mitochondrial genome plays a significant role in adaption to hypoxic conditions.

To test our hypothesis, we first examined the role of ancient human mtDNA variation in adaptation to high altitute and hypoxia. For this, in collaboration with scientists at the Third Military Medical University (Chongqing, China) and the Wake Forest University (Winston-Salem, NC) we collected samples from six Tibetan villages located above 3,000-m elevation. These high-altitude samples were compared with three low-altitude Chinese datasets that were collected in collaboration with scientists at UCI and the National Taiwan University Hospital (Taipei, Taiwan). Additionally, more than 7,000 complete mtDNA sequences were downloaded from NCBI. All sequences were haplotyped and analyzed at the variant and haplogroup level. Our mtDNA sequence analysis revealed that the NADH dehydrogenase subunit 1 (ND1) nucleotide 3394 T > C (Y30H) variant occurs on five different haplogroup backgrounds in high-altitude Tibetan and Indian populations.

Additionally, our highly precise mitochondrial complex I assay showed that on the M9 background, the 3394C variant is associated with a complex I activity that is equal to or higher than that of the 3394T variant found on the low-altitute B4c or F1 backgrounds. Additionally, the 3394C variant has been associated with LHON disease in low-altitute J, M9, or D4 samples.

Taken together, our results suggest that the mtDNA variation is significantly associated with high altitute, and that the 3394C variant can be either beneficial or deleterious depending on its haplogroup and environmental context.

mtDNA sequence analysis--MITOMAP

The MITOMAP database of human mitochondrial DNA (mtDNA) information has been an important compilation of mtDNA variation for researchers, clinicians and genetic counselors for the past twenty-five years. The MITOMAP protocol shows how users may look up human mitochondrial gene loci, search for public mitochondrial sequences, and browse or search for reported general population nucleotide variants as well as those reported in clinical disease. Within MITOMAP is the powerful sequence analysis tool for human mitochondrial DNA, MITOMASTER. The MITOMASTER protocol gives step-by-step instructions showing how to submit sequences to identify nucleotide variants relative to the rCRS, to determine the haplogroup, and to view species conservation. User-supplied sequences, GenBank identifiers and single nucleotide variants may be analyzed.

mtDNA & disease: autism

Autism Spectrum Disorders (ASD) are a group of childhood-onset neurodevelopmental conditions characterized by social impairment, language deficits, and particularly restricted interests and/or stereotypical repetitive behaviors. The clinical presentation and disease progression, after diagnosis at 2-3 years of age, is highly variable. Variability is also observed in other simultaneously existing conditions, such as intellectual disability, anxiety, depression, gastro-intestinal problems, and epileptic episodes. The phenotypic variability of ASD is mirrored in its genetics. Genome wide association studies, whole exome or genome sequencing, and candidate gene re-sequencing studies have reported hundreds of genetic point or structural variants—de novo, rare, or common—as ASD contributing factors.

Besides its phenotypic and genetic variability, ASD displays the rare 4:1 male to female ratio among patients. The male predilection in the neurodevelopmental ASD is inconsistent with Mendelian expectations but regularly observed in the milder neurodegenerative mtDNA diseases, particularly Leber’s Hereditary Optic Neuropathy. Numerous studies have reported physiological features in ASD patients consistent with mild mitochondrial defects .

ASD as a neurodevelopmental state is highly dependent on energy. Because energy production relies heavily on mitochondria, mitochondrial function may influence neurodevelopment and contribute to autism. Based on this syllogism, we hypothesized that human mtDNA variation is associated with ASD risk. To determine whether inherited mtDNA variation contributes to ASD risk, we analyzed the Autism Genetic Resource Exchange (AGRE) family cohort.

In our study, based on 1624 patients with ASD and 2417 healthy parents and siblings from 933 AGRE families, individuals with European haplogroups I, J, K, O-X, T, and U and Asian and Native American haplogroups A and M are at significantly increased risk of ASD compared with the most common European haplogroup HHV. Therefore mitochondrial haplogroups, with their associated functional variants, contribute a significant proportion of ASD risk, thus confirming that mitochondrial dysfunction is a significant factor in the cause of ASD. The interaction between the ancient haplogroup functional variants, recent heteroplasmic mtDNA mutations, mutation or deletion of 1 or more nDNA genes, and environmental insults that modulate bioenergetics may all combine to explain many of the unusual features of ASD genetics.

mtDNA & disease: metabolic syndrome

Metabolic syndrome (MS) is a cluster of conditions — increased blood pressure, a high blood sugar level, excess body fat around the waist and abnormal cholesterol levels — that occur together, increasing the risk of heart disease, stroke and diabetes.

Mitochondria are critical regulators of cell metabolism. Therefore mitochondrial dysfunction is associated with many metabolic disorders. The latter can be explained by defects in oxidative phosphorylation, reactive oxygen species production, or mtDNA mutations. In collaboration with Lee-Ming Chuang (NTU) and Ping H. Wang (UCI), we  examined the association between mtDNA variation and various phenotypic parameters of MS in a large saple of diabetic, obese, or hypertension patients and age-matched controls from Taiwan. We showed that that functional mtDNA variants may contribute to the risk of developing T2DM and MS.

mtDNA & adaptation: from arctic to tropics

Global studies have shown that the different human mtDNA haplotypes fit into a single dichotomous tree with an African root and specific branches radiating into the different continents giving region-specific haplogroups. Also, these studies have revealed two striking discontinuities in mtDNA diversity: the first between northeastern Africa and Eurasia, in which the enormous diversity of African mtDNA lineages encompassed by macro-haplogroup L was truncated to only two founding mtDNA haplotypes that generated Eurasian macro-haplogroups M and N; and the second between Central Asia and northeastern Siberia, where the plethora of Asian mtDNA M and N-derived types  became reduced to essentially only three haplogroup lineages A, C, and D.

Since there are no major geographical barriers between Central Asia and northeastern Siberia, the latter should have received a random sample of Asian mtDNA lineages but it did not. Consequently, it has been hypothesized that natural selection has influenced the regional differences between mtDNA lineages, and that adaptive selection has acted on the mtDNA types that survived the migration into the more northern regions.

The above mentioned hypothesis has been supported by evolutionary studies that revealed that: a) the ω (Ka/Ks) ratio of functional mtDNA variants is strikingly different among indigenous human populations, and b) specific amino acid substitutions on the internal nodes of the human mtDNA tree have been positively selected during the human adaptation to the arctic climate.

To establish that nodal mtDNA substitutions have been important in human adaptation to climate, we need to establish that new functional mtDNA variants accumulate on specific mtDNA lineages when exposed to new environments.

The migration of Siberians into the Americas provides the perfect natural experiment. Arctic adapted Siberians carrying mtDNA haplogroups A, C, or D crossed the Bering Land Bridge into the Americas about 20,000, and A again about 7 to 9,000 YBP and then migrated South back into the temperate and then tropical zones.

We hypothesize that the populations that moved south should have acquired additional mtDNA mutations that increased their fitness for the warmer climates. To test our hypothesis, we have compared the mtDNA sequence variation between indigenous peoples from Siberia and Central and South America.

mtDNA & disease: preterm birth

Preterm birth (PTB) is defined as birth before 37 completed weeks of gestation and its rate has risen alarmingly over the past twenty years. Possible explanations for these high rates include the increases in multiple births, older maternal age, elective caesarean sections before 37 weeks of gestation, and the use of assisted reproductive technologies. Also, many environmental contributors to PTB such as stress, smoking, and inflammation, are identified. Evidence also shows there is a large racial disparity in the etiology of PTB. While evidence suggests that PTB is not inherited in a classic Mendelian autosomal recessive or dominant fashion, a predisposition to PTB clearly runs in families.

The maternal and non-Mendelian inheritance of PTB and its solid association with ethnicity led us to hypothesize that mtDNA variation contributes to its etiology. In collaboration with Pathik Wadhwa (UCI) and Robert Romero (WSU, NICHD), we are examining the association between mtDNA variation and PTB in two independent large datasets.

mtDNA & disease: chronic obstructive pulmonary disease

COPD is one of the major causes of morbidity and mortality worldwide, affecting between 4 and 6% of the population over the age of 45 years. It is a highly heterogeneous disease of progressive airflow obstruction that is strongly associated with a history of cigarette smoking. However, not all smokers develop COPD indicating that either genetic or other environmental factors are important in its etiology. 

Metabolic and molecular biology studies have showed that smoking produces chronic oxidative stress. Current genetic data implicate reactive oxygen species toxicity and mitochondrial dysfunction in COPD as underlying factors in the progression from smoking toxicity to obstructive lung disease.

We hypothesize that mitochondrial dysfunction is an important factor in the etiology of COPD. In collaboration with GlaxoSmithKline, we are investigating the role of various classes of mtDNA mutations (ancient adaptive, recent deleterious, and somatic) in COPD.