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Alston CL, Rocha MC, Lax NZ, Turnbull DM, Taylor RW. The genetics and
pathology of mitochondrial disease. Journal of Pathology 2017, 241(2), 236-
250.
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© 2016 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of
Pathological Society of Great Britain and Ireland.
This is an open access article under the terms of the Creative Commons Attribution License, which
permits use, distribution and reproduction in any medium, provided the original work is properly cited.
DOI link to article:
http://dx.doi.org/10.1002/path.4809
Date deposited:
09/03/2017
Journal of Pathology
J Pathol 2017; 241: 236–250
Published online 2 November 2016 in Wiley Online Library
(wileyonlinelibrary.com)
DOI: 10.1002/path.4809
INVITED REVIEW
The genetics and pathology of mitochondrial disease
Charlotte L Alston, Mariana C Rocha, Nichola Z Lax, Doug M Turnbull and Robert W Taylor
*
Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, UK
*Correspondence to: R Taylor, Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle
University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK. E-mail: robert.taylor@ncl.ac.uk
Abstract
Mitochondria are double-membrane-bound organelles that are present in all nucleated eukaryotic cells and are
responsible for the production of cellular energy in the form of ATP. Mitochondrial function is under dual genetic
control – the 16.6-kb mitochondrial genome, with only 37 genes, and the nuclear genome, which encodes the
remaining ∼1300 proteins of the mitoproteome. Mitochondrial dysfunction can arise because of defects in either
mitochondrial DNA or nuclear mitochondrial genes, and can present in childhood or adulthood in association with
vast clinical heterogeneity, with symptoms affecting a single organ or tissue, or multisystem involvement. There is
no cure for mitochondrial disease for the vast majority of mitochondrial disease patients, and a genetic diagnosis is
therefore crucial for genetic counselling and recurrence risk calculation, and can impact on the clinical management
of affected patients. Next-generation sequencing strategies are proving pivotal in the discovery of new disease
genes and the diagnosis of clinically affected patients; mutations in >250 genes have now been shown to cause
mitochondrial disease, and the biochemical, histochemical, immunocytochemical and neuropathological charac-
terization of these patients has led to improved diagnostic testing strategies and novel diagnostic techniques. This
review focuses on the current genetic landscape associated with mitochondrial disease, before focusing on advances
in studying associated mitochondrial pathology in two, clinically relevant organs – skeletal muscle and brain.
© 2016 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain
and Ireland.
Keywords: mitochondria; mitochondrial disease; mtDNA; respiratory chain deciency; genetic diagnosis; muscle pathology;
immunohistochemistry; neuropathology
Received 31 August 2016; Revised 15 September 2016; Accepted 16 September 2016
No conicts of interest were declared.
Introduction
Mitochondria are double-membrane-bound organelles
present in all nucleated eukaryotic cells, and are respon-
sible for numerous cellular processes, including calcium
homeostasis, iron–sulphur cluster biogenesis, apopto-
sis, and the production of cellular energy (ATP) by
oxidative phosphorylation (OXPHOS) [1,2]. With bac-
terial origins, a historical symbiotic relationship evolved
during which mitochondria became normal constituents
of eukaryotic cells [3]. Their ancestry remains apparent
from their own multicopy genetic material [mitochon-
drial DNA (mtDNA)], with copy number varying greatly
between individuals and across different tissues from the
same individual. The 16.6-kb circular mtDNA molecule
encodes 13 subunits of the OXPHOS components, 22
mitochondrial tRNAs, and two subunits of the mitori-
bosomes [4]. Additionally, the mitoproteome requires a
further ∼1300 nuclear-encoded proteins for producing,
assembling or supporting the ve multimeric OXPHOS
complexes (I–V) and ancillary mitochondrial processes
[5]. It stands to reason that mitochondrial dysfunction
can result from either mtDNA or nuclear gene defects,
and can occur as a primary, congenital condition or a
secondary, age-associated effect attributable to somatic
mutation [6].
The umbrella term ‘mitochondrial disease’ refers
to a clinically heterogeneous group of primary mito-
chondrial disorders in which the tissues and organs
that are most often affected are those with the high-
est energy demands. Clinical symptoms can arise in
childhood or later in life, and can affect one organ in
isolation or be multisystemic [7]; the minimum dis-
ease prevalence in adults is ∼12.5 per 100 000 [8], and
∼4.7 per 100 000 in children [9]. There is a general
lack of genotype–phenotype correlations in many mito-
chondrial disorders, which means that establishing a
genetic diagnosis can be a complicated process, and
remains elusive for many patients. This review pro-
vides a concise update on three areas where there have
been major advances in our understanding in recent
years [10], i.e. the molecular genetics, muscle pathology
and neuropathology associated with mitochondrial dis-
ease, highlighting the range of new techniques that are
improving the diagnosis of patients with suspected mito-
chondrial disease, with the aim of providing options to
families at risk of an otherwise incurable condition.
© 2016 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any
medium, provided the original work is properly cited.
Mitochondrial genetic disease 237
The genetics of mitochondrial disease
Mitochondrial disease caused by mtDNA
Unlike nuclear DNA, which is diploid and follows
Mendelian laws of inheritance, mtDNA is exclusively
maternally inherited [11]. The multicopy nature of
mtDNA gives rise to heteroplasmy, a unique aspect of
mtDNA-associated genetics that occurs when there is
coexistence of a mix of mutant and wild-type mtDNA
molecules (heteroplasmy). In contrast, homoplasmy
occurs when all of the mtDNA molecules have the
same genotype. Heteroplasmic mutations often have
a variable threshold, i.e. a level to which the cell can
tolerate defective mtDNA molecules [12]. When the
mutation load exceeds this threshold, metabolic dys-
function and associated clinical symptoms occur. Point
mutations and large-scale mtDNA deletions represent
the two most common causes of primary mtDNA dis-
ease, the former usually being maternally inherited, and
the latter typically arising de novo during embryonic
development.
mtDNA point mutations
mtDNA point mutations (including small indel muta-
tions) constitute a signicant cause of human disease,
with an estimated population prevalence of one in 200
[13]. Mutations have been reported in every mtDNA
gene, and have been associated with clinical symp-
toms ranging from non-syndromic sensorineural deaf-
ness to MELAS, a devastating syndromic neurological
condition whose predominant features, i.e. mitochon-
drial encephalopathy, lactic acidosis, and stroke-like
episodes, give rise to the acronym. Clinical symptoms
can present in child or adulthood, and mutations can
be inherited (∼75% cases) or occur de novo (∼25%
cases) [14]. Maternally transmitted mtDNA defects may
involve a clinically unaffected mother who harbours the
familial mtDNA mutation below the threshold required
for cellular dysfunction, although her oocytes harbour
varying mutation loads, owing to the selection pres-
sures of the mitochondrial bottleneck [15]. It is there-
fore almost impossible to predict the recurrence risk
for subsequent pregnancies, although prenatal testing of
embryonic tissues by the use of chorionic villus biopsy
or amniocentesis can provide an accurate measure of
mtDNA heteroplasmy in the fetus, which can inform
reproductive choices [16]. The recurrence risk of de
novo mtDNA point mutations is very low, except for the
risk of germline mosaicism in maternal oocytes [14].
Single, large-scale mtDNA deletions
Single, large-scale mtDNA deletions have a population
frequency of 1.5/100 000 [8], with three main associated
phenotypes: chronic progressive external ophthalmople-
gia (PEO) (∼65% of cases), Kearns–Sayre syndrome
(KSS) (∼30% of cases), and Pearson syndrome (<5%
of cases) [17]. Pearson syndrome is the most severe
presentation associated with single, large-scale mtDNA
deletions; patients present early in life with sideroblastic
anaemia and pancreatic dysfunction, and the condition
is often fatal in infancy [18]. KSS patients present
before the of age 20 years with ptosis and/or PEO and
pigmentary retinopathy, and may have multisystem
involvement, including myopathy, ataxia, or cardiac
conduction defects [17]. PEO is the more benign pre-
sentation attributable to single mtDNA deletions, and
is associated with ophthalmoplegia, ptosis, and myopa-
thy [19]. Unlike nuclear gene rearrangements, single,
large-scale mtDNA deletions often arise sporadically
during embryonic development and have a low recur-
rence risk [20]. Clinically affected women who harbour
a large-scale mtDNA deletion have a low (<10%) risk
of transmission [20], and prenatal testing is informative
for at-risk pregnancies [16].
Secondary mtDNA mutations
Large-scale mtDNA deletions and point mutations rep-
resent primary mtDNA defects, but secondary defects
are other common causes of mitochondrial disease.
Defective mtDNA maintenance, transcription, or protein
translation, or a defective ancillary process such as mito-
chondrial import, can cause either quantitative (deple-
tion of mtDNA copy number) or qualitative (affecting
mtDNA genome integrity, resulting in multiple large
mtDNA deletions) effects. These result from mutations
affecting nuclear genes, and inheritance occurs in a
Mendelian (or de novo) fashion.
Mitochondrial disease caused by nuclear
mitochondrial genes
The majority of the genes encoding the mitoproteome
are in the nuclear genome [5] and follow Mendelian
inheritance patterns. De novo, X-linked, dominant and
recessive inheritance cases have been reported in the lit-
erature [21–24]. The rst nuclear mitochondrial gene
mutation was identied in 1995 in SDHA, encoding a
structural subunit of complex II [25], and there has been
monumental progress in the discovery of mitochondrial
disease candidate genes since then. New proteomic and
transcriptomic approaches are being applied to models
of human disease to uncover new candidates [26,27],
and patient analyses are validating their involvement in
human pathology [28]. The traditional approach of link-
age analysis by the use of multiple affected family mem-
bers has given way to massively parallel sequencing
strategies, including whole exome sequencing (WES),
either of affected singletons or of proband–parent trios,
and new disease genes are still emerging over 20 years
later. Of the ∼1300 proteins in the mitoproteome, muta-
tions have been reported in >250 genes [29], and both
new genes and new mechanisms involving genes already
implicated in human disease through alternative path-
ways are being reported [30]. It is apparent that more
severe clinical phenotypes are often associated with
recessive defects, presumably because of varying het-
eroplasmy levels in clinically affected tissues and the
© 2016 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd J Pathol 2017; 241: 236 –250
on behalf of Pathological Society of Great Britain and Ireland. www.pathsoc.org www.thejournalofpathology.com
238 CL Alston et al
Figure 1. Schematic of the OXPHOS complexes, their component subunits, and associated ancillary factors. Multimeric protein complexes
I–IV shuttle electrons along the respiratory chain, facilitated by the reduction of the cofactors coenzyme Q
10
(Q) and cytochrome c (cyt c).
Electron transfer is coupled to the transfer of protons (H
+
) across the inner mitochondrial membrane to generate a proton motive force,
which is used by complex V (ATP synthase) to synthesize ATP. Characterization of OXPHOS complexes has identied the constitutive subunits
that are either mtDNA-encoded or nuclear-encoded, and many of the nuclear-encoded proteins involved in complex assembly, biogenesis,
or ancillary function; genes in which mutations have been identied are shown in bold, and the rst report of disease-causing mutations
is shown in blue.
dichotomous effect of recessive mutations; therefore,
mtDNA mutations are more common in adults, whereas
nuclear gene defects are overrepresented in paediatric
cases [31].
In this review, we delineate the nuclear mitochondrial
disease genes into those that cause isolated and those
that cause multiple respiratory chain complex decien-
cies, for simplicity and brevity.
Mitochondrial disease caused by nuclear
mitochondrial genes: isolated respiratory chain
complex deciencies
Histochemical and biochemical evidence of an isolated
respiratory chain complex deciency can be suggestive
of a mutation affecting either a structural subunit or an
assembly/ancillary factor of one of the ve OXPHOS
complexes. Our current knowledge of the structural sub-
units and ancillary factors for each complex is summa-
rized in Figure 1.
Isolated complex I deciency
Complex I (NADH dehydrogenase) is composed
of 44 structural subunits (seven of which are
mtDNA-encoded) with at least 14 ancillary/assembly
factors [32,33]. Isolated complex I deciency represents
the biochemical phenotype for ∼30% of paediatric
patients [34], of whom 70–80% have a nuclear gene
defect [35]. The clinical symptoms associated with
complex I deciency are heterogeneous, although
the prognosis is typically poor, with rapid progres-
sion. Lactic acidosis is a common feature, although
it is often present with other symptoms, such as car-
diomyopathy or leukodystrophy. Mutations have been
identied in 19 of the 37 structural subunits, and in 10
of 14 identied assembly factors. Although there are
a few exceptions, such as the p.Trp22Arg NDUFB3
[36] and p.Gly212Val TMEM126B European founder
mutations [28,37], and the p.Cys115Tyr NDUFS6
Caucasus Jewish founder mutation [38], studies have
revealed the majority of complex I deciency mutations
© 2016 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd J Pathol 2017; 241: 236 –250
on behalf of Pathological Society of Great Britain and Ireland. www.pathsoc.org www.thejournalofpathology.com
Mitochondrial genetic disease 239
to be private and non-recurrent [39]. NDUFS2 and
ACAD9 mutations account for a signicant proportion
of diagnoses, although it is likely that clearer genetic
diagnostic trends will emerge from large diagnostic
next-generation sequencing (NGS) datasets [40].
Isolated complex II deciency
Succinate dehydrogenase (SDH), unlike any of the other
complexes of the mitochondrial OXPHOS system, is
entirely nuclear-encoded, and is involved in both the tri-
carboxylic acid cycle (where it metabolizes succinate to
fumarate) and the respiratory chain (transferring elec-
trons from FADH
2
to reduce ubiquinone to ubiquinol).
Complex II deciency is rare (2–8% of mitochon-
drial disease cases [41,42]), with <50 patients having
been reported. Biallelic mutations have been associ-
ated with congenital metabolic presentations, predomi-
nantly affecting either the central nervous system (CNS)
or heart (hypertrophic cardiomyopathy, leukodystrophy,
Leigh syndrome, and encephalopathy) [43], whereas
heterozygous mutations are associated with cancer sus-
ceptibility, particularly pheochromocytoma and para-
ganglioma [44]. Although SDH was initially believed to
have distinct genotype–phenotype relationships (SDHA
and SDHAF1 being linked to mitochondrial disease, and
SDHB/SDHC/SDHD/SDHAF2 being linked with cancer
susceptibility), it is emerging that there is phenotypic
overlap, prompting tumour surveillance of unaffected
relatives heterozygous for SDHx mutations [45,46].
Isolated complex III deciency
Ubiquinol–cytochrome c oxidoreductase, complex III
of the respiratory chain, functions as a homodimer to
transfer electrons from ubiquinol to cytochrome b, and
then to cytochrome c. Complex III is composed of 11
structural subunits plus two heme groups and the Rieske
iron–sulphur protein. Exercise intolerance is the clini-
cal phenotype reported for >50% of patients with muta-
tions in the mtDNA MTCYB gene, but cardiomyopa-
thy and encephalomyopathy have also been noted [47].
Pathogenic mutations have been reported in four of
the nuclear-encoded structural subunits plus ve assem-
bly/ancillary factors [48], with presentations including
developmental delay, encephalopathy, lactic acidosis,
liver dysfunction, renal tubulopathy, and muscle weak-
ness [48,49].
Isolated complex IV deciency
Cytochrome c oxidase (COX), complex IV of the res-
piratory chain, is embedded in the inner mitochon-
drial membrane, and functions as a dimer, with two
copper-binding sites, two heme groups, one magnesium
ion, and one zinc ion [50]. Complex IV pumps protons
across the inner mitochondrial membrane, contributing
to the proton motive force for ATP synthase exploitation,
and donates electrons to oxygen at the respiratory chain
termini to form water. Complex IV has 13 structural
subunits, and at least 26 additional proteins involved in
assembly and biogenesis [51]. NDUFA4 was originally
described as a complex I subunit gene, but has since been
reassigned to complex IV, following functional studies
[52] supported by the presence of NDUFA4 defects in
a patient with severe COX deciency [53]. Mutations
have been reported in structural COX subunits, but most
defects affect biogenesis/assembly proteins. Some pro-
teins are linked tightly with specic aspects of COX
biogenesis (e.g. COA6, involved in copper-dependent
COX2 biogenesis [54]), and others have more diverse
roles [55]. Clinically, presentations are often early onset
and devastating, predominantly affecting the heart and
CNS (e.g. SURF1, in which >80 different mutations
have been reported to cause Leigh syndrome [56]),
although a milder Charcot–Marie–Tooth phenotype has
been associated with biallelic COX6A1 variants [57].
Isolated complex V deciency
ATP synthase, complex V, is the multimeric molec-
ular motor that drives ATP production through phos-
phorylation of ADP. Utilizing the proton motive force
generated by electron transport and proton pumping
by the respiratory chain, the 600-kDa complex con-
sists of 13 different subunits (some of which have dif-
ferent isoforms; for example, ATP5G1, ATP5G2 and
ATP5G3 encode subunit c isoforms), and involves at
least three ancillary factors. Defects have been reported
in only four nuclear complex V genes to date, with
varied clinical phenotypes. The most common defects
involve TMEM70, including a Roma TMEM70 founder
mutation causing lactic acidosis and cardiomyopathy
[58], although encephalopathy and cataracts have been
reported in other populations [59].
Mitochondrial disease caused by nuclear
mitochondrial genes: multiple respiratory chain
defects
Mitochondrial function is regulated and maintained by
∼1300 nuclear genes; these nuclear genes are trans-
lated by cytosolic translational machinery, and the 5
′
mitochondrial targeting sequence directs transport of the
translated proteins into the mitochondrion, where they
are required for diverse functions. These include the
transcription of mitochondrial mRNA (e.g. POLRMT
[60]), mitochondrial DNA maintenance (e.g. POLG
[61]), regulation of mitochondrial dNTP pools (e.g.
RRM2B [62]), cellular signalling (e.g. SIRT1 [63]), and
the translation of mtDNA-derived proteins. Numerous
subgroups of proteins are involved in mitochondrial
gene translation: mitochondrial aminoacyl tRNA syn-
thetases, which are responsible for charging each mito-
chondrial tRNA molecule with the appropriate amino
acid (e.g. AARS2 [64]), proteins involved in RNA pro-
cessing (e.g. MTPAP [65]), mitoribosomal proteins (e.g.
MRPL44 [66]), and proteins involved in mitochondrial
tRNA modication (e.g. TRMU [67]). Defects in ≥250
nuclear mitochondrial genes have now been reported in
© 2016 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd J Pathol 2017; 241: 236 –250
on behalf of Pathological Society of Great Britain and Ireland. www.pathsoc.org www.thejournalofpathology.com