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OPEN The Spectrum of Mitochondrial

Ultrastructural Defects in
Mitochondrial Myopathy
received: 07 April 2016 Amy E. Vincent1, Yi Shiau Ng1, Kathryn White2, Tracey Davey2, Carmen Mannella3,
accepted: 07 July 2016 Gavin Falkous1, Catherine Feeney1, Andrew M. Schaefer1, Robert McFarland1,
Published: 10 August 2016 Grainne S. Gorman1, Robert W. Taylor1, Doug M. Turnbull1 & Martin Picard4,5
Mitochondrial functions are intrinsically linked to their morphology and membrane ultrastructure.
Characterizing abnormal mitochondrial structural features may thus provide insight into the
underlying pathogenesis of inherited and acquired mitochondrial diseases. Following a systematic
literature review on ultrastructural defects in mitochondrial myopathy, we investigated skeletal
muscle biopsies from seven subjects with genetically defined mtDNA mutations. Mitochondrial
ultrastructure and morphology were characterized using two complimentary approaches: transmission
electron microscopy (TEM) and serial block face scanning EM (SBF-SEM) with 3D reconstruction. Six
ultrastructural abnormalities were identified including i) paracrystalline inclusions, ii) linearization
of cristae and abnormal angular features, iii) concentric layering of cristae membranes, iv) matrix
compartmentalization, v) nanotunelling, and vi) donut-shaped mitochondria. In light of recent
molecular advances in mitochondrial biology, these findings reveal novel aspects of mitochondrial
ultrastructure and morphology in human tissues with implications for understanding the mechanisms
linking mitochondrial dysfunction to disease.

Skeletal muscle fibers contain large numbers of mitochondria classically known for their role in ATP synthesis
through oxidative phosphorylation (OXPHOS), which fuels the energy-demanding process of muscle contraction1,2.
However, research in recent decades has revealed that beyond energy production mitochondria also per-
form a number of additional functions. They contribute to Ca2+ homeostasis3,4 and redox signalling5,6, release
pro-apoptotic factors regulating cell death7, synthesize essential macromolecules including heme molecules8,
regulate nuclear gene expression9,10, and can release immunogenic pro-inflammatory molecules into the cyto-
plasm and systemic circulation11. Beyond expanding our fundamental understanding of mitochondrial biology12,
these advances have challenged the commonly reported view of mitochondria as a cellular powerhouse and thus
revealed new cellular mechanisms whereby mitochondrial dysfunction causes clinical disease13–16.
Of particular interest to neuromuscular disorders is the link between mitochondrial ultrastructure and
function17–19. Abnormal mitochondrial ultrastructure, particularly the highly conserved inner mitochondrial
membrane (IMM) cristae where a number of OXPHOS enzymes reside, is linked to altered mitochondrial func-
tion and signalling that may contribute to pathophysiology (e.g., ref. 20). Furthermore, the molecular machinery
that regulates mitochondrial morphology and ultrastructural transitions has in part been defined and experi-
mental manipulation of various components in model systems has reinforced causal links between mitochondrial
structures and functions21. Thus, the determinants of mitochondrial ultrastructure and its functional bearings
have implications for understanding the pathophysiology in human mitochondrial disease22. However, mito-
chondrial ultrastructural defects in mitochondrial myopathy have not been thoroughly examined in light of
recent molecular advances in mitochondrial biology.
The first description of mitochondrial structures in human skeletal muscle using electron microscopy
appeared in the 1960s23–25. Abnormal skeletal muscle mitochondrial morphology and ultrastructure has since

1
Wellcome Trust Centre for Mitochondrial Research, Institute of Neurosciences, Newcastle University, Newcastle
upon Tyne, UK. 2EM Research Services, Newcastle University, Newcastle upon Tyne, UK. 3Wadsworth Center, New
York State Department of Health, Albany, NY, USA. 4Department of Psychiatry, Division of Behavioral Medicine,
Columbia University Medical Center, New York, NY, USA. 5Department of Neurology and Columbia Translational
Neuroscience Initiative, H. Houston Merritt Center, Columbia University Medical Center, New York, NY, USA.
Correspondence and requests for materials should be addressed to M.P. (email: [email protected])

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Figure 1. Normal mitochondrial ultrastructure. (A) Transmission electron micrograph of normal

mitochondria in human skeletal muscle showing typical tubular cristae, and crista junctions. (B) Schematic
representation of crista junctions, associated structures, and parameters measured in this study. (C) Three-
dimensional schematic of normal tubular cristae structure. The outer mitochondrial membrane (OMM,
red), and three functionally distinct regions of the inner mitochondrial membrane (IMM): inner boundary
membrane (blue), crista junction (orange), and crista membrane (green). (D) Same image as in A with
pseudocolored adjacent but distinct mitochondria and outlined crisate membranes undergoing trans-
mitochondrial cristae coordination (see ref. 34 and text for discussion). (E) Unprocessed and (F) pseudocolored
transmission electron micrographs of normal human skeletal muscle illustrating mitochondria with normal
shapes and sizes, with electron-dense curvilinear cristae, with some exhibiting trans-mitochondrial cristae
coordination.

been reported in the context of aging and several neuromuscular disorders, but most previous studies involved
only a limited spectrum of defects and/or poorly-defined genetic disorders (e.g., refs 26, 27 see Table S1). Previous
investigations of mitochondrial ultrastructure in clinical samples were also limited to standard (single-plane)
transmission electron microscopy (TEM), precluding analysis of complex three-dimensional mitochondrial
structures of potential functional significance.
Here, we first conducted a systematic review of the literature to document mitochondrial ultrastructural
abnormalities in skeletal muscle of individuals with mitochondrial disease published to date. We then combined
two electron microscopy methods: TEM and serial block face scanning electron microscopy (SBF-SEM) to exam-
ine muscle biopsies from individuals with molecularly defined mitochondrial DNA (mtDNA) mutations. This in
depth re-examination of skeletal muscle mitochondrial ultrastructure in light of recent advances in mitochondrial
biology reveals abnormal features not previously reported in human tissues, thus expanding the spectrum of
mitochondrial EM pathology in mitochondrial disease.

Results
Systematic review of the literature. We first performed a systematic review of the literature that iden-
tified 135 publications reporting EM findings in skeletal muscle biopsies of individuals with mitochondrial dis-
ease. These are summarized in Table S1, including information about the muscle biopsied, subject ages, clinical
phenotype, and genetic diagnosis where available. Among the most commonly reported features were enlarged
mitochondrial size with swelling, paracrystalline inclusions (PCIs), and electron-dense precipitates in the
mitochondrial matrix. This systematic review indicated that most articles were case studies, published prior to
technological progress enabling genetic diagnosis, or prior to recent discoveries of the molecular aspects of mito-
chondrial ultrastructure, thus limiting the interpretation of these observations.

Normal mitochondrial ultrastructure. Parameters for normal mitochondrial ultrastructure are estab-
lished (e.g., refs 28–30) and were confirmed in biopsies from two individuals with normal skeletal muscle
mitochondrial histochemistry. Mitochondria are double membrane organelles with the inner (IMM) and
outer mitochondrial membranes (OMM) surrounding the mitochondrial matrix and intermembrane space,
respectively (Fig. 1). The convoluted IMM bends inwards31,32 and can be divided into three regions; inner

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Age at Genetic Heteroplasmy (if Lactate

Patient # Sex biopsy diagnosis applicable) % deficiency % RRF CK (IU/L) (mmol/L) Clinical phenotype Diagnostic notes
Large-scale single CPEO, proximal
1 F 47 N/A 20 10 226 2.4 —
mtDNA deletion myopathy
Large-scale single CPEO, proximal
2 F 62 34 20 15 122–197 2.1–3.1 —
mtDNA deletion myopathy
Large-scale single CPEO, proximal
3 F 70 22 18 9 318–1238 1.4–2 Asymmetric myopathy
mtDNA deletion myopathy
Axial, proximal
4 F 22 m.8344A>G 97 97 10 145–291 7.4 myopathy, lactic —
acidosis
5 F 50 m.8344A>G 63 22 7 43 1.6 Mild myopathy Mother of patient 4
6 F 20 m.8344A>G 40 COX intermediate 0 267 1.2 Asymptomatic Sister of patient 4
Diabetes mellitus,
7 F 69 m.3243A>G 21 3 2 180–375 1.3 deafness, gut —
dysmotility

Table 1. Case information for patients with mitochondrial disease. N/A: non-available; % COX: proportion
of myofibers with cytochrome c oxidase deficiency; RRF: ragged red fibers; CK: creatine kinase; CPEO: chronic
progressive external opthalmoplegia; HCM: hypertrophic cardiomyopathy; OA: optic atrophy; MERRF: myoclonic
epilepsy with ragged red fibers. Deletions position and sizes for patient 1: N/A; patient 2: m.8482-13460, 4978 bp;
patient 3: m.8576-12968, 4392 bp. Normal clinical range for CK: 25–200 IU/L; lactate: <​2.2 mmol/L. All biopsies
from the tibialis anterior muscle.

Linearization
and
Patient Type I Type geometrical Concentric Hyperbranching/
# PCI II PCI features cristae Compartmentalisation Nanotunneling hyperfusion Projections
1 +​+​+​ −​ −​ −​ −​ −​ +​+​ −​
2 −​ −​ −​ −​ −​ +​ +​ −​
3 −​ −​ −​ −​ ​ ​
+​++ +​ −​ +​+​+​
4 −​ +​ ​ ​
+​++ +​+​ −​ −​ −​ −​
5 +​ −​ −​ −​ +​+​ −​ −​ +​
6 −​ −​ −​ +​ −​ −​ +​+​ +​
7 −​ −​ −​ −​ −​ +​+​+​ +​+​+​ ​ ​
+​++

Table 2. Summary of mitochondrial ultrastructural abnormalities identified in patient skeletal muscle

biopsies. PCI: Paracrystalline inclusion; +​: Few; +​+​: Frequent; +​+​+​: Very frequent; −​: none.

boundary membrane, the crista junction, and the cristae membrane (Fig. 1B,C)33. In some cases where mitochon-
dria are tethered by an inter-mitochondrial junction (IMJ), trans-mitochondrial cristae coordination between
distinct organelles can be observed34 (Fig. 1A,D). Also in normal mitochondria, the matrix is a single continuous
space that contains enzymes involved in biochemical transformations and biosynthetic reactions, as well as sev-
eral copies of the mitochondrial genome. Although frequently depicted as ovoid or bean-shaped, mitochondria
oscillate between tubular and spherical morphology determined by highly dynamic fusion and fission processes,
which also determine their sizes21.
Here, we aimed to document deviations from normal mitochondrial ultrastructure in molecularly-defined
cases of mitochondrial disease. We examined muscle biopsies from seven patients who harboured a primary
mtDNA mutation: single large-scale mtDNA deletion (n =​  3), m.8344A>G tRNALys (n =​  3), or m.3243A>G
tRNALeu(UUR) (n =​ 1). Six mitochondrial ultrastructural abnormalities were identified as candidate features linked
to known myopathic mechanisms. Demographic, genetic, biochemical, and clinical information for each subject
is provided in Table 1. A summary of ultrastructural findings for all subjects is provided in Table 2. Each observed
feature is first presented below, and their potential biological and clinical significance subsequently discussed in
light of recent advanced in mitochondrial biology.

Paracrystalline inclusions (PCIs). PCIs were observed in a patient harbouring a single, large-scale mtDNA
deletion (patient 1) and chronic progressive external opthalmoplegia (CPEO) and in two patients manifesting
with myopathy with the m.8344A>G mutation (patients 4 and 5). PCIs present as rigid rectangular crystals of
approximately 250 nm in length and 50 nm in width. They consist of stacked sheets that either run obliquely
(Fig. 2A,D) or parallel (Fig. 2B,C) relative to the length of the paracrystal. Their rigidity is evidenced by their
occasional deformation or rupture of membranes (Fig. 2C). As for the other defects discussed below, substantial
heterogeneity existed in PCI distribution even within single cells, with some mitochondria exhibiting normal
ultrastructure, and other containing PCIs of various types and sizes. Although PCIs were observed in both sub-
sarcolemmal (SS, beneath the plasma membrane and near nuclei) and intermyofibrillar (IMF, between myofibrils)
compartments, PCIs were generally more prevalent in SS mitochondria (Fig. 2E,F).

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Figure 2. Paracrystalline inclusions (PCIs). (A) Type I PCIs occupying most of a mitochondrion’s volume in skeletal
muscle with a single mtDNA deletion (patient 1). (B) Linear Type I PCI in mitochondrion from a case of m.8344A>G
(patient 5). (C) Disruption of IMM and OMM (arrowhead) by a rigid type II PCI, and (D) other examples of type II
PCIs from a case of m.8344A>G (patient 4). (E) Subsarcolemmal region of a muscle fiber showing the extracellular
space (EC, yellow) and sarcolemma, profile of a nucleus (N, blue), myofibrils (MF), mitochondria with PCI (red)
and normal mitochondria (green), with (F) pseudocolored mask (patient 1). Note the greater abundance of PCI-
containing mitochondria in the perinuclear SS compartment compared to the intermyofibrillar compartment,
consistent with the distinctive requirement for de novo protein synthesis for PCI formation.

PCIs are classified in two major types characterized by defined structural pattern, size, and location within
the mitochondria35. Both type-I PCIs comprised of stacked sheets with discernible structure forming rectangular
inclusions in the intracristae space (Fig. 2A,B) and type-II PCIs with electron dense substructure and residing in
the intracristae and intermembrane space (Fig. 2D) were observed here. Consistent with previous observations35,
we found type-I and type-II PCIs to be mutually exclusive within individual patients; type-I PCIs were identified
in patients 1 and 5, whereas type-II PCIs were observed in patient 4.

Cristae linearization and angular features. In contrast to the normal invaginations of the IMM (Fig. 1),
we observed linearization of cristae membranes and abnormal angular (i.e., geometrical) features in patient 4
(Fig. 3). These structures included rigid linear cristae juxtaposed at angles of 124.7 ±​ 7.4° (Fig. 3A,B), often in
association with electron dense inclusions (Fig. 3C,D). Linear cristae segments show enhanced electron den-
sity, suggesting the presence of large molecular weight proteins and/or substantial change in membrane lipid
composition. Three-dimensional reconstruction from SBF-SEM data demonstrated the organization of line-
arized electron-dense cristae as continuous sheets encompassing cargo, rather than isolated tubular structures
(Fig. 3E,F).

Concentric cristae or “onion-like” mitochondria. In normal mitochondria the inner boundary mem-
brane periodically invaginates into tubular or fenestrated laminar cristae, with the resulting crista junctions forming
pores between the intermembrane and intracristae spaces (Fig. 1). Contrary to this pattern, in TEM from patients 4
and 6 with the m.8344A>G mutation we observed several mitochondria devoid of normal cristae and crista junc-
tions (CJs), but with abnormal “onion-like” concentric membranes free of fenestration (Fig. 4), also previously
referred to as “tubular parallel cristae” or “concentric laminated bodies” (see Table S1). Three-dimensional recon-
structions confirmed the tight layering of discontinuous concentric membranes sheets (Fig. 4C,D).
The intermembrane space separating the OMM-IMM was similar between mitochondria with concen-
tric (7.1 ±​ 1.6 nm) and normal cristae (7.9 ±​ 1.2 nm, P =​ 0.45). However, the width of the intracristae spaces
(Fig. 1B) was reduced by approximately 15% in mitochondria with concentric cristae (7.78 ±​ 1.0 nm) com-
pared to normal mitochondria (9.20 ±​ 1.0 nm, P <​ 0.05), indicating a tightening of cristae membranes in

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Figure 3. Linearization and geometrical cristae features. (A,B) Enlarged mitochondria containing linearized
cristae juxtaposed at nearly identical angles, and (C) linearized cristae forming various geometrical shapes, and
(D) linearized IMM segments (arrows) joined by curved segments from a case of m.8344A>G (patient 4).
(E) SBF-SEM image with example of linearized cristae and geometrical shapes and (F) three-dimensional
reconstruction of mitochondrion in E (patient 4).

Figure 4. Concentric “onion-shaped” cristae. (A) Multiple overlaid layers of double OMM/IMM membranes
forming two major compartments in a case of the m.8344A>G (patient 4), and (B) two-dimensional
reconstruction of membrane structures. (C) Example of concentric cristae compartments (patient 4) imaged
with SBF-SEM, with (D) corresponding three-dimensional reconstruction.

onion-like mitochondria. Furthermore, as expected the distance between two adjacent cristae (Fig. 1B, intercris-
tae space) was substantially smaller in mitochondria with concentric cristae (22.5 ±​ 4.5 nm) than in normal mito-
chondria (60.2 ±​ 9.9 nm, P <​ 0.001), indicating denser packaging of membranes in dysfunctional mitochondria.

Compartmentalisation. Normal mitochondria consist of 2 compartments: a single mitochondrial matrix

compartment, and a contiguous intermembrane/intracristae space. We observed an increased number of com-
partments per mitochondrion particularly in patient 3 with a single, large-scale mtDNA deletion and CPEO,
and patient 5 with a m.8344A>G mutation and mild myopathy. Abnormal compartments were bound by a
single or double membrane with distinct molecular or ionic composition evidenced by differences in electron
density between each compartment (Fig. 5A,B), dense amorphous material (Fig. 5C), occasionally bounded by
electron-dense linearized membranes (Fig. 5D). Notably, compartmentalization appears to involve the complete

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Figure 5. Compartmentalization. (A) Example of membrane-bound sub-mitochondrial compartments located

centrally and (B) peripherally in contact with the inner boundary membrane, from cases of m.8344A>G mutation
(patient 5) and single mtDNA deletion (patient 3), respectively. (C) Electron-dense round compartments distributed
in the mitochondrial matrix in a case of single mtDNA deletion (patient 3). (D) Compartment bound by linearized
electron-dense membranes in a case of m.8344A>G (patient 4). (E) Cross-sectional image of a mitochondrion with
two distinct compartments of different electron density, and (F) three-dimensional reconstruction from SBF-SEM.
(G,H) Examples of OMM protrusion and distension consistent with the release of mitochondrial components in
the cytoplasm in a case of m.8344A>G mutation (patient 4). Pseudocolored areas indicate the major compartment
bound by the OMM (green), and sub-compartments (red and blue).

absence of crista junction and normal cristae structures. Three-dimensional reconstruction of mitochondria
exhibiting apparent compartmentalization in cross-section confirmed the complete spatial isolation of individual
compartments without connection to the outer boundary membrane (Fig. 5E,F). Localized distension of the
OMM with apparent release of mitochondrial matrix content into the cytoplasm was also observed (Fig. 4G,H).

Nanotunneling. We observed mitochondrial nanotunnels (Fig. 6A,B) in three of the seven patients (patients
2, 3 and 7). The average diameter of nanotunnels was 62.3 ±​ 10.7 nm (Fig. 6C) and was similar between patients.
Three-dimensional reconstructions further demonstrated that nanotunnels consist of thin tubular projections extend-
ing from one or more mitochondria. The nanotunnel length averaged 623 nm, ranging from 206 nm to 2.3 μ​m (Fig. 6D).

Hyperbranching and donut mitochondria. Extensively branched mitochondria were particularly abun-
dant in a case of m.3243A>G with 21% heteroplasmy (patient 7) (Fig. 6E,F). Interestingly, donut-shaped mito-
chondria arising from self-fusion of a mitochondrion were also observed in cases single mtDNA deletion at
34% heteroplasmy (patient 2) and m.8344A>G at 40% heteroplasmy (patient 6) (Fig. 6G,H). Three-dimensional
reconstruction confirmed the unique toroid nature of donut mitochondria (Fig. 6H).

Discussion
Mitochondrial biology is replete with examples where mitochondrial ultrastructure is mechanistically linked
to functions17,18, and vice versa. In an attempt to understand the pathogenesis of mitochondrial disease, early
electron microscopy investigations identified common ultrastructural abnormalities such as swelling and PCIs.
However, most observations were mainly made prior to the identification of molecular determinants of mito-
chondrial structure and function (Table S1), thus limiting the spectrum of conceivable observations and the
interpretation of their mechanistic significance. Improved diagnosis enable the identification of pathogenic muta-
tions in an unprecedentedly large proportion of patients36. Here, building from recent advances in mitochondrial
biology imaging technology, and genetic diagnosis, we examined the spectrum of mitochondrial ultrastructural
features in a clinically characterized group of patients with genetically defined mitochondrial disease.
The literature to date characterizes what constitutes normal mitochondrial morphology in human and mouse
skeletal muscle, including the organization of the IMM into cristae (Fig. 1). Using our electron microscopy
approaches, we documented comparable normal mitochondrial morphology in two individuals with normal skel-
etal muscle mitochondrial function34, confirming that our biopsy and imaging methods preserved normal mito-
chondrial ultrastructure. Normal ultrastructure notably included the physical coordination of cristae between
pairs of distinct mitochondria linked by an inter-mitochondrial junction (Fig. 1A,D), a phenomenon which has
been shown to be resistant to genetic disruption of respiratory chain function in mice, independent of mitofusins,

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Figure 6. Nanotunelling and hyperbranching. (A,B) Examples of mitochondrial nanotunnels composed of

both OMM and IMM, but devoid of cristae in a case of m.3243A>G (patient 7). (C) Variation in nanotunnel
diameter, with each datapoint representing the average of the smallest and largest diameters measured
for individual nanotunnels across all subjects (n =​  26). (D) Three-dimensional reconstruction of three
mitochondria connected via nanotunnels from a case of m.3242A>G (patient 7). (E,F) Examples of highly
branched mitochondria (hyperfusion) from cases of m.3243A>G (patient 7) (G) Donut-shaped mitochondrion
denoting self-fusion from a case of single mtDNA deletion (patient 2). (H) Three-dimensional reconstruction of
a donut-shaped mitochondrion from a case of m.8344A>G (patient 6).

evolutionary conserved from mollusk to mammals, and inducible to some extent by the physical rapprochement
of energized mitochondria in vitro34. In general, from a methodological perspective, it must be noted that con-
sistent with the mosaic distribution of affected and non-affected cells in mitochondrial myopathy, substantial
heterogeneity and mosaicism in mitochondrial ultrastructure exists between individuals, between muscle fibers,
and even within single cells (Fig. S1).
Overall, the electron microscopic survey described here expands the spectrum of mitochondrial ultrastruc-
tural abnormalities known to exist in human. Some previously reported features are non-specific pathological
hallmarks of mitochondrial myopathy such as PCIs, enlarged mitochondria, concentric “onion-like” cristae.
Other features not previously reported include linearization and angular arrangement of cristae, localized mem-
brane distension, nanotunnels, and donut-shaped mitochondria. These features are discussed below in context
of recent findings in mitochondrial biology, with an emphasis on their potential significance to mitochondrial
function and pathology.

Paracrystalline inclusions. Although sample size was small, type-I (n =​ 2) and type-II (n =​ 1) PCIs were
found to be mutually exclusive similar to previous reports35. The cause of this mutual exclusivity is, to date,
unknown. Notably, two related patients with the m.8344A>G mutation (mother and daughter, patients 4 and 5)
manifested different PCIs, indicating that factors other than the mtDNA mutation and nuclear background likely
interact to determine disease phenotype. PCI analysis in larger cohorts of patients would be required to under-
stand the specific conditions leading to different types of PCIs. However, it is worth noting that in our study
occurrence of type II PCIs correlated clinically with most severe cytochrome c oxidase deficiency and lactic aci-
dosis, and structurally with highest occurrence of concentric and linearized inner membranes.
We further note that PCIs appear more commonly in subsarcolemmal mitochondria. PCIs are composed of
crystallized mitochondrial creatine kinase (CK)37, likely as a result of a compensatory upregulation of CK due
to a deficiency of creatine phosphate shuttle activity. Reduced shuttle activity likely results from reduced ATP
synthesis secondary to OXPHOS defects, leading to CK protein accumulation and PCI formation. Thus, contrary
to most known pathognomonic processes triggered by loss-of-function mutations (i.e., absence of a protein or
functional mutation), PCI formation involves the accumulation of a functional protein. Protein accumulation
requires de novo synthesis, which depends upon upregulation of the CK gene in the nuclear compartment, and
local translation of the gene product. This molecular requirement for PCI could explain the preferential abun-
dance in the SS mitochondria that are inherently closer to myonuclei than IMF mitochondria.

Linearized cristae membranes. Linearized cristae membranes with altered electron density and a rigid
angular appearance were observed in a single patient (patient 4). These were commonly found in association with
PCIs and changes to both membrane and matrix electron density. Altered protein composition or supramolecular

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assembly of protein complexes, particularly of the ATP synthase, which is heavily involved in determining IMM
folding32,38, influence membrane curvature. Changes in the fluidity or rigidity of the IMM could also be caused
by altered cardiolipin content in the IMM39–41. Interestingly, we noted linearized cristae membranes juxtaposed at
an angle of approximately 120°. Domènech et al. also reported hexagonal structures with membranes exhibiting
120° angles in cardiolipin-containing phospholipid bilayer42, suggesting that cristae linearization and abnormal
angular features in mitochondrial myopathy could result from altered membrane lipid composition. The sole case
with prominent linearized inner membranes in our study (patient 4) was concurrent with the only example of
type II PCIs.

Concentric cristae. Concentric cristae were limited to two related patients (patients 4 and 6) with the
m.8344A>G mutation. Nevertheless, the existence of onion-like IMM organisation in human tissue extends pre-
vious observations in cultured human (HeLa) cells and yeast where down-regulation or knock down of mito-
chondrial contact site and cristae organising system (MICOS) components causes membrane stacking and/or
onion-like concentric layering33,43-45. Abnormal dimerization of the ATP-synthase in yeast also promotes concen-
tric cristae formation46.
Measurement of the intra- and inter- cristae space in normal mitochondria and those with concentric cristae
demonstrated a significant reduction in size in concentric cristae indicating tighter packing of cristae membranes.
The widths of intermembrane and intracristae spaces (Fig. 1) are regulated by specific proteins and are believed
to be of functional relevance19,47. We did not observe cristae junctions in mitochondria with concentric cristae.
Based on studies in model systems, potential causes of crista junction dysfunction and the resulting layering pat-
tern include defects of nuclear-encoded MICOS components, or other crista junction or IMS proteins interacting
with both OMM and IMM.

Compartmentalization. An increase in the number of compartments observed within mitochondria was

noted in two patients (patients 3 and 5). Sub-mitochondrial compartmentalization could be the product of par-
tial or hemi-fusion subsequent to OMM fusion in the absence of IMM fusion, thus resulting in a single enlarged
mitochondrion with multiple matrix spaces from the original smaller precursor mitochondria48. Consistent with
this hypothesis, suppression of the IMM pro-fusion Opa1 homologue eat-3 in Caenorhabditis elegans causes a
similar compartmentalisation phenotype49.
We observed localized distension of the OMM with apparent release of mitochondrial matrix content into the
cytoplasm (Fig. 4G,H). This occurred without gross alteration of mitochondrial ultrastructure, distinguishing
this process from permeability transition-induced swelling. Interestingly, recent evidence indicates that mito-
chondrial proteins (e.g. prohibitin, Hsp60) and mtDNA (in oxidized form) are released into the cytoplasm and
systemic circulation11. Such ectopic mitochondrial material acts as damage associated mitochondrial proteins
(DAMPs) or “alarmins”, triggering activation of inflammatory responses both intracellularly and systemically11.
The factors determining mitochondrial compartmentalization and local release of mitochondrial material, and
their relevance to myopathy, remain to be established.

Nanotunneling. To our knowledge, this is the first report of nanotunnels in human skeletal muscle. The
existence of “nanotunnels” was initially demonstrated in rat cardiomyocytes50. Consistent with earlier reports
where similar structures were observed51,52, mitochondrial nanotunnels are stretches of both IMM and OMM
devoid of cristae (Fig. 5A, inset), measure 50–200 nm in diameter50, able to transport large soluble proteins such
as GFP between non-adjacent mitochondria50. Such communication system may be particularly relevant for
physically constrained mitochondria in striated muscle, which cannot easily move and undergo fusion50.
In vitro, nanotunnels appear to grow between mitochondria in a kinesin KIF5B-dependent mechanism within
seconds53. However, upon fusion with a distant mitochondrion newly established nanotunnels may increase in
diameter, accommodate respiratory complexes via diffusion through the IMM, and thus contribute to the expan-
sion of mitochondrial tubules and of the mitochondrial network53. Alternatively, nanotunnels could result from
failed or stalled fission, a possibility supported by the fact that nanotunnels have a diameter at the lower limit of
the constrictions (60–150 nm) induced by the dynamin Dnm1 during mitochondrial fission in yeast54. Failed
fission could contribute to accelerate the spread of molecular defects across the mitochondrial network55.
Understanding the physiological and pathological conditions that promote or inhibit mitochondrial nano-
tunelling could offer new insights into the pathogenesis of mitochondriopathies, mutation load threshold, and
progression of mitochondrial myopathy. It is worth noting that in this study nanotunnels were observed in spec-
imens from three of seven patients, exclusively in those lacking PCIs. Nanotunnels were also observed in normal
muscle without mitochondrial disease (n =​ 2), but not in those with the highest heteroplasmy levels and the most
severe mitochondrial dysfunction. Therefore, nanotunnels may be indicative of normal or moderately impaired
mitochondrial respiratory chain function.

Hyperbranching and donut mitochondria. Excessive mitochondrial fusion or absence of fission leads
to mitochondrial elongation and hyperbranching, possibly representing a compensatory acute response to mito-
chondrial stress56. Dose-response increase in the m.3243A>G mutation load in vitro also leads to progressive
mitochondrial elongation9, and has been observed in aged mouse sarcopenic muscle57. Thus, hyperbranching and
donut mitochondria may reflect cellular stress58 in mitochondrial myopathy patients with intermediate states of
dysfunction, such as patient 7 (Fig. 6E,F).
Further to this we observe donut mitochondria in a further two patients (patients 2 and 6). The donut shape
results from self-fusion or “splitting” of mitochondria and are induced experimentally by respiratory chain inhi-
bition and oxidative stress in vitro59, and have been reported in brain presynaptic boutons of aged cognitively

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impaired non-human primates60. The presence of these features in human skeletal muscle may be reflective of the
degree or nature of mitochondrial dysfunction, although more work is required to establish their physiological
significance.
Some limitations of the present study should be noted. The aim of this investigation was to characterize the
spectrum of mitochondrial ultrastructural features in human skeletal muscle. Accordingly, our approach con-
sisted in capturing a large number of images depicting specific mitochondrial ultrastructural abnormalities,
targeting myofibers with clear signs of pathology. While this sampling approach enabled the identification of
multiple examples for known and novel ultrastructural defects, it is not compatible with a systematic unbiased
quantification of the prevalence or frequency of the ultrastructural defects. Furthermore, muscle biopsies were
collected from a convenience sample of consecutive individuals attending the diagnostic clinic, yielding a rela-
tively small group of patients with different genetic defects. While this precludes conclusions regarding disease
specificity, it has allowed to document and characterize a larger spectrum of ultrastructural abnormalities, and
conclude that some structural defects are in fact not unique to specific mutations.

Conclusion
Collectively, these results advance our understanding of mitochondrial dysfunction in several ways. First, in
seeking to understand the relative contributions of sub-cellular compartmentalization in disease pathogenesis
and progression, the recognition that certain features (i.e. PCIs) require the accumulation rather than the deple-
tion of proteins may offer new insights into both the kinetics and nature of the underlying bioenergetics defects.
Second, some of the reported features were previously observed in vitro or in model organisms following genetic
disruption of specific mitochondrial proteins. For example, alteration of MICOS components disrupt CJs in var-
ious model systems (e.g., ref. 61), and could contribute to some observed features such as compartmentalization
that completely lack CJs, and concentric cristae formation where CJs are rare. This opens the door to investi-
gating the pathophysiological signficance of MICOS components in primary mtDNA diseases. Third, the ori-
gin of transcriptional dysregulation and pro-inflammatory gene activation in certain musculoskeletal disorders
remains unclear. Given that mitochondria can transcriptionally regulate a large number of nuclear genes9,10 and
trigger intracellular inflammatory processes11, localized membrane distension (Fig. 5G,H) or PCI-induced mem-
brane rupture (Fig. 2C) could contribute to the cytoplasmic release of mitochondrial material that trigger these
“non-energetic” pathogenic features. Finally, nanotunnel formation, donut-shaped mitochondria, and hyper-
branching could represent evolutionary conserved compensatory responses to “mild” mitochondrial stress56,62.
Systematic assessment of mitochondrial morphology using quantitative EM methodologies sensitive mitochondrial
size, shape, and branching complexity (e.g., refs 29,57), and particularly three-dimensional reconstruction methods
such as serial block face (SBF-SEM) and focused-ion beam (FIB-SEM), will be required to ascertain the role of struc-
tural remodelling in certain mitochondrial and other musculoskeletal diseases. In addition, the functional significance
of these changes will also need to be established through targeted molecular studies coupled to clinical investigations of
mitochondrial ultrastructure. Expanding the spectrum of mitochondrial ultrastructure in human tissues should help
us identify different mechanisms by which mitochondrial dysfunction contributes to disease.

Material and Methods

Literature review. Scopus, Embase and Medline were searched using the following search terms: “electron
microscop*​AND muscle AND human AND mitochondria*​”. Filtering these for “full text” and “human” yielded
1549 results from Scopus, 1670 results from Embase and 922 results from Medline. Duplicates were removed,
and search results screened on the basis of the following criteria: full text availability, English language, human,
skeletal muscle, mitochondrial disease, any publication date up to the end of 2015. All included studies reported
on patients with either a clinical or genetic diagnosis of mitochondrial disease; publications including cases where
a diagnosis could not be reached have not been included. This resulted in 131 primary articles and four reviews
(total n =​ 135). All articles were screened for the specific mitochondrial pathology reported, and for the diag-
nostic methodology used, which included restriction site mutation (RSM) assay, southern blotting, PCR, Sanger
sequencing, restriction fragment length polymorphism (RFLP), solid phase mini sequencing, sequencing (gen-
eral), next generation sequencing, or method not specified. Table S1 reports in chronological order the biopsied
muscle, age of subjects, clinical features, genetic diagnosis, and a summary of mitochondrial ultrastructural and
morphological feature(s).

Patient cohort. This study was approved by the Newcastle and North Tyneside Local Research Ethics
Committees (reference 2002/205) and prior informed consent was obtained from each participant. All exper-
iments were carried out in accordance with the approved guidelines. Samples were collected in our diagnostic
service over a period of approximately ten weeks where 11 consecutive cases underwent a muscle biopsy, seven
of which were diagnosed with a primary mtDNA defect and reported upon here. For cases of single, large scale
mtDNA deletions, sequencing was performed in two of the three cases to determine the breakpoint and size.
Muscle biopsies were performed using the conchotome method under local anaesthesia (2% lidocaine) from
tibialis anterior muscle of all diagnosed patients. Biopsy specimens were subsequently dissected and processed
for electron microscopy. Demographic information and clinical data for each patient is summarized in Table 1.

Transmission electron microscopy (TEM). Muscle fiber bundles were teased from a fresh biopsy and
fixed overnight in 2% glutaradehyde in 0.1 M Sorenson’s buffer (pH 7.4) at 4 °C as described previously29. Briefly,
fibers were post fixed in 1% osmium tetroxide for 1 hour. Samples are dehydrated in a graded series of acetone
(25%, 50%, 75%, 100%) before being embedded in epoxy resin (TAAB medium grade) and polymerised at 60 °C.
Sections are cut on a Leica EM UC7 ultramicrotome, firstly semi-thin sections (0.5 um) are stained with toluidine
blue for LM to identify the area of interest/confirm orientation of tissue. Ultrathin sections (70 nm) were then

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transferred to copper grids, and stained with uranyl acetate and lead citrate, and examined on a Phillips CM 100
Compustage (FEI) transmission electron microscope and digital micrographs were captured with an AMT CCD
camera (Deben). On average seven individual fibers were thoroughly examined for each patient, for a total of 750
analysed images. Mitochondrial respiratory chain deficiency exists as a mosaic in skeletal muscle and cannot be
conclusively ascertained for individual muscle fibers in ultrathin sections. We therefore focused our survey on
myofibers with the highest mitochondrial content and/or showing signs of pathology at low magnification, such
as vacuolization, mitochondrial hyperproliferation, or myofibrillar disarray. Regions of interest were scanned
at 5,800x, images were captured at magnifications between 7,900x and 96,000x. Muscle fibers were examined in
longitudinal and transverse orientations using methodology reported previously29.

Serial block face scanning electron microscopy (SBF-SEM). Tissue was fixed in 2% glutaraldehyde
in 0.1 M cacodylate buffer (pH 7.4), and processed with heavy metal impregnation as described previously63.
Briefly, tissue was immersed in 3% potassium ferrocyanide and 2% osmium tetroxide, followed by 0.1% thio-
carbohydrazide, then 2% osmium tetroxide and finally left overnight in 1% uranyl acetate (with water washes
between each step). The next day the samples were immersed in 0.6% lead aspartate solution and then dehydrated
in graded acetone and embedded in epoxy tab 812 hard resin. After polymerisation blocks were trimmed and
sectioned for standard TEM to identify areas of interest for SBF-SEM imaging. Fibers with high mitochondrial
content were selected from cases with specific mitochondrial pathology and a series of serial images interspersed
by 30–50 nm were captured at a magnification of 8,000–12,000x on a Zeiss Sigma scanning electron microscope
with Gatan 3view system and digital micrograph software.

Analysis and statistics. Image stacks were exported, processed, and used for reconstruction of abnormal
features with IMOD 3dmod (IMOD 4.7, Boulder Laboratory for 3-D Electron Microscopy of Cells). Abnormal
ultrastructure features detected in patients 4, 6 and 7 were reconstructed in 3dmod. Ultrastructural features were
manually traced in consecutive image series and meshed. Surface transparency and smoothness were adjusted to
facilitate visualization of features of interest in final reconstructed models. Each ultrastructural component was
analysed separately to accurately quantify 3-dimensional features. Mitochondrial were pseudocolored (Keynote
6.6.1) to facilitate visualization of distinct organelles and structrures of interest.
Quantitative measurement of two-dimensional features (nanotunnel diameter and length, intracristae and
intercristae distance, and intermembrane space) were performed in Image J (NIH, version 1.47v). For nanotun-
nel width measurements, the narrowest and widest regions of each nanotunnel were averaged, yielding a mean
diameter for each nanotunnel (n =​ 26). Segments used for analysis were defined on the basis of lacking cristae
and being of constant width. Data are reported as means ±​ S.D. Two-tailed T-test assuming unequal variance was
used to evaluate differences in cristae measurements between normal and abnormal mitochondria, with the level
of significance set at 0.05.

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Acknowledgements
This work was supported by grants from the Biotechnology and Biological Sciences Research Council BB/
M012093/1, Engineering and Physical Sciences Research Council, Economic and Social Research Council
and Medical Research Council G0700718, The Wellcome Trust Centre for Mitochondrial Research G906919,
The MRC Centre for Translational Research in Neuromuscular Disease Mitochondrial Disease Patient Cohort
G0800674, the UK NIHR Biomedical Research Centre in Age and Age Related Diseases award to the Newcastle
upon Tyne Hospitals NHS Foundation Trust, The Lily Foundation and the UK NHS Specialist Commissioners
“Rare Mitochondrial Disorders of Adults and Children” Service. AEV is funded by an MRC studentship (MR/
K501074/1) as part of the MRC Centre for Neuromuscular disease (MR/K000608/1).

Author Contributions
Experimental conception and design: M.P., D.M.T. and A.E.V. Facilitation of tissue acquisition and clinical
information: Y.S.N., D.M.T., R.W.T., G.F., C.F., A.M.S. and R.M.F. Acquisition of data: A.E.V., K.W., T.D. and M.P.
Analysis and interpretation of data: A.E.V. and M.P. Drafting of manuscript: A.E.V., M.P. and D.M.T. Critical
revision of manuscript: C.M., Y.S.N., R.W.T., G.S.G. and R.M.F.

Additional Information
Supplementary information accompanies this paper at http://www.nature.com/srep
Competing financial interests: The authors declare no competing financial interests.
How to cite this article: Vincent, A. E. et al. The Spectrum of Mitochondrial Ultrastructural Defects in
Mitochondrial Myopathy. Sci. Rep. 6, 30610; doi: 10.1038/srep30610 (2016).
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