Association of G-quadruplex forming sequences with human mtDNA deletion breakpoints

BACKGROUND

Mitochondrial DNA (mtDNA) deletions cause disease and accumulate during aging, yet our understanding of the molecular mechanisms underlying their formation remains rudimentary. Guanine-quadruplex (GQ) DNA structures are associated with nuclear DNA instability in cancer; recent evidence indicates they can also form in mitochondrial nucleic acids, suggesting that these non-B DNA structures could be associated with mtDNA deletions. Currently, the multiple types of GQ sequences and their association with human mtDNA stability are unknown.

RESULTS

Here, we show an association between human mtDNA deletion breakpoint locations (sites where DNA ends rejoin after deletion of a section) and sequences with G-quadruplex forming potential (QFP), and establish the ability of selected sequences to form GQ in vitro. QFP contain four runs of either two or three consecutive guanines (2G and 3G, respectively), and we identified four types of QFP for subsequent analysis: intrastrand 2G, intrastrand 3G, duplex derived interstrand (ddi) 2G, and ddi 3G QFP sequences. We analyzed the position of each motif set relative to either 5' or 3' unique mtDNA deletion breakpoints, and found that intrastrand QFP sequences, but not ddi QFP sequences, showed significant association with mtDNA deletion breakpoint locations. Moreover, a large proportion of these QFP sequences occur at smaller distances to breakpoints relative to distribution-matched controls. The positive association of 2G QFP sequences persisted when breakpoints were divided into clinical subgroups. We tested in vitro GQ formation of representative mtDNA sequences containing these 2G QFP sequences and detected robust GQ structures by UV-VIS and CD spectroscopy. Notably, the most frequent deletion breakpoints, including those of the "common deletion", are bounded by 2G QFP sequence motifs.

CONCLUSIONS

The potential for GQ to influence mitochondrial genome stability supports a high-priority investigation of these structures and their regulation in normal and pathological mitochondrial biology. These findings emphasize the potential importance of helicases that subsequently resolve GQ to maintain the stability of the mitochondrial genome.

Two-dimensional intact mitochondrial DNA agarose electrophoresis reveals the structural complexity of the mammalian mitochondrial genome

The mitochondrial genome exists in numerous structural conformations, complicating the study of mitochondrial DNA (mtDNA) metabolism. Here, we describe the development of 2D intact mtDNA agarose gel electrophoresis (2D-IMAGE) for the separation and detection of approximately two-dozen distinct topoisomers. Although the major topoisomers were well conserved across many cell and tissue types, unique differences in certain cells and tissues were also observed. RNase treatment revealed that partially hybridized RNAs associated primarily with covalently closed circular DNA, consistent with this structure being the template for transcription. Circular structures composed of RNA:DNA hybrids contained only heavy-strand DNA sequences, implicating them as lagging-strand replication intermediates. During recovery from replicative arrest, 2D-IMAGE showed changes in both template selection and replication products. These studies suggest that discrete topoisomers are associated with specific mtDNA-directed processes. Because of the increased resolution, 2D-IMAGE has the potential to identify novel mtDNA intermediates involved in replication or transcription, or pathology including oxidative linearization, deletions or depletion.

Reconstitution of mitochondria derived vesicle formation demonstrates selective enrichment of oxidized cargo

The mechanisms that ensure the removal of damaged mitochondrial proteins and lipids are critical for the health of the cell, and errors in these pathways are implicated in numerous degenerative diseases. We recently uncovered a new pathway for the selective removal of proteins mediated by mitochondrial derived vesicular carriers (MDVs) that transit to the lysosome. However, it was not determined whether these vesicles were selectively enriched for oxidized, or damaged proteins, and the extent to which the complexes of the electron transport chain and the mtDNA-containing nucloids may have been incorporated. In this study, we have developed a cell-free mitochondrial budding reaction in vitro in order to better dissect the pathway. Our data confirm that MDVs are stimulated upon various forms of mitochondrial stress, and the vesicles incorporated quantitative amounts of cargo, whose identity depended upon the nature of the stress. Under the conditions examined, MDVs did not incorporate complexes I and V, nor were any nucleoids present, demonstrating the specificity of cargo incorporation. Stress-induced MDVs are selectively enriched for oxidized proteins, suggesting that conformational changes induced by oxidation may initiate their incorporation into the vesicles. Ultrastructural analyses of MDVs isolated on sucrose flotation gradients revealed the formation of both single and double membranes vesicles of unique densities and uniform diameter. This work provides a framework for a reductionist approach towards a detailed examination of the mechanisms of MDV formation and cargo incorporation, and supports the emerging concept that MDVs are critical contributors to mitochondrial quality control.

The mitochondrial transcription factor TFAM coordinates the assembly of multiple DNA molecules into nucleoid-like structures

Packaging DNA into condensed structures is integral to the transmission of genomes. The mammalian mitochondrial genome (mtDNA) is a high copy, maternally inherited genome in which mutations cause a variety of multisystem disorders. In all eukaryotic cells, multiple mtDNAs are packaged with protein into spheroid bodies called nucleoids, which are the fundamental units of mtDNA segregation. The mechanism of nucleoid formation, however, remains unknown. Here, we show that the mitochondrial transcription factor TFAM, an abundant and highly conserved High Mobility Group box protein, binds DNA cooperatively with nanomolar affinity as a homodimer and that it is capable of coordinating and fully compacting several DNA molecules together to form spheroid structures. We use noncontact atomic force microscopy, which achieves near cryo-electron microscope resolution, to reveal the structural details of protein-DNA compaction intermediates. The formation of these complexes involves the bending of the DNA backbone, and DNA loop formation, followed by the filling in of proximal available DNA sites until the DNA is compacted. These results indicate that TFAM alone is sufficient to organize mitochondrial chromatin and provide a mechanism for nucleoid formation.

The human cytochrome c oxidase assembly factors SCO1 and SCO2 have regulatory roles in the maintenance of cellular copper homeostasis

Human SCO1 and SCO2 are metallochaperones that are essential for the assembly of the catalytic core of cytochrome c oxidase (COX). Here we show that they have additional, unexpected roles in cellular copper homeostasis. Mutations in either SCO result in a cellular copper deficiency that is both tissue and allele specific. This phenotype can be dissociated from the defects in COX assembly and is suppressed by overexpression of SCO2, but not SCO1. Overexpression of a SCO1 mutant in control cells in which wild-type SCO1 levels were reduced by shRNA recapitulates the copper-deficiency phenotype in SCO1 patient cells. The copper-deficiency phenotype reflects not a change in high-affinity copper uptake but rather a proportional increase in copper efflux. These results suggest a mitochondrial pathway for the regulation of cellular copper content that involves signaling through SCO1 and SCO2, perhaps by their thiol redox or metal-binding state.

Aconitase couples metabolic regulation to mitochondrial DNA maintenance

Mitochondrial DNA (mtDNA) is essential for cells to maintain respiratory competency and is inherited as a protein-DNA complex called the nucleoid. We have identified 22 mtDNA-associated proteins in yeast, among which is mitochondrial aconitase (Aco1p). We show that this Krebs-cycle enzyme is essential for mtDNA maintenance independent of its catalytic activity. Regulation of ACO1 expression by the HAP and retrograde metabolic signaling pathways directly affects mtDNA maintenance. When constitutively expressed, Aco1p can replace the mtDNA packaging function of the high-mobility-group protein Abf2p. Thus, Aco1p may integrate metabolic signals and mtDNA maintenance.

Human SCO1 and SCO2 have independent, cooperative functions in copper delivery to cytochrome c oxidase

Human SCO1 and SCO2 are paralogous genes that code for metallochaperone proteins with essential, but poorly understood, roles in copper delivery to cytochrome c oxidase (COX). Mutations in these genes produce tissue-specific COX deficiencies associated with distinct clinical phenotypes, although both are ubiquitously expressed. To investigate the molecular function of the SCO proteins, we characterized the mitochondrial copper delivery pathway in SCO1 and SCO2 patient backgrounds. Immunoblot analysis of patient cell lines showed reduced levels of the mutant proteins, resulting in a defect in COX assembly, and the appearance of a common assembly intermediate. Overexpression of the metallochaperone COX17 rescued the COX deficiency in SCO2 patient cells but not in SCO1 patient cells. Overexpression of either wild-type SCO protein in the reciprocal patient background resulted in a dominant-negative phenotype, suggesting a physical interaction between SCO1 and SCO2. Chimeric proteins, constructed from the C-terminal copper-binding and N-terminal matrix domains of the two SCO proteins failed to complement the COX deficiency in either patient background, but mapped the dominant-negative phenotype in the SCO2 background to the N-terminal domain of SCO1, the most divergent part of the two SCO proteins. Our results demonstrate that the human SCO proteins have non-overlapping, cooperative functions in mitochondrial copper delivery. Size exclusion chromatography suggests that both the proteins function as homodimers. We propose a model in which COX17 delivers copper to SCO2, which in turn transfers it directly to the CuA site at an early stage of COX assembly in a reaction that is facilitated by SCO1.

A function for the mitochondrial chaperonin Hsp60 in the structure and transmission of mitochondrial DNA nucleoids in Saccharomyces cerevisiae

The yeast mitochondrial chaperonin Hsp60 has previously been implicated in mitochondrial DNA (mtDNA) transactions: it is found in mtDNA nucleoids associated with single-stranded DNA; it binds preferentially to the template strand of active mtDNA ori sequences in vitro; and wild-type (ρ⁺) mtDNA is unstable in hsp60 temperature-sensitive (t^s) mutants grown at the permissive temperature. Here we show that the mtDNA instability is caused by a defect in mtDNA transmission to daughter cells. Using high resolution, fluorescence deconvolution microscopy, we observe a striking alteration in the morphology of mtDNA nucleoids in ρ⁺ cells of an hsp60-t^s mutant that suggests a defect in nucleoid division. We show that ρ⁻ petite mtDNA consisting of active ori repeats is uniquely unstable in the hsp60-t^s mutant. This instability of ori ρ⁻ mtDNA requires transcription from the canonical promoter within the ori element. Our data suggest that the nucleoid dynamics underlying mtDNA transmission are regulated by the interaction between Hsp60 and mtDNA ori sequences.

An unusual cystic appearance of disseminated low-grade gliomas

We report five cases of pediatric disseminated low-grade gliomas of the brainstem or spinal cord that exhibited an unusual, cystic pattern. Leptomeningeal disease was present in three of these at diagnosis, and was detected shortly afterwards in the other two. Four patients are alive up to 5 years later, following minimal to no intervention, while one is dead.

Evaluating pediatric brain tumor cellularity with diffusion-tensor imaging

OBJECTIVE

MR imaging of central nervous system (CNS) malignancies falls short of a definitive evaluation. Tissue diagnosis remains the gold standard. Diffusion-tensor MR imaging measures the apparent diffusion coefficient and diffusion anisotropy of water in tissue. The purpose of this study was to test the hypothesis that the apparent diffusion coefficient may improve the MR imaging evaluation of newly diagnosed CNS neoplasms. We examined the relationship between the apparent diffusion coefficient, anisotropy, and tumor cellularity in 12 pediatric patients.

MATERIALS AND METHODS

On the basis of histopathologic evaluation, tumors in this case series were segregated into three types: low-grade gliomas, embryonal tumors, and nonembryonal high-grade tumors. Mean apparent diffusion coefficient and anisotropy values obtained from the solid components of each tumor were compared with cellularity, total cellular area, and total nuclear area derived from biopsy material.

RESULTS

The apparent diffusion coefficient ratio (tumor to normal brain) correlated well with tumor classification (p = 0.001). Anisotropy was decreased similarly in all tumor classifications. The absolute apparent diffusion coefficient correlated well with cellularity (p = 0.014) and total nuclear area (p = 0.005) per high-power field. The correlation between apparent diffusion coefficient and total cellular area per high-power field was not statistically significant.

CONCLUSION

The apparent diffusion coefficient may be predictive of tumor classification and may be a useful tool in characterizing tumor cellularity and total nuclear area. These parameters are not available in standard MR imaging. Therefore, diffusion-tensor imaging may enhance the diagnostic process in pediatric CNS malignancies.

Large cell/anaplastic medulloblastomas and medullomyoblastomas: clinicopathological and genetic features

OBJECT

Medulloblastoma is the most common malignant central nervous system neoplasm found in children. A distinct variant designated large cell/anaplastic (LC/A) medulloblastoma is characterized by frequent dissemination of cerebrospinal fluid (CSF) at presentation and a more aggressive clinical course. The authors report on their examination of the clinicopathological and genetic features of seven such cases encountered at their institution.

METHODS

Eighty cases of medulloblastomas were reviewed and seven (8.8%) of these were believed to fit the histological and immunohistochemical criteria for LC/A medulloblastoma. In three cases (43%) either desmoplastic or classic medulloblastoma was the underlying subtype, and in two cases (28%) the LC/A tumor was found within the setting of medullomyoblastoma. Fluorescence in situ hybridization was used in six of the seven cases to characterize the presence of isochromosome 17q, deletion of chromosome 22q (a deletion characteristically found in atypical teratoid/rhabdoid tumors), and c-myc amplification. The patients' clinical histories revealed CSF dissemination in all cases and lymph node metastasis in one case. Isochromosome 17q was found in five (83%) of six cases. Evidence of chromosomal gains indicated aneuploidy in three tumors (50%), and amplification of c-myc was found in three tumors (50%). No 22q deletions were encountered.

CONCLUSIONS

A high percentage of LC/A medulloblastomas arise within a background of typical medulloblastomas or medullomyoblastomas. As is the case in conventional medulloblastomas, the presence of 17q is a common early tumorigenic event; however, in a significant percentage of specimens there is also evidence of aneuploidy and/or amplification of c-myc. These findings indicate that LC/A morphological characteristics reflect a more advanced tumor stage than that found in pure medulloblastomas or in typical medullomyoblastomas.

Prepontine lesions with chiari II malformation. Report of two cases

In 2 cases of infants with the Chiari II malformation, a prepontine cyst presented in association with the hindbrain abnormalities characteristic of the Chiari II syndrome. Both infants presented with bulbar dysfunction and had poor outcome despite decompression of the cerebellar tonsillar herniation and drainage of the prepontine cysts. No such association between prepontine lesions and Chiari II has been described previously.

In organello formaldehyde crosslinking of proteins to mtDNA: identification of bifunctional proteins

The segregating unit of mtDNA is a protein-DNA complex called the nucleoid. In an effort to understand how nucleoid proteins contribute to mtDNA organization and inheritance, we have developed an in organello formaldehyde crosslinking procedure to identify proteins associated with mtDNA. Using highly purified mitochondria, we observed a time-dependent crosslinking of protein to mtDNA as determined by sedimentation through isopycnic cesium chloride gradients. We detected approximately 20 proteins crosslinked to mtDNA and identified 11, mostly by mass spectrometry. Among them is Abf2p, an abundant, high-mobility group protein that is known to function in nucleoid morphology, and in mtDNA transactions. In addition to several other proteins with known DNA binding properties or that function in mtDNA maintenance, we identified other mtDNA-associated proteins that were not anticipated, such as the molecular chaperone Hsp60p and a Krebs cycle protein, Kgd2p. Genetic experiments indicate that hsp60-ts mutants have a petite-inducing phenotype at the permissive temperature and that a kgd2Delta mutation increases the petite-inducing phenotype of an abf2Delta mutation. Crosslinking and DNA gel shift experiments show that Hsp60p binds to single-stranded DNA with high specificity for the template strand of a putative origin of mtDNA replication. These data identify bifunctional proteins that participate in the stability of rho(+) mtDNA.

Ventricular anatomy and shunt catheters

A functioning shunt must have a patent proximal catheter within the cerebrospinal fluid space. Occlusion with choroid plexus or ependymal tissue might be expected if these tissues are in contact with the proximal inlets. This study was undertaken to define the intraventricular distances available for a standard-placement shunt cather and to compare the available distances with actual ventricular catheter inlets. In 52 normal subjects (age range from 1 month to 20 years; median 7.7 years) magnetic resonance imaging was used to measure the dimensions of the anterior horn in planes typically used for cather placement. For anterior placements, the intraventricular length (ventricle entry to the foramen of Monro) was measured for a standardized catheter route ('As') and for a route yielding a maximum lenght ('Amax'). For posterior placements, the length (ventricle tip to foramen of Monro) was obtained for a standardized catheter placement to the ipsilateral ('Pi') and the contralateral ventricle ('Pc') as well as measuring a maximum length in a curved trajectory ('Pmax'). The average length (and range) in centimeters for the various trajectories was: As = 1.5 (1.1-1.9), Amax = 1.7 (1.2-2.2), Pi = 1.6 (1.2-2.1), Pc = 2.0 (1.4-2.9), and Pmax = 2.8/3.1 (2.1-3.6). Minor variations from a standard shunt insertion site did not affect the length of catheter within the ventricle. Current ventricular catheters have proximal inlets extending 1.6-2.4 cm from the catheter tip. Variations in standard ventricular catheter placement should have no measurable effect on how much ventricle is available for the proximal catheter. It may not be possible to place a standard ventricular catheter and keep the inlets within the ventricle and placed consistently away from choroid plexus and ependyma, regardless of approach. This may contribute to the similar proximal occlusion rates reported for the differing placements. Subsequent studies of shunt placement should correlate proximal occlusion rates with ventricular size. To prevent ventricular size from directly affecting proximal conclusion, consideration should be given to altering the design of ventricular catheters by placing inlets over a shorter distance (1.0 cm) from the tip.

Complex cervical spine neoplastic disease: reconstruction after surgery by using a vascularized fibular strut graft. Case report

The authors report a case of an aggressive chordoma in the cervical spine of a 15-year-old girl who underwent radical resection followed by reconstruction using an anterior vascularized fibular strut graft and posterior arthrodesis prior to receiving immediate postoperative radiation therapy. The patient had successful graft incorporation 4 months postoperatively. The authors review the advantages of using vascularized fibular strut grafts for the treatment of multilevel cervical spine neoplastic disease and discuss the theoretical advantages of using vascularized grafts that tolerate therapeutic levels of radiation.

Posterior vermal split syndrome

We have studied a battery of movements in 5 children (age, 6-15 years) after transection of the posterior inferior cerebellar vermis. In each case, the surgery destroyed the midline vermis only (ranging from lobules VI-X). Tandem gait was badly impaired in all subjects. No subjects had impairments of kicking, reaching, pinching, or speech. Regular gait, standing, and hopping on one leg were relatively unimpaired. Cutting the parallel fibers that cross the midline may be the critical variable causing incoordination in tandem gait.

Management of uncomplicated skull fractures in children: is hospital admission necessary?

OBJECTIVE

This study was undertaken to determine the necessity for routine hospital admission of children with skull fractures, a normal neurological exam, a normal head CT, and no other injuries ('uncomplicated skull fracture').

METHODS

A prospective study of closed-head injuries in children was done over a 2-year period at St. Louis Children's Hospital. All patients with closed head injuries underwent skull radiographs and a head CT scan. From this cohort, children with uncomplicated skull fractures were identified and studied. For comparison, a retrospective analysis was also performed of the hospital admission records of children admitted over a 5-year period (1990-1994) with the diagnosis of epidural hematoma (EDH) to identify the typical time intervals between injury and documentation of the lesion in these cases.

RESULTS

Forty-four patients with uncomplicated skull fractures were identified; all had been admitted for observation. Mean age was 1.8 years. Average time between injury and hospital admission was 6.35 h with half of this time being spent in the emergency room. Average LOS was 35 h, but 50% of patients were hospitalized less than 24 h. No patient in this study group suffered a complication related to their inury. Twenty-three patients with EDH had been admitted during the 5-year review period. Slightly more than one-half of patients had their EDH detected within 6 h of injury. The others were diagnosed more than 6 h after injury due to a delay in medical evaluation or a delay in obtaining a computed tomographic (CT) scan after an initial medical evaluation.

CONCLUSIONS

Patients with uncomplicated skull fractures, in the absence of recurrent emesis and/or evidence of child abuse, can be considered for discharge home. The definition of an uncomplicated skull fracture requires that a head CT be performed on these patients.

Intracranial tumor in children: MR imaging findings within 24 hours of craniotomy

PURPOSE

To evaluate whether very early magnetic resonance (MR) imaging enables distinction of residual tumor from benign postoperative change in children.

MATERIALS AND METHODS

Forty-six postoperative MR examinations were performed in 43 children with intracranial tumors within 24 hours of the completion of surgery during a 2-year period. These examinations were categorized according to whether residual tumor could be definitely identified or excluded, or whether the diagnosis was uncertain.

RESULTS

Contrast enhancement occurred in 33 of 46 MR examinations performed within 24 hours of surgery. In 18 instances, this was associated with obvious residual tumor. In 15 patients, only small amounts of linear or patchy enhancement were seen. Of these, seven patients (46%) were disease-free for an average of 4.5 years. Assessment for postoperative enhancement was hampered in seven patients because of the presence of methemoglobin in the tumor bed. Contrast enhancement was not observed in two patients before surgery.

CONCLUSION

Surgically induced, MR-detectable contrast enhancement and extracellular methemoglobin formation occurs within 24 hours of the completion of intracranial surgery. This can interfere with the detection of small amounts of residual tumor.

Normal diameter of filum terminale in children: in vivo measurement

The hallmarks of tethered cord syndrome are a low-lying conus medullaris and a thick filum terminale. In diagnosing the tethered cord syndrome, the thick filum terminale is often defined as that greater than 2 mm in diameter. The cutoff of 2 mm in diameter was derived from myelographic measurements a few decades ago, and the true normal diameter of the filum terminale diameter in children or adults remains unknown. We measured the diameters of the filum terminale in vivo in the operating room on 31 children (age range = 2-14 years; mean age = 5 years) undergoing selective dorsal rhizotomy for spastic cerebral palsy. None of them had clinical evidence of tethered cord syndrome. The conus medullaris and filum terminale were videotaped intraoperatively and images were transferred to an image analyzer; the filum diameters at 10 and 15 mm caudal to the conus medullaris were then measured extraoperatively using the computer graphics system. The diameter of the filum at 10 and 15 mm caudal to the conus was 1,211 +/- 209 and 1,163 +/- 245 microm (mean +/- SD), respectively. In all children except one, the conus medullaris ended above the L2 level. The data indicate that filum terminales greater than 2 mm in diameter in children are abnormally thick.