A circadian enhancer mediates PER-dependent mRNA cycling in Drosophila melanogaster

Genes expressed under circadian-clock control are found in organisms ranging from prokaryotes to humans. In Drosophila melanogaster, the period (per) gene, which is required for clock function, is transcribed in a circadian manner. We have identified a circadian transcriptional enhancer within a 69-bp DNA fragment upstream of the per gene. This enhancer drives high-amplitude mRNA cycling under light-dark-cycling or constant-dark conditions, and this activity is per protein (PER) dependent. An E-box sequence within this 69-bp fragment is necessary for high-level expression, but not for rhythmic expression, indicating that PER mediates circadian transcription through other sequences in this fragment.

MAPK/ERK signalling mediates VEGF-induced bone marrow stem cell differentiation into endothelial cell

Multi-potent adult progenitor cells (MAPCs) differentiate into endothelial cells (ECs) in the presence of vascular endothelial growth factor (VEGF). The mechanism(s) of VEGF-induced differentiation of MAPCs to ECs are not yet known. We, therefore, examined the role of mitogen-activated protein kinase/extracellular signal-regulated kinase (p42/44-MAPK/ERK1/2) signalling in endothelial differentiation from bone marrow stem cells. We observed that VEGF stimulation of MAPCs for 14 days results in a significant expression of endothelial-specific gene and/or proteins including von Willebrand factor (vWF), vascular endothelial-cadherin (VE-cadherin), VEGF receptor-2 (VEGFR2), and CD31. Up-regulation of EC-specific markers was accompanied by a cobblestone morphology, expression of endothelial nitric oxide synthase (eNOS), and Dil-Ac-LDL uptake, typical for EC morphology and function. VEGF induced a sustained activation of p42 MAPK/ERK, but not that of p44 MAPK/ERK during the course of MAPCs differentiation in a time-dependent manner up to 14 days. VEGF-induced activation of p42 MAPK/ERK also led to the nuclear translocation of MAPK/ERK1/2. Incubation of MAPCs with MAPK/ERK1/2 phosphorylation inhibitor PD98059 blocked the sustained VEGF-induced MAPK/ERK1/2 phosphorylation as well as its nuclear translocation in the differentiating MAPCs. Inhibition of MAPK/ERK1/2 phosphorylation by PD98059 also blocked the expression of EC-specific genes in these cells and their differentiation to ECs. These data suggest that VEGF induces MAPC differentiation into EC via a. MAPK/ERK1/2 signalling pathway-mediated mechanism in vitro.

T cell independence of bleomycin-induced pulmonary fibrosis

The role of T cells and cytokines in bleomycin (BLM)-induced fibrosis was evaluated in susceptible and resistant strains of normal and SCID mice. Histology and hydroxyproline analysis showed that BLM induced pulmonary fibrosis in C57BL/6 and (C57BL/6 x BALB/c)F1 mice, whereas BALB/c mice were resistant to the disease. To test whether lymphocytes were required for the induction of BLM-induced pulmonary fibrosis, SCID mice were injected intratracheally with BLM and evaluated for the development of pulmonary inflammation and fibrosis. Similar morphological changes and increases in hydroxyproline were observed in both C57BL/6 SCID and (C57BL/6 x CB.17)F1 SCID animals compared to those seen in wild-type C57BL/6 and (C57BL/6 x BALB/c)F1 mice. In contrast, CB.17 SCID mice, which are genetically similar to BALB/c mice, were resistant to disease induction. Analysis of the cellular infiltrate in BLM-treated C57Bl/6 SCID mice confirmed a lack of T cells in the lungs of SCID mice and demonstrated a pronounced accumulation of eosinophils in areas of developing pulmonary fibrosis. NK cells were significantly elevated in untreated SCID mice and did not increase further after BLM treatment. Analysis of selected cytokines 1 day after initiation of BLM-induced pulmonary fibrosis indicated that the levels of TNF-alpha and IFN-gamma appeared to segregate with fibrosis in both the SCID and wild-type mice. The data demonstrate that T cells are not required for the induction of fibrosis by BLM and suggest that responses by non-lymphoid cells may be sufficient for the induction of fibrosis.

cisRED: a database system for genome-scale computational discovery of regulatory elements

We describe cisRED, a database for conserved regulatory elements that are identified and ranked by a genome-scale computational system (www.cisred.org). The database and high-throughput predictive pipeline are designed to address diverse target genomes in the context of rapidly evolving data resources and tools. Motifs are predicted in promoter regions using multiple discovery methods applied to sequence sets that include corresponding sequence regions from vertebrates. We estimate motif significance by applying discovery and post-processing methods to randomized sequence sets that are adaptively derived from target sequence sets, retain motifs with p-values below a threshold and identify groups of similar motifs and co-occurring motif patterns. The database offers information on atomic motifs, motif groups and patterns. It is web-accessible, and can be queried directly, downloaded or installed locally.

Phospho-ΔNp63α is a key regulator of the cisplatin-induced microRNAome in cancer cells

Head and neck squamous cell carcinoma (HNSCC) cells exposed to cisplatin (CIS) displayed a dramatic ATM-dependent phosphorylation of ΔNp63α that leads to the transcriptional regulation of downstream mRNAs. Here, we report that phospho (p)-ΔNp63α transcriptionally deregulates miRNA expression after CIS treatment. Several p-ΔNp63α-dependent microRNA species (miRNAs) were deregulated in HNSCC cells upon CIS exposure, including miR-181a, miR-519a, and miR-374a (downregulated) and miR-630 (upregulated). Deregulation of miRNA expression led to subsequent modulation of mRNA expression of several targets (TP53-S46, HIPK2, ATM, CDKN1A and 1B, CASP3, PARP1 and 2, DDIT1 and 4, BCL2 and BCL2L2, TP73, YES1, and YAP1) that are involved in the apoptotic process. Our data support the notion that miRNAs are critical downstream targets of p-ΔNp63α and mediate key pathways implicated in the response of cancer cells to chemotherapeutic drugs.

The biological clock of very premature primate infants is responsive to light

Each year more than 250,000 infants in the United States are exposed to artificial lighting in hospital nurseries with little consideration given to environmental lighting cycles. Essential in determining whether environmental lighting cycles need to be considered in hospital nurseries is identifying when the infant's endogenous circadian clock becomes responsive to light. Using a non-human primate model of the developing human, we examined when the circadian clock, located in the hypothalamic suprachiasmatic nuclei (SCN), becomes responsive to light. Preterm infant baboons of different ages were exposed to light (5,000 lux) at night, and then changes in SCN metabolic activity and gene expression were assessed. After exposure to bright light at night, robust increases in SCN metabolic activity and gene expression were seen at ages that were equivalent to human infants at 24 weeks after conception. These data provide direct evidence that the biological clock of very premature primate infants is responsive to light.

Molecular cloning of the cDNA for the catalytic subunit of human DNA polymerase delta

The cDNA of human DNA polymerase delta was cloned. The cDNA had a length of 3.5 kb and encoded a protein of 1107 amino acid residues with a calculated molecular mass of 124 kDa. Northern blot analysis showed that the cDNA hybridized to a mRNA of 3.4 kb. Monoclonal and polyclonal antibodies to the C-terminal 20 residues specifically immunoblotted the human pol delta catalytic polypeptide. A multiple sequence alignment was constructed. This showed that human pol delta is closely related to yeast pol delta and the herpes virus DNA polymerases. The levels of pol delta message were found to be induced concomitantly with DNA pol delta activity and DNA synthesis in serum restimulated proliferating IMR90 cultured cells. The human pol delta gene was localized to chromosome 19 by Southern blotting of EcoRI digested DNA from a panel of rodent/human cell hybrids.

Mechanisms of human mitochondrial DNA maintenance: the determining role of primary sequence and length over function

Although the regulation of mitochondrial DNA (mtDNA) copy number is performed by nuclear-coded factors, very little is known about the mechanisms controlling this process. We attempted to introduce nonhuman ape mtDNA into human cells harboring either no mtDNA or mutated mtDNAs (partial deletion and tRNA gene point mutation). Unexpectedly, only cells containing no mtDNA could be repopulated with nonhuman ape mtDNA. Cells containing a defective human mtDNA did not incorporate or maintain ape mtDNA and therefore died under selection for oxidative phosphorylation function. On the other hand, foreign human mtDNA was readily incorporated and maintained in these cells. The suicidal preference for self-mtDNA showed that functional parameters associated with oxidative phosphorylation are less relevant to mtDNA maintenance and copy number control than recognition of mtDNA self-determinants. Non-self-mtDNA could not be maintained into cells with mtDNA even if no selection for oxidative phosphorylation was applied. The repopulation kinetics of several mtDNA forms after severe depletion by ethidium bromide treatment showed that replication and maintenance of mtDNA in human cells are highly dependent on molecular features, because partially deleted mtDNA molecules repopulated cells significantly faster than full-length mtDNA. Taken together, our results suggest that mtDNA copy number may be controlled by competition for limiting levels of trans-acting factors that recognize primarily mtDNA molecular features. In agreement with this hypothesis, marked variations in mtDNA levels did not affect the transcription of nuclear-coded factors involved in mtDNA replication.

Are A3 adenosine receptors expressed in the brain?

An increasing number of reports suggest a role for A3 adenosine receptors (A3ARs) in mediating adenosine action in the central nervous system. However, studies of A3AR localization in the brain have yet to be performed. To provide insights into the central sites of A3AR action, we compared patterns of A1 and A3AR mRNA and binding site expression in the brains of rats, mice and humans. We also assessed whether A3 agonists are selective for A3ARs. Whereas it was possible to detect high-level A1AR expression in many brain regions, it was not possible to detect either A3AR gene or binding site expression in the central nervous system. When we examined the affinities of the A3AR agonists CI-IAB-MECA and IAB-MECA for A1ARs, we found that these compounds bound to A1ARs with high affinity. These observations suggest that studies using A3-agonists need to consider potential effects of A1ARs activation, as A1ARs are abundantly expressed in the nervous system whereas A3AR expression in the brain cannot be directly demonstrated.

A disease-associated G5703A mutation in human mitochondrial DNA causes a conformational change and a marked decrease in steady-state levels of mitochondrial tRNA(Asn)

We introduced mitochondrial DNA (mtDNA) from a patient with a mitochondrial myopathy into established mtDNA-less human osteosarcoma cells. The resulting transmitochondrial cybrid lines, containing either exclusively wild-type or mutated (G5703A transition in the tRNA[Asn] gene) mtDNA, were characterized and analyzed for oxidative phosphorylation function and steady-state levels of different RNA species. Functional studies showed that the G5703A mutation severely impairs oxidative phosphorylation function and mitochondrial protein synthesis. We detected a marked reduction in tRNA(Asn) steady-state levels which was not associated with an accumulation of intermediate transcripts containing tRNA(Asn) sequences or decreased transcription. Native polyacrylamide gel electrophoresis showed that the residual tRNA(Asn) fraction in mutant cybrids had an altered conformation, suggesting that the mutation destabilized the tRNA(Asn) secondary or tertiary structure. Our results suggest that the G5703 mutation causes a conformational change in the tRNA(Asn) which may impair aminoacylation. This alteration leads to a severe reduction in the functional tRNA(Asn) pool by increasing its in vivo degradation by mitochondrial RNases.

Functional and molecular mitochondrial abnormalities associated with a C --> T transition at position 3256 of the human mitochondrial genome. The effects of a pathogenic mitochondrial tRNA point mutation in organelle translation and RNA processing

We have previously identified a mitochondrial DNA polymorphism (a C --> T transition at position 3256, within the mitochondrial tRNALeu(UUR) gene in a patient with a multisystem disorder. Although there were several indicators suggesting a pathogenetic role for this mtDNA polymorphism, its heteroplasmic nature made functional and molecular studies difficult to interpret. We have now fused enucleated fibroblasts from the patient with a mtDNA-less cell line to generate transmitochondrial cybrids harboring different proportions of mutated and wild-type mtDNA. Individual clones harboring essentially 100% wild-type or > 99% mutated mtDNAs were characterized and studied for respiratory capacity, respiratory chain enzymes activity, mitochondrial protein synthesis, and RNA steady-state levels and processing. Our results showed that cell lines containing exclusively mutated mtDNAs respire poorly, overproduce lactic acid, and have significantly impaired activity of respiratory complexes I and IV. Molecular studies showed that mutant clones have a decrease in steady-state levels of mitochondrial tRNALeu(UUR), and a partial impairment of mitochondrial protein synthesis and steady-state levels, suggesting that these molecular abnormalities are involved in the pathogenetic mechanism of the mtDNA 3256 mutation.

Suppression of a mitochondrial tRNA gene mutation phenotype associated with changes in the nuclear background

We previously have characterized a pathogenic mtDNA mutation in the tRNAAsn gene. This mutation (G5703A) was associated with a severe mitochondrial protein synthesis defect and a reduction in steady-state levels of tRNAAsn. We now show that, although transmitochondrial cybrids harboring homoplasmic levels of the mutation do not survive in galactose medium, several galactose-resistant clones could be obtained. These cell lines had restored oxidative phosphorylation function and 2-fold higher steady-state levels of tRNAAsn when compared with the parental mutant cell line. The revertant lines contained apparently homoplasmic levels of the mutation and no other detectable alteration in the tRNAAsn gene. To investigate the origin of the suppression, we transferred mtDNA from the revertants (143B/206 TK-) to a different nuclear background (143B/207 TK-, 8AGr). These new transmitochondrial cybrids became defective once again in oxidative phosphorylation and regained galactose sensitivity. However, galactose-resistant clones could also be obtained by growing the 8AGr transmitochondrial cybrids under selection. Because the original rate of reversion was higher than that expected by a classic second site nuclear mutation, and because of the aneuploid features of these cell lines, we searched for the presence of chromosomal alterations that could be associated with the revertant phenotype. These studies, however, did not reveal any gross changes. Our results suggest that modulation of the dosage or expression of unknown nuclear-coded factor(s) can compensate for a pathogenic mitochondrial tRNA gene mutation, suggesting new strategies for therapeutic intervention.

Osmotic Swelling Pressure Response of Smart Hydrogels Suitable for Chronically-Implantable Glucose Sensors

In the last few years, a new type of glucose-sensitive hydrogel (GSH) has been developed that shrinks with increasing glucose concentration due to the formation of reversible crosslinks The first osmotic swelling pressure results measured for any member of this new class of GSH are reported, so that their suitability for use in sensors combining pressure transducers and smart gels can be evaluated. Comparison is also made with results obtained for an older type of GSH that expands with increasing glucose concentration due to an increase in the concentration of counterions within the gel. The newer type of GSH exhibits both faster kinetics and weaker fructose interference, and therefore is more suitable for in vivo glucose sensing.

Aberrant MFN2 transcription facilitates homocysteine-induced VSMCs proliferation via the increased binding of c-Myc to DNMT1 in atherosclerosis

It is well‐established that homocysteine (Hcy) is an independent risk factor for atherosclerosis. Hcy can promote vascular smooth muscle cell (VSMC) proliferation, it plays a key role in neointimal formation and thus contribute to arteriosclerosis. However, the molecular mechanism on VSMCs proliferation underlying atherosclerosis is not well elucidated. Mitofusin‐2 (MFN2) is an important transmembrane GTPase in the mitochondrial outer membrane and it can block cells in the G0/G1 stage of the cell cycle. To investigate the contribution of aberrant MFN2 transcription in Hcy‐induced VSMCs proliferation and the underlying mechanisms. Cell cycle analysis revealed a decreased proportion of VSMCs in G0/G1 and an increased proportion in S phase in atherosclerotic plaque of APOE^−/− mice with hyperhomocystinaemia (HHcy) as well as in VSMCs exposed to Hcy in vitro. The DNA methylation level of MFN2 promoter was obviously increased in VSMCs treated with Hcy, leading to suppressed promoter activity and low expression of MFN2. In addition, we found that the expression of c‐Myc was increased in atherosclerotic plaque and VSMCs treated with Hcy. Further study showed that c‐Myc indirectly regulates MFN2 expression is duo to the binding of c‐Myc to DNMT1 promoter up‐regulates DNMT1 expression leading to DNA hypermethylation of MFN2 promoter, thereby inhibits MFN2 expression in VSMCs treated with Hcy. In conclusion, our study demonstrated that Hcy‐induced hypermethylation of MFN2 promoter inhibits the transcription of MFN2, leading to VSMCs proliferation in plaque formation, and the increased binding of c‐Myc to DNMT1 promoter is a new and relevant molecular mechanism.

A mouse model of a human multiple GIST family with KIT-Asp820Tyr mutation generated by a knock-in strategy

Several families exhibiting multiple gastrointestinal stromal tumours (GISTs) and germline c-kit gene mutations at exons 8, 11, 13, or 17 have been reported. These patients also exhibit diffuse hyperplasia of the interstitial cells of Cajal (ICCs) as a pre-existing lesion of multiple GISTs. We generated a mouse model of a family with germline c-kit gene mutation at exon 17, and compared the phenotypes between the mice and humans. The mouse counterpart (KIT-Asp818Tyr) of the human KIT-Asp820Tyr mutation was transmitted into germline by a knock-in strategy. Mating of male and female heterozygotes (KIT-Asp818Tyr/+) resulted in the generation of homozygotes (KIT-Asp818Tyr/KIT-Asp818Tyr). Histological examination revealed that all heterozygotes had both a small KIT-positive mesenchymal tumour at the caecum, consistent with GIST, and KIT-positive diffuse spindle-shaped cell proliferation in the distal oesophagus, stomach, proximal duodenum, and colon consistent with ICC hyperplasia. All homozygotes exhibited a larger caecal tumour and more prominent spindle-shaped cell proliferation compared with the heterozygous mice, and they usually died within 10 weeks after birth, likely due to ileus. The small intestine of both genotypes showed no apparent morphological abnormality, and autonomous contraction of the ileal segments appeared normal. Western blotting demonstrated that the caecal tumours expressed phosphorylated KIT, MAPK, Stat1, and Stat5. These mutant mice are considered to be useful for further investigation of the mechanism of GIST development as a result of ICC hyperplasia and for assessment of the in vivo effects of drugs against molecular targets.

Developing circadian rhythmicity

Circadian rhythms are endogenously generated rhythms with a period length of about 24-hours. Evidence gathered over the past decade indicates that the circadian timing system develops prenatally, and the suprachiasmatic nuclei, the site of a circadian clock, is present by midgestation in human and nonhuman primates. Recent evidence also shows that the circadian system of primate infants is responsive to light at very premature stages and that low intensity lighting can regulate the developing clock. After birth, there is progressive maturation of the circadian system outputs, with pronounced rhythms in sleep-wake and hormone secretion generally developing after 2 months of age. With the continued elucidation of circadian system development and influences on human physiology and illness, it is anticipated that consideration of circadian biology will become an increasingly important component of neonatal care.

Meta-analysis of alkaline phosphatase and prognosis for osteosarcoma

Many studies have evaluated the relationships between alkaline phosphatase (ALP) levels and the prognosis for osteosarcoma. However, a consensus has yet to be reached. We completed a meta-analysis to assess the significance of ALP and prognosis for osteosarcoma. We retrieved eligible documents from the PubMed and Embase databases and extracted related data from those documents. The overall survival (OS), hazard ratio (HR) and event-free survival (EFS) HR were obtained after combination to evaluate the impacts of ALP levels on prognosis for osteosarcoma. After screening, a total of 12 documents published between 1999 and 2013 were included. The ALP levels on OS were evaluated in nine documents. The pooled HRs was 1.78 (95% CI: 1.52-2.07, p < .05). The ALP levels on EFS were determined in eight documents. The pooled HRs was 1.58 (95% CI: 1.37-1.82, p < .05). Begg's test (OS, p > .754; EFS, p > .386) and Egger's test (OS, p > .649; EFS, p > .274) showed that there was no significant publication bias during analytic process. In summary, our meta-analysis shows that a higher level of ALP can decrease the OS and EFS in patients with osteosarcoma and ALP is an important biological indicator for patients with osteosarcoma.

A comprehensive characterization of lymphoepithelial cyst associated with the pancreas

BACKGROUND

Lymphoepithelial cyst of the pancreas is a rare but distinctive cystic lesion lined by a mature, keratinizing squamous epithelium and surrounded by lymphoid tissue.

METHODS

To gain more insights into this entity, we describe 5 examples of lymphoepithelial cyst of the pancreas (2 of which were briefly described before) and compare them with similar cases in the literature for a total of 19 cases.

RESULTS

The male:female ratio was 16:3; patients' ages ranged from 32 to 73 years (mean and median 51). The lymphoepithelial cyst was incidentally found at autopsy in 4 patients (21%) or during evaluation for unrelated diseases in another 4 patients (21%). In the remaining 11 patients, the cyst was associated with abdominal pain in 9 (47% of all patients), nausea/vomiting in 3 (16%), diarrhea in 1 (5%), and nonspecific systemic symptoms in 6 (32%) (some patients had more than 1 associated symptom). Computed axial tomography scan, with or without ultrasonographic study, was done in 16 cases and uniformly displayed a single, well-circumscribed, cystic mass protruding beyond the surface of the pancreas; the rest of the pancreas was normal. Intraoperatively, the cyst was readily apparent once the lesser sac was entered and the surface of the pancreas exposed; the cyst was located at the head (3 cases), neck (1 case), body (6 cases), and tail (9 cases). Surgery was done for all 15 clinical cases and included local excision of the cyst with a thin rim of attached, underlying pancreas (6 cases), or distal pancreatectomy with (4 cases) or without (3 cases) splenectomy. Follow-up information, available in 7 cases, showed that all symptoms disappeared and the patients were alive and well up to 6 years after surgery.

CONCLUSIONS

This rare cyst of the pancreas has a uniform and characteristic clinicopathologic profile, enabling easy and accurate diagnosis. Although the histogenesis of lymphoepithelial cysts is not known, they are benign and can be cured by local excision.

Prevalence of myasthenia gravis and associated autoantibodies in paraneoplastic pemphigus and their correlations with symptoms and prognosis

BACKGROUND

Paraneoplastic pemphigus (PNP) involves multiple organs, but little is known about its neurological involvement.

OBJECTIVES

To investigate the symptoms, prognosis and profiles of associated autoantibodies in myasthenia gravis (MG), and their correlations in patients with PNP.

METHODS

Fifty-eight patients with PNP were assessed for myasthenic symptoms and laboratory evidence. Serum autoantibodies against acetylcholine receptor (AChR), acetylcholinesterase (AChE), titin, ryanodine receptor (RyR) and muscle-specific kinase (MuSK) were measured by enzyme-linked immunosorbent assay. Patients with pemphigus vulgaris (PV), pemphigus foliaceus (PF), connective tissue disease (CTD) and non-PNP MG (NP-MG), and healthy donors, served as controls. These autoantibodies in PNP were also compared in the presence or absence of dyspnoea or muscle weakness. Cox regression and log-rank tests were used for survival analysis.

RESULTS

Overall 39% of patients with PNP experienced muscle weakness, and 35% were diagnosed with MG. Moreover, 35% had positive anti-AChR and 28% had anti-AChE antibodies, similarly to NP-MG (33% and 17%, respectively, P > 0·05). However, both were negative in all patients with PV, PF and CTD and healthy donors (P < 0·005). No other antibodies showed significant differences among groups. Anti-AChR and anti-AChE antibody levels were significantly increased in patients with PNP with dyspnoea, while anti-AChR, anti-titin and anti-RyR were significantly increased in patients with PNP with muscle weakness (P < 0·05). Nevertheless, levels and positive rates of these autoantibodies showed no significant differences between PNP with Castleman disease and thymoma. Although anti-AChE levels impacted survival duration (P  =  0·027, odds ratio 3·14), MG complications did not affect the overall survival percentage in PNP.

CONCLUSIONS

MG is a complication of PNP. Anti-AChR and anti-AChE antibodies are prominent in patients with PNP, especially those with dyspnoea.

Specific sequences outside the E-box are required for proper per expression and behavioral rescue

A 69 bp circadian regulatory sequence (CRS) upstream of the per gene is sufficient to drive circadian transcription, mediate proper spatial expression, and rescue behavioral rhythmicity in per01 flies. Within the CRS, an E-box is required for transcriptional activation by two basic-helix-loop-helix (bHLH) PERARNT-SIM (PAS) transcription factors, dCLOCK (dCLK) and CYCLE (CYC). To define sequences within the CRS that are required for spatial expression, circadian expression, and behavioral rhythmicity, a series of mutants that alter blocks of 3 to 12 nucleotides across the entire CRS were used to drive lacZ or per expression in vivo. As expected, the E-box within the CRS is necessary for high-level expression and behavioral rhythmicity, but sequences outside the E-box are also required for transcriptional activation, proper spatial expression, and behavioral rhythmicity. These results indicate that the dCLK-CYC target site extends beyond the E-box and that factors other than dCLK and CYC modulate per transcription.

Phenotype-genotype correlations in skeletal muscle of patients with mtDNA deletions

Large-scale deletions of mitochondrial DNA (mtDNA) have been associated with a subgroup of mitochondrial encephalomyopathies, usually characterized by progressive external ophthalmoplegia (PEO) and mitochondrial proliferation in muscle fibers. We and others have shown that muscle from patients with mtDNA deletions have variable cytochrome c oxidase (COX) deficiency and reduction of mitochondrially-synthesized polypeptides in affected muscle fibers. The present work summarizes the phenotype-genotype correlations observed in patients' muscle. In situ hybridization revealed that, while most COX-deficient fibers had increased levels of mutant mtDNA, they almost invariably had reduced levels of normal mtDNA. PCR quantitation of both deleted and wild-type mtDNAs in normal and respiration-deficient muscle fibers from patients with the "common deletion" showed that deleted mtDNAs were present in normal fibers (31 +/- 26%), but their percentages were much higher in affected fibers (95% +/- 2%). Absolute levels of deleted mtDNA were also increased in affected fibers, whereas absolute levels of wild-type mtDNA were significantly reduced. Taken together, our results suggest that although a specific ratio between mutant and wild-type mitochondrial genomes is probably the major determinant of the respiratory chain deficiency associated with mtDNA deletions, the reduction in the absolute amounts of wild-type mtDNA may also play a significant pathogenetic role.