Mutagenesis, tumorigenicity, and apoptosis: are the mitochondria involved?

Salivary Biomarkers for Oral Cancer Detection: Insights from Human DNA and RNA Analysis

Oral cancer is a significant global health concern, with a high mortality rate mainly due to late-stage diagnosis. Early detection plays a critical role in improving patient outcomes, highlighting the need for non-invasive and accessible screening methods. Salivary biomarkers have emerged as a promising avenue for oral cancer detection, leveraging advancements in human DNA and RNA analysis. Several DNA-based biomarkers, such as genetic mutations, chromosomal aberrations, and epigenetic alterations, have shown promise in detecting oral cancer at various stages. Likewise, RNA-based biomarkers, including microRNAs, long non-coding RNAs, and messenger RNAs, have demonstrated potential for diagnosing oral cancer and predicting treatment outcomes. The integration of high-throughput sequencing technologies, such as next-generation sequencing and transcriptomic profiling, has enabled the identification of novel biomarkers and provided deeper insights into the molecular mechanisms underlying oral cancer development and progression. Despite the promising results, challenges remain in standardizing sample collection, establishing robust biomarker panels, and validating their clinical utility. Nevertheless, salivary biomarkers hold great promise as a non-invasive, cost-effective, and accessible approach for oral cancer detection, ultimately leading to improved patient outcomes through early diagnosis and intervention. The analysis of genetic material obtained from saliva offers several advantages, including ease of collection, non-invasiveness, and the potential for repeated sampling. Furthermore, saliva reflects the physiological and pathological status of the oral cavity, making it an ideal source for biomarker discovery and validation. This article presents a comprehensive review of the current research on salivary biomarkers for oral cancer detection, focusing on insights gained from human DNA and RNA analysis.

The Fractal Viewpoint of Tumors and Nanoparticles

Even though the promising therapies against cancer are rapidly improved, the oncology patients population has seen exponential growth, placing cancer in 5th place among the ten deadliest diseases. Efficient drug delivery systems must overcome multiple barriers and maximize drug delivery to the target tumors, simultaneously limiting side effects. Since the first observation of the quantum tunneling phenomenon, many multidisciplinary studies have offered quantum-inspired solutions to optimized tumor mapping and efficient nanodrug design. The property of a wave function to propagate through a potential barrier offer the capability of obtaining 3D surface profiles using imaging of individual atoms on the surface of a material. The application of quantum tunneling on a scanning tunneling microscope offers an exact surface roughness mapping of tumors and pharmaceutical particles. Critical elements to cancer nanotherapeutics apply the fractal theory and calculate the fractal dimension for efficient tumor surface imaging at the atomic level. This review study presents the latest biological approaches to cancer management based on fractal geometry.

Mitochondrial NADH Dehydrogenase Subunit 3 (MTND3) Polymorphisms are Associated with Gastric Cancer Susceptibility

Accumulating evidence indicates that mitochondrial DNA alterations contribute to cancer development and progression. In this study, we evaluated the relationship between polymorphisms of mitochondrial NADH dehydrogenase subunit 3 (MTND3) and the risk of gastric cancer (GC). Five single nucleotide polymorphisms (SNPs; rs28358278, rs2853826, rs201397417, rs41467651, and rs28358275) were identified and genotyped in 377 patients with GC patients and 363 controls by direct sequencing. The rs41467651 T allele was significantly associated with GC risk [adjusted odds ratio (OR) = 2.11, 95% confidence interval (CI) = 1.25-3.55, P = 0.005). In stratified analysis, rs28358278, rs2853826, and rs41467651 were associated with subgroups of GC, with the rs28358278 G, rs2853826 T, and rs41467651 T alleles associated with an increased GC risk in females (adjusted OR = 1.70, 95% CI = 1.08-2.69, P = 0.023; adjusted OR = 1.78, 95% CI = 1.11-2.85, P = 0.016; adjusted OR = 2.07, 95% CI = 1.04-4.12, P = 0.038, respectively). The rs441467651 T allele was also related with GC risk in diffuse-type subjects compared to that of controls (adjusted OR = 2.61, 95% CI = 1.43-4.89, P = 0.002). In addition, The rs441467651 T allele was significantly related with increased GC risk regardless of lymph node metastasis (LNM), T classification, and tumor stage compared to that of controls (adjusted OR = 2.00, 95% CI = 1.12-3.55, P = 0.019 in LNM-negative subjects; adjusted OR = 2.10, 95% CI = 1.05-4.22, P = 0.0379 in LNM-positive subjects; adjusted OR = 1.82, 95% CI = 1.02-3.24, P = 0.042 in T1/T2 subjects; adjusted OR = 2.60, 95% CI = 1.29-5.24, P = 0.007 in T3/T4 subjects; adjusted OR = 1.91, 95% CI = 1.09-3.34, P = 0.025 in tumor stage I (A+B)/II (A+B+C) subjects; adjusted OR = 2.36, 95% CI = 1.12-5.13, P = 0.025 in tumor stage III (A+B+C) subjects) compared to that of controls. Our findings suggest that the rs28358278, rs2853826, and rs41467651 polymorphisms of MTND3 increase the susceptibility to GC development.

Tamoxifen promotes apoptosis and inhibits invasion in estrogen‑positive breast cancer MCF‑7 cells

Tamoxifen (TAM) is the earliest non-steroidal antiestrogen drug, which has been widely used in endocrine therapy targeting breast cancer. The aim of the present study was to investigate the effect of TAM on the proliferation, apoptosis, migration and invasion of the estrogen‑positive (ER+) breast cancer cell line MCF‑7 in vitro, and elucidate its mechanisms. It was demonstrated that TAM suppressed proliferation, migration and invasion, and induced apoptosis in MCF‑7 cells. Further investigation revealed that the mitochondrial membrane potential and the amount of ATP were significantly decreased following the treatment of MCF‑7 cells with TAM. Mitochondria are an important source of reactive oxygen species (ROS) and they are also the target of ROS as well. In the present study, TAM promoted the formation of ROS in MCF‑7 cells. In conclusion, these results reveal the underlying mechanism by which TAM induces ER+ breast cancer cell apoptosis and inhibits invasion, thereby supporting the use of TAM in breast cancer treatment.

Changes in mitochondrial homeostasis and redox status in astronauts following long stays in space

The effects of long-term exposure to extreme space conditions on astronauts were investigated by analyzing hair samples from ten astronauts who had spent six months on the International Space Station (ISS). Two samples were collected before, during and after their stays in the ISS; hereafter, referred to as Preflight, Inflight and Postflight, respectively. The ratios of mitochondrial (mt) to nuclear (n) DNA and mtRNA to nRNA were analyzed via quantitative PCR. The combined data of Preflight, Inflight and Postflight show a significant reduction in the mtDNA/nDNA in Inflight, and significant reductions in the mtRNA/nRNA ratios in both the Inflight and Postflight samples. The mtRNA/mtDNA ratios were relatively constant, except in the Postflight samples. Using the same samples, the expression of redox and signal transduction related genes, MnSOD, CuZnSOD, Nrf2, Keap1, GPx4 and Catalase was also examined. The results of the combined data from Preflight, Inflight and Postflight show a significant decrease in the expression of all of the redox-related genes in the samples collected Postflight, with the exception of Catalase, which show no change. This decreased expression may contribute to increased oxidative stress Inflight resulting in the mitochondrial damage that is apparent Postflight.

Variants in mitochondrial tRNA gene may not be associated with thyroid carcinoma

Thyroid cancer is a very common form of endocrine system malignancy. To date, the molecular mechanism underlying thyroid cancer remains poorly understood. Studies of oncocytic tumors have led to a hypothesis which proposes that defects in oxidative phosphorylation (OX- PHOS) may result in a compensatory increase in mitochondrial replication and gene expression. As a result, mitochondrial DNA (mtDNA) mutation analysis has become a useful tool to explore the molecular basis of this disease. Among these mutations, mitochondrial transfer RNAs (mttRNAs) are the hot spots for pathogenic mutations associated with thyroid cancer. However, due to its high mutation rate, the role of mt-tRNA variants in thyroid cancer is still controversial. To address this problem, in this study, we reassessed seven reported mt-tRNA variants: tRNA^Asp G7521A, tRNA^Arg T10411C and T10463C, tRNA^Leu(CUN) A12308G, tRNA^Ile G4292C and C4312T, and tRNA^Ala T5655C, in clinical manifestations of thyroid cancer. We first performed the phylogenetic conservation analysis for these variants; moreover, we used a bioinformatic tool to compare the minimum free energy (G) of mt-tRNA with and without mutations. Most strikingly, none of these variants caused the significant change of the G between the wild-type and the mutant form, suggesting that they may not play an important roles in thyroid cancer. In addition, we screened the frequency of the “pathogenic” A12308G alternation in 300 patients with thyroid cancer and 200 healthy controls. We found that there were five patients and three control subjects carrying this variant. It seemed that the A12308G variant may be a common polymorphism in the human population. Taken together, our study indicated that variants in mt-tRNA genes may not play active roles in patients with thyroid cancer.

Relationship between mutations of mitochondrial DNA control region and tumors

The mitochondrion is the main place of cell respiration and participates in the process of cell apoptosis and proliferation, nucleic acid synthesis, and the production of free radicals. Mitochondrial DNA (mtDNA) is susceptible to the attack by oxygen free radicals and their products, and tends to develop somatic mutations, because of the lack of protection by histones and complete repair system. Somatic mutations in mtDNA will finally promote tumorigenesis. The control region of mtDNA is a region with a high mutation frequency. The association between control region mutations and tumorigenesis has attracted wide attention. Therefore, it is of great significance to elucidate the relationship between mtDNA control region mutations and tumorigenesis.

Who controls the ATP supply in cancer cells? Biochemistry lessons to understand cancer energy metabolism

Applying basic biochemical principles, this review analyzes data that contrasts with the Warburg hypothesis that glycolysis is the exclusive ATP provider in cancer cells. Although disregarded for many years, there is increasing experimental evidence demonstrating that oxidative phosphorylation (OxPhos) makes a significant contribution to ATP supply in many cancer cell types and under a variety of conditions. Substrates oxidized by normal mitochondria such as amino acids and fatty acids are also avidly consumed by cancer cells. In this regard, the proposal that cancer cells metabolize glutamine for anabolic purposes without the need for a functional respiratory chain and OxPhos is analyzed considering thermodynamic and kinetic aspects for the reductive carboxylation of 2-oxoglutarate catalyzed by isocitrate dehydrogenase. In addition, metabolic control analysis (MCA) studies applied to energy metabolism of cancer cells are reevaluated. Regardless of the experimental/environmental conditions and the rate of lactate production, the flux-control of cancer glycolysis is robust in the sense that it involves the same steps: glucose transport, hexokinase, hexosephosphate isomerase and glycogen degradation, all at the beginning of the pathway; these steps together with phosphofructokinase 1 also control glycolysis in normal cells. The respiratory chain complexes exert significantly higher flux-control on OxPhos in cancer cells than in normal cells. Thus, determination of the contribution of each pathway to ATP supply and/or the flux-control distribution of both pathways in cancer cells is necessary in order to identify differences from normal cells which may lead to the design of rational alternative therapies that selectively target cancer energy metabolism.

Decoding the Pluripotency Network: The Emergence of New Transcription Factors

Since the successful isolation of mouse and human embryonic stem cells (ESCs) in the past decades, massive investigations have been conducted to dissect the pluripotency network that governs the ability of these cells to differentiate into all cell types. Beside the core Oct4-Sox2-Nanog circuitry, accumulating regulators, including transcription factors, epigenetic modifiers, microRNA and signaling molecules have also been found to play important roles in preserving pluripotency. Among the various regulations that orchestrate the cellular pluripotency program, transcriptional regulation is situated in the central position and appears to be dominant over other regulatory controls. In this review, we would like to summarize the recent advancements in the accumulating findings of new transcription factors that play a critical role in controlling both pluripotency network and ESC identity.

Mitochondria malfunctions as mediators of stem-cells' related carcinogenesis: a hypothesis that supports the highly conserved profile of carcinogenesis

Cancer development is an evolutionary process that has been highly conserved among centuries within organisms. Based on this, the interest in cancer research focuses on cells, organelles and genes that possess a genetic conservatism from yeasts to human. Towards this thought, mitochondria, the highly conserved and responsible for the cellular bioenergetic activity organelles, might play crucial role in carcinogenesis. Interestingly, tumors with low bioenergetic signature have worse prognosis and show a decreased expression of ATPase protein. Furthermore, according to the stem-cell theory of carcinogenesis, aggressive tumors are characterized by an increase number of malignant stem-like cell population and their resistance to chemotherapy has been found to be mitochondrially driven. The above considerations triggered us to hypothesize that mitochondrial bioenergetic processes in stem-like cancer cells plays a crucial role in the highly conserved process of carcinogenesis. Specifically, we support that mitochondrial and/or nuclear DNA alterations that control stem cells' ATP production drive stem cells to "immortalization" (Otto Warburg theory) that mediates cancer initiation and progression. Substantiation of our hypothesis requires evidence that: (1) alterations in mitochondria bioenergetic metabolites and enzymes encoded either from the mtDNA or the nuclear DNA are linked to human cancer and (2) mitochondrial functions are regulated by highly conserved genes involved in cancer-related cellular processes such as apoptosis, aging and autophagy. Experimental approach on how this hypothesis might be tested and promising strategies in cancer therapeutics are also discussed. In case the hypothesis of stem-cell bioenergetic malformations' related carcinogenesis proves to be correct, it would contribute to the development of new prognostic, diagnostic and even more effective therapeutic interventions against various types of cancer.

Molecular mechanism for the selective impairment of cancer mitochondrial function by a mitochondrially targeted vitamin E analogue

The effects of α-tocopheryl succinate (α-TOS), α-tocopheryl acetyl ether (α-TEA) and triphenylphosphonium-tagged vitamin E succinate (mitochondrially targeted vitamin E succinate; MitoVES) on energy-related mitochondrial functions were determined in mitochondria isolated from AS-30D hepatoma and rat liver, bovine heart sub-mitochondrial particles (SMPs), and in rodent and human carcinoma cell lines and rat hepatocytes. In isolated mitochondria, MitoVES stimulated basal respiration and ATP hydrolysis, but inhibited net state 3 (ADP-stimulated) respiration and Ca(2+) uptake, by collapsing the membrane potential at low doses (1-10μM). Uncoupled mitochondrial respiration and basal respiration of SMPs were inhibited by the three drugs at concentrations at least one order of magnitude higher and with different efficacy: MitoVES>α-TEA>α-TOS. At high doses (>10μM), the respiratory complex II (CII) was the most sensitive MitoVES target. Acting as an uncoupler at low doses, this agent stimulated total O(2) uptake, collapsed ∆ψ(m), inhibited oxidative phosphorylation and induced ATP depletion in rodent and human cancer cells more potently than in normal rat hepatocytes. These findings revealed that in situ tumor mitochondria are preferred targets of the drug, indicating its clinical relevance.

Mitochondrial transcription factor A regulates BCL2L1 gene expression and is a prognostic factor in serous ovarian cancer

Mitochondrial transcription factor A (mtTFA) is necessary for both transcription and maintenance of mitochondrial DNA (mtDNA). Recently, we reported that mtTFA is expressed not only in mitochondria, but also in nuclei. However, the function of mtTFA in the nucleus has not been clearly elucidated. In the present study, we examined nuclear mtTFA expression in 60 tissue samples of serous ovarian cancer using immunohistochemical analysis and found that 56.7% of serous ovarian cancer patients were positive for mtTFA, whereas 43.3% were negative. Univariate survival analysis showed that the overall 5-year survival rate was significantly worse for patients with mtTFA-positive cancer compared with mtTFA-negative cancer (32%vs 42%, respectively; P = 0.021). To elucidate the function of mtTFA in the nucleus, we investigated BCL2L1, a target gene of mtTFA. There was a significant correlation between nuclear mtTFA expression and BCL2L1 expression in seven ovarian cancer cell lines and in specimens of clinical ovarian cancer. Cellular BCL2L1 was downregulated following transfection of siRNA against mtTFA. BCL2L1 promoter activity was increased after transfection of mtTFA expression plasmid, but decreased after siRNA knockdown of mtTFA. Chromatin immunoprecipitation assays showed that mtTFA was bound to the BCL2L1 promoter region. These results suggest that mtTFA is a prognostic factor for a poor outcome of ovarian cancer and may function as an antiapoptotic factor, regulating genes such as BCL2L1. Furthermore, mtTFA may be a promising molecular target for novel therapeutic strategies for the treatment of ovarian cancer.

Increased expression but not sensitivity to Fas/CD95 in glioblastoma cells depleted of mitochondrial DNA

Mitochondria and Fas (CD95) play a role in tumorigenicity and apoptosis. In the present study, the functional relationship of mitochondria to Fas in mediating apoptosis was investigated. Glioblastoma cells (DBTRGO5MG, U87) were depleted of mitochondrial DNA (mtDNA) by treatment with ethidium bromide (Rho(-) cells). Compared to Rho(+) cells, Rho(-) cells showed enhanced expression of Fas at the cell surface. Indeed, when Rho(+) cells were treated with mitochondrial respiratory chain complex inhibitors, Fas cell surface expression was noted to increase in a similar fashion to the depletion of mtDNA in both cell lines. However, when cells were evaluated for sensitivity to apoptosis using Fas-engagement, there was no difference between the Rho(+) and Rho(-) cells in either cell line. By contrast, sensitivity to the cytotoxic agent cis-diammine-dichloroplatinum (cisplatin) was markedly increased in the Rho(-) cells, which expressed higher levels of cell surface Fas. Expression of Fas is increased with the depletion of mtDNA and respiratory complex inhibitors. However, this increase in expression does not necessarily translate to an increase in sensitivity to Fas-engagement, although there is an increase in the sensitivity of depleted cells to cytotoxic agents such as cisplatin.

Number of somatic mutations in the mitochondrial D-loop region indicates poor prognosis in breast cancer, independent of TP53 mutation

The objective of this study was to investigate whether somatic mutations in the mitochondrial DNA (mtDNA) D-loop region correlate with known prognostic factors, namely, age, tumor size, lymph node status, metastasis, tumor-node-metastasis stage, lymphovascular invasion, and status of the progesterone receptor, estrogen receptor, ERBB2 (alias HER2/neu), and TP53 proteins (as determined by immunohistochemistry) and to investigate their relationship, if any, to TP53 mutations in human breast cancer. Thirty breast tumors without BRCA mutation, along with adjacent nontumorous tissues, were genotyped for the mtDNA D-loop region and for the promoter as well as the coding region of the TP53 gene. Clinicopathological parameters were recorded and assessed. In all, 17 somatic mtDNA D-loop mutations were identified, in 13 of 30 tumor samples (43%); two mutations were novel: 544C>T and 16510A>C. Four TP53 mutations were found in six tumor samples (20%), and two (c.437G>A and c.706T>C) were novel. Only progesterone receptor status correlated with the number of somatic mtDNA D-loop mutations (likelihood chi-square test; P < 0.05). Somatic mutations in the mtDNA D-loop and in TP53 were independent of each other (Fisher's exact test; P > 0.05). These results suggest that the number of somatic mtDNA D-loop mutations may be an indicator of poor prognosis through a mechanism independent of TP53.

Do alterations in mitochondrial DNA play a role in breast carcinogenesis?

A considerable body of evidence supports a role for oxidative stress in breast carcinogenesis. Due to their role in producing energy via oxidative phosphorylation, the mitochondria are a major source of production of reactive oxygen species, which may damage DNA. The mitochondrial genome may be particularly susceptible to oxidative damage leading to mitochondrial dysfunction. Genetic variants in mtDNA and nuclear DNA may also contribute to mitochondrial dysfunction. In this review, we address the role of alterations in mtDNA in the etiology of breast cancer. Several studies have shown a relatively high frequency of mtDNA mutations in breast tumor tissue in comparison with mutations in normal breast tissue. To date, several studies have examined the association of genetic variants in mtDNA and breast cancer risk. The G10398A mtDNA polymorphism has received the most attention and has been shown to be associated with increased risk in some studies. Other variants have generally been examined in only one or two studies. Genome-wide association studies may help identify new mtDNA variants which modify breast cancer risk. In addition to assessing the main effects of specific variants, gene-gene and gene-environment interactions are likely to explain a greater proportion of the variability in breast cancer risk.

Quantitative mitochondrial redox imaging of breast cancer metastatic potential

Predicting tumor metastatic potential remains a challenge in cancer research and clinical practice. Our goal was to identify novel biomarkers for differentiating human breast tumors with different metastatic potentials by imaging the in vivo mitochondrial redox states of tumor tissues. The more metastatic (aggressive) MDA-MB-231 and less metastatic (indolent) MCF-7 human breast cancer mouse xenografts were imaged with the low-temperature redox scanner to obtain multi-slice fluorescence images of reduced nicotinamide adenine dinucleotide (NADH) and oxidized flavoproteins (Fp). The nominal concentrations of NADH and Fp in tissue were measured using reference standards and used to calculate the Fp redox ratio, Fp(NADH+Fp). We observed significant core-rim differences, with the core being more oxidized than the rim in all aggressive tumors but not in the indolent tumors. These results are consistent with our previous observations on human melanoma mouse xenografts, indicating that mitochondrial redox imaging potentially provides sensitive markers for distinguishing aggressive from indolent breast tumor xenografts. Mitochondrial redox imaging can be clinically implemented utilizing cryogenic biopsy specimens and is useful for drug development and for clinical diagnosis of breast cancer.

[Metabolic markers of the head and neck cancers--clinical applications and the biochemical background]

The problem of diagnosis in the field of head and neck region is still valid. Specific diagnosis and precise estimation of the tumor's size with the use of CT and MRI imaging is generally unsatisfactory. The Positron Emission Tomography (PET) supports this process with additional information about the tumor's metabolism. Numerous publications show that PET-CT has a great influence on the evaluation of the size of the tumor, presence of lymph node metastases, choice of treatment and the prognosis of the recurrence. Cancer cells represent a specific metabolic state. These cells intake large quantities of glucose and utilize it in the process of glycolysis. The oxidative phosphorylation is not efficient in the transformed cells and defects in mitochondrial functions are at the heart of malignant cell transformation. Disruption of the oxidative phosphorylation chain has been described in the neoplasms. As a consequence, in cancer the glycolysis is active even in the normoxic environment. This metabolic shift in cell transformation has been described in early XX century and so called Warburg's hypothesis profoundly influenced the present perception of cancer metabolism, positioning what is termed aerobic glycolysis in the mainstream of clinical oncology. Today we know that neoplastic cells differ at the proteomic level. A subset of different proteins such as hexokinase II or HIF are upregulated. These abnormalities might be used as the neoplastic markers.

Chapter 9: Oxidative stress in malignant progression: The role of Clusterin, a sensitive cellular biosensor of free radicals

Clusterin/Apolipoprotein J (CLU) gene is expressed in most human tissues and encodes for two protein isoforms; a conventional heterodimeric secreted glycoprotein and a truncated nuclear form. CLU has been functionally implicated in several physiological processes as well as in many pathological conditions including ageing, diabetes, atherosclerosis, degenerative diseases, and tumorigenesis. A major link of all these, otherwise unrelated, diseases is that they are characterized by increased oxidative injury due to impaired balance between production and disposal of reactive oxygen or nitrogen species. Besides the aforementioned diseases, CLU gene is differentially regulated by a wide variety of stimuli which may also promote the production of reactive species including cytokines, interleukins, growth factors, heat shock, radiation, oxidants, and chemotherapeutic drugs. Although at low concentration reactive species may contribute to normal cell signaling and homeostasis, at increased amounts they promote genomic instability, chronic inflammation, lipid oxidation, and amorphous aggregation of target proteins predisposing thus cells for carcinogenesis or other age-related disorders. CLU seems to intervene to these processes due to its small heat-shock protein-like chaperone activity being demonstrated by its property to inhibit protein aggregation and precipitation, a main feature of oxidant injury. The combined presence of many potential regulatory elements in the CLU gene promoter, including a Heat-Shock Transcription Factor-1 and an Activator Protein-1 element, indicates that CLU gene is an extremely sensitive cellular biosensor of even minute alterations in the cellular oxidative load. This review focuses on CLU regulation by oxidative injury that is the common molecular link of most, if not all, pathological conditions where CLU has been functionally implicated.

Mitochondrial genomic instability in colorectal cancer: no correlation to nuclear microsatellite instability and allelic deletion of hMSH2, hMLH1, and p53 genes, but prediction of better survival for Dukes' stage C disease

PURPOSE

Malfunction of mismatch repair (MMR) system and p53 produces nuclear genomic instability and is involved in colorectal tumorigenesis. In addition to a nuclear genome, eukaryotic cells have cytoplasmic genomes that are compartmentalized in the mitochondria. The aims of this study were to detect the mitochondrial genomic instability (mtGI) in colorectal carcinomas, and to explore its relationship with nuclear genetic alterations and its prognostic meaning.

METHODS

Eighty-three colorectal carcinomas with corresponding normal mucosa were analyzed for mtGI, nuclear microsatellite instability (nMSI), and loss of heterozygosity (LOH) of hMSH2, hMLH1, and p53 genes. Mitochondrial and nuclear alterations were examined for mutual correlation and for associations with clinicopathological features and clinical outcomes.

RESULTS

Out of 83 cases, mtGI was identified in 23 carcinomas (27.7%), whereas nMSI was detected in 11 (13.3%). Of the 23 cases with mtGI, only two showed nMSI simultaneously. The frequencies of LOH of hMSH2, hMLH1, and p53 were 16.1%, 11.6%, and 65.3%, respectively. There was no significant association between mtGI and these allelic losses. Notably, Dukes' C patients with mtGI had better disease-free and overall survival than those lacking this feature (p = 0.0516 and 0.0313, respectively).

CONCLUSIONS

Mitochondrial genomic instability occurs with a high frequency in colorectal carcinomas but is independent of nMSI and allelic deletion of hMSH2, hMLH1, and p53 genes. The results suggest that, instead of nuclear MMR system, there might be different mechanisms involving mitochondrial genomic integrity, and mtGI confers a better prognosis in Dukes' C colorectal cancer.

Quantitative magnetic resonance and optical imaging biomarkers of melanoma metastatic potential

Noninvasive or minimally invasive prediction of tumor metastatic potential would facilitate individualized cancer management. Studies were performed on a panel of human melanoma xenografts that spanned the full range of metastatic potential measured by an in vivo lung colony assay and an in vitro membrane invasion culture system. Three imaging methods potentially transferable to the clinic [dynamic contrast-enhanced (DCE) MRI, T(1(rho))-MRI, and low-temperature fluorescence imaging (measurable on biopsy specimens)] distinguished between relatively less metastatic and more metastatic human melanoma xenografts in nude mice. DCE-MRI, analyzed with the shutter-speed relaxometric algorithm and using an arterial input function simultaneously measured in the left ventricle of the mouse heart, yielded a blood transfer rate constant, K(trans), that measures vascular perfusion/permeability. K(trans) was significantly higher in the core of the least metastatic melanoma (A375P) than in the core of the most metastatic melanoma (C8161). C8161 melanoma had more blood vascular structures but fewer functional blood vessels than A375P melanoma. The A375P melanoma exhibited mean T(1(rho)) values that were significantly higher than those of C8161 melanoma. Measurements of T(1) and T(2) relaxation times did not differ significantly between these 2 melanomas. The mitochondrial redox ratio, Fp/(Fp + NADH), where Fp and NADH are the fluorescences of oxidized flavoproteins and reduced pyridine nucleotides, respectively, varied linearly with the in vitro invasive potential of the 5 melanoma cell lines (A375P, A375M, A375P10, A375P5, and C8161). This study shows that a harsh microenvironment may promote melanoma metastasis and provides potential biomarkers of metastatic potential.

Sequencing strategy for the whole mitochondrial genome resulting in high quality sequences

Background

It has been demonstrated that a reliable and fail-safe sequencing strategy is mandatory for high-quality analysis of mitochondrial (mt) DNA, as the sequencing and base-calling process is prone to error. Here, we present a high quality, reliable and easy handling manual procedure for the sequencing of full mt genomes that is also appropriate for laboratories where fully automated processes are not available.

Results

We amplified whole mitochondrial genomes as two overlapping PCR-fragments comprising each about 8500 bases in length. We developed a set of 96 primers that can be applied to a (manual) 96 well-based technology, which resulted in at least double strand sequence coverage of the entire coding region (codR).

Conclusion

This elaborated sequencing strategy is straightforward and allows for an unambiguous sequence analysis and interpretation including sometimes challenging phenomena such as point and length heteroplasmy that are relevant for the investigation of forensic and clinical samples.

High rate of mutation in mitochondrial DNA displacement loop region in human colorectal cancer

PURPOSE

Mitochondrial DNA mutations are found in many kinds of human cancer and the 1.1 kb displacement loop region has been identified as a "hot spot" for mutation in mitochondrial DNA of tumors. This study evaluated the mutation frequencies in hypervariable regions of mitochondrial displacement loop in patients with colorectal cancer.

METHODS

We examined the frequency of mutations in the mitochondrial DNA displacement loop region of 40 colorectal cancer samples in comparison to 150 samples from people without any type of familial cancer history, by automated DNA sequencing. Alignment was made with the revised Cambridge Reference Sequence and any differences recorded as single base substitution, insertions, and deletions.

RESULTS

Our results showed that the rate of displacement loop variations was higher in colorectal cancer patients than controls. Nineteen single nucleotide polymorphisms were found; among them eighteen occurred in the displacement loop region.

CONCLUSIONS

Mutations in mtDNA D-loop region probably do not cause colorectal cancer but are more likely to be epiphenomena; patients with the high mtDNA variants are at a higher risk of colorectal cancer.

Expression of beta-F1-ATPase and mitochondrial transcription factor A and the change in mitochondrial DNA content in colorectal cancer: clinical data analysis and evidence from an in vitro study

PURPOSE

Mitochondria play an important role in regulating apoptosis and thus may be involved in tumor progression. This study was conducted to elucidate the role of mitochondrial dysfunction in colorectal cancer (CRC).

METHODS

Mitochondrial DNA (mtDNA) content was analyzed with real-time polymerase chain reaction in 153 CRC patients who had received surgery at the Taipei Veterans General Hospital from January 1999 to December 2000. The expression of mitochondrial transcription factor A (TFAM) and beta-F1-ATPase were analyzed using immunohistochemistry. HCT116 cells were cultured in 1% O(2) for at least 20 passages. Mitochondrial biogenesis, ATP production, and the apoptotic response to 5-fluorouracil were analyzed in the derived cells.

RESULTS

Disease stage was associated with changes in mtDNA content (p < 0.001), expression of TFAM (p = 0.004), and/or beta-F1-ATPase (p < 0.001). CRCs with low expression of TFAM or beta-F1-ATPase had a lower mtDNA content. In the multivariate analysis, disease stage was the most significant prognostic factor [95% confidence interval (CI), 2.82-6.23], followed by beta-F1-ATPase [95% CI, 1.10-4.10]. In patients receiving 5-FU based chemotherapy, the 5-year disease-free survival rate was only 27% in CRC patients with a low beta-F1-ATPase tumor and was significantly lower than that in those with a high beta-F1-ATPase tumor (60%; p = 0.042). In the hypoxia-treated cells, mitochondrial mass increased, mtDNA content decreased, sensitivity to 5-fluorouracil decreased, and beta-F1-ATPase expression decreased.

CONCLUSION

Mitochondrial dysfunction may be associated with poor outcomes in CRC patients.

Brain mitochondrial lipid abnormalities in mice susceptible to spontaneous gliomas

Alterations in mitochondrial function have long been considered a hallmark of cancer. We compared the lipidome and electron transport chain activities of non-synaptic brain mitochondria in two inbred mouse strains, the C57BL/6J (B6) and the VM/Dk (VM). The VM strain is unique in expressing a high incidence of spontaneous brain tumors (1.5%) that are mostly gliomas. The incidence of gliomas is about 210-fold greater in VM mice than in B6 mice. Using shotgun lipidomics, we found that the mitochondrial content of ethanolamine glycerophospholipid, phosphatidylserine, and ceramide was higher, whereas the content of total choline glycerophospholipid was lower in the VM mice than in B6 mice. Total cardiolipin content was similar in the VM and the B6 mice, but the distribution of cardiolipin molecular species differed markedly between the strains. B6 non-synaptic mitochondria contained 95 molecular species of cardiolipin that were symmetrically distributed over 7 major groups based on mass charge. In contrast, VM non-synaptic mitochondria contained only 42 molecular species that were distributed asymmetrically. The activities of Complex I, I/III, and II/III enzymes were lower, whereas the activity of complex IV was higher in the mitochondria of VM mice than in B6 mice. The high glioma incidence and alterations in electron transport chain activities in VM mice compared to B6 mice could be related to the unusual composition of mitochondrial lipids in the VM mouse brain.

Depletion of mitochondrial DNA up-regulates the expression of MDR1 gene via an increase in mRNA stability

The mutation and reduction of mitochondrial DNA (mtDNA) have been suggested as factors in the carcinogenesis. However, whether the depletion of mtDNA induces multidrug resistance in cancer cells has not been fully investigated. To elucidate the association of cellular mtDNA content and drug resistance, we generated HCT-8 colon cancer cells which revealed a marked decrease in cellular mtDNA and ATP content, concomitant with a lack of mRNAs encoded by mtDNA. The mtDNA-depleted cells showed a decreased sensitivity and accumulation of anti-cancer drugs, suggesting that mtDNA depletion could develop multidrug resistance (MDR) phenotype in HCT-8 cells. We found that the expression level of MDR1 mRNA and its translated product P-glycoprotein was increased in the mtDNA-depleted cells, indicating that the decrease of sensitivity and accumulation of anti-cancer drug in the mtDNA-depleted cells might be due to a substantial increase in the expression of P-glycoprotein. Furthermore, increased expression of MDR1 mRNA and P-glycoprotein was due to an increase of mRNA stability rather than transcriptional activation. Taken together, these results indicate that mtDNA depletion can induce an increased P-glycoprotein expression via an increase of mRNA stability and suggest that the mtDNA depletion in cancer cells plays an important role in the induction of MDR phenotype.

Elucidating the interactions between the adhesive and transcriptional functions of -catenin in normal and cancerous cells

Wnt signalling is involved in a wide range of physiological and pathological processes. The presence of an extracellular Wnt stimulus induces cytoplasmic stabilisation and nuclear translocation of beta-catenin, a protein that also plays an essential role in cadherin-mediated adhesion. Two main hypotheses have been proposed concerning the balance between beta-catenin's adhesive and transcriptional functions: either beta-catenin's fate is determined by competition between its binding partners, or Wnt induces folding of beta-catenin into a conformation allocated preferentially to transcription. The experimental data supporting each hypotheses remain inconclusive. In this paper we present a new mathematical model of the Wnt pathway that incorporates beta-catenin's dual function. We use this model to carry out a series of in silico experiments and compare the behaviour of systems governed by each hypothesis. Our analytical results and model simulations provide further insight into the current understanding of Wnt signalling and, in particular, reveal differences in the response of the two modes of interaction between adhesion and signalling in certain in silico settings. We also exploit our model to investigate the impact of the mutations most commonly observed in human colorectal cancer. Simulations show that the amount of functional APC required to maintain a normal phenotype increases with increasing strength of the Wnt signal, a result which illustrates that the environment can substantially influence both tumour initiation and phenotype.

Mitochondrial DNA G10398A polymorphism imparts maternal Haplogroup N a risk for breast and esophageal cancer

Mitochondria are the major source of Reactive Oxygen Species (ROS) and mtDNA G10398A (Ala-->Thr) polymorphism, proposed to be involved in increased ROS production, has been shown in association with invasive breast cancer in African-American (AA) women [J.A. Canter, A.R. Kallianpur, F.F. Parl, R.C. Millikan, Mitochondrial DNA G10398A polymorphism and invasive breast cancer in African-American women, Cancer Res. 65 (2005) 8028-8033] and prostate cancer in AA men [M.P. Mims, T.G. Hayes, S. Zheng, S.M. Leal, A. Frolov, M.M. Ittmann, et al., Mitochondrial DNA G10398A polymorphism and invasive breast cancer in African-American women, Cancer Res. 66 (2006) 1880; author reply 1880-1881]. The role of mitochondria, however, in cancer development has been in question recently [A. Salas, Y.G. Yao, V. Macaulay, A. Vega, A. Carracedo, H.J. Bandelt, A critical reassessment of the role of mitochondria in tumorigenesis, PLoS Med. 2 (2005) e296], which has made it pertinent to analyze the data and test the hypotheses by conducting fresh case-control studies. This study, therefore, makes an attempt to validate the exclusive presence of mtG10398A (Ala-->Thr) polymorphism in a haplotype constituting mtDNA haplogroup N and its sublineages, imparting this group a higher risk for breast cancer, based on the re-analyses of approximately 1000 complete human mtDNA sequences worldwide and collated information on 2334 individuals belonging to 18 regions in India. The conclusion drawn of mt10398A allele providing a risk towards cancer is confirmed in a case-control comparison study of 124 sporadic breast cancer patients and 273 controls; and 55 squamous cell carcinoma of esophagus, ESCC, and 163 controls, matched for age, ethnicity and sex from north India. It is further apparent from the study that such a mtDNA polymorphism background provides a higher risk for the cancers of the tissues which could be affected by environmental insults directly as in the ESCC, observed with a high acquired (somatic) rate of mutation in p53 when compared to the breast cancer, suggesting that the mtDNA variants that arose as energetic adaptations, influence our health differentially under different environment conditions and a given genetic background of the mt genome.

Extraction and identification of mitochondrial DNA and nuclear DNA from human esophageal squamous cell carcinoma tissues

AIM: To extract mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) simultaneously from the same tissues and evaluate its efficiency by comparative analysis.

METHODS: Both mtDNA and nDNA were extracted simultaneously from the same tissues using agent kit. Agarose gel electrophoresis and polymerase chain reaction were used to identify the obtained mtDNA and nDNA.

RESULTS: mtDNA and nDNA were successfully extracted from the mitochondria and nucleus of the same tissue, respectively. The efficiency of this method for extracting mtDNA and nDNA simultaneously from the same tissue was similar to that of the traditional method (extracting mtDNA and nDNA from different tissues), and there was a close relationship between these two methods.

CONCLUSION: It is timesaving and economical to extract mtDNA and nDNA simultaneously from the same tissues, which is a better way for DNA study.

The biological significance of cancer: mitochondria as a cause of cancer and the inhibition of glycolysis with citrate as a cancer treatment

In this article, I present the hypothesis that cancer presents due to the domination of the cell by mitochondria, which, from an evolution viewpoint, appeared in multi-cellular living being with the incorporation of a bacteria into a primitive cell, the bacteria sustained itself as mitochondria and these conserved their identity and bacterial characteristics, based on this, the hypothesis is suggested of the biological competition between the cell and the mitochondria; the mitochondria, on establishing itself as an independent entity within the cell, created the need to permanently remain in the cytoplasm of the cell, thus, from an energy viewpoint, when a cell becomes malignant, the mitochondria are the sole beneficiaries, as there is an ideal environment at the cellular level for the mitochondria to sustain their functions, and from this hypothesis, the treatment for fighting cancer consists of inhibiting glycolysis, being the principal source of energy for the mitochondria, this is achieved by administering citrate to cancer patients, as the citrate inhibits the phosphofructokinase enzyme, the pyruvate dehydrogenase complex and the succinate dehydrogenase enzyme of Krebs cycle, thus, the mitochondria will be forced to limit their metabolism and, secondarily, will lower the reproduction capacity of the cell in general.

Mitochondrial DNA mutations in differentiated thyroid cancer with respect to the age factor

INTRODUCTION

Increased numbers of mitochondria in differentiated thyroid cancer and, most strikingly, mutations in human mitochondrial DNA (mtDNA) in older people have led to speculation that mtDNA mutations might contribute to aging or accumulate in postmitotic tissues with age. Mutation analyses of mtDNA in papillary (PTCs) and follicular (FTCs) thyroid carcinomas have been limited to date. The significance and frequency of mtDNA mutations in PTC and FTC are therefore controversial, as is age dependence.

METHODS

We analyzed eight sample pairs of PTC and six of FTC tissue with the corresponding normal thyroid tissue. DNA was extracted from frozen and formaldehyde-fixed tissue using the QIAmp Tissue Kit. Sequence differences in the mtDNA between tumor and normal tissue were detected using appropriate polymerase chain reaction (PCR) products for heteroduplex analysis in a denaturing high performance liquid chromatography (HPLC) Wave System (Transgenomic). Mutations were confirmed and identified by sequencing the PCR products of conspicuous chromatograms. The samples were obtained from 346 patients with PTC and 105 patients with FTC. We analyzed the whole mitochondrial genome from seven PTC and three FTC tumors along with the corresponding normal thyroid tissue. 3/7 PTC samples showed two heteroplasmic mutations and one polymorphism; all 3 FTCs showed homoplasmic and/or heteroplasmic mutations.

RESULTS

All but one of these tumors are well documented in the mitochondrial database MITOMAP. MtDNA mutations were found in all three patients aged 45 years and older. There was no correlation, however, in this small group to clinical prognostic factors for recurrence and especially for survival in differentiated thyroid carcinomas, such as histology, tumor size, lymph node metastases, distant metastases, and gender, most likely because of the short follow-up. While univariate analysis of the findings in the whole cohort of 346 patients with PTC suggested that age is a significant prognostic factor for survival (P = 0.0237) but not for recurrence (P = 0.65), this was not the case in the 105 patients with FTC.

CONCLUSIONS

Although we found accumulation of mutations in two older patients with PTC and one patient with FTC (all three patients older than 45 years had mtDNA mutations), the low frequency of these mutations in the small group of 10 analyzed patients did not correlate with statistically validated clinical prognosticators for recurrence or survival, especially not with age. The low power of our data are therefore not able to support or refute the hypothesis that these mtDNA mutations are related to age-dependent tumor progression in the thyroid or that they "may be involved in thyroid tumorigenesis."

Association studies on human mitochondrial DNA: methodological aspects and results in the most common age-related diseases

Mitochondrial DNA (mtDNA) follows direct maternal inheritance and, as such, can be used in phylogenetic studies to determine a human lineage tree. The presence of common polymorphisms allows a classification of mtDNA in haplogroups and sub-haplogroups, according to the branch they belong to. Thanks to the rapidly growing number of mtDNA sequences available, this classification is being corrected and redefined to be more accurate. In parallel with this process, several studies are trying to identify an association between common mtDNA polymorphisms and common complex traits, as hypothesized by the common disease-common variant theory. Here we review the associations already reported with the main age-related complex diseases and we identify the critical points (sample size, size of the recruiting area, careful matching between cases and controls regarding geographical origin and ethnicity, data quality checking) to be taken in account in planning such studies. On the whole, this research area is opening a new perspective as an important component of "mitochondrial medicine", capable of identifying new molecular targets for the diagnosis, prevention and treatment of common complex diseases.

Nuclear HMGA1 nonhistone chromatin proteins directly influence mitochondrial transcription, maintenance, and function

We have previously demonstrated that HMGA1 proteins translocate from the nucleus to mitochondria and bind to mitochondrial DNA (mtDNA) at the D-loop control region [G.A. Dement, N.R. Treff, N.S. Magnuson, V. Franceschi, R. Reeves, Dynamic mitochondrial localization of nuclear transcription factor HMGA1, Exp. Cell Res. 307 (2005) 388-401.] [11]. To elucidate possible physiological roles for such binding, we employed methods to analyze mtDNA transcription, mitochondrial maintenance, and other organelle functions in transgenic human MCF-7 cells (HA7C) induced to over-express an HA-tagged HMGA1 protein and control (parental) MCF-7 cells. Quantitative real-time (RT) PCR analyses demonstrated that mtDNA levels were reduced approximately 2-fold in HMGA1 over-expressing HA7C cells and flow cytometric analyses further revealed that mitochondrial mass was significantly reduced in these cells. Cellular ATP levels were also reduced in HA7C cells and survival studies showed an increased sensitivity to killing by 2-deoxy-D-glucose, a glycolysis-specific inhibitor. Flow cytometric analyses revealed additional mitochondrial abnormalities in HA7C cells that are consistent with a cancerous phenotype: namely, increased reactive oxygen species (ROS) and increased mitochondrial membrane potential (Delta Psi(m)). Additional RT-PCR analyses demonstrated that gene transcripts from both the heavy (ND2, COXI, ATP6) and light (ND6) strands of mtDNA were up-regulated approximately 3-fold in HA7C cells. Together, these mitochondrial changes are consistent with many previous reports and reveal several possible mechanisms by which HMGA1 over-expression, a common feature of naturally occurring cancers, may affect tumor progression.

Peptide deformylase inhibitors as potent antimycobacterial agents

Peptide deformylase (PDF) catalyzes the hydrolytic removal of the N-terminal formyl group from nascent proteins. This is an essential step in bacterial protein synthesis, making PDF an attractive target for antibacterial drug development. Essentiality of the def gene, encoding PDF from Mycobacterium tuberculosis, was demonstrated through genetic knockout experiments with Mycobacterium bovis BCG. PDF from M. tuberculosis strain H37Rv was cloned, expressed, and purified as an N-terminal histidine-tagged recombinant protein in Escherichia coli. A novel class of PDF inhibitors (PDF-I), the N-alkyl urea hydroxamic acids, were synthesized and evaluated for their activities against the M. tuberculosis PDF enzyme as well as their antimycobacterial effects. Several compounds from the new class had 50% inhibitory concentration (IC50) values of <100 nM. Some of the PDF-I displayed antibacterial activity against M. tuberculosis, including MDR strains with MIC90 values of <1 microM. Pharmacokinetic studies of potential leads showed that the compounds were orally bioavailable. Spontaneous resistance towards these inhibitors arose at a frequency of < or =5 x 10(-7) in M. bovis BCG. DNA sequence analysis of several spontaneous PDF-I-resistant mutants revealed that half of the mutants had acquired point mutations in their formyl methyltransferase gene (fmt), which formylated Met-tRNA. The results from this study validate M. tuberculosis PDF as a drug target and suggest that this class of compounds have the potential to be developed as novel antimycobacterial agents.

Interaction between yeast mitochondrial and nuclear genomes: null alleles of RTG genes affect resistance to the alkaloid lycorine in rho0 petites of Saccharomyces cerevisiae

Some nuclear genes in Saccharomyces cerevisiae (S. cerevisiae) respond to signals from the mitochondria in a process called by Butow (Cell Death Differ. 9 (2002) 1043-1045) retrograde regulation. Expression of these genes is activated in cells lacking mitochondrial function by involvement of RTG1, RTG2 and RTG3 genes whose protein products bind to "R-boxes" in the promoter region; RTG2p is a cytoplasmic protein. Since S. cerevisiae rho0 strains, lacking the entire mitochondrial genome, are resistant to lycorine, an alkaloid extracted from Amaryllis plants, it could be hypothesized that in rho0 cells the dysfunctional mitochondrial status stimulates overexpression of nuclear genes very likely involved in both nuclear and mitochondrial DNA replication. In this report we show that the resistance of rho0 cells to lycorine is affected by the deletion of RTG genes.

Mitochondrial DNA mutations and mitochondrial DNA depletion in gastric cancer

Gastric carcinoma is one of the most common types of cancer in Taiwan. Somatic mitochondrial DNA (mtDNA) alteration in gastric carcinoma and its association with clinicopathologic features remain unclear. When we used polymerase chain reaction (PCR) and direct sequencing, 15 of the 31 (48%) gastric carcinomas displayed somatic mutations in the D-loop region, a hot spot for mutations in mtDNA of human cancers. Ten (67%) cancers with the somatic mutations in the D-loop had insertion or deletion mutations in nucleotide position (np) 303-309 in the mononucleotide repeat region. One carcinoma carried tandem duplication and triplication flanked by mononucleotide repeats starting at np 311 and 568, respectively, in the D-loop. We also detected the common 4,977-bp deletion in 17 (55%) of the noncancerous tissue samples, but only in three (9%) carcinomas. Moreover, we quantified the mtDNA content using a competitive PCR technique and found that mtDNA depletion occurred in 17 (55%) of the gastric carcinomas. Although no significant association was found between clinicopathologic features and the mtDNA mutations in the D-loop, mtDNA depletion was observed significantly in the ulcerated, infiltrating (Borrmann's type III) and diffusely thick (Borrmann's type IV) types of gastric carcinomas (P = 0.018). Our results suggest that somatic mtDNA mutations and mtDNA depletion occur in gastric cancer and that mtDNA depletion is involved in carcinogenesis and/or cancer progression of gastric carcinoma.

Mitochondrial DNA G10398A Polymorphism and Invasive Breast Cancer in African-American Women

Mitochondria generate oxygen-derived free radicals that damage mitochondrial DNA (mtDNA) as well as nuclear DNA and in turn promote carcinogenesis. The mtDNA G10398A polymorphism alters the structure of Complex I in the mitochondrial electron transport chain, an important site of free radical production. This polymorphism is associated with several neurodegenerative disorders. We hypothesized that the 10398A allele is also associated with breast cancer susceptibility. African mitochondria harbor the 10398A allele less frequently than Caucasian mitochondria, which predominantly carry this allele. Mitochondrial genotypes at this locus were therefore determined in two separate populations of African-American women with invasive breast cancer and in controls. A preliminary study at Vanderbilt University (48 cases, 54 controls) uncovered an association between the 10398A allele and invasive breast cancer in African-American women, [odds ratio (OR), 2.90; 95% confidence interval (95% CI), 0.61-18.3; P = 0.11]. We subsequently validated this finding in a large, population-based, case-control study of breast cancer, the Carolina Breast Cancer Study at the University of North Carolina (654 cases, 605 controls). African-American women in this study with the 10398A allele had a significantly increased risk of invasive breast cancer (OR, 1.60; 95% CI, 1.10-2.31; P = 0.013). The 10398A allele remained an independent risk factor after adjustment for other well-accepted breast cancer risk factors. No association was detectable in white women (879 cases, 760 controls; OR, 1.03; 95% CI, 0.81-1.31; P = 0.81). This study provides novel epidemiologic evidence that the mtDNA 10398A allele influences breast cancer susceptibility in African-American women. mtDNA polymorphisms may be underappreciated factors in breast carcinogenesis.

Mitochondrial DNA as a cancer biomarker

As part of a national effort to identify biomarkers for the early detection of cancer, we developed a rapid and high-throughput sequencing protocol for the detection of sequence variants in mitochondrial DNA. Here, we describe the development and implementation of this protocol for clinical samples. Heteroplasmic and homoplasmic sequence variants occur in the mitochondrial genome in patient tumors. We identified these changes by sequencing mitochondrial DNA obtained from tumors and blood from the same individual. We confirmed previously identified primary lung tumor changes and extended these findings in a small patient cohort. Eight sequence variants were identified in stage I to stage IV tumor samples. Two of the sequence variants identified (22%) were found in the D-loop region, which accounts for 6.8% of the mitochondrial genome. The other sequence variants were distributed throughout the coding region. In the forensic community, the sequence variations used for identification are localized to the D-loop region because this region appears to have a higher rate of mutation. However, in lung tumors the majority of sequence variation occurred in the coding region. Hence, incomplete mitochondrial genome sequencing, designed to scan discrete portions of the genome, misses potentially important sequence variants associated with cancer or other diseases.

Searching for non-RET molecular alterations in medullary thyroid carcinoma: expression analysis by mRNA differential display

Some 25%-70% of sporadic medullary thyroid carcinomas (MTCs) are associated with somatic mutations within the RET proto-oncogene. In a significant number of MTCs, however, no such genetic variations can be detected, which implies alternative pathogenic molecular alterations. To assess altered RET mutation-specific gene expression, and to identify yet unknown gene transcripts involved in the tumorigenesis of MTC, we performed an expression analysis by mRNA differential display (RT-DD). Snap-frozen tumor tissues and corresponding normal thyroid tissues of 8 patients suffering from MTC (6 sporadic, 2 hereditary tumors) were included in the study; 5/8 MTCs harbored RET point mutations (codons 618, 634, 918). The RT-DD method was refined by use of fluorescence-labeled arbitrary oligonucleotides, electrophoresis on an automated sequencer, and a novel fragment-recovery technique utilizing a high-performance fluorescence scanner. More than 400 differentially expressed mRNA transcripts--representing upregulated or downregulated genes in the compared tissues--were detected. In all, 28 selected fragments were recovered, cloned, sequenced, and identified. Differential expression of gene transcripts with known association to cell proliferation or tumor progression--such as annexin A2, Rab11a, trefoil proteins, superoxide dismutase (SOD1), mitochondrial displacement loop (D-loop), and G protein subunit gamma11--as well as of the neuroendocrine marker chromogranin was observed. Furthermore, several mRNA transcripts of yet unknown genes displayed mutation-specific upregulation or downregulation in MTC. Illumination of the molecular basis especially of C-cell carcinomas without detectable alterations of the RET receptor tyrosine kinase will be required for the development of therapeutic strategies for advanced tumors that cannot be bridled or cured by surgical interventions alone.

Absence of pathogenic mitochondrial DNA mutations in mouse brain tumors

BACKGROUND

Somatic mutations in the mitochondrial genome occur in numerous tumor types including brain tumors. These mutations are generally found in the hypervariable regions I and II of the displacement loop and unlikely alter mitochondrial function. Two hypervariable regions of mononucleotide repeats occur in the mouse mitochondrial genome, i.e., the origin of replication of the light strand (OL) and the Arg tRNA.

METHODS

In this study we examined the entire mitochondrial genome in a series of chemically induced brain tumors in the C57BL/6J strain and spontaneous brain tumors in the VM mouse strain. The tumor mtDNA was compared to that of mtDNA in brain mitochondrial populations from the corresponding syngeneic mouse host strain.

RESULTS

Direct sequencing revealed a few homoplasmic base pair insertions, deletions, and substitutions in the tumor cells mainly in regions of mononucleotide repeats. A heteroplasmic mutation in the 16srRNA gene was detected in a spontaneous metastatic VM brain tumor.

CONCLUSION

None of the mutations were considered pathogenic, indicating that mtDNA somatic mutations do not likely contribute to the initiation or progression of these diverse mouse brain tumors.

Increased mitochondrial DNA content in saliva associated with head and neck cancer

Alterations of the mitochondrial DNA (mtDNA) have been described in human tumors and in other tissues in association with smoking exposure. We did quantitative PCR of cytochrome c oxidase I (Cox I) and cytochrome c oxidase II (Cox II) genes on oral rinse samples obtained from 94 patients with primary head and neck squamous cell carcinoma (HNSC) and a control group of 656 subjects. Mitochondrial DNA/nuclear DNA in saliva from HNSC patients and controls in relationship to smoking exposure, ethanol intake, and tumor stage were examined. Mean levels of Cox I and Cox II in saliva samples were significantly higher in HNSC patients: Cox I, 0.076 [95% confidence interval (95% CI), 0.06-0.09] and Cox II, 0.055 (95% CI, 0.04-0.07) in comparison with controls Cox I, 0.054 (95% CI, 0.05-0.06), P < 0.0001 and Cox II, 0.046 (95% CI, 0.04-0.05), P = 0.003 (t test). MtDNA levels were elevated in primary tumors when compared with matched, pretreatment saliva and significant correlation was noted (Cox I, r = 0.30, P = 0.005 and Cox II r = 0.33, P = 0.002, respectively, Pearson's correlation). On univariate analysis, smoking, age, HNSC diagnosis, and advanced stage of HNSC were associated with higher level of mtDNA content in saliva. Multivariate analysis showed a significant and independent association of HNSC diagnosis, age, and smoking with increasing mtDNA/nuclear DNA for Cox I and Cox II. mtDNA content alteration is associated with HNSC independently of age and smoking exposure, can be detected in saliva, and may be due to elevation in mtDNA content in primary HNSC.