Remarks on Mitochondrial Myopathies.

Mitochondrial myopathies represent a heterogeneous group of diseases caused mainly by genetic mutations to proteins that are related to mitochondrial oxidative metabolism. Meanwhile, a similar etiopathogenetic mechanism (i.e., a deranged oxidative phosphorylation and a dramatic reduction of ATP synthesis) reveals that the evolution of these myopathies show significant differences. However, some physiological and pathophysiological aspects of mitochondria often reveal other potential molecular mechanisms that could have a significant pathogenetic role in the clinical evolution of these disorders, such as: i. a deranged ROS production both in term of signaling and in terms of damaging molecules; ii. the severe modifications of nicotinamide adenine dinucleotide (NAD)+/NADH, pyruvate/lactate, and α-ketoglutarate (α-KG)/2- hydroxyglutarate (2-HG) ratios. A better definition of the molecular mechanisms at the basis of their pathogenesis could improve not only the clinical approach in terms of diagnosis, prognosis, and therapy of these myopathies but also deepen the knowledge of mitochondrial medicine in general.

Immunological Role of IgG Subclasses.

The loss of tolerance to self-antigens is the unequivocal "red line" of autoimmunity: both development of autoreactive T and B cells and production of polyclonal autoantibodies represent seminal keys to the pathogenesis of protean autoimmune diseases. Most of these autoantibodies are immunoglobulins G (IgG), functionally distinguished in four subclasses named IgG1, IgG2, IgG3, and IgG4, due to structural differences in the hinge and heavy chain constant regions. Different studies analyzed serum levels of IgG subclasses in the course of different disorders, showing that they might have a pathogenic role by regulating interactions among immunoglobulins, Fc-gamma receptors, and complement. To date, the mechanisms promoting different IgG subclasses distribution during the natural history of most autoimmune diseases remain somewhat unclear. Evidence from the medical literature shows that the serum IgG profile is peculiar for many autoimmune diseases, suggesting that different subclasses could be specific for the underlying driving autoantigens. A better knowledge of IgG subsets may probably help to elucidate their pathological task, but also to define their relevance for diagnostic purposes, patients' personalized management, and prognosis assessment.

Mitochondrial Metabolism in Cancer. A Tangled Topic. Which Role for Proteomics?

Given the role of mitochondria in modulating many cellular functions, it is not surprising that they can play a crucial role also in molecular pathophysiology of cancer. In particular, the discovery in recent decades of a link between cancer metabolic processes, alterations of mitochondrial DNA, oncogenes and tumor suppressors has led not only to a renaissance of interest in Warburg's pioneering work, but also to a reexamination of his original observations above all in relation to the current knowledge in cancer cell metabolism. It follows that, although mitochondrial contribution to the pathogenesis of cancer has historically tended to be neglected, it is now evident that reprogrammed mitochondria can contribute to a complex bioenergetic adjustment that sustains not only tumor formation but also its progression. Most importantly, cancer cell metabolism seems to have a role in diversified aspects related to cancer pathophysiology (i.e., aggressiveness, recurrence, metastatic dissemination). Hence, it is imperative to always consider cancer cell metabolism, its adaptability, its influences but, above all, its functional heterogeneity in a single tumor, for a really rational and valid approach towards molecular biology of cancer.

Toward the Standardization of Mitochondrial Proteomics: The Italian Mitochondrial Human Proteome Project Initiative.

The Mitochondrial Human Proteome Project aims at understanding the function of the mitochondrial proteome and its crosstalk with the proteome of other organelles. Being able to choose a suitable and validated enrichment protocol of functional mitochondria, based on the specific needs of the downstream proteomics analysis, would greatly help the researchers in the field. Mitochondrial fractions from ten model cell lines were prepared using three enrichment protocols and analyzed on seven different LC-MS/MS platforms. All data were processed using neXtProt as reference database. The data are available for the Human Proteome Project purposes through the ProteomeXchange Consortium with the identifier PXD007053. The processed data sets were analyzed using a suite of R routines to perform a statistical analysis and to retrieve subcellular and submitochondrial localizations. Although the overall number of identified total and mitochondrial proteins was not significantly dependent on the enrichment protocol, specific line to line differences were observed. Moreover, the protein lists were mapped to a network representing the functional mitochondrial proteome, encompassing mitochondrial proteins and their first interactors. More than 80% of the identified proteins resulted in nodes of this network but with a different ability in coisolating mitochondria-associated structures for each enrichment protocol/cell line pair.

The epithelial-mesenchymal transition in cancer: a potential critical topic for translational proteomic research.

The epithelial-mesenchymal transition (EMT) is a morphogenetic process that results in a loss of epithelial characteristics and the acquisition of a mesenchymal phenotype. First described in embryogenesis, the EMT has been recently implicated in carcinogenesis and tumor progression. In addition, recent evidence has shown that stem-like cancer cells present the hallmarks of the EMT. Some of the molecular mechanisms related to the interrelationships between cancer pathophysiology and the EMT are well-defined. Nevertheless, the precise molecular mechanism by which epithelial cancer cells acquire the mesenchymal phenotype remains largely unknown. This review focuses on various proteomic strategies with the goal of better understanding the physiological and pathological mechanisms of the EMT process.

Cancer Biomarkers: A Status Quo.

At present, there are a growing number of biomolecules under investigation to understand their potential role as cancer biomarker for diagnostic, prognostic and therapeutic purposes. Intriguingly, the state of art on cancer biomarkers research shows interesting and promising results together to clamorous failures. Also from a clinical point of view, there are contradictory results on routine clinical use of the present cancer biomarkers. Some patients may be simply monitored in their course by a periodic blood sample, but sometimes this monitoring show dramatic limits. A lot of patients show serious and extensive relapses without significant change in serum concentrations of biomarkers tested. Often the physician who should utilize these biomarkers does not entirely know their limits and the total potential applications as well and sometimes this knowledge is influenced by economical and marketing strategies. This limited and "polluted" knowledge may have dramatic consequences for patient. A critical approach towards old and new cancer biomarkers should foster a deepened and useful understanding of the diagnostic and prognostic index of these fundamental parameters of laboratory medicine and in the same time can facilitate the research of new and more sensitive-specific signals of the cancer cell proliferation.

The Role of CA 125 as Tumor Marker: Biochemical and Clinical Aspects.

CA 125 also known as mucin 16 or MUC16 is a large membrane glycoprotein belonging to the wide mucin family, encoded by the homonymous MUC16 gene. Following its discovery in the blood of some patients with specific types of cancers or other benign conditions, CA125 has found application as a tumor marker of ovarian cancer. Thirty years after its discovery, use of CA 125 is still FDA-recommended to monitor response to therapy in patients with epithelial ovarian cancer and to detect residual or recurrent disease in patients who have undergone first-line therapy and would be considered for second-look procedures. However, due to its limited specificity and sensitivity, CA 125 alone cannot still be an ideal biomarker. Increased clinical performance, in terms of better sensitivity and specificity in identifying epithelial ovarian cancer relapse, has been obtained by combined use of CA 125 with HE4, another ovarian cancer marker recently introduced in clinical use. Significant advancements have been achieved more recently, due to the introduction of FDA-approved ROMA and OVA1 algorithms to evaluate the risk of ovarian cancer for patients with a pelvic mass.

CA 19-9: Biochemical and Clinical Aspects.

CA19-9 (carbohydrate antigen 19-9, also called cancer antigen 19-9 or sialylated Lewis a antigen) is the most commonly used and best validated serum tumor marker for pancreatic cancer diagnosis in symptomatic patients and for monitoring therapy in patients with pancreatic adenocarcinoma. Normally synthesized by normal human pancreatic and biliary ductal cells and by gastric, colon, endometrial and salivary epithelia, CA 19-9 is present in small amounts in serum, and can be over expressed in several benign gastrointestinal disorders. Importantly, it exhibits a dramatic increase in its plasmatic levels during neoplastic disease. However, several critical aspects for its clinical use, such as false negative results in subjects with Lewis (a-b-) genotype and false positive elevation, occasional and transient, in patients with benign diseases, together with its poor positive predictive value (72.3 %), do not make it a good cancer-specific marker and renders it impotent as a screening tool. In the last years a large number of putative biomarkers for pancreatic cancer have been proposed, most of which is lacking of large scale validation. In addition, none of these has showed to possess the requisite sensitivity/specificity to be introduced in clinical use. Therefore, although with important limitations we well-know, CA 19-9 continues being the only pancreatic cancer marker actually in clinical use.

Neuron-Specific Enolase as a Biomarker: Biochemical and Clinical Aspects.

Neuron-specific enolase (NSE) is known to be a cell specific isoenzyme of the glycolytic enzyme enolase. In vertebrate organisms three isozymes of enolase, expressed by different genes, are present: enolase α is ubiquitous; enolase ß is muscle-specific and enolase γ is neuron-specific. The expression of NSE, which occurs as γγ- and αγ-dimer, is a late event in neural differentiation, thus making it a useful index of neural maturation.NSE is a highly specific marker for neurons and peripheral neuroendocrine cells. As a result of the findings of NSE in specific tissues under normal conditions, increased body fluids levels of NSE may occur with malignant proliferation and thus can be of value in diagnosis, staging and treatment of related neuroendocrine tumours (NETs).NSE is currently the most reliable tumour marker in diagnosis, prognosis and follow-up of small cell lung cancer (SCLC), even though increased levels of NSE have been reported also in non-small cell lung cancer (NSCLC). The level of NSE correlates with tumour burden, number of metastatic sites and response to treatment.NSE can be also useful at diagnosis of NETs and gastroenteropancreatic (GEP)-NETs.Raised serum levels of NSE have been found in all stages of neuroblastoma, although the incidence of increased concentration is greater in widespread and metastatic disease. Moreover, NSE determination in cord blood offers an early postnatal possibility of confirming the diagnosis of neuroblastoma in newborns.NSE has been demonstrated to provide quantitative measures of brain damage and/or to improve the diagnosis and the outcome evaluation in ischaemic stroke, intracerebral hemorrhage, seizures, comatose patients after cardiopulmonary resuscitation for cardiac arrest and traumatic brain injury.Increased NSE serum levels have also been found associated with melanoma, seminoma, renal cell carcinoma, Merkel cell tumour, carcinoid tumours, dysgerminomas and immature teratomas, malignant phaechromocytoma, Guillain-Barré syndrome and Creutzfeldt-Jakob disease.

A Critical Approach to Clinical Biochemistry of Chromogranin A.

Chromogranin A (CGA) is a member of the granin family of proteins which are widespread in endocrine, neuroendocrine, peripheral, and central nervous tissues, where they are typically found in secretory granules. It is well accepted that CGA cooperates to regulate synthesis and secretion of these various granule signaling molecules.Because of its ubiquitous distribution within neuroendocrine tissues, CGA can be a useful diagnostic marker for neuroendocrine neoplasms, including carcinoids, pheochromocytomas, neuroblastomas, medullary thyroid carcinomas (MTC), some pituitary tumors, functioning and nonfunctioning islet cell tumors and other amine precursor uptake and decarboxylation (APUD) tumors. It is also useful as a prognostic marker for detection of recurrence and monitoring of response to different treatments. As other tumor markers, it is imperative to know its physiology and pathophysiology, its sensitivity and specificity in different neuroendocrine tumors (NETs), and carefully integrate these data with the clinical data of the single patient, to maximize its diagnostic/prognostic index.

Circulating tumour cells and cancer stem cells: a role for proteomics in defining the interrelationships between function, phenotype and differentiation with potential clinical applications.

Research on the discovery and implementation of valid cancer biomarkers is one of the most challenging fields in oncology and oncoproteomics in particular. Moreover, it is generally accepted that an evaluation of cancer biomarkers from the blood could significantly enable biomarker assessments by providing a relatively non-invasive source of representative tumour material. In this regard, circulating tumour cells (CTCs) isolated from the blood of metastatic cancer patients have significant promise. It has been demonstrated that localised and metastatic cancers may give rise to CTCs, which are detectable in the bloodstream. Despite technical difficulties, recent studies have highlighted the prognostic significance of the presence and number of CTCs in the blood. Future studies are necessary not only to detect CTCs but also to characterise them. Furthermore, another pathogenically significant type of cancer cells, known as cancer stem cells (CSCs) or more recently termed circulating tumour stem cells (CTSCs), appears to have a significant role as a subpopulation of CTCs. This review discusses the potential application of proteomic methodologies to improve the isolation and characterisation of CTCs and to distinguish between CTCs with a poor clinical significance and those with important biological and clinical implications.

Mitochondria and cancer: a growing role in apoptosis, cancer cell metabolism and dedifferentiation.

At the beginning of the twentieth century, Otto Warburg demonstrated that cancer cells have a peculiar metabolism. These cells preferentially utilise glycolysis for energetic and anabolic purposes, producing large quantities of lactic acid. He defined this unusual metabolism "aerobic glycolysis". At the same time, Warburg hypothesised that a disruption of mitochondrial activities played a precise pathogenic role in cancer. Because of this so-called "Warburg effect", mitochondrial physiology and cellular respiration in particular have been overlooked in pathophysiological studies of cancer. Over time, however, many studies have shown that mitochondria play a fundamental role in cell death by apoptosis or necrosis. Moreover, metabolic enzymes of the Krebs cycle have also recently been recognised as oncosuppressors. Recently, a series of studies were undertaken to re-evaluate the role of oxidative mitochondrial metabolism in cancer cell growth and progression. Some of these data indicate that modulation of mitochondrial respiration may induce an arrest of cancer cell proliferation and differentiation (pseudodifferentiation) and/or or death, suggesting that iatrogenic manipulation of some mitochondrial activities may induce anticancer effects. Moreover, studying the role of mitochondria in cancer cell dedifferentiation/differentiation processes may allow further insight into the pathophysiology and therapy of so-called cancer stem cells.

Mitochondria and drugs.

Mitochondria play a central role in the life and death of cells. They are not merely the centre for energy metabolism, but are also the headquarters for different catabolic and anabolic processes, calcium fluxes, and various signalling pathways. Mitochondria maintain homeostasis in the cell by interacting with reactive oxygen-nitrogen species and responding adequately to different stimuli. In this context, the interaction of pharmacological agents with mitochondria is an aspect of molecular biology that is too often disregarded, not only in terms of toxicology but also from a therapeutic point of view, especially considering the potential therapeutic applications related to the modulation of mitochondrial activity.At the mitochondrial level, there are several potential drug targets that can lead to toxicity, but only for few of them, a real clinical counterpart has been demonstrated. Recently, antiviral nucleoside analogues have shown mitochondrial toxicity through the inhibition of DNA polymerase-gamma. Other drugs targeted to different components of the mitochondrial channels can disrupt ion homeostasis or affect the mitochondrial permeability transition pore. Many molecules are known inhibitors of the mitochondrial electron transport chain, interfering with one or more of the complexes in the respiratory chain. Some drugs, including non-steroidal anti-inflammatory drugs (NSAIDs), may lead to uncoupling of oxidative phosphorylation, while the mitochondrial toxicity of other drugs seems to depend on the production of free radicals, although this mechanism has yet to be defined. Besides toxicity, other drugs have been targeted to mitochondria to treat mitochondrial dysfunctions. Many drugs have been recently developed to target the mitochondria of cancer cells in order to trigger apoptosis or necrosis. The aim of this chapter is to underline the role of mitochondria in pharmacology and toxicology, stressing all the potential therapeutic approaches being due to iatrogenic modulation of the multitude of mitochondrial activities.

Mitochondrial proteomic approaches for new potential diagnostic and prognostic biomarkers in cancer.

Mitochondrial dysfunction and mutations in mitochondrial DNA have been implicated in a wide variety of human diseases, including cancer. In recent years, considerable advances in genomic, proteomic and bioinformatic technologies have made it possible the analysis of mitochondrial proteome, leading to the identification of over 1,000 proteins which have been assigned unambiguously to mitochondria. Defining the mitochondrial proteome is a fundamental step for fully understanding the organelle functions as well as mechanisms underlying mitochondrial pathology. In fact, besides giving information on mitochondrial physiology, by characterizing all the components of this subcellular organelle, the application of proteomic technologies permitted now to study the proteins involved in many crucial properties in cell signaling, cell differentiation and cell death and, in particular, to identify mitochondrial proteins that are aberrantly expressed in cancer cells. An improved understanding of the mitochondrial proteome could be essential to shed light on the connection between mitochondrial dysfunction, deregulation of apoptosis and tumorigenesis and to discovery new therapeutic targets for mitochondria-related diseases.

Mitochondrial Respiratory Complexes as Targets of Drugs: The PPAR Agonist Example.

Mitochondrial bioenergetics are progressively acquiring significant pathophysiological roles. Specifically, mitochondria in general and Electron Respiratory Chain in particular are gaining importance as unintentional targets of different drugs. The so-called PPAR ligands are a class of drugs which not only link and activate Peroxisome Proliferator-Activated Receptors but also show a myriad of extrareceptorial activities as well. In particular, they were shown to inhibit NADH coenzyme Q reductase. However, the molecular picture of this intriguing bioenergetic derangement has not yet been well defined. Using high resolution respirometry, both in permeabilized and intact HepG2 cells, and a proteomic approach, the mitochondrial bioenergetic damage induced by various PPAR ligands was evaluated. Results show a derangement of mitochondrial oxidative metabolism more complex than one related to a simple perturbation of complex I. In fact, a partial inhibition of mitochondrial NADH oxidation seems to be associated not only with hampered ATP synthesis but also with a significant reduction in respiratory control ratio, spare respiratory capacity, coupling efficiency and, last but not least, serious oxidative stress and structural damage to mitochondria.

A proteomic approach to characterizing ciglitazone-induced cancer cell differentiation in Hep-G2 cell line.

Drug induced cell differentiation represents a promising experimental model for proteomic analysis of cancer cells. In fact, by modulating and monitoring neoplastic cell differentiation it could be possible to identify cytodifferentiation related protein expression changes that can be subsequently utilized in vivo as potential cancer biomarkers. One main advantage of this approach is the significant reduction of biological variability normally observed in clinical biomarker research, with important implications also in prognosis and therapy. At this regard, a new class of differentiating agents is emerging, the so called PPAR-ligands, which however are characterized by a debated mechanism of action that has not been yet studied through a proteomic approach. To this aim, we investigated ciglitazone-induced differentiation of a human hepatocarcinoma HepG2 cell line, by monitoring biochemical and cellular parameters of cytodifferentiation and modifications of cellular protein profiles through 2-DE and MALDI-TOF analysis. Independent of the hypothesized mechanism of action of this intriguing PPARgamma agonist, results indicated that ciglitazone is a strong differentiating agent for the HepG2 cell line and that this process is associated with modifications of protein expression related to cell antioxidant systems, the cell cycle apparatus, signal transduction pathways, cellular stress and invasiveness. At last, considering these and other published data, a proteomic profile related to the cancer aggressiveness is beginning to emerge.

Resveratrol treatment induces redox stress in red blood cells: a possible role of caspase 3 in metabolism and anion transport.

Resveratrol, an important phytoalexine found in many plants, has been shown to be significantly effective in the treatment of several pathological conditions such as cancer, coronary heart disease and osteoarthritis. This study focuses on the effects of this drug on human red blood cells. In particular, we have examined the influence of resveratrol on Band 3, the anion exchanger protein, and hemoglobin as a function of the oxygenation-deoxygenation cycle. Moreover, special attention has been given to the metabolic changes imposed by caspase 3 activation. Resveratrol has proved to lower superoxide production, thereby decreasing heme-iron oxidation and saving the reducing power required for met-hemoglobin reduction. Oxygen binding experiments showed that resveratrol interacts with hemoglobin, shifting the T→R conformational transition towards the higher-affinity R state. This might contribute to altering the metabolic balance of the cell through an intensification of the pentose phosphate pathway. Moreover, at high oxygenation levels of the erythrocytic hemoglobin, resveratrol induces a significant activation of caspase 3, the action of which on Band 3 has a strong impact on cellular metabolism and anion transport.

The Tangled Mitochondrial Metabolism in Cancer: An Innovative Pharmacological Approach.

BACKGROUND: Mitochondria are remarkably gaining significant and different pathogenic roles in cancer (i.e., to sustain specific metabolism, to activate signaling pathways, to promote apoptosis resistance, to favor cancer cell dissemination, and finally to facilitate genome instability). Interestingly, all these roles seem to be linked to the fundamental activity of mitochondria, i.e. oxidative metabolism. Intriguingly, a typical modification of mitochondrial oxidative metabolism and reactive oxygen species production/ neutralization seems to have a central role in all these tangled pathogenic roles in cancer. On these bases, a careful understanding of the molecular relationships between cancer and mitochondria may represent a fundamental step to realize therapeutic approaches blocking the typical cancer progression. The main aim of this review is to stress some neglected aspects of oxidative mitochondrial metabolism of cancer cells to promote more translational research with diagnostic and therapeutic potential. METHODS: We reviewed the available literature regarding clinical and experimental studies on various roles of mitochondria in cancer, with attention to the cancer cell mitochondrial metabolism. RESULTS: Mitochondria are an important source of reactive oxygen species. Their toxic effects seem to increase in cancer cells. However, it is not clear if damage depends on ROS overproduction and/or defect in detoxification. Failure of both these processes is likely a critical component of the cancer process and is strictly related to the actual microenvironment of cancer cells. CONCLUSIONS: Mitochondria, also by ROS production, have a fundamental pathogenetic role in promoting and maintaining cancer and its spreading. To carefully understand the tangled redox state of cancer cells mitochondria represents a fundamental step to realize therapeutic approaches blocking the typical cancer progression.

Derangement of erythrocytic AE1 in beta-thalassemia by caspase 3: pathogenic mechanisms and implications in red blood cell senescence.

Considering its complex molecular pathophysiology, beta-thalassemia could be a good in vivo model to study some aspects related to erythrocyte functions with potential therapeutic implications not only within the frame of this particular hemoglobinopathy but also with respect to conditions in which the cellular milieu, altered by a deranged anion exchanger, could display a significant pathogenetic role (i.e., erythrocyte senescence, complications of red cell storage, renal tubular acidosis and some abnormal protein thesaurismosis). This work evaluates the anionic influx across band 3 protein in normal and beta-thalassemic red blood cells (RBCs) and ghosts. Since redox-mediated injury is an important pathway in the destruction of beta-thalassemic RBCs, we studied the anion transport and the activity of caspase 3 in the absence and presence of t-butylhydroperoxide in order to evaluate the effect of an increase of cellular oxidative stress. Interestingly, beta-thalassemic erythrocytes show a faster rate of anion exchange than normal RBCs and absence of any modulation mechanism of anion influx. These findings led us to formulate a hypothesis about the metabolic characteristics of beta-thalassemic erythrocytes, outlining that one of the main targets of caspase 3 in RBCs is the cytoplasmic domain of band 3 protein.

The plasma membrane of erythrocytes plays a fundamental role in the transport of oxygen, carbon dioxide and nitric oxide and in the maintenance of the reduced state of the heme iron.

Here we review new insights into the role of the erythrocyte membrane and the implications of its architecture on the several functions accomplished by the red blood cells. The picture which emerges highlights the capability of Hb and band 3 to modulate erythrocyte metabolism and to meet the needs of the cell.