Mild orotic aciduria in UMPS heterozygotes: a metabolic finding without clinical consequences.

BACKGROUND: Elevated urinary excretion of orotic acid is associated with treatable disorders of the urea cycle and pyrimidine metabolism. Establishing the correct and timely diagnosis in a patient with orotic aciduria is key to effective treatment. Uridine monophosphate synthase is involved in de novo pyrimidine synthesis. Uridine monophosphate synthase deficiency (or hereditary orotic aciduria), due to biallelic mutations in UMPS, is a rare condition presenting with megaloblastic anemia in the first months of life. If not treated with the pyrimidine precursor uridine, neutropenia, failure to thrive, growth retardation, developmental delay, and intellectual disability may ensue. METHODS AND RESULTS: We identified mild and isolated orotic aciduria in 11 unrelated individuals with diverse clinical signs and symptoms, the most common denominator being intellectual disability/developmental delay. Of note, none had blood count abnormalities, relevant hyperammonemia or altered plasma amino acid profile. All individuals were found to have heterozygous alterations in UMPS. Four of these variants were predicted to be null alleles with complete loss of function. The remaining variants were missense changes and predicted to be damaging to the normal encoded protein. Interestingly, family screening revealed heterozygous UMPS variants in combination with mild orotic aciduria in 19 clinically asymptomatic family members. CONCLUSIONS: We therefore conclude that heterozygous UMPS-mutations can lead to mild and isolated orotic aciduria without clinical consequence. Partial UMPS-deficiency should be included in the differential diagnosis of mild orotic aciduria. The discovery of heterozygotes manifesting clinical symptoms such as hypotonia and developmental delay are likely due to ascertainment bias.

Two Novel TEX15 Mutations in a Family with Nonobstructive Azoospermia.

AIM: Genetic investigations explain only a small percentage of cases of nonobstructive azoospermia (NOA), a condition that affects up to 2% of infertile couples. This study aimed to identify further genomic variants that are associated with primary spermatogenic failure within the testis. METHODS: One family with 2 infertile siblings affected by NOA was genotyped by whole-exome sequencing. DNA variants were filtered based on quality score, allele frequency, and functional roles of genes in spermatogenesis. RESULTS: Both NOA males were compound heterozygotes for a nonsense mutation and a single nucleotide deletion leading to premature stop codons in the TEX15 gene (c.2419A>T, p.Lys807*, and c.3040delT, p.Ser1014Leufs*5, respectively). The single mutations were identified only on one allele in 6 family members, including 3 fertile males who conceived naturally. CONCLUSION: This is the second reported case of a TEX15 deleterious mutation cosegregating with NOA in a family in which the infertile phenotype is reminiscent of the one observed in the TEX15-knockout mouse, confirming that TEX15 plays a critical role in normal spermatogenesis and its defects may be responsible for a number of NOA cases.

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.

Functional analysis of six uncharacterised mutations in LDLR gene.

BACKGROUND AND AIMS: Familial hypercholesterolemia (FH) is a primary hyperlipemia. It is an autosomal dominant genetic disorder of lipoproteins metabolism mainly caused by mutations in the low density lipoprotein receptor gene (LDLR). We aimed to investigate the functional impact on the low density lipoprotein receptor (LDLR) activity of six uncharacterised variants located in the coding region of the LDLR gene, namely c.428G > T, c.640T > C, c.1708C > T, c.1736A > T, c.1981C > G and c.2114C > G (NM_000527.4) and to attempt to define their clinical status. METHODS: Functional studies were carried out using site-directed mutagenesis techniques and expression of LDLR protein in vitro. Results were correlated with clinical data and in silico analyses in order to assess the physiopathological role of these variants. RESULTS: This work provides functional information about 6 uncharacterised mutations in LDLR. CONCLUSIONS: The six variants studied here appeared to affect the LDLR function in vitro to different degrees, ranging from receptors with normal to slightly reduced activity to receptors exhibiting less than 10% of the wild-type activity. According to these studies and The American College of Medical Genetics and Genomics (ACMG) Standards and Guidelines, two variants could be classified as "Likely Benign" (p.(Ala705Gly) and p.(Leu570Phe)), three variants as "Pathogenic" (p.(Asp579Val), p.(Cys143Phe) and p.(Trp214Arg)) and one variant as "Likely Pathogenic" (p.(Pro661Ala)).

Caution in interpretation of disease causality for heterozygous loss-of-function variants in the MYH8 gene associated with autosomal dominant disorder.

To date, the NM_002472.2(MYH8):c.2021G>A (p.Arg674Gln) missense variant in the MYH8 gene is the only known genetic change in individuals with autosomal dominant trismus-pseudocamptodactyly syndrome with unknown molecular mechanism. Next-generation sequencing (NGS), including targeted gene panels and whole-exome sequencing, is routinely performed in many clinical diagnostic laboratories as standard-of-care testing aimed at identifying disease-causing genomic variants. Whole-exome sequencing has revealed loss-of-function variants in the MYH8 gene. To properly classify the MYH8 loss-of-function variants, we either retrieved them from public databases or retrospectively collected them from individuals genetically tested by custom NGS panels or by whole-exome sequencing and confirmed using Sanger sequencing. We further evaluated the respective clinical presentations of these individuals with the MYH8 loss-of-function variants. Heterozygous loss-of-function variants in the MYH8 gene were detected in 16 individuals without trismus-pseudocamptodactyly syndrome. Four of these 16 individuals had a pathogenic or likely pathogenic variant detected in another gene that could explain their clinical presentation. Moreover, there are ∼100 MYH8 heterozygous protein-truncating and splice site variants in the ExAC database in different populations. Our results, combined with the population data, indicate that loss-of-function variants in the MYH8 gene do not cause autosomal dominant trismus-pseudocamptodactyly syndrome, and the clinical significance of these variants remains unknown at present. This result highlights the importance of considering the molecular mechanism of disease, variants published in the medical literature, and population genomic data for the correct interpretation of loss-of-function variants in genes associated with autosomal dominant diseases.

The multikinase inhibitor Sorafenib enhances glycolysis and synergizes with glycolysis blockade for cancer cell killing.

Although the only effective drug against primary hepatocarcinoma, the multikinase inhibitor Sorafenib (SFB) usually fails to eradicate liver cancer. Since SFB targets mitochondria, cell metabolic reprogramming may underlie intrinsic tumor resistance. To characterize cancer cell metabolic response to SFB, we measured oxygen consumption, generation of reactive oxygen species (ROS) and ATP content in rat LCSC (Liver Cancer Stem Cells) -2 cells exposed to the drug. Genome wide analysis of gene expression was performed by Affymetrix technology. SFB cytotoxicity was evaluated by multiple assays in the presence or absence of metabolic inhibitors, or in cells genetically depleted of mitochondria. We found that low concentrations (2.5-5 µM) of SFB had a relatively modest effect on LCSC-2 or 293 T cell growth, but damaged mitochondria and increased intracellular ROS. Gene expression profiling of SFB-treated cells was consistent with a shift toward aerobic glycolysis and, accordingly, SFB cytotoxicity was dramatically increased by glucose withdrawal or the glycolytic inhibitor 2-DG. Under metabolic stress, activation of the AMP dependent Protein Kinase (AMPK), but not ROS blockade, protected cells from death. We conclude that mitochondrial damage and ROS drive cell killing by SFB, while glycolytic cell reprogramming may represent a resistance strategy potentially targetable by combination therapies.

The proteomics of cancer stem cells: potential clinical applications for innovative research in oncology.

Cancer stem cells (CSCs) or tumour-maintaining cells are becoming an important new reality in oncology. The intriguing molecular pathophysiology of CSCs may justify some of the obscure pathogenetic, diagnostic, prognostic, and above all, therapeutic aspects of cancer and, eventually, lead to new solutions in oncology. CSC is a cell within the tumour that possesses the capacity to self-renew and, in doing so, gives rise to the heterogeneous lineages that comprise the tumour. The precise identification of this peculiar subpopulation of cancer cells, which has some intriguing similarities to normal stem cells, is becoming an important and urgent topic in oncology. In fact, some debated CSC markers have been already adopted by pharmacological research as targets of new and/or old anticancer drugs, showing an intriguing therapeutic index. These discussed identification markers include cell surface proteins, different activated signalling pathways, several molecules of the stem cell niche, various drug resistance mechanisms (ABCG2 and ALDH), telomerase, oncogenes and oncosuppressors (p16INK4 - Rb) and lastly, various microRNAs. In this new promising area of cancer research, proteomics, in general, and oncoproteomics, in particular, can and must play a significant role if the methodological approaches and the experimental protocols are correctly designed and interpreted.

Cancer stem cells: the development of new cancer therapeutics.

INTRODUCTION: Cancer stem cells (CSCs) are a subpopulation of tumor cells with indefinite proliferative potential that drive the growth of tumors. CSCs seem to provide a suitable explanation for several intriguing aspects of cancer pathophysiology. AREAS COVERED: An explosion of therapeutic options for cancer treatment that selectively target CSCs has been recorded in the recent years. These include the targeting of cell-surface proteins, various activated signalling pathways, different molecules of the stem cell niche and various drug resistance mechanisms. Importantly, approaching cancer research by investigating the pathogenesis of these intriguing cancer cells is increasing the knowledge of the pathophysiology of the disease, emphasizing certain molecular mechanisms that have been partially neglected. EXPERT OPINION: The characterization of the molecular phenotype of these cancer stem-like cells, associated with an accurate definition of their typical derangement in cell differentiation, can represent a fundamental advance in terms of diagnosis and therapy of cancer. Preliminary results seem to be promising but further studies are required to define the therapeutic index of this new anticancer treatment. Moreover, understanding the pathogenetic mechanisms of CSCs can expand the therapeutic applications of normal adult stem cells by reducing the risk of uncontrolled tumorigenic stem cell differentiation.

Pharmacological modulation of nitric oxide release: new pharmacological perspectives, potential benefits and risks.

Nitric oxide is becoming an increasingly important signalling molecule implicated in a growing number of physiological and pathophysiological processes. Moreover, with the recent advances in nitric oxide biochemistry, many well known drugs have been shown to act totally or partially by modulating NO metabolism with varying therapeutic results. The classic organic nitrates have been shown to exhibit beneficial therapeutic but suffer from some well known pitfalls (tolerability induction, abrupt cephalea and hypotension). Similarly, sydnonimines, another well known class of NO donor drugs, have a characteristically low therapeutic index (i.e., cyanide toxicity). At present, pharmacological researchers are designing and synthesising various chemical compounds capable of modulating NO metabolism for therapeutic purposes that also possess an optimal therapeutic index. Specifically, various new classes of NO donors are under intense pharmacological investigation (such as S-nitrosothiols, diazeniumdiolates, furoxans, zeolites and so on), each characterised by a particular pharmacokinetic and pharmacodynamic profile. To known the pharmacological development of these new NO donor drugs could help to ameliorate the use of these molecules in various therapeutic protocols. In fact, the pharmacologically modulated nitric oxide release showed to have an important therapeutic impact in the treatment of diseases such as arteriopathies, various acute and chronic inflammatory conditions, and several degenerative diseases. At present, the most important obstacle in the field of new NO donor drugs seems to be carefully targeting NO release to a particular tissue at an optimal concentration, so as to achieve a beneficial action and to limit possible toxic effects.

Revisiting the Warburg effect in cancer cells with proteomics. The emergence of new approaches to diagnosis, prognosis and therapy.

Most cancer cells exhibit elevated levels of glycolysis and this metabolic pathway seems to be related to a greater glucose uptake. This phenomenon, known as the Warburg effect, is considered one of the most fundamental metabolic alterations during malignant transformation. Originally, Warburg hypothesised that the aerobic glycolysis of cancer cells could be just an aspect of a more complex metabolic adaptation. However, this intriguing discovery was partially misinterpreted and disregarded over time. In recent years, the peculiarities of cancer cell metabolism have been re-evaluated in light of new metabolic data that seem to confirm and to widen the original concept of the Warburg effect. In fact, biochemical, molecular, and, above all, proteomic studies on the multifaceted roles of glycolytic enzymes in cancer cells in general, and in cancer stem cells in particular, seem to suggest more complex functional adaptations. These adaptations result in significantly altered protein expression patterns, and they have fundamental implications for diagnosis, prognosis and therapy. Revisiting the Warburg effect in cancer cells with a proteomic approach could deepen our knowledge of cancer cell metabolism and of cancer cell biology in general. Moreover, by identifying useful diagnostic, prognostic and therapeutic targets, it could significantly impact clinical practice.

Glycolytic enzyme inhibitors in cancer treatment.

BACKGROUND: The radio- and chemotherapeutics currently used for the treatment of cancer are widely known to be characterized by a low therapeutic index. An interesting approach to overcoming some of the limits of these techniques is the exploitation of the so-called Warburg effect, which typically characterizes neoplastic cells. Interestingly, this feature has already been utilized with good results, but only for diagnostic purposes (PET and SPECT). From a pharmacological point of view, drugs able to perturb cancer cell metabolism, specifically at the level of glycolysis, may display interesting therapeutic activities in cancer. OBJECTIVE: The pharmacological actions of these glycolytic enzyme inhibitors, based primarily on ATP depletion, could include: i) amelioration of drug selectivity by exploiting the particular glycolysis addiction of cancer cell; ii) inhibition of energetic and anabolic processes; iii) reduction of hypoxia-linked cancer-cell resistance; iv) reduction of ATP-dependent multi-drug resistance; and v) cytotoxic synergism with conventional cancer treatments. CONCLUSION: Several glycolytic inhibitors are currently in preclinical and clinical development. Their clinical value as anticancer agents, above all in terms of therapeutic index, strictly depends on a careful reevaluation of the pathophyiological role of the unique metabolism of cancer cells in general and of Warburg effect in particular.

The human muscle proteome in aging.

The aim of the present study was to assess age-dependent changes of proteins in the vastus lateralis muscle of physically active elderly and young subjects by a combination of two-dimensional difference gel electrophoresis, SDS-PAGE and ESI-MS/MS. The differences observed in the elderly group included down-regulation of regulatory myosin light chains, particularly the phosphorylated isoforms, a higher proportion of myosin heavy chain isoforms 1 and 2A, and enhanced oxidative and reduced glycolytic capacity.

Peptide and protein separations by capillary electrophoresis in the presence of mono- and diquaternarized diamines.

Two compounds, derivatives of 1,4-diazobicyclo[2,2,2]octane (DABCO), have been evaluated as potential quenchers of silanol interactions with peptides and proteins during their capillary zone electrophoresis (CZE) separations. They are: 1-(4-iodobutyl)4-aza-1-azoniabicyclo[2,2,2]octane iodide (M7C4I) and 1,4-didecyl-1,4-diazoniabicyclo [2,2,2]octane dibromide (C10M7C10). The first compound is known to react with the wall, by forming a covalent bond via alkylation of silanols. On the contrary, the second one (C10M7C10) can only loosely interact with silica due to lack of reactive iodine and to a much too short distance (a C(2)) between the two quaternary nitrogens. Very good peptide maps of protein digests can be obtained in isoelectric glutamic acid (Glu) buffer, at pH 3.52 by utilizing the M7C4I. However, in the case of total tissue extracts, excellent resolution is obtained only with the first eluting part of the analyte spectrum (i.e., peptides and smaller proteins). With larger proteins, interaction with the wall and loss of resolution is experienced. When using the C10M7C10, good resolution of di- and tripeptides is obtained, while a loss of resolution is observed with entire protein digest. M7C4I does not seem to interact with the peptide/protein analytes, and simply repels them from the wall via its positive charges; it is believed that disalt (C10M7C10) acts by interacting with the same compounds, possibly by forming micelles in solution.