Personalized Medicine: Pharmacogenomics and Drug Development.

Acta Med Iran. 2017 Mar;55(3):150-165

Authors: Mirsadeghi S, Larijani B

Abstract
Personalized medicine aims is to supply the proper drug to the proper patient within the right dose. Pharmacogenomics (PGx) is to recognize genetic variants that may influence drug efficacy and toxicity. All things considered, the fields cover a wide area, including basic drug discovery researches, the genetic origin of pharmacokinetics and pharmacodynamics, novel drug improvement, patient genetic assessment and clinical patient administration. At last, the objective of Pharmacogenomics is to anticipate a patient's genetic response to a particular drug as a way of presenting the best possible medical treatment. By predicting the drug response of an individual, it will be possible to increase the success of therapies and decrease the incidence of adverse side effect.

PMID: 28282716 [PubMed - in process]

Personalized Regenerative Medicine.

Acta Med Iran. 2017 Mar;55(3):144-149

Authors: Arjmand B, Goodarzi P, Mohamadi-Jahani F, Falahzadeh K, Larijani B

Abstract
Personalized medicine as a novel field of medicine refers to the prescription of specific therapeutics procedure for an individual. This approach has established based on pharmacogenetic and pharmacogenomic information and data. The terms precision and personalized medicines are sometimes applied interchangeably. However, there has been a shift from "personalized medicine" towards "precision medicine". Although personalized medicine emerged from pharmacogenetics, nowadays it covers many fields of healthcare. Accordingly, regenerative medicine and cellular therapy as the new fields of medicine use cell-based products in order to develop personalized treatments. Different sources of stem cells including mesenchymal stem cells, embryonic stem cells and induced pluripotent stem cells (iPSCs) have been considered in targeted therapies which could give many advantages. iPSCs as the novel and individual pluripotent stem cells have been introduced as the appropriate candidates for personalized cell therapies. Cellular therapies can provide a personalized approach. Because of person-to-person and population differences in the result of stem cell therapy, individualized cellular therapy must be adjusted according to the patient specific profile, in order to achieve best therapeutic results and outcomes. Several factors should be considered to achieve personalized stem cells therapy such as, recipient factors, donor factors, and the overall body environment in which the stem cells could be active and functional. In addition to these factors, the source of stem cells must be carefully chosen based on functional and physical criteria that lead to optimal outcomes.

PMID: 28282715 [PubMed - in process]

Dietary intake and lipid profile in children and adolescents with cystic fibrosis.

J Cyst Fibros. 2017 Mar 07;:

Authors: Woestenenk JW, Schulkes DA, Schipper HS, van der Ent CK, Houwen RH

Abstract
BACKGROUND: Cystic fibrosis (CF) patients are advised to derive 35% of their daily energy intake from dietary fat. Whether this high fat intake is associated with dyslipidaemia is unknown. We described the lipid profile and dietary intake in paediatric patients with CF.
METHODS: 110 fasting lipid concentrations of 110 Dutch patients with CF were studied, along with 86 measurements of dietary intake. For the total group and for boys and girls separately, the lipid profile and the dietary intake were investigated. The cross-sectional relationship between the lipid concentrations and dietary intake was determined.
RESULTS: The mean dietary fat intake was ≥35% of the total energy intake, along with a considerable consumption of saturated fat. We found lower concentrations of cholesterol, high-density lipoprotein cholesterol and low-density lipoprotein cholesterol, and increased concentrations of triglyceride and triglyceride to high-density lipoprotein cholesterol ratios. Lipid concentrations were not associated with dietary fat intake.
CONCLUSION: This study lacks variation in dietary fat intake to exclude an effect on lipid concentrations as the distribution of dietary fat intake remained constant at a high level. Elevated triglyceride concentrations and triglyceride to high-density lipoprotein cholesterol ratios suggest an increased risk of cardiovascular disease. Any negative consequences of a high dietary fat intake on the overall lipid profile later in life cannot be excluded.

PMID: 28283399 [PubMed - as supplied by publisher]

Interactions between Neutrophils and Pseudomonas aeruginosa in Cystic Fibrosis.

Pathogens. 2017 Mar 09;6(1):

Authors: Rada B

Abstract
Cystic fibrosis (CF) affects 70,000 patients worldwide. Morbidity and mortality in CF is largely caused by lung complications due to the triad of impaired mucociliary clearance, microbial infections and chronic inflammation. Cystic fibrosis airway inflammation is mediated by robust infiltration of polymorphonuclear neutrophil granulocytes (PMNs, neutrophils). Neutrophils are not capable of clearing lung infections and contribute to tissue damage by releasing their dangerous cargo. Pseudomonas aeruginosa is an opportunistic pathogen causing infections in immunocompromised individuals. P. aeruginosa is a main respiratory pathogen in CF infecting most patients. Although PMNs are key to attack and clear P. aeruginosa in immunocompetent individuals, PMNs fail to do so in CF. Understanding why neutrophils cannot clear P. aeruginosa in CF is essential to design novel therapies. This review provides an overview of the antimicrobial mechanisms by which PMNs attack and eliminate P. aeruginosa. It also summarizes current advances in our understanding of why PMNs are incapable of clearing P. aeruginosa and how this bacterium adapts to and resists PMN-mediated killing in the airways of CF patients chronically infected with P. aeruginosa.

PMID: 28282951 [PubMed - in process]

Exome sequencing identified a novel SMAD2 mutation in a Chinese family with early onset aortic aneurysms.

Clin Chim Acta. 2017 Mar 07;:

Authors: Zhang W, Zeng Q, Xu Y, Ying H, Zhou W, Cao Q, Zhou W

Abstract
Aortic aneurysm remains a devastating disease due to its fatal complications, such as aortic dissection and rupture. A subset of aortic aneurysm is caused by genetic defect and to date more than a dozen of disease-causing genes have been discovered to account for the disease. In this study, by using whole exome sequencing, we identified a novel heterozygous missense mutation (c.833C>T, p.A278V) in the SMAD2 gene in a family with early onset aortic aneurysms. The mutation segregated in this family, was high conserved among species and predicted to be pathogenic by multiple in silico programs. To our knowledge, this is the second report that link the SMAD2 mutations to aortic aneurysm. We recommend that SMAD2 should be included in the expanding panel of genetic testing for patients with unexplained aortic aneurysms, which will facilitate genotype-phenotype correlation of SMAD2 mutations. Given the current wide application of molecular diagnosis in clinical setting, identification of the defected gene allows recognition of additional family members at risk for aortic diseases and gene-based management of the carriers.

PMID: 28283438 [PubMed - as supplied by publisher]

The Application of Proteomics to Traumatic Brain and Spinal Cord Injuries.

Curr Neurol Neurosci Rep. 2017 Mar;17(3):23

Authors: Sarkis GA, Mangaonkar MD, Moghieb A, Lelling B, Guertin M, Yadikar H, Yang Z, Kobeissy F, Wang KK

Abstract
Traumatic brain injury (TBI) and traumatic spinal cord injury (SCI), collectively termed neurotrauma, are two parallel neurological conditions that can cause long-lasting neurological impairment and other comorbidities in patients, while at the same time, can create a high burden to society. To date, there are still no FDA-approved therapeutic interventions for either TBI or SCI. Recent advances in proteomic technologies, including tandem mass spectrometry, as well as imaging mass spectrometry, have enabled new approaches to study the differential proteome in TBI and SCI with the use of either animal disease models and/or biosamples from clinical observational studies. Thus, the applications of state-of-the-art proteomic method hold promises in shedding light on identifying clinically useful neurotrauma "biomarkers" and/or in identifying distinct and, otherwise, unobvious systems pathways or "key drivers" that can be further exploited as new therapeutic intervention targets.

PMID: 28283963 [PubMed - in process]

Estimating the Efficiency of Phosphopeptide Identification by Tandem Mass Spectrometry.

J Am Soc Mass Spectrom. 2017 Mar 10;:

Authors: Hsu CC, Xue L, Arrington JV, Wang P, Paez Paez JS, Zhou Y, Zhu JK, Tao WA

Abstract
Mass spectrometry has played a significant role in the identification of unknown phosphoproteins and sites of phosphorylation in biological samples. Analyses of protein phosphorylation, particularly large scale phosphoproteomic experiments, have recently been enhanced by efficient enrichment, fast and accurate instrumentation, and better software, but challenges remain because of the low stoichiometry of phosphorylation and poor phosphopeptide ionization efficiency and fragmentation due to neutral loss. Phosphoproteomics has become an important dimension in systems biology studies, and it is essential to have efficient analytical tools to cover a broad range of signaling events. To evaluate current mass spectrometric performance, we present here a novel method to estimate the efficiency of phosphopeptide identification by tandem mass spectrometry. Phosphopeptides were directly isolated from whole plant cell extracts, dephosphorylated, and then incubated with one of three purified kinases-casein kinase II, mitogen-activated protein kinase 6, and SNF-related protein kinase 2.6-along with (16)O4- and (18)O4-ATP separately for in vitro kinase reactions. Phosphopeptides were enriched and analyzed by LC-MS. The phosphopeptide identification rate was estimated by comparing phosphopeptides identified by tandem mass spectrometry with phosphopeptide pairs generated by stable isotope labeled kinase reactions. Overall, we found that current high speed and high accuracy mass spectrometers can only identify 20%-40% of total phosphopeptides primarily due to relatively poor fragmentation, additional modifications, and low abundance, highlighting the urgent need for continuous efforts to improve phosphopeptide identification efficiency. Graphical Abstract ᅟ.

PMID: 28283928 [PubMed - as supplied by publisher]

Transcriptomic Insights into Genetic Diversity of Protein-Coding Genes in X. laevis.

Dev Biol. 2017 Mar 07;:

Authors: Savova V, Pearl EJ, Boke E, Nag A, Adzhubei I, Horb ME, Peshkin L

Abstract
We characterize the genetic diversity of Xenopus laevis strains using RNA-seq data and allele-specific analysis. This data provides a catalogue of coding variation, which can be used for improving the genomic sequence, as well as for better sequence alignment, probe design, and proteomic analysis. In addition, we paint a broad picture of the genetic landscape of the species by functionally annotating different classes of mutations with a well-established prediction tool (PolyPhen-2). Further, we specifically compare the variation in the progeny of four crosses: inbred genomic (J)-strain, outbred albino (B)-strain, and two hybrid crosses of J and B strains. We identify a subset of mutations specific to the B strain, which allows us to investigate the selection pressures affecting duplicated genes in this allotetraploid. From these crosses we find the ratio of non-synonymous to synonymous mutations is lower in duplicated genes, which suggests that they are under greater purifying selection. Surprisingly, we also find that function-altering ("damaging") mutations constitute a greater fraction of the non-synonymous variants in this group, which suggests a role for subfunctionalization in coding variation affecting duplicated genes.

PMID: 28283406 [PubMed - as supplied by publisher]

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Topical phenytoin for the treatment of neuropathic pain.

J Pain Res. 2017;10:469-473

Authors: Kopsky DJ, Keppel Hesselink JM

Abstract
We developed and tested a new putative analgesic cream, based on the anticonvulsant phenytoin in patients suffering from treatment refractory neuropathic pain. The use of commercial topical analgesics is not widespread due to the facts that capsaicin creams or patches can give rise to side effects, such as burning, and analgesic patches (e.g., lidocaine 5% patches) have complex handling, especially for geriatric patients. Only in a few countries, compounded creams based on tricyclic antidepressants or other (co-)analgesics are available. Such topical analgesic creams, however, are easy to administer and have a low propensity for inducing side effects. We, therefore, developed a new topical cream based on 5% and 10% phenytoin and described three successfully treated patients suffering from neuropathic pain. All patients were refractory to a number of other analgesics. In all patients, phenytoin cream was effective in reducing pain completely, without any side effects, and the tolerability was excellent. The onset of action of the phenytoin creams was within 30 minutes. Phenytoin cream might become a new treatment modality of the treatment of neuropathic pain.

PMID: 28280381 [PubMed - in process]

Therapeutic strategies of drug repositioning targeting autophagy to induce cancer cell death: from pathophysiology to treatment.

J Hematol Oncol. 2017 Mar 09;10(1):67

Authors: Yoshida GJ

Abstract
The 2016 Nobel Prize in Physiology or Medicine was awarded to the researcher that discovered autophagy, which is an evolutionally conserved catabolic process which degrades cytoplasmic constituents and organelles in the lysosome. Autophagy plays a crucial role in both normal tissue homeostasis and tumor development and is necessary for cancer cells to adapt efficiently to an unfavorable tumor microenvironment characterized by hypo-nutrient conditions. This protein degradation process leads to amino acid recycling, which provides sufficient amino acid substrates for cellular survival and proliferation. Autophagy is constitutively activated in cancer cells due to the deregulation of PI3K/Akt/mTOR signaling pathway, which enables them to adapt to hypo-nutrient microenvironment and exhibit the robust proliferation at the pre-metastatic niche. That is why just the activation of autophagy with mTOR inhibitor often fails in vain. In contrast, disturbance of autophagy-lysosome flux leads to endoplasmic reticulum (ER) stress and an unfolded protein response (UPR), which finally leads to increased apoptotic cell death in the tumor tissue. Accumulating evidence suggests that autophagy has a close relationship with programmed cell death, while uncontrolled autophagy itself often induces autophagic cell death in tumor cells. Autophagic cell death was originally defined as cell death accompanied by large-scale autophagic vacuolization of the cytoplasm. However, autophagy is a "double-edged sword" for cancer cells as it can either promote or suppress the survival and proliferation in the tumor microenvironment. Furthermore, several studies of drug re-positioning suggest that "conventional" agents used to treat diseases other than cancer can have antitumor therapeutic effects by activating/suppressing autophagy. Because of ever increasing failure rates and high cost associated with anticancer drug development, this therapeutic development strategy has attracted increasing attention because the safety profiles of these medicines are well known. Antimalarial agents such as artemisinin and disease-modifying antirheumatic drug (DMARD) are the typical examples of drug re-positioning which affect the autophagy regulation for the therapeutic use. This review article focuses on recent advances in some of the novel therapeutic strategies that target autophagy with a view to treating/preventing malignant neoplasms.

PMID: 28279189 [PubMed - in process]

Splenic rupture and mediastinal mass associated with rare TdT-negative T-LBL/T-ALL lead to sudden death of a juvenile.

Forensic Sci Med Pathol. 2016 Dec;12(4):523-526

Authors: Gascho D, Huber B, Bolliger SA, Thali MJ, Schaerli S

PMID: 27778145 [PubMed - indexed for MEDLINE]

An extreme case of platypnoea-orthodeoxia syndrome.

Clin Med (Lond). 2016 Oct;16(5):453-454

Authors: O'Gallagher K, Chou E, Jeyabraba S, Sinha A, Robb D, Byrne J

Abstract
An 80-year-old female presented with progressive breathlessness, worse on sitting or standing and relieved by lying flat. Subsequent investigations identified a patent foramen ovale (PFO) with right-to-left flow across the interatrial septum (IAS). A diagnosis of platypnoea orthodeoxia syndrome secondary to inter-atrial shunting was made. Technical features precluded a percutaneous PFO closure so an open surgical repair was performed with complete resolution of symptoms. We discuss the pathophysiology and management of platypnoea orthodeoxia syndrome.

PMID: 27697809 [PubMed - indexed for MEDLINE]

[Concepts applied to psychiatry pharmacogenomics].

Vertex. 2016 Sep;XXVII(129):383-392

Authors: Zorrilla Zubilete MA

Abstract
Pharmacogenetics studies the action of a drug in order to predict the response based on the genetic makeup of an individual. The objective of pharmacogenetic studies is to minimize the adverse effects and to ensure therapeutic benefit. Since psychotropic drugs have a high rate of variability in patient response, the aim of this paper is to update the pharmacogenetic concepts in psychopharmacology in a review that provides tools for rigorous analysis when prescribing a psychotropic drug. The purpose of clinical pharmacogenetic testing is to be able to distinguish between patients who are more or less responders to certain drugs, or on contrary, who are at increased risk for adverse events. The goal is to choose a drug therapy that can maximize the effectiveness in the treatment and minimize the risks of adverse reactions, thus improving the benefit / risk ratio.
IN CONCLUSION: technology is not a limiting factor nowadays; the challenge remains, however, to further develop research for clinical use, establishing an appropriate validation test, that is accurate, repeatable and reproducible, in order to safely detect gene sequences of clinical interest.

PMID: 28282076 [PubMed - in process]

Genetic risk variants as therapeutic targets for Crohn's disease.

Expert Opin Ther Targets. 2017 Apr;21(4):381-390

Authors: Gabbani T, Deiana S, Marocchi M, Annese V

Abstract
INTRODUCTION: The pathogenesis of Inflammatory bowel diseases (IBD) is multifactorial, with interactions between genetic and environmental factors. Despite the existence of genetic factors being largely demonstrated by epidemiological data and several genetic studies, only a few findings have been useful in term of disease prediction, disease progression and targeting therapy. Areas covered: This review summarizes the results of genome-wide association studies in Crohn's disease, the role of epigenetics and the recent discovery by genetic studies of new pathogenetic pathways. Furthermore, it focuses on the importance of applying genetic data to clinical practice, and more specifically how to better target therapy and predict potential drug-related toxicity. Expert opinion: Some genetic markers identified in Crohn`s disease have allowed investigators to hypothesize about, and in some cases, prove the usefulness of new specific therapeutic agents. However, the heterogeneity and complexity of this disease has so far limited the daily clinical use of genetic information. Finally, the study of the implications of genetics on therapy, either to predict efficacy or avoid toxicity, is considered still to be in its infancy.

PMID: 28281904 [PubMed - in process]

Transmembrane Domain Single-Nucleotide Polymorphisms Impair Expression and Transport Activity of ABC Transporter ABCG2.

Pharm Res. 2017 Mar 09;:

Authors: Sjöstedt N, van den Heuvel JJ, Koenderink JB, Kidron H

Abstract
PURPOSE: To study the function and expression of nine naturally occurring single-nucleotide polymorphisms (G406R, F431L, S441N, P480L, F489L, M515R, L525R, A528T and T542A) that are predicted to reside in the transmembrane regions of the ABC transporter ABCG2.
METHODS: The transport activity of the variants was tested in inside-out membrane vesicles from Sf9 insect and human derived HEK293 cells overexpressing ABCG2. Lucifer Yellow and estrone sulfate were used as probe substrates of activity. The expression levels and cellular localization of the variants was compared to the wild-type ABCG2 by western blotting and immunofluorescence microscopy.
RESULTS: All studied variants of ABCG2 displayed markedly decreased transport in both Sf9-ABCG2 and HEK293-ABCG2 vesicles. Impaired transport could be explained for some variants by altered expression levels and cellular localization. Moreover, the destructive effect on transport activity of variants G406R, P480L, M515R and T542A is, to our knowledge, reported for the first time.
CONCLUSIONS: These results indicate that the transmembrane region of ABCG2 is sensitive to amino acid substitution and that patients harboring these ABCG2 variant forms could suffer from unexpected pharmacokinetic events of ABCG2 substrate drugs or have an increased risk for diseases such as gout where ABCG2 is implicated.

PMID: 28281205 [PubMed - as supplied by publisher]

First Case of Foot Drop Associated with Capecitabine in a Patient with Thymidylate Synthase Polymorphism.

Cureus. 2017 Jan 24;9(1):e995

Authors: Wilks AB, Saif MW

Abstract
Capecitabine, an oral prodrug of 5-FU, has been approved by the FDA for use in patients with breast and colon cancers. In addition, capecitabine is commonly used in patients with other malignancies such as pancreatic, gastroesophageal, and hepatobiliary tract cancers. Though cerebellar toxicity is a rare but well-known side effect of intravenous 5-FU therapy, peripheral neuropathy with capecitabine has only been described in rare cases. In this case report, we describe a 79-year-old patient with locally advanced adenocarcinoma of the pancreas undergoing chemoradiation therapy with capecitabine who developed peripheral sensorimotor neuropathy. To the best of our knowledge, this is the first patient in the literature who was found to have two mutations (2R) of a 28 base-pair tandem repeat in the 5' promoter enhancer region (5'-TSER) on both alleles (2R/2R) of thymidylate synthetase (TYMS) gene, possibly responsible for the neurotoxicity.

PMID: 28280649 [PubMed - in process]

Hepatic Induction of Fatty Acid Binding Protein 4 Plays a Pathogenic Role in Sepsis in Mice.

Am J Pathol. 2017 Mar 06;:

Authors: Hu B, Li Y, Gao L, Guo Y, Zhang Y, Chai X, Xu M, Yan J, Lu P, Ren S, Zeng S, Liu Y, Xie W, Huang M

Abstract
Sepsis is defined as the host's deleterious systemic inflammatory response to microbial infections. Herein, we report an essential role of the fatty acid binding protein 4 (FABP4; alias adipocyte protein 2 or aP2), a lipid-binding chaperone, in sepsis response. Bioinformatic analysis of the Gene Expression Omnibus data sets showed the level of FABP4 was higher in the nonsurvival sepsis patients' whole blood compared to the survival cohorts. The expression of Fabp4 was induced in a liver-specific manner in cecal ligation and puncture (CLP) and lipopolysaccharide treatment models of sepsis. The induction of Fabp4 may have played a pathogenic role, because ectopic expression of Fabp4 in the liver sensitized mice to CLP-induced inflammatory response and worsened the animal's survival. In contrast, pharmacological inhibition of Fabp4 markedly alleviated the CLP responsive inflammation and tissue damage and improved survival. We conclude that FABP4 is an important mediator of the sepsis response. Early intervention by pharmacological inhibition of FABP4 may help to manage sepsis in the clinic.

PMID: 28279656 [PubMed - as supplied by publisher]

Genetic variants in CETP increase risk of intracerebral hemorrhage.

Ann Neurol. 2016 11;80(5):730-740

Authors: Anderson CD, Falcone GJ, Phuah CL, Radmanesh F, Brouwers HB, Battey TW, Biffi A, Peloso GM, Liu DJ, Ayres AM, Goldstein JN, Viswanathan A, Greenberg SM, Selim M, Meschia JF, Brown DL, Worrall BB, Silliman SL, Tirschwell DL, Flaherty ML, Kraft P, Jagiella JM, Schmidt H, Hansen BM, Jimenez-Conde J, Giralt-Steinhauer E, Elosua R, Cuadrado-Godia E, Soriano C, van Nieuwenhuizen KM, Klijn CJ, Rannikmae K, Samarasekera N, Al-Shahi Salman R, Sudlow CL, Deary IJ, Morotti A, Pezzini A, Pera J, Urbanik A, Pichler A, Enzinger C, Norrving B, Montaner J, Fernandez-Cadenas I, Delgado P, Roquer J, Lindgren A, Slowik A, Schmidt R, Kidwell CS, Kittner SJ, Waddy SP, Langefeld CD, Abecasis G, Willer CJ, Kathiresan S, Woo D, Rosand J, Global Lipids Genetics Consortium and International Stroke Genetics Consortium

Abstract
OBJECTIVE: In observational epidemiologic studies, higher plasma high-density lipoprotein cholesterol (HDL-C) has been associated with increased risk of intracerebral hemorrhage (ICH). DNA sequence variants that decrease cholesteryl ester transfer protein (CETP) gene activity increase plasma HDL-C; as such, medicines that inhibit CETP and raise HDL-C are in clinical development. Here, we test the hypothesis that CETP DNA sequence variants associated with higher HDL-C also increase risk for ICH.
METHODS: We performed 2 candidate-gene analyses of CETP. First, we tested individual CETP variants in a discovery cohort of 1,149 ICH cases and 1,238 controls from 3 studies, followed by replication in 1,625 cases and 1,845 controls from 5 studies. Second, we constructed a genetic risk score comprised of 7 independent variants at the CETP locus and tested this score for association with HDL-C as well as ICH risk.
RESULTS: Twelve variants within CETP demonstrated nominal association with ICH, with the strongest association at the rs173539 locus (odds ratio [OR] = 1.25, standard error [SE] = 0.06, p = 6.0 × 10(-4) ) with no heterogeneity across studies (I(2)  = 0%). This association was replicated in patients of European ancestry (p = 0.03). A genetic score of CETP variants found to increase HDL-C by ∼2.85mg/dl in the Global Lipids Genetics Consortium was strongly associated with ICH risk (OR = 1.86, SE = 0.13, p = 1.39 × 10(-6) ).
INTERPRETATION: Genetic variants in CETP associated with increased HDL-C raise the risk of ICH. Given ongoing therapeutic development in CETP inhibition and other HDL-raising strategies, further exploration of potential adverse cerebrovascular outcomes may be warranted. Ann Neurol 2016;80:730-740.

PMID: 27717122 [PubMed - indexed for MEDLINE]