Pharmacogenomics- The Promise of Personalized Medicine

Introduction: Pharmacogenomics (PGx) is the study of the genetic basis of variability among individuals in response to drugs. It is the newest discipline of medicine and is becoming a very active area of research, with the pharmaceutical industry gaining experience applying it, integrating it into the drug development process, and also learning to better manage the expectations of the medical community. Methodology: A comprehensive review of the literature on the principles, applications, challenges and prospects of pharmacogenomics was performed. Results: Pharmacogenomics tailors therapies to the genetic makeup of an individual and can therefore offer treatments that are more efficacious and have fewer side effects. Despite these benefits, personalized medicine has not been embraced by large pharmaceutical companies. It is expected that the first wave of successful pharmacogenomics products will be used in acute treatments for which current therapies have and severe side effects. These products should also be good candidates for premium pricing. Personalized medicine (PM), based on the genetic makeup of a patient, may result in not only an improved therapeutic response but also a clinically important reduction in adverse drug reactions. The experience to date is mixed, with a few successes but many frustrations. Conclusion: However, for pharmacogenomics to be truly embraced, the benefits of this technology must become more widely accepted in terms of economic, public, regulatory and ethical issues. DOI: http://dx.doi.org/10.3329/bjms.v12i4.11041 Bangladesh Journal of Medical Science Vol. 12 No. 04 October ’13 Page 346-356

Functional differences between aggregated and dispersed insulin-producing cells

AIMS/HYPOTHESIS

Beta cells situated in the islet of Langerhans respond more vigorously to glucose than do dissociated beta cells. Mechanisms for this discrepancy were studied by comparing insulin-producing MIN6 cells aggregated into pseudoislets with MIN6 monolayer cells and mouse and human islets.

METHODS

MIN6 monolayers, pseudoislets and mouse and human islets were exposed to glucose, α-ketoisocaproic acid (KIC), pyruvate, KIC plus glutamine and the phosphatidylinositol 3-kinase (PI3K) inhibitors LY294002 or wortmannin. Insulin secretion (ELISA), cytoplasmic Ca(2+) concentration ([Ca(2+)]c; microfluorometry), glucose oxidation (radiolabelling), the expression of genes involved in mitochondrial metabolism (PCR) and the phosphorylation of insulin receptor signalling proteins (western blotting) were measured.

RESULTS

Insulin secretory responses to glucose, pyruvate, KIC and glutamine were higher in pseudoislets than monolayers and comparable to those of human islets. Glucose oxidation and genes for mitochondrial metabolism were upregulated in pseudoislets compared with single cells and monolayers, respectively. Phosphorylation at the inhibitory S636/639 site of IRS-1 was significantly higher in monolayers and dispersed human and mouse cells than pseudoislets and intact human and mouse islets. PI3K inhibition only slightly attenuated glucose-stimulated insulin secretion from monolayers, but substantially reduced that from pseudoislets and human and mouse islets without suppressing the glucose-induced [Ca(2+)]c response.

CONCLUSIONS/INTERPRETATION

We propose that islet architecture is critical for proper beta cell mitochondrial metabolism and IRS-1 signalling, and that PI3K regulates insulin secretion at a step distal to the elevation of [Ca(2+)]c.

New HBV subgenotype D9, a novel D/C recombinant, identified in patients with chronic HBeAg-negative infection in Eastern India

Genome diversity is a hallmark of hepatitis B virus (HBV), which allowed its classification into 10 genotypes (A-J) and numerous subgenotypes. Among them, Genotype D is currently segregated into eight subgenotypes (D1-D8). Here, we report the identification and characterization of a novel subgenotype within genotype D of HBV from chronic hepatitis B e antigen (HBeAg)-negative patients of Eastern India. Phylogenetic tree analysis based on complete genome sequences revealed that six of 39 HBV/D isolates formed a distinct cluster supported by high bootstrap value and had nucleotide divergence >4% relative to the known D subgenotypes (D1-D8), justifying their assignment into a new subgenotype (D9). By comparing the amino acid sequences of the four ORFs of HBV/D9 with D1-D8, 36 specific residues, including a unique one (E(112) in the core region), were identified that could be considered as a signature of D9. Further analysis by Simplot, BootScan and jpHMM demonstrated that D9 resulted from a discrete recombination with genotype C over the precore-core region. This type of recombination has not been described previously as all C/D recombinants reported so far possessed genotype C backbones with mosaic fragments derived from HBV/D. Interestingly, compared to other subgenotypes of HBV/D, D9 isolates had a higher frequency of mutations (A1762T and G1764A) in the basal core promoter region that had been implicated in the development of hepatocellular carcinoma. Further investigations are needed to determine the overall prevalence and clinical significance of these newly characterized D9 strains and to assess the impact of inter-genotypic recombination on viral properties.

Tracking the naturally occurring mutations across the full-length genome of hepatitis B virus of genotype D in different phases of chronic e-antigen-negative infection

Hepatitis B e-antigen (HBeAg)-negative chronic HBV infection is highly prevalent in several parts of the world, including India, with the clinical spectrum ranging from inactive carrier (IC) state to chronic 'e-negative' hepatitis B (CHB) and culminating in advanced liver disease such as cirrhosis (LC). The present study has for the first time investigated the natural diversity of HBV belonging to genotype D in treatment-naïve Indian patients representing the above phases of HBeAg-negative infection to identify candidate mutations associated with each disease state. Studies of full-length HBV/D sequences revealed that the progressive accumulation and persistence of mutations in basal core promoter, negative regulatory element, Pre-core region, the B- and T-cell epitopes of X protein as well as deletions in the PreS region contribute significantly to disease progression from IC through CHB to LC. In addition, the development of CHB was associated with a significant increase in viral variants characterized by mutations in enhancer II, preS1 promoter, T-cell epitope of core and B-cell epitope region of PreS1. While few of the mutations were previously reported in the context of HBV genotypes B and C, others had not been documented before. Our results thus highlight a distinct pattern of mutation in HBV/D that may help in predicting clinical outcomes of HBeAg-negative infection and have implications for better clinical management of the patients.

Identification of Hookworm Species in Stool By Harada Mori Culture

This cross sectional study was done from January 2009 to June 2010 in Microbiology department of Dhaka Medical College, Dhaka to identify hookworm species and to compare different laboratory methods for diagnosis of hookworm infections. Among the 375 stool samples evaluated, 26 (6.93%) samples were positive for hookworms. Ankylostoma duodenale were 3 (11.50%) and Necator americanus were 23 (88.50%). Harada Mori culture was found as the most effective method for detection of hookworms.DOI: http://dx.doi.org/10.3329/bjmm.v4i2.10821 

Preparation and evaluation of gastroretentive floating pellets of metronidazole using Na-alginate and hydroxyl propyl methyl cellulose polymers

Gastroretentive floating pellets of metronidazole were formulated to prolong the gastric residence time in order to obtain controlled release characteristics of the drug. Nine formulations of metronidazole floating pellets such as AX, BX, CX, AY, BY, CY, AZ, BZ and CZ were prepared by extrusion method using different quantities of hydroxyl propyl methyl cellulose (HPMC) polymers such as methocel K4M premium and methocel K100LV premium in the ratio of 2:1, 1:2 and 1.5:1.5 while the amount of Na-alginate used in the formulations was 3.50, 5.25 and 7.0 g, respectively. The in vitro dissolution studies were carried out in 900 mL of phosphate buffer (pH 1.2) at 37 +/- 0.5 degrees C and 50 rpm for 6 h using USP XXIV paddle method and the content of drug release was done by UV spectrophotometer at 277 nm. It was found that the percent release of metronidazole from different formulations was different with passing of time. The drug release profile of the formulation (AX) having Na-alginate 3.50 g methocel K4M premium and methocel K100LV premium in the ratio of 2:1 showed best fit to Higuchi release kinetics with R2 value of 0.994. Finally, it might be concluded that the polymers had significant effect on drug release kinetics of metronidazole from floating pellets. The selection and use of suitable polymers in appropriate ratio might be very important in designing floating pellets and using the capabilities of these polymers, suitable floating pellets of metronidazole with desirable release rate could be formulated. Thus, in vivo research studies by the future researchers will confirm the appropriateness of these formulated metronidazole floating pellets.

Acute poisoning in southern part of Bangladesh--the case load is decreasing

This retrospective study was carried out in the Medicine Department of Khulna Medical College, the biggest tertiary hospital in the southern part of Bangladesh to observe the trends of poisoning in southern part of Bangladesh over four years including age and sex variation, mode of poisoning, type of poison used and outcome of poisoning. The hospital medical records of all patients, aged 10 years and above with history of acute poisoning from January, 2003 to December, 2006 were enrolled. Patients were categorized into four age group including Group (Gr.) I, Gr. II, Gr. III & Gr. IV having age range of 10-20, 21-30, 31-40 & >40 respectively. Underlying causes of poisoning were also observed totally and individually in different mode with male, female ratio and the percentage. Death cases according to mode of poisoning with demographic alignment were also observed. Statistical analysis were done using epi-info version 3.5.1 and measures were presented as proportion and percentage. Among 1903 cases, 1012 (53.1%) were male and 891 (46.8%) female with a ratio of 1.4: 1. The year wise total number of cases were progressively decreased from 627 (2003) to 353 (2006). Most commonly found toxic agent was Organo-Phosphate compound (526; 27.64%) with a very little sexual variation & this trend remained same in all study years. Poisoning with unknown substance was the second leading cause (16.03%) followed by Copper-sulphate (14.03%), Sedative (13.35%), Snakebite (12.93%) etc. Incidence of unknown poisoning, sedatives, snake-bite and corrosives were found to be gradually decreased over the study years. Male were found mostly affected in majority type of poisoning except Copper-sulphate, kerosene, puffer fish, paracetamol and other drugs category. Age group II (710; 37.3%) was the most vulnerable group with male (57.89%) preponderance followed by group I (643; 33.7%), III (329; 17.2%) and IV (221; 11.6%) respectively. Highest 1308 (68.7%) cases were suicidal in mode followed by 304 (15.9%) accidental and 291 (15.2%) homicidal. Out of 1903, 140 (7.3%) patients died. Death rate was highest in OPC poisoning (52.1%) followed by unknown substance (13.5%), snakebite and copper-sulphate (11.4%) etc. In an agro-based country like Bangladesh, it's very difficult to reduce the poisoning cases and mortality. Prospectively designed multi-centered studies are needed to reflect the epidemiological properties of poisonings throughout Bangladesh, and would be very valuable for the determination of preventive measures.

Novel Pure Organic Particles for Copper CMP at Low Down Force

It is generally accepted that there is a minimum hardness requirement for abrasive particles to be used in CMP (Chemical Mechanical Polishing) slurries. For copper CMP, the common abrasives are various types of alumina and silica. It has also long been suspected that a softer organic based abrasive could significant reduce the defects during polishing. In this study, for the first time, we demonstrated the usefulness of an organic particle as abrasive in formulating copper CMP slurry. The unexpected consequence of using such soft hydrophilic particles is its low sensitivity of material removal rate for copper towards polishing down force and platen speed. In addition, due to its unique particle surface properties, the slurry gives high selectivity in removal rate for copper over barrier, cap, and dielectric materials. In this paper, some basic physical and chemical characteristics of the particles and slurry will be first presented. The performance of this new slurry in relation to conventional slurries on blanket and patterned wafers will be discussed.

Obscure GI bleeding in the tropics: impact of introduction of double-balloon and capsule endoscopies on outcome

BACKGROUND

Innovative but costly small-bowel enteroscopies, capsule endoscopy (CE), and double-balloon endoscopy (DBE) have revolutionized the management of obscure GI bleeding (OGIB).

OBJECTIVE

To measure the impact of these procedures on outcomes of OGIB in a resource-poor setting.

DESIGN

Prospective cohort study and comparison with a historical cohort.

SETTING

Tertiary-care center in India.

PATIENTS

Fifty-three patients with OGIB, diagnosed by American Gastroenterological Association criteria.

INTERVENTIONS

DBE and/or CE were performed. Patients were then offered specific treatment and/or hematinics.

MAIN OUTCOME MEASUREMENTS

The etiology of OGIB in a tropical country and yield of DBE and/or CE. The number of investigations required, follow-up hemoglobin, rebleeds, and interventions/transfusions needed were compared between the present and historical cohort.

RESULTS

Mean age was 46.4 years with hemoglobin (mean +/- standard deviation) of 8.3 +/- 2.3 g/dL at evaluation. OGIB was overt in 33 and occult in 20. They underwent 173 investigations before referral. DBE and/or CE localized the source of bleeding in 43 (yield 81%). Angiodysplasias, tumors, Crohn's disease, intestinal tuberculosis, and hookworm infestation were predominant etiologies. Compared with the historical cohort, DBE and/or CE have reduced the number of investigations per patient, increased the yield of mid intestinal source of OGIB, and reduced the number of surgeries, especially emergency laparotomies. There was no significant alteration in the overall yield, mortality, and rebleeding rates.

LIMITATION

Small cohort without economic analysis.

CONCLUSIONS

The demographic profile and etiological spectrum of OGIB in the tropics is different. DBE and/or CE have made a favorable impact on management.

Memory effects for the heat conductivity of random suspensions of spheres

The presence of a particulate phase defines the effective response of a suspension to changes of the average heat flux. Using the random-point approximation we show that within the first order in the concentration, one needs to solve the problem for the temperature field created by a single inclusion in a matrix subject to an unsteady temperature gradient at infinity. We solve this problem by means of Laplace transform and use the solution as the first-order kernel in the functional expansion. From this kernel, we find the statistical average for the heat flux, which turns out to be a memory integral of the spatially averaged time-dependent temperature gradient. Thus, we discover that the constructive relationship between the average flux and averaged temperature gradient is not local in time, but rather involves a convolution integral that represents the memory due to the heterogeneity of the system. This is a novel result, which inter alia gives a rigorous justification to the usage of generalizations of the heat conduction law involving fractional time derivatives. The decay of the kernel is very close to t −1/2 for dimensionless times lesser than one and abruptly changes to t −3/2 for larger times.

Isolation of a bacteriophage specific for CS7-expressing strains of enterotoxigenic Escherichia coli

Enterotoxigenic Escherichia coli (ETEC) is the most common bacterial cause of childhood diarrhoea in Bangladesh. Among the virulence factors of ETEC, toxins and colonization factors (CFs) play a major role in pathogenesis. Unlike Vibrio cholerae, the relationship between ETEC and ETEC-specific phages is poorly understood and the possible role of ETEC phages in the evolution of ETEC strains in the environment is yet to be established. This study was designed specifically to isolate phages that are specific for ETEC virulence factors. Among the 49 phages isolated from 12 different surface water samples, 13 were tested against 211 ETEC strains collected from clinical and environmental sources. One phage, designated IMM-001, showed a significant specificity towards CS7 CF as it attacked all the CS7-expressing ETEC. Electron microscopic analyses showed that the isolated phage possessed an isomeric hexagonal head and a long filamentous tail. An antibody blocking method and phage neutralization assay confirmed that CS7 pilus is required for the phage infection process, indicating the role of CS7 fimbrial protein as a potential receptor for IMM-001. In summary, this study showed the presence of a lytic phage in environmental water that is specific for the CS7 CF of ETEC.

Alterations in natural killer cells and natural killer T cells during acute viral hepatitis E

The mechanism of liver damage in acute hepatitis E is poorly understood. In this study, we assessed the frequency and activation status of natural killer (NK) and natural killer T (NKT) cells and cytotoxic activity of NK cells in the peripheral blood mononuclear cells (PBMCs) obtained from patients with hepatitis E (n = 41) and healthy controls (n = 61). Flow cytometry was used to assess NK (CD3(-)/CD56(+)) and NKT cell (CD3(+)/CD56(+)) fractions (% of PBMCs) and activation status (CD69(+); % of NK, NKT cells). NK cell cytotoxicity was assessed using major histocompatibilities complex-deficient K562 cells as target cells. In 14 patients, the studies were repeated during the convalescence period. Patients had fewer median (range) NK cells [8.9% (2.4-47.0) vs 11.2% (2.6-35.4)] and NKT cells [8.7% (2.8-34.1) vs 13.6% (2.3-36.9)] than controls (P < 0.05 each). Activation markers were present on large proportion of NK cells [43.5% (11.2-58.6) vs 15.5% (3.0-55.8)] and NKT cells [41.5% (17.4-71.1) vs 12.8% (3.3-63.2); P < 0.05 each] from patients. NK cell cytotoxicity was similar in patients and controls. During convalescence, all the parameters normalized. In conclusion, reversible alterations in NK and NKT cell number and activation status during acute hepatitis E suggest a role of these cells in the pathogenesis of this disease.

Prevalence of major neurological disorders among geriatric population in the metropolitan city of Kolkata

Well-conducted neuroepidemiological studies for the geriatric population are rare in India. In view of the growing aging population, we planned to determine the prevalence of common neurological disorders among the elderly population in the city of Kolkata. This was a cross-sectional study of a stratified random sample of the city population and carried in two stages through house to house survey. Initially, trained non-medical workers screened the cases with a validated family questionnaire and then a neurologist examined all the screened positive cases. A validated neuropsychological screening test was also applied among the elderly population with cognitive complaints. Results showed prevalence rates (per 1000 elderly population--> or = 60 years) of following disorders in decreasing order: stroke--33.93, essential tremor--13.76, dementia--7.89, Parkinsonism--3.30 and epilepsy--2.57. Sex-specific prevalence showed that stroke was commoner among men and that of other disorders among women. Age-specific prevalence recorded progressive increase in the rates of all disorders among both genders, though not uniformly among women. Overall the crude prevalence of neurological disorders was 60.9 per 1000. The present study shows higher rate of stroke as compared to other neurological disorders among elderly population in India, which needs urgent attention.