Saikrishna Lakkakula

Functional PstI/RsaI Polymorphisms in the CYP2E1 Gene among South Indian Populations

Human cytochrome P4502E1 (CYP2E1) is a well-conserved xenobiotic-metabolizing enzyme expressed in liver, kidney, nasal mucosa, brain, lung, and other tissues. CYP2E1 is inducible by ethanol, acetone, and other low-molecular weight substrates and may mediate development of chemically-mediated cancers. CYP2E1 polymorphisms alter the transcriptional activity of the gene. This study was conducted in order to investigate the allele frequency variation in different populations of Andhra Pradesh. Two hundred and twelve subjects belonging to six populations were studied. Genotype and allele frequency were assessed through TaqMan allelic discrimination (rs6413419) and polymerase chain reaction-sequencing (-1295G>C and -1055C>T) after DNA isolation from peripheral leukocytes. The data were compared with other available world populations. The SNP rs6413419 is monomorphic in the present study, -1295G>C and -1055C>T are less polymorphic and followed Hardy-Weinberg equilibrium in all the populations studied. The -1295G>C and -1055C>T frequencies were similar and acted as surrogates in all the populations. Analysis of HapMap populations data revealed no significant LD between these markers in all the populations. Low frequency of CYP2E1 c2 could be useful in the understanding of south Indian population gene composition, alcohol metabolism, and alcoholic liver disease development. However, screening of additional populations and further association studies are necessary. The heterogeneity of Indian population as evidenced by the different distribution of CYP2E1 c2 may help in understanding the population genetic and evolutionary aspects of this gene.

Gene Frequencies of the Human GSTT1 (Null Allele) and GSTP1 (Ile105Val) Polymorphisms among South Indian Populations

Background: Glutathione S-transferases (GSTs) are members of the phase II biotransformation enzymes that play a key role in cellular detoxification of chemical carcinogens and xenobiotics. Variations at GST genes have been reported in different human populations, and some association studies have reported increased risk for cancers and other disease end points. The present study was conducted to investigate the allele frequency variations in south Indian populations. Methods: GSTT1 null allele and GSTP1 Ile105Val polymorphisms were genotyped in two hundred and twelve subjects (aged 34 to 60 years old) belong to six populations using PCR and PCR-RFLP techniques respectively. Results: Both GSTT1 ins-del and GSTP1 Ile105Val are polymorphic in all populations. GSTP1 Ile105Val followed the Hardy-Weinberg equilibrium. The GSTT1 null allele frequencies ranged from 11.6% to 22.2% and GSTP1 Ile105Val “Val” allele frequency ranged from 20.0% to 38.2% in the study populations. HapMap data showed the highest frequency of Val105 allele in African populations followed by European populations. East Asian populations showed the lowest frequency of Val105 allele. Conclusion: The variations observed in allelic distribution of GST genes may presumably be due to the selective pressure exerted on populations of that region. In conclusion, the present study reports the frequency of GSTT1 null allele and GSTP1 Ile105Val polymorphisms in Indian populations which provides foundation for potential epidemiological and clinical studies.

NAT2 genetic variations among South Indian populations

The N-acetyltransferases (NATs) are xenobiotic-metabolizing enzymes involved in the metabolism of drugs, environmental toxins and the aromatic amine carcinogens present in cigarette smoke. Genetic variations in NAT2 have long been recognized as the cause of variable enzymatic activity or stability, leading to slow or rapid acetylation. In the present study, we genotyped three single-nucleotide polymorphisms (SNPs) from the NAT2 gene (rs1799929, rs1799930 and rs1799931), using TaqMan allelic discrimination, among 212 individuals from six major South Indian populations and compared the results with other available Indian and worldwide data. All three of the markers followed Hardy–Weinberg equilibrium and were highly polymorphic in the studied populations. The constructed haplotypes showed a high level of heterozygosity. All of the populations in the present study commonly shared only four haplotypes out of the eight possible three-site haplotypes. The haplotypes exhibited fairly high frequencies across multiple populations, where three haplotypes were shared by all six populations with a cumulative frequency ranging from 88.2% (Madiga) to 97.0% (Balija). We also observed a tribal-specific haplotype. A strong linkage disequilibrium (LD) between rs1799929 and rs1799930 was consistent in all of the studied populations, with the exception of the Madiga. A comparison of the genomic regions 20-kb up- and downstream of rs1799930 in a large number of worldwide samples showed a strong LD of this SNP with another NAT2 SNP, rs1112005, among the majority of the populations. Moreover, our lifestyle test (hunter–gatherer versus agriculturist) in comparison with the NAT2 variant suggested that two of the studied populations (Balija and Madiga) have likely shifted their diet more recently.

EPHX1 gene polymorphisms among south Indian populations

Microsomal epoxide hydrolase is a smooth endoplasmic reticulum enzyme and is expressed relatively ubiquitously in most tissues and in many species. The microsomal epoxide hydrolase (mEH) encoded by EPHX1 is a biotransformation enzyme that metabolizes numerous reactive epoxide intermediates to more water-soluble trans-dihydrodiol derivatives. In the present study, we genotyped two SNPs of the EPHX1 gene [(Exon 3: Tyr113His; rs1051740) and (Exon 4: His139 Arg; rs2234922)], using TaqMan allelic discrimination among 212 individuals of six major south Indian populations, and compared with other available world populations data. Both polymorphisms followed Hardy-Weinberg equilibrium and were highly polymorphic in the studied populations. The haplotype based analysis revealed remarkable variation among the study populations. Linkage disequilibrium (LD) between Tyr113 His and His139Arg loci was not significant in any of the population studied. Calculation of LD in the 20kb up and downstream regions from Tyr113His and His 139Arg loci in HapMap populations revealed no significant LD between these markers in all the populations. Analysis of predicted EPHX1 activity status of all samples revealed that the prevalence of low activity samples is more than the intermediate and high activity samples in all populations studied. Screening of additional populations and computation of genetic distances between populations at SNP sites may help in understanding the population genetic and evolutionary aspects of this gene.

Small molecule tyrosine kinase inhibitors and pancreatic cancer—Trials and troubles

Pancreatic cancer (PC) is an aggressive carcinoma and the fourth cause of cancer deaths in Western countries. Although surgery is the most effective therapeutic option for PC, the management of unresectable, locally advanced disease is highly challenging. Our improved understanding of pancreatic tumor biology and associated pathways has led to the development of various treatment modalities that can control the metastatic spread of PC. This review intends to present trials of small molecule tyrosine kinase inhibitors (TKIs) in PC management and the troubles encountered due to inevitable acquired resistance to TKIs.

Pain Management Issues as Part of the Comprehensive Care of Patients with Sickle Cell Disease

Background: Vaso‐occlusive pain crisis is one of the primary complications of sickle cell disease (SCD) and is responsible for the majority of hospital visits in patients with SCD. Stints of severe pain can last for hours to days and are difficult to treat and manage, often resulting in drastically reduced quality of life. Purpose: Our purpose is to provide an overview of pain management issues in SCD populations. Methods: We explored literature using PubMed and Embase for the etiology and management of pain in SCD. Databases were searched employing the following terms: sickle cell, pain pathways, pain perception, pharmacological therapies, psychological therapies, physical therapies and genetics. Results: Pain in SCD can vary from acute to chronic (persistent) or mixed and understanding of the underlying mechanisms is important for proper pain management. Currently, there are many means of managing pain in children with SCD, which involve pharmacological and non‐pharmacological approaches. A combination of psychotherapy and pain medications can be used for treatment of pain and other psychosocial co‐morbidities in complex persistent pain. Conclusions: Providing more appropriate medication and optimal dosage based on individuals genomic variations is the future of medicine, and this will allow the physicians to hone in on optimal pain management in patients with SCD.

Retrospection of the effect of hydroxyurea treatment in patients with sickle cell disease

Abstract Sickle cell anemia (SCA) is one of the inherited hemoglobin disorders with substantial morbidity and early mortality. Hydroxyurea is the US Food and Drug Administration (FDA)-approved medication that has emerged as the primary disease-modifying therapy for SCA. Our purpose is to summarize the available evidence regarding the pharmacology, clinical efficacy, and safety of hydroxyurea therapy for the treatment of SCA. The electronic databases PubMed and Embase were searched from their starting dates to May 31, 2016. Databases were searched using the following terms: sickle cell, hydroxyurea, nitric oxide, dosing, therapeutic, and safety monitoring. Hydroxyurea therapy may cause severe myelosuppression when used in patients with SCA. SCA patients are initially treated with hydroxyurea at 10 or 20 mg/kg, and then the dose- is escalated to mild myelosuppression using a standardized regimen. Routine blood monitoring should be performed while the patient receives hydroxyurea treatment. Hydroxyurea can increase fetal hemoglobin (HbF) level and ameliorate some of the vascular symptoms in patients with SCA. Hydroxyurea therapy may help to avoid frequent hospitalizations, especially in patients with vaso-occlusive crisis. Taken together, available evidence suggests that hydroxyurea represents an inexpensive and effective treatment option that should be offered to patients with SCA.

CBS c.844ins68 Polymorphism Frequencies in Control Populations: Implications on Nonsyndromic Cleft Lip With or Without Cleft Palate

Introduction Nonsyndromic cleft lip with or without cleft palate (NSCLP) is a common birth defect with substantial clinical and social impact. Folate deficiency is one of the factors that have been associated with increased risk for NSCLP. Polymorphisms in folate and homocysteine pathway genes may act as susceptibility factors. Objective The objective of this study was to evaluate prevalence estimates of cystathionine beta-synthase (CBS) insertion of 68-bp (c.844ins68) polymorphisms and their correlation with NSCLP. Material and Methods A total of 236 unrelated individuals from seven Indian populations and an additional 355 cases with NSCLP and 357 controls without NSCLP were included in this study. We investigated the CBS c.844ins68 polymorphism in all samples. Genotyping was performed with polymerase chain reaction and electrophoresis. The data were statistically analyzed using the chi-square test. Results The CBS c.844ins68 allele is present in six of the seven populations analyzed, and allele frequencies range from 1.5% in Balija to 9.1% in Sugali populations. The CBS c.844ins68 polymorphism showed a significant protective effect on NSCLP at both genotype (WW versus WI: odds ratio [OR] = 0.54, 95% confidence interval [CI] = 0.31 to 0.95, P = .149) and allele levels (W versus I: OR = 0.56, 95% CI = 0.32 to 0.96, P = .033). Conclusions The current study observed significant differences in the frequency of the CBS 844ins68 allele across populations. There is a significant association between CBS c.844ins68 polymorphism and cleft lip and palate in the Indian population. Additional studies are warranted to identify the functional variants in the genes controlling homocysteine as etiological contributors to the formation of oral clefts.