Microarray based comparative genome-wide expression profiling of major subtypes of leukemia

The uncontrolled proliferation of hematopoietic cells with no capacity to differentiate into mature blood cells leads to leukemia. Though considerable amount of work has been done in understanding the molecular basis and gene expression profiles of hematologic malignancies viz., chronic lymphocytic leukemia (CLL), chronic myelogenous leukemia (CML), acute lymphocytic leukemia (ALL) and acute myelogenous leukemia (AML), the role of various underlying genes and mechanisms predisposing the disease are poorly understood. To develop the early diagnosis, preventive and therapeutic strategies, identification of population specific novel mutations and candidate genes are required. Micro array based gene expression profiling was performed for total of 18 samples (4 from each subtype of leukemia that is, CLL, CML, ALL, AML and 2 controls) from Indian population using single color hybridization. The expression of all genes presented in terms of fold variation was subjected to F-test. The microarray data of genes showing differential regulation with respect to the control samples have been obtained from total 50, 238 probes covering 14,992 genes on Agilent’s Human 8X60K Array. The experiment was conducted with expectation to have similar patterns of result in terms of gene expression but it demonstrates statistically significant relationship only among CML and ALL which are of myeloid and lymphoid origin, respectively, in contrast to other combinations. Gene expression profiles of four subtypes of leukemia were compared to each other to ascertain the overall association and significance of genes for occurrence of different types of leukemiawhich would guide in the development of common probable biomarkers for leukemias followed by effective diagnosis, prognosis and treatment. Based on their geomean fold values, the highly upregulated genes found in this study are listed.Keywords: Leukemia, microarray, gene expression profiling, fold variation, lymphoid, myeloid, geomean foldAfrican Journal of Biotechnology, Vol. 13(10), pp. 1174-1181, 5 March, 201

The Effect of Socioeconomic Factors and Indoor Residual Spraying on Malaria in Mangaluru, India: A Case-Control Study

India faces 0.5 million malaria cases annually, including half of all Plasmodium vivax malaria cases worldwide. This case–control study assessed socioeconomic determinants of urban malaria in coastal Mangaluru, Karnataka, southwestern India. Between June and December 2015, we recruited 859 malaria patients presenting at the governmental Wenlock Hospital and 2190 asymptomatic community controls. We assessed clinical, parasitological, and socioeconomic data. Among patients, p. vivax mono-infection (70.1%) predominated. Most patients were male (93%), adult (median, 27 years), had no or low-level education (70.3%), and 57.1% were daily labourers or construction workers. In controls (59.3% male; median age, 32 years; no/low-level education, 54.5%; daily labourers/construction workers, 41.3%), 4.1% showed asymptomatic Plasmodium infection. The odds of malaria was reduced among those who had completed 10th school grade (aOR, 0.3; 95% CI, 0.26–0.42), lived in a building with a tiled roof (aOR, 0.71; 95% CI, 0.53–0.95), and reported recent indoor residual spraying (aOR, 0.02; 95% CI, 0.01–0.04). In contrast, migrant status was a risk factor for malaria (aOR, 2.43; 95% CI, 1.60–3.67). Malaria in Mangaluru is influenced by education, housing condition, and migration. Indoor residual spraying greatly contributes to reducing malaria in this community and should be promoted, especially among its marginalised members.Peer Reviewe

A study on the ayurveda intervention (Virechana - therapeutic purgation and Rasayana - rejuvenation) on molecular gene expression profiling in familial breast cancer patients

Background: The study was conducted to assess the ayurvedic intervention Virechana - therapeutic purgation and Rasayana - rejuvenation on predisposed familial breast cancer expression profiling of BRCA1 and BRCA2 genes. Materials and Methods: The total RNA was extracted from blood of five subjects of familial breast cancer predisposition patients using PAX Gene Blood RNA Kit who had undergone the ayurvedic intervention Virechana - therapeutic purgation and Rasayana - rejuvenation therapy. BRCA1 and BRCA2 gene expression was assessed by reverse transcription polymerase chain reaction and quantitative polymerase chain reaction (qPCR). The qPCR-based BRCA1 gene expression results were analyzed for fold variation based on Ct values using the following formula: 2 (−ΔΔCt), where ΔCt is the Ct (GOI) − avg.(Ct (HKG)), GOI is the gene of interest, and HKG is the housekeeping gene. Results: In one subject (S1), the upregulation (61.82) showed further increase (843.36) by therapeutic purgation and then decreased below the baseline level (11.3) in the rejuvenation phase. In three subjects (S2, S3, and S5), the upregulated genes (1488.87, 15825.9, and 19.16) showed down trend continuously till rejuvenation phase (1.92, 4.17, and 3.97) but not to downregulation. Another subject (S4) showed reversal of genetic expression, i.e., downregulated gene (−1) showed upregulation (237,900.70) continuously throughout the therapy, which is in conformity of the proposed hypothesis, i.e., biopurification (therapeutic purgation) followed by rejuvenation leads to upregulation of gene. Conclusion: With the available limited and diversified data, it may be concluded that therapeutic purgation followed by rejuvenation (Narasimha Rasayana) therapy exerted effect on gene expression, but further study needs to be conducted with more number of samples

Clinical profile of hemophilia B patients from Karnataka

Background: The most prevalent severe inherited hemorrhagic condition is hemophilia, which means “love of blood.” Hemophilia A and B are caused by a lack or malfunction of the factor VIII and factor IX proteins. Objective: The present study is to determine the prevalence and clinical profile of hereditary coagulation disorder, particularly hemophilia B, in Karnataka. Methods: The study comprised 150 HB patients with a mean age of 25, nmale = 148 and nfemale = 2. The samples were collected from hemophilia societies across Karnataka. The detailed history of HB patients was recorded in a predesigned Performa regarding family history, age, time of first bleed, site of the bleed, and bleeding history. Result: In our study cohort, the majority of the 58 (38.7%) cases belong to 21–30 years of age. The mean age of onset was 2.0 ± 1.0 years in severe, 7.5 ± 2.8 0 years in moderate, and 10.0 ± 3.5 years in mild HB patients. Out of 150 HB cases, 102 (68%) cases were diagnosed as severe, 30 (20%) as moderate, and 18 (12%) as mild. Mean factor IX levels were 0.6 ± 0.2, 2.5 ± 1.3, and 8.0 ± 2.6 in the severe, moderate, and mild group, respectively. A family history of bleeding was observed in 97 [64.7%] HB patients. Forty-seven (32.3%) HB patients had a history of consanguinity. The most common initial site of bleed was in joints in 86 [57.3%]. Conclusion: The present study is one of the fewer studies from Karnataka studying the demographic and clinicopathological features of hemophilia B. Early diagnosis can be only helpful with knowledge of spectral presentation of hemophilia B in a local population

Parkinson's disease in North Karnataka An epidemiological perspective

Abstract: Parkinson's disease (PD) is a progressive disorder of the brain. It occurs when certain neurons in substantia nigr

Mutation analysis of the LDL receptor gene in Indian families with familial hypercholesterolemia

Objective: Familial Hypercholesterolemia (FH) is a metabolic disorder inherited as an autosomal dominant trait characterized by an increased plasma Low-density Lipoprotein (LDL) level. The disease is caused by several different mutations in the LDL Receptor (LDLR) gene. Several mutations have been reported in this gene in patients from several ethnic groups. Early identification of individuals carrying the defective gene could be useful in reducing the risk of atherosclerosis and myocardial infraction by the available therapeutic methods. The techniques available for determining the number of the functional LDLR molecules are difficult to carry out and expensive. Our study presents mutation analysis of the LDLR gene in 24 Indian families with FH. Material & Methods: Peripheral blood samples were obtained form individuals after taking informed consent on the condition that each of these individuals had at least one first-degree relative affected with FH. Genomic DNA was isolated, exon-specific intronic primers were designed and used to amplify DNA samples from individuals. PCR products were directly subjected to automated DNA sequencing to detect the mutations. Along with the affected individuals, ten ethnically matched controls were also analyzed to determine the presence of the same mutations. Patients with Nephrotic Syndrome admitted to hospital were excluded from the study. Results: All the 24 patients had total cholesterol level above 300 mg/dl and LDL cholesterol level above 200mg/dl. Sequence analysis of the LDL Receptor (LDLR) gene showed 3 novel mutations which have never been reported elsewhere. In exon 10 we reported g.29372_29373insC, which was found in all the 24 patients and was missence mutation coding for C (cysteine) instead of V (valine). Conclusion: Our study reported 3 novel mutations in 24 Indian families. These novel mutations are predicted to produce change in the amino acid and thus leading to the conformational changes in the structure of LDLR protein. Change in the LDLR protein makes the LDL receptor unable to transport the cholesterol in to the cell and hence cholesterol starts accumulating in the blood stream and leads to FH

A comparative study of cDNA microarray analysis of familial and sporadic breast cancer in India

Many genes and signalling pathways controlling cell proliferation, death and differentiation, as well as genomic integrity, are involved in cancer development. Techniques, such as cDNA microarrays, have enabled measurement of the expression of thousands of genes in a single experiment, revealing many new, potentially important cancer genes. Human breast cancer is usually caused by genetic alterations of somatic cells of the breast, but occasionally, susceptibility to the disease is inherited. As a step towards understanding the differences between familial and sporadic breast cancer in humans, gene expression patterns were examined in breast tumours. Sporadic (n = 7) and familial (n = 6) tissue samples, and normal breast tissue (n = 3) samples, were collected from women who underwent breast surgery at Karnataka Cancer Therapy and Research Institute (KCTRI), Hubli. Total RNA was isolated and subjected to cDNA microarray for 14,992 genes on Agilent’s Human 8x15K Array. Gene expression profiles were analysed using Genespring software. F-Test was carried out to find the variance in terms of gene expression patterns between familial and sporadic breast cancer tissue samples. Our study revealed, that, there is no significant variation between sporadic and familial breast cancer in terms of gene expression profiles. With this, it can be concluded that both familial and sporadic breast cancers are similar in terms of the gene expression profiles. This will guide in development of common biomarkers for both familial and sporadic breast cancer and will also help in diagnosis, prognosis and treatment