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

  • Harendra Modak
  • Sujayendra Kulkarni
  • Suyamindra S Kulkarni
  • Prabhanjan Gai
  • Umesh Hallikeri
  • Pramod B Gai

Abstract

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 fold

African Journal of Biotechnology, Vol. 13(10), pp. 1174-1181, 5 March, 2014

Author Biographies

Harendra Modak
Centre for Excellence in Molecular Haemato-oncology, Department of Applied Genetics, Karnatak University, India
Sujayendra Kulkarni
Centre for Excellence in Molecular Haemato-oncology, Department of Applied Genetics, Karnatak University, India
Suyamindra S Kulkarni
Karnataka Institute for DNA Research,Dharwad, India
Prabhanjan Gai
Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
Umesh Hallikeri
Karnataka Cancer therapy and Research Institute, Karnataka, India
Pramod B Gai
Centre for Excellence in Molecular Haemato-oncology, Department of Applied Genetics, Karnatak University, India; Karnataka Institute for DNA Research,Dharwad, India
Published
2015-05-27
Section
Articles

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eISSN: 1684-5315