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Online Journal of Bioinformatics ©
Volume 16(3): 327-343, 2015.
Gene expression in sickle cell patients: Putative genes associated with variability in pleiotropic phenotype
1,2Das I MSc, 3Mishra H MBBS MTech PhD, 3Khodiar PK MBBS MD, 1,3*Patra PK MBBS MD.
1Pt. J.N.M. Medical College, Raipur, 2 Surguja University, Ambikapur, 3Sickle Cell Institute Chhattisgarh, Raipur, India.
Das I, Mishra H, Khodiar PK, Patra PK., Gene expression in sickle cell patients: Putative genes associated with variability in pleiotropic phenotype, Onl J Bioinform., 16(3): 327-343, 2015. Sickle cell disease (SCD) is a hemoglobinpathy prevalent in areas of India. Clinical features are pleiotropic due to anemia, vaso-occlusion and inflammation, leading to gradual multiple organ failure. Vaso-occlusive crisis (VOC) is a common cause of severe pain and morbidity. We evaluate gene expression in patients of SCD for up-regulated genes in VOC to find putative genes associated with variability in phenotype. Seven subjects from sickle cell steady (HbSS SS) and 7 from VOC groups (HbSS VOC), and 6 healthy controls (HbAA) were studied. Whole blood transcriptome was compared between groups. 154 and 84 genes were found to be up-regulated in HbSS VOC and HbSS SS respectively, compared with HbAA subjects. Similarly, 6 genes were found to be up-regulated in HbSS VOC compared to HbSS SS (gene expression fold change cut-off ≥2, corrected p-value of <0.05) subjects. Annotation and pathway analysis was performed for up-regulated genes. Pathway analyses showed that majority of genes belonged to inflammatory and stress response, cell signaling and cell cycle regulation. Validation of gene expression was done through quantitative real time PCR (qRT PCR). Polymorphisms in these genes may be studied for their possible implication in pleiotropic phenotype of SCD.
Key words: Sickle cell disease, Vaso-occlusive crisis, Gene expression, Pleiotropic phenotype, Candidate genes.