Post Doctoral work:

Upon completion of my doctoral work, I pursued postdoctoral research with Dr. Guido Guidotti at Harvard University, Cambridge, MA. In the Guidotti’s lab, I effectively developed a novel Bioassay for the detection and quantification of ATP hydrolysis enzymes, and working in a project for recombinant production of Apyrase. I gained experience in cell culturing (Insect cells, COS-7) and exposed to high-throughput and microarray technology.  Furthermore, I was involved in developing a single molecule DNA sequencing technology.

As a junior faculty at Boston University School of Medicine, Boston, MA, I developed an interest to expertise in mapping the genetic basis of common complex disease in human population based and proband sampling based studies using various DNA technologies.

Framingham Heart Study Genetics

In June 2000, Dr. Karamohamed was interviewed for the position of Director of Assay Development for the Framingham Heart Study (FHS) genetic research in an effort to identify biological markers for several traits. The FHS population was initially selected using random sampling. With the enrollment of the “Offspring Study” in 1971 and the “Third Generation” in 2002, the study has accumulated several hundred large extended kindreds. The longitudinal follow up of the FHS cohorts and families makes it an ideal population for the investigation of gene-gene and gene-environment interaction in the understanding of human diseases. DNA from participants has been collected since 1987 and used in first generation genome scans and linkage analysis to implicate loci conferring increased susceptibility to a multitude of diseases, risk factors and traits. We are currently mapping and seeking to clone several novel disease genes and biomarkers for risk factors. Finally, we are beginning to explore the cellular and molecular basis for the major clinical disease endpoints studied in the FHS.

The focus of his position was the same area of his interest is identifying genetic risk factors for various diseases.  The approach used for gene discovery by Dr. Karamohamed in the FHS focuses on a normal population. Common genetic polymorphisms predisposing to a particular disease and the risk associated with them are identified directly. In contrast, traditional disease-based studies collect individuals with extreme clinical phenotypes from families showing strong Mendelian transmission of a trait. These studies aim to identify gene variants segregating in these families and then show that this allele or other common variant is associated with increased risk of disease in the general population.

Another difference in the approach used by Dr. Karamohamed in FHS is the use of sub-phenotypes rather than a single clinical disease as measurement outcomes.

Some of my major projects are as follow:

Parkinson’s disease

Parkinson’s disease (PD) is a common neurodegenerative disorder with an average age at onset of about 60 years. More than one percent of persons 55 years of age or older and more than three percent of those over 75 years of age are PD-affected. The disease has long been viewed as “multifactorial” with both genetic and environmental influences, but we have suggested that much of the complexity is at the level of phenotype. Using the GenePD study cohort and the candidate gene approach as described above, I am trying to understand the contribution of genetics with the hope of identifying a gene or genes that contribute to Parkinson’s disease risk. Recently, we completed a genome wide scan and I followed up with more STRs targeting specific linkage peaks to narrow and resolve linkage under the peaks. For example, linkage on chromosome 2 was further refined and an association study focused on candidate genes under the peak. As a result, we identified a haplotype that influences age at onset of PD which published recently in Neurology (2003). We are trying to find the effect of the identified haplotype on the expression of the implicated gene in brain samples of PD patients. I also investigated the presence of six reported genetic variations in the SCNA, NR4A2, and DJ-1 genes in 292 cases of familial Parkinson's disease from the GenePD study. The results were recently published (Mov Disord. 2005). I investigated the role of BDNF in PD. We identified various alleles to be associated with PD. For example, homozygosity for the rare allele of the functional BDNF G196A (Val66Met) variant was associated with a 5.3-year older onset age (p = 0.0001). The results were published in Neurology (2005). Furthermore, in an effort to simplify this complex disease, we sought to define a more homogeneous definition of the phenotype by exploring the heritability Dementia and Tremor in the GenePD study cohort. We identified the familial aggregation of “tremor predominant” and “akinetic-rigid predominant” families. This new phenotypic distinction may assist in defining specific regions associated with each form. We also identified a genetic marker that is highly associated with the ‘tremor-rigid’ dichotomy. Further work to understand and define the role of genes in the clinical expression of PD is currently under investigation.

Diabetes Mellitus 2 (DM2) and Alzheimer’s Diseases

In the last few years, researchers focused on understanding the genetics of several metabolic syndromes using various human cohorts. I used the Framingham Heart Study cohort in an effort to further understand the role of genetics in DM2 as a complex disease. My first effort was focused on chromosome 10 as previous studies had identified linkage to fasting plasma glucose, mean fasting plasma, and the ratio of fasting insulin to fasting glucose on that chromosome. I identified new polymorphisms in the Insulin degrading enzyme (IDE) that are associated with several DM2 phenotypes. The results were published recently in Diabetes (2003). Using mammalian cell lines from the same cohort, we are initiating studies of molecular mechanisms underlying the link of IDE to fasting plasma glucose, mean fasting plasma, and the ratio of fasting insulin to fasting glucose. Currently, I am trying to capture the functional SNPs by identifying associated altered expression patterns in the IDE gene.

Insulin-degrading enzyme (IDE) is a protein known to play a role in eliminating amyloid peptides that cause destructive plaques and tangles in the brains of Alzheimer's patients. The idea of identifying an IDE protein form or SNPs that is associated with Alzheimer’s is a particular interest.

Pulmonary Disease (COPD)

Chronic obstructive pulmonary disease (COPD) has been described as the fifth most significant global health problem, and is expected to become the third leading cause of death in the first quarter of the next century. About 2.8 million persons in the United States aged 17 to 75 years have COPD, as well as 1.7 million persons over the age of 45 years. Genetic risk factors that contribute to COPD and other pulmonary diseases have been a focus of several studies including the FHS. We used a number of measures representing sub-phenotypes for pulmonary

functions, including forced expiratory volume in 1 sec (FEV1) and forced vital capacity (FVC), to determine the hereditability of pulmonary function and to identify by linkage analysis candidate gene(s) and associated candidate pathways.

Using the FHS, we identified linkage to 6q for pulmonary function measures. We further fine mapped the region with additional microsatellite and SNP markers and conducted follow-up linkage and association studies for candidate genes. Using SNPs in both an unrelated and family-based cohorts of the FHS participants, we found a strong association in for FEV1 and FVC to SNPS near “Secreted Modular calcium-binding protein 2” (SMOC2). More biological studies to verify the functional SNP using RT-PCR and RNA expression are underway. This study will appear shortly in the American Journal of Human Genetics. We are also seeking to further understand the complexity of pulmonary disease

from a phenotype perspective. We suspect that other sub-phenotypes that not been considered, such as bronchitis, are contributing to disease complexity. The approach is in collaboration with several pulmonologists.