Microbial organisms such as bacteria and fungi are known to produce natural compounds. These natural compounds are primarily classified into four groups as polyketides (PKS), non-ribosomal peptides (NRPS), terpene or hybrid molecules (PKS-NRPS or PKS-terpenes). Generally, drug-like encoding genes are organized in gene clusters called biosynthetic gene clusters (BGCs). Genome sequencing and characterization of these microbial organisms are a rapid way of identification of their BGCs and corresponding future drug-like compounds. These compounds are highly relevant for drug discovery, particularly for new antibiotics, anticancer drugs and pharmaceuticals. We have developed collaborative projects with partner organizations like Kiel University (Marine fungal genomics), Allahabad University (four bacterial genomes) and CSIR-National Botanical Research Institute (Lichen genomics).
Conotruncal heart defects (CTDs) are characterized by the cardiac structural malformations of the outflow tract and are the most common subgroup of congenital heart defects. CTDs are presented as both syndromic and non-syndromic forms. Although CTDs are known to be affected by genetic, epigenetic, or environmental factors, several recent studies have strongly supported the genetic causes of CTDs. The complex genetic basis, disease pathogenesis, and the underlying molecular mechanisms of the heart development are yet to be elucidated. In collaboration with Dr. Patil from Mazumdar Shaw Medical Centre (MSMC), Bangalore, we have recruited 55 Indian families with different subtypes of CTDs, to investigate the genetic basis of these complex cardiac disorders. The existing low-resolution cytogenetics and molecular techniques used for diagnosis of CTDs result in a significant diagnostic delay as numerous genetic syndromes and >60 CTD genes were reported to date. Hence, we initiated MLPA to be followed by chromosomal microarray techniques in combination with whole exome sequencing and/or whole genome sequencing technologies to identify the causative genetic variants in CTD patients. Further, in vitro cell line models will be generated to study the disease pathogenesis of the novel genetic variants identified in the patients using standard molecular techniques.
Acromegaly is caused by excessive growth hormone production, most often due to pituitary adenomas. Characterized by acral growth, the disease manifests insidiously in adults and can be potentially life-threatening. In growing children, the disease presentation is dramatic with disproportionate linear growth leading to gigantism. Inaccessibility of the gland for biopsy, lack of functional cell lines and tumor heterogeneity has constrained the elucidation of molecular etiology of the disease. In collaboration with PGIMER, Chandigarh, we initiated whole-exome sequencing (WES) studies to identify genetic basis of acromegaly in Indian patients, which will aid in clinical assessment of pathogenecity. In familial cases, genetic studies are carried out and the clinician is informed of the risk factors to facilitate genetic counseling to the family.
Hearing impairment is one of the most frequent sensory defects and can be classified into congenital and acquired. Congenital hearing loss can be caused by hereditary and non-hereditary genetic factors. The identification of the causal hereditary mutation leading to congenital hearing impairment is important for early diagnosis, clinical follow-up and genetic counseling. India is a country with high ethnic diversity and high degree of consanguinity in some pockets. In collaboration with Command Hospital, Bangalore, we initiated a whole-exome sequencing project to identify causative novel variants/genes in this genetically heterogeneous recessive disease.
Genetic diagnosis of primary immune deficiency (PID) diseases in India is subject to numerous obstacles in terms of evaluation, characterization and turnaround time for definitive diagnosis and treatment. Few established centers in the country provide comprehensive genetic and prenatal diagnosis for primary immune deficiencies. Additionally, a diverse range of infections endemic to our country and nutritional deficiencies serve to further complicate PID diagnosis. Obtaining a specific molecular diagnosis has significant implications for patient management, including genetic counseling and providing prenatal diagnosis. Therefore, it becomes important to establish facilities for quicker diagnosis of the underlying genetic defect. Higher degree of consanguinity and ethnic diversity in India also necessitates the need for molecular confirmation of the genetic players suspected to be related to a particular PID case. In collaboration with National Institute of Immunohematology in Mumbai, we have now initiated studies to identify the variants/genes involved in disease pathogenecity.
Intellectual disability (ID) previously referred to as mental retardation (MR) is a neuro developmental disorder with significant limitations in intellectual functioning and adaptive behavior. XLID is a clinically and genetically heterogeneous disorder, and exists in both syndromic and non-syndromic forms. Family based association studies have identified more than 100 genes known to be implicated in XLID. However, the cause of the disease is still unknown for the non-syndromic form of XLID and is poorly studied. In collaboration with Dr. Girimaji from NIMHANS, we collected samples from more than 40 families with more than 80 individuals affected with moderate to severe ID. Due to genetic variability of XLID, cytogenetic tests followed by array comparative genomic hybridization were performed to investigate copy number alterations and larger chromosomal deletions/duplications in all the families. Whole-exome sequencing was initiated to identify novel variants/genes involved in intellectual disability.
Kinases and phosphatases have an equal role to play in phosphorylation and dephosphorylation of proteins that are responsible for transmitting signals from an external stimulus to the final expression of required functional genes through a cascade of signaling molecules. However, actions of phosphatases are less investigated as opposed to kinases. We are identifying substrates of protein tyrosine phosphatases that are involved in human diseases in a global scale using substrate trapping mutants of protein tyrosine phosphatases in order to evaluate their functional aspects that will result in the identification of lead molecules for therapeutic interventions.
Esophageal cancer is the third leading cancer in males and fourth leading in females in India, but not much is known about the molecular etiology of the disease. We have used DNA microarray technology for high throughput identification of molecular gene expression profiles. We observed 881 genes significantly upregulated in ESCC samples as compared to the adjacent normal epithelium. The expression of two previously unreported overexpressed genes, ORAOV2 and FAP, was validated at the protein level by immunohistochemical labeling of tissue microarrays and archival tissue sections. Overall, using this approach, we have identified a number of promising novel candidates that can be validated further for their potential to serve as biomarkers for ESCC. This is a collaborative effort between IOB, Kidwai Memorial Institute of Oncology and Johns Hopkins School of Medicine. Similarly, we are working on copy number variations in ESCC using arrayCGH.
Similar approaches are adopted for diverse cancers such as pancreatic cancer, gastric adenocarcinoma, gall bladder carcinoma, hepatocellular carcinoma, leukoplakia and oral squamous cell carcinoma, cervical cancer and retinoblastoma. Other diseases for which transcriptomic profiling are being done include temporal lobe epilepsy, tuberculous meningitis, rheumatoid arthritis, osteoarthritis, spondyloarthropathy and reactive arthritis. We also use this technology to identify subset of genes which are responsible for the development of skin lesions in arsenic exposed patients.
