Highlights

Systematic Analysis and Functional Annotation of Variations in the Genome of an Indian Individual. Patowary et. al. Hum Mutat. 2012 Mar 27. doi: 10.1002/humu.22091. [Epub ahead of print]

Personal Genomics- the rapid and complete sequencing of an individual’s genome in the hope of predicting susceptibility to diseases, drug efficacy and even life span is the first step to predictive medicine. IGIB announced the sequencing of the first Indian genome previously. Vinod Scaria and Sridhar Sivasubbu, with collaborators, now report a detailed analysis of the polymorphisms in this genome.

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Nonprocessive [2 + 2]e- off-loading reductase domains from mycobacterial nonribosomal peptide synthetases. Chhabra A et. al. Proc Natl Acad Sci U S A. 2012 Apr 10;109(15):5681-6.

Exploring the assembly line methodology of enzymes like polyketide synthases and nonribosomal peptide synthetases involved in production of lipidic metabolites in mycobacteria, Rajesh S. Gokhale and collaborators demonstrate that mycobacterial NRPSs performs two consecutive [2 + 2]e(-) reductions to release thioester-bound lipopeptides as corresponding alcohols.

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Chemical chaperones assist intracellular folding to buffer mutational variations. Bandyopadhyay et. al. Nature Chemical Biology 2012; 8, 238–245

A significant fraction of genetic differences might be silenced by active mechanisms collectively termed as genetic buffering. Kausik Chakraborty’s group found that the chemical milieu of a cell may contribute to the buffering capacity of an organism by assisting different mutant proteins in reaching their native state.

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The tuberculosis drug streptomycin as a potential cancer therapeutic: inhibition of miR-21 function by directly targeting its precursor. Bose et. al. Angew Chem Int Ed Engl. 2012; 51(4):1019-23.

A molecular screen for small molecule inhibitors of microRNA expression by Souvik Maiti and colleagues show that Streptomycin, the well known anti-tubercular drug can decrease the expression of the oncogenic microRNA, miR-21, perhaps by interfering in the dicer mediated maturation of the microRNA.

Let-7 microRNA-mediated regulation of IL-13 and allergic airway inflammation. Kumar et. al. J Allergy Clin Immunol 2011, 128(5):1077-85

IL-13 is a cytokine secreted by T(H)2 lymphocytes that modulates allergic inflammation and tissue remodeling. This work from Balaram Ghosh’s laboratory shows that the microRNA let7 can target IL-13. Intranasal delivery of let-7 decreased IL-13 levels, airway inflammation and other signs of asthma in mice.

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EGLN1 involvement in high-altitude adaptation revealed through genetic analysis of extreme constitution types defined in Ayurveda. Aggarwal et. al. Proc Natl Acad Sci U S A. 2010;107(44):18961-6

This study by Mitali Mukerji and colleagues has provided a link between common variations in an oxygen sensor gene EGLN1, that differs between Prakriti (constitution) types to differences in high altitude adaptation and susceptibility to high altitude pulmonary edema. This provides a novel framework for personalized medicine through integration of Ayurveda, genomics and modern medicine.

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Systematic Analysis and Functional Annotation of Variations in the Genome of an Indian Individual
Patowary A, Purkanti R, Singh M, Chauhan RK, Bhartiya D, Dwivedi OP, Chauhan G, Bharadwaj D, Sivasubbu S, Scaria V.
Hum Mutat. 2012 Mar 27. doi: 10.1002/humu.22091. [Epub ahead of print].

ABSTRACT: Whole genome sequencing of personal genomes has revealed a large repertoire of genomic variations and has provided a rich template for identification of common and rare variants in genomes in addition to understanding the genetic basis of diseases. The widespread application of personal genome sequencing in clinical settings for predictive and preventive medicine has been limited due to the lack of comprehensive computational analysis pipelines. We have used next-generation sequencing technology to sequence the whole genome of a self-declared healthy male of Indian origin. We have generated around 28X of the reference human genome with over 99% coverage. Analysis revealed over 3 million single nucleotide variations and about 490,000 small insertion deletion events including several novel variants. Using this dataset as a template, we designed a comprehensive computational analysis pipeline for the systematic analysis and annotation of functionally relevant variants in the genome. This study follows a systematic and intuitive data analysis workflow to annotate genome variations and its potential functional effects. Moreover, we integrate predictive analysis of pharmacogenomic traits with emphasis on drugs for which pharmacogenomic testing has been recommended. This study thus provides the template for genome-scale analysis of personal genomes for personalized medicine.


Nonprocessive [2 + 2]e- off-loading reductase domains from mycobacterial nonribosomal peptide synthetases
Chhabra A, Haque AS, Pal RK, Goyal A, Rai R, Joshi S, Panjikar S, Pasha S, Sankaranarayanan R, Gokhale RS.
Proc Natl Acad Sci U S A. 2012 Apr 10;109(15):5681-6.

Abstract
In mycobacteria, polyketide synthases and nonribosomal peptide synthetases (NRPSs) produce complex lipidic metabolites by using a thio-template mechanism of catalysis. In this study, we demonstrate that off-loading reductase (R) domain of mycobacterial NRPSs performs two consecutive [2 + 2]e(-) reductions to release thioester-bound lipopeptides as corresponding alcohols, using a nonprocessive mechanism of catalysis. The first crystal structure of an R domain from Mycobacterium tuberculosis NRPS provides strong support to this mechanistic model and suggests that the displacement of intermediate would be required for cofactor recycling. We show that 4e(-) reductases produce alcohols through a committed aldehyde intermediate, and the reduction of this intermediate is at least 10 times more efficient than the thioester-substrate. Structural and biochemical studies also provide evidence for the conformational changes associated with the reductive cycle. Further, we show that the large substrate-binding pocket with a hydrophobic platform accounts for the remarkable substrate promiscuity of these domains. Our studies present an elegant example of the recruitment of a canonical short-chain dehydrogenase/reductase family member as an off-loading domain in the context of assembly-line enzymology.


Chemical chaperones assist intracellular folding to buffer mutational variations
Anannya Bandyopadhyay, Kanika Saxena, Neha Kasturia, Vijit Dalal, Niraj Bhatt, Asher Rajkumar,Shuvadeep Maity, Shantanu Sengupta & Kausik Chakraborty
Nature Chemical Biology 8, 238–245 (2012)

Hidden genetic variations have the potential to lead to the evolution of new traits. Molecular chaperones, which assist protein folding, may conceal genetic variations in protein-coding regions. Here we investigate whether the chemical milieu of cells has the potential to alleviate intracellular protein folding, a possibility that could implicate osmolytes in concealing genetic variations. We found that the model osmolyte trimethylamine N-oxide (TMAO) can buffer mutations that impose kinetic traps in the folding pathways of two model proteins. Using this information, we rationally designed TMAO-dependent mutants in vivo, starting from a TMAO-independent protein. We show that different osmolytes buffer a unique spectrum of mutations. Consequently, the chemical milieu of cells may alter the folding pathways of unique mutant variants in polymorphic populations and lead to unanticipated spectra of genetic buffering.


Let-7 microRNA-mediated regulation of IL-13 and allergic airway inflammation
Kumar M, Ahmad T, Sharma A, Mabalirajan U, Kulshreshtha A, Agrawal A, Ghosh B.
J Allergy Clin Immunol. 2011 Nov;128(5):1077-85.e1-10. Epub 2011 May 25.

Abstract
BACKGROUND: IL-13, a cytokine secreted by T(H)2 lymphocytes and other cells, critically modulates allergic inflammation and tissue remodeling in allergic asthma. Although much is known about transcriptional regulation of IL-13, posttranscriptional regulation is poorly understood.
OBJECTIVE: Because many inflammatory pathways are known to be regulated by microRNAs, permitting a rapid and fine-tuned response, the role of microRNA-mediated regulation of IL-13 was investigated using both in vitro and in vivo studies.
METHODS: A combination of in silico approaches and in vitro transfections in A549 cells and primary cultured T cells was used to demonstrate the involvement of let-7 in IL-13 regulation. Furthermore, intranasal delivery of let-7 microRNA mimic in mice was performed to study its effects in allergic airway inflammatory conditions.
RESULTS: Using a combination of bioinformatics and molecular approaches, we demonstrate that the let-7 family of microRNAs regulates IL-13 expression. Induced levels of IL-13 in cultured T cells were inversely related to let-7 levels. In an IL-13-dependent murine model of allergic airway inflammation, we observed that inflammation was associated with a reduction in most of the members of the let-7 family. Exogenous administration of let-7 mimic to lungs of mice with allergic inflammation resulted in a decrease in IL-13 levels, resolution of airway inflammation, reduction in airway hyperresponsiveness, and attenuation of mucus metaplasia and subepithelial fibrosis.
CONCLUSION:Let-7 microRNAs inhibit IL-13 expression and represent a major regulatory mechanism for modulating IL-13 secretion in IL-13-producing cell types and thereby T(H)2 inflammation.


EGLN1 involvement in high-altitude adaptation revealed through genetic analysis of extreme constitution types defined in Ayurveda
Aggarwal S, Negi S, Jha P, Singh PK, Stobdan T, Pasha MA, Ghosh S, Agrawal A; Indian Genome Variation Consortium, Prasher B, Mukerji M.
Proc Natl Acad Sci U S A. 2010 Nov 2;107(44):18961-6. Epub 2010 Oct 18.

Abstract
It is being realized that identification of subgroups within normal controls corresponding to contrasting disease susceptibility is likely to lead to more effective predictive marker discovery. We have previously used the Ayurvedic concept of Prakriti, which relates to phenotypic differences in normal individuals, including response to external environment as well as susceptibility to diseases, to explore molecular differences between three contrasting Prakriti types: Vata, Pitta, and Kapha. EGLN1 was one among 251 differentially expressed genes between the Prakriti types. In the present study, we report a link between high-altitude adaptation and common variations rs479200 (C/T) and rs480902 (T/C) in the EGLN1 gene. Furthermore, the TT genotype of rs479200, which was more frequent in Kapha types and correlated with higher expression of EGLN1, was associated with patients suffering from high-altitude pulmonary edema, whereas it was present at a significantly lower frequency in Pitta and nearly absent in natives of high altitude. Analysis of Human Genome Diversity Panel-Centre d'Etude du Polymorphisme Humain (HGDP-CEPH) and Indian Genome Variation Consortium panels showed that disparate genetic lineages at high altitudes share the same ancestral allele (T) of rs480902 that is overrepresented in Pitta and positively correlated with altitude globally (P < 0.001), including in India. Thus, EGLN1 polymorphisms are associated with high-altitude adaptation, and a genotype rare in highlanders but overrepresented in a subgroup of normal lowlanders discernable by Ayurveda may confer increased risk for high-altitude pulmonary edema.