Publications

Comprehensive genomic analysis of malignant pleural mesothelioma identifies recurrent mutations, gene fusions and splicing alterations

Raphael Bueno1,8, Eric W Stawiski2,3,8, Leonard D Goldstein2,3,8, Steffen Durinck2,3,8, Assunta De Rienzo1,8, Zora Modrusan3,8, Florian Gnad2,8, Thong T Nguyen3,8, Bijay S Jaiswal3,8, Lucian R Chirieac4, Daniele Sciaranghella1, Nhien Dao1, Corinne E Gustafson1, Kiara J Munir1, Jason A Hackney2, Amitabha Chaudhuri5, Ravi Gupta5, Joseph Guillory3, Karen Toy3, Connie Ha3, Ying-Jiun Chen3, Jeremy Stinson3, Subhra Chaudhuri3, Na Zhang3, Thomas D Wu2, David J Sugarbaker6, Frederic J de Sauvage7, William G Richards1 & Somasekar Seshagiri3

We analyzed transcriptomes (n = 211), whole exomes (n = 99) and targeted exomes (n = 103) from 216 malignant pleural mesothelioma (MPM) tumors. Using RNA-seq data, we identified four distinct molecular subtypes: sarcomatoid, epithelioid, biphasic-epithelioid (biphasic-E) and biphasic-sarcomatoid (biphasic-S). Through exome analysis, we found BAP1, NF2, TP53, SETD2, DDX3X, ULK2, RYR2, CFAP45, SETDB1 and DDX51 to be significantly mutated (q-score ≥ 0.8) in MPMs. We identified recurrent mutations in several genes, including SF3B1 (~2%; 4/216) and TRAF7 (~2%; 5/216). SF3B1-mutant samples showed a splicing profile distinct from that of wild-type tumors. TRAF7 alterations occurred primarily in the WD40 domain and were, except in one case, mutually exclusive with NF2 alterations. We found recurrent gene fusions and splice alterations to be frequent mechanisms for inactivation of NF2, BAP1 and SETD2. Through integrated analyses, we identified alterations in Hippo, mTOR, histone methylation, RNA helicase and p53 signaling pathways in MPMs.

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A novel H395R mutation in MKKS/BBS6 causes retinitis pigmentosa and polydactyly without other findings of Bardet-Biedl or McKusick-Kaufman syndrome

John D. Hulleman, Annie Nguyen, V.L. Ramprasad, Sakthivel Murugan, Ravi Gupta, Avinash Mahindrakar, Ravi Angara, Chandrasekhar Sankurathri, V. Vinod Mootha (2016). Molecular Vision, 22, 73-81.

Retinitis pigmentosa (RP) is the most common inherited form of retinal degeneration, affecting nearly 1/4,000 individuals [1]. RP is caused by progressive rod photoreceptor degeneration ultimately leading to peripheral vision loss, night blindness, and, sometimes, complete blindness. Mutations in more than 50 genes have been identified to cause nonsyndromic RP, while mutations in a smaller subset of genes have been found to cause syndromic RP (i.e., RP combined with additional symptoms in other tissues/organs). Common forms of syndromic RP include Usher syndrome [2], Refsum disease [3], and Bardet-Biedl syndrome (BBS) [4]. Of these disorders, BBS is one of the most studied.

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First Report of Kufor-Rakeb Syndrome (PARK 9) from India, and a Novel Nonsense Mutation in ATP13A2 Gene

L.K. Prashanth, Sakthivel Murugan, Vikram Kamath, Ravi Gupta, Rakesh Jadav, S. Sreekantaswamy and Vedam L. Ramprasad (2015). Movement Disorders - Clinical Practice, Vol. 2, Issue 3.

Kufor-Rakeb syndrome (KRS; PARK 9) is a rare autosomal-recessive form of juvenile-onset Parkinson's disease (PD) caused by ATP13A2 gene mutations. The classical description of KRS is that of rapidly progressive symptoms in the form of parkinsonism, spasticity, supranuclear upgaze paresis, facial-faucial-finger minimyoclonus, visual hallucinations, oculogyric dystonic spasms, and dementia, usually noted between 12 and 16 years of age, resulting in early severe motor handicap.[1] World-wide prevalence of KRS is unknown, with only case reports/series being published.[2, 3] We report on the first case of KRS from India, with previously unreported nonsense mutation in exon 22 ofATP13A2 gene (chr1: 17316187; G>A).

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Identification of novel mutations in ABCA4 gene: Clinical and Genetic analysis of Indian patients with Stargardt disease

Rajani Battu, Anshuman Verma, Ramesh Hariharan, Shuba Krishna, Ravi Kiran, Jemima Jacob, Aparna Ganapathy, Vedam L. Ramprasad, Govindasamy Kumaramanickavel, Nallathambi Jeyabalan, and Arkasubhra Ghosh (2015). BioMed Research International, Volume 2015, Article ID 940864..

Stargardt disease (STGD) is the leading cause of juvenile macular degeneration associated with progressive central vision loss, photophobia and color vision abnormalities. The purpose of this study is to describe the clinical and genetic features of Stargardt patients from an Indian cohort.

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Evolution of targeted therapies in cancer: opportunities and challenges in the clinic

Sam Santhosh, Prasanna Kumar, Vedam Ramprasad and Amitabha Chaudhuri (2015). Future Oncology, Vol. 11, No. 2, 279-293.

Targeted therapies have changed the course of cancer treatment in recent years. By reducing toxicity and improving outcome, these new generations of precision medicines have extended patient lives beyond what could be achieved by the use of non-targeted therapies. In the last 2 years, several new molecular entities targeting signaling proteins and immune pathways have gone through successful clinical development resulting in their approval. These new targeted therapies require patient selection and the discovery of biomarkers of response. This review discusses the evolution of targeted therapies in cancer and challenges in translating the concepts into clinical practice.

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Prevalence of genetic variants associated with cardiovascular disease risk and drug response in the Southern Indian population of Kerala

Lakshmi Mahadevan, Ancy Yesudas, PK Sajesh, S Revu, Prasanna Kumar, Devi Santhosh, Sam Santhosh, JM Sashikumar, VK Gopalakrishnan, Joji Boben, Changanamkandath Rajesh (2014). Indian Journal of Human Genetics, Vol. 20, Issue: 2, 175-184.

We have identified that certain variants associated with cardiovascular disease and related drug response in the five genes, especially those in VKORC1, CYP2C19 and MYBPC3, are highly prevalent in the Kerala population, with almost 2 times higher prevalence of CYP2C19*2 variant compared with other regions in the country. Since the variants chosen in this study have relevance in disease phenotype and/or drug response, and are detected at a higher frequency, this study is likely to encourage clinicians to perform genetic testing before prescribing therapy.

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Regulation of macrophage polarization by RON receptor tyrosine kinase signaling

Amit Chaudhuri (2014). Frontiers in Immunology, 5, 546.

The M1 and M2 states of macrophage polarization are the two extremes of a physiologic/phenotypic continuum that is dynamically influenced by environmental signals. The M1/M2 paradigm is an excellent framework to understand and appreciate some of the diverse functions that macrophages perform. Molecular analysis of mouse and human macrophages indicated that they gain M1 and M2-related functions after encountering specific ligands in the tissue environment. In this perspective, I discuss the function of recepteur d’origine nantais (RON) receptor tyrosine kinase in regulating the M2-like state of macrophage activation Besides decreasing pro-inflammatory cytokine production in response to toll-like receptor-4 activation, macrophage-stimulating protein strongly suppresses nitric oxide synthase and at the same time upregulates arginase, which is the rate limiting enzyme in the ornithine biosynthesis pathway. Interestingly, RON signaling preserved some of the characteristics of the M1 state, while still promoting the hallmarks of M2 polarization. Therefore, therapeutic modulation of RON activity can shift the activation state of macrophages between acute and chronic inflammatory states.

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Cost-efficient HIV-1 drug resistance surveillance using multiplexed high-throughput amplicon sequencing: implications for use in low- and middle-income countries

Halime Ekici, Shwetha D. Rao, Anders Sönnerborg, Vedam L. Ramprasad, Ravi Gupta and Ujjwal Neogi (2014). J. Antimicrob. Chemother., 69 (12), 3349-3355.

Increased trends of primary drug resistance mutations (DRMs) among treatment-naive HIV-1-infected patients in low- and middle-income countries (LMICs) and the non-availability of pre-antiretroviral therapy (ART) genotypic resistance testing (GRT) may severely affect future therapeutic outcomes. The main objective of this study was therefore to develop a simplified, cost- and labour-efficient but high-throughput GRT protocol to be applied in the large-scale surveillance of DRMs in LMICs.

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Recessive Mutations in SLC38A8 Cause Foveal Hypoplasia and Optic Nerve Misrouting without Albinism

James A. Poulter, Musallam Al-Araimi, Ivan Conte, Maria M. van Genderen, Eamonn Sheridan, Ian M. Carr, David A. Parry, Mike Shires, Sabrina Carrella, John Bradbury, Kamron Khan, Phillis Lakeman, Panagiotis I. Sergouniotis, Andrew R. Webster, Anthony T. Moore, Bishwanath Pal, Moin D. Mohamed, Anandula Venkataramana, Vedam Ramprasad, Rohit Shetty, Murugan Saktivel, Govindasamy Kumaramanickavel, Alex Tan, David A. Mackey, Alex W. Hewitt, Sandro Banfi, Manir Ali, Chris F. Inglehearn, and Carmel Toomes (2013). The American Journal of Human Genetics, 93, 1143–1150.

Foveal hypoplasia and optic nerve misrouting are developmental defects of the visual pathway and only co-occur in connection with albinism; to date, they have only been associated with defects in the melanin-biosynthesis pathway. Here, we report that these defects can occur independently of albinism in people with recessive mutations in the putative glutamine transporter gene SLC38A8. Nine different mutations were identified in seven Asian and European families. Using morpholino-mediated ablation of Slc38a8 in medaka fish, we confirmed that pigmentation is unaffected by loss of SLC38A8. Furthermore, by undertaking an association study with SNPs at the SLC38A8 locus, we showed that common variants within this gene modestly affect foveal thickness in the general population. This study reveals a melanin-independent component underpinning the development of the visual pathway that requires a functional role for SLC38A8.

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Sequencing and analysis of a South Asian-Indian personal genome

Ravi Gupta, Aakrosh Ratan, Changanamkandath Rajesh, Rong Chen, Hie Lim Kim, Richard Burhans, Webb Miller, Sam Santhosh, Ramana V Davuluri, Atul J Butte, Stephan C Schuster, Somasekar Seshagiri and George Thomas (2012). BMC Genomics, 13, 440.

With over 1.3 billion people, India is estimated to contain three times more genetic diversity than does Europe. Next-generation sequencing technologies have facilitated the understanding of diversity by enabling whole genome sequencing at greater speed and lower cost. While genomes from people of European and Asian descent have been sequenced, only recently has a single male genome from the Indian subcontinent been published at sufficient depth and coverage. In this study we have sequenced and analyzed the genome of a South Asian Indian female (SAIF) from the Indian state of Kerala

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