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PERUMAL LAB

Virology | HBV Pathogenesis | G-Quadruplexes | Non-Coding RNA

 

  Research  

Hepatitis B Virus
Pathogenesis

Hepatitis B Virus (HBV) infection is a major global problem with over 300 million chronic HBV carriers.  About 0.5-1% of all Indians are chronically infected with HBV.  We investigate molecular mechanisms of HBV replication using a cell culture model.  We also study the role of HBV proteins in HBV-related liver cancer.  Furthermore, we screen for anti-HBV activity of synthetic molecules and compounds derived from traditional medicine concoctions.  

G-Quadruplexes in
Viruses

G-quadruplexes are nucleic acid secondary structures that regulate transcription, translation, splicing and recombination. The role of G-quadruplexes in viruses is not well understood. We identify G-quadruplex motifs in virus genomes and investigate their functional role in virus replication, latency and virus evolution. 

CpG dinucleotides in virus pathogenesis and evolution

The methylation of cytosines (within CpG dinucleoitides) in vertebrate genomes has been linked to the depletion CpG dinucleotides.  Viruses infecting vertebrates can be methylated by the host DNA methyltrasnferases, leading to CpG depletion in their genomes. The CpG content of virus genomes has been recently linked to virus replication and pathogenesis.  We are studying the CpG content of HIV-1 and its role in determining virus pathogenesis, temporal evolution of virulence. 

Dr. Vivekanandan Perumal

Education

B.Sc. (Medical Laboratory Technology); Christian Medical College, Vellore, India

M.Sc. (Medical Microbiology); Christian Medical College, Vellore, India

Ph.D. (Basic Medical Sciences); Christian Medical College, Vellore, India.

Experience

2004-2006- Research scholar, Johns Hopkins University, Baltimore, MD,USA.

2006-2009 – Postdoctoral Fellow, Johns Hopkins University, Baltimore, MD,USA.

2010-2016 – Assistant professor, Kusuma School of Biological Sciences, IIT Delhi.

2016-till date - Associate professor, Kusuma School of Biological Sciences, IIT Delhi

 

  Lab Members  

 Postdoctoral Fellows 

JAYANTA BORKAKOTI

  Alumni  

1. Jasmine Samal (PhD, 2016)

Current Position - Post Doctoral Fellow, Graduate School of Public Health, University of Pittsburgh

2. Mohita Upadhyay (PhD, 2016)

Current Position - Scientific writer, Scientific Services Practice, PLS, Novartis Healthcare Pvt. Ltd., Hyderabad

3. Manish Kandpal (PhD, 2017)

Current Position - Post Doctoral Fellow, Mass. Eye and Ear, Harvard Medical School, Boston

4. Banhi Biswas (PhD 2018)

Current Position - Post Doctoral Fellow, National Cancer Institute, Frederick, USA

 

  Publications and Patents  

2018

Kamuju V, Kumar S, Khan WH, Vivekanandan P. Hypervirulent Clostridium difficile ribotypes are CpG depleted. Virulence. 2018;9(1):1422-1425. doi: 10.1080/21505594.2018.

 

G-quadruplexes: more than just a kink in microbial genomes. N Saranathanan and Vivekanandan P .  Trends in Microbiology (accepted). 

 

Narain, A Pandey, S Gupta, J Gomes*, R Bhatia*, P Vivekanandan*. Targeted next generation sequencing reveals novel and rare variants in Indian patients with Amyotrophic Lateral Sclerosis. Neurobiology of Aging (In press).

 

Vadivel K, Mageshbabu R, Sankar S, Jain A, Perumal V, Srikanth P, Ranjan GA, Nair A, Simoes EAF, Nandagopal B, Sridharan G. Detection of parvovirus B19 in selected high-risk patient groups & their phylogenetic & selection analysis. Indian J Med Res. 2018 Apr;147(4):391-399. doi: 10.4103/ijmr.IJMR_241_16.

 

Patil, S Aravindan, MK Wasson, P Vivekanandan, PV Rao. Fast Fabrication of Superhydrophobic Titanium Alloy as Antibacterial Surface Using Nanosecond Laser Texturing. Journal of Micro and Nano-Manufacturing. 2018; 6 (1), 011002.

 

Biswas B, Kumari P, Vivekanandan P. Pac1 Signals of Human Herpesviruses Contain a Highly Conserved G-Quadruplex Motif.  ACS Infect Dis. 2018 Mar 1. doi: 10.1021/acsinfecdis.7b00279.

 

Sankar S, Borkakoti J, Ramamurthy M,  Nandagopal B, Vivekanandan P, Sridharan G. Identification of tell-tale patterns in the 3′ non-coding region of hantaviruses that distinguish HCPS-causing hantaviruses from HFRS-causing hantaviruses. Emerging Microbes and Infection. 2018; 7 (1); 32.

 

2017

Samal J, Kandpal M, Vivekanandan P. HBeAg-induced miR-106b promotes cell growth by targeting the retinoblastoma gene. Sci Rep. 2017 Oct 30;7(1):14371. doi: 10.1038/s41598-017-14652-x. PubMed PMID: 29085029; PubMed Central PMCID:PMC5662563.

 

 

Biswas B, Kandpal M, Vivekanandan P. A G-quadruplex motif in an envelope gene promoter regulates transcription and virion secretion in HBV genotype B. Nucleic Acids Res. 2017 Nov 2;45(19):11268-11280. doi: 10.1093/nar/gkx823. PubMed PMID:28981800; PubMed Central PMCID: PMC5737607.

 

 

Wasson MK, Borkakoti J, Kumar A, Biswas B, Vivekanandan P. The CpG dinucleotide content of the HIV-1 envelope gene may predict disease progression. Sci Rep. 2017 Aug 15;7(1):8162. doi: 10.1038/s41598-017-08716-1. PubMed PMID:28811638; PubMed Central PMCID: PMC5557942.

 

 

Narain P, Gomes J, Bhatia R, Singh I, Vivekanandan P. C9orf72 hexanucleotide repeat expansions and Ataxin 2 intermediate length repeat expansions in Indian patients with amyotrophic lateral sclerosis. Neurobiol Aging. 2017 Aug;56:211.e9-211.e14.

doi: 10.1016/j.neurobiolaging.2017.04.011. Epub 2017 Apr 26. PubMed PMID: 28527524.

 

2016

Biswas B, Kandpal M, Jauhari UK, Vivekanandan P. Genome-wide analysis of G-quadruplexes in herpesvirus genomes. BMC Genomics. 2016 Nov 21;17(1):949. PubMed PMID: 27871228; PubMed Central PMCID: PMC5117502.

 

 

6: Singh S, Upadhyay M, Sharma J, Gupta S, Vivekanandan P, Elangovan R. A portable immunomagnetic cell capture system to accelerate culture diagnosis of bacterial infections. Analyst. 2016 May 23;141(11):3358-66. doi: 10.1039/c6an00291a. PubMed PMID: 27118505.

 

2015

Upadhyay M, Vivekanandan P. Depletion of CpG Dinucleotides in Papillomaviruses and Polyomaviruses: A Role for Divergent Evolutionary Pressures. PLoS One. 2015 Nov 6;10(11):e0142368. doi: 10.1371/journal.pone.0142368. eCollection 2015.

PubMed PMID: 26544572; PubMed Central PMCID: PMC4636234.

 

 

Kandpal M, Samal J, Biswas B, Negi A, Mishra VC, Tyagi N, Raina V, Vivekanandan P. Enhanced hepatitis B virus (HBV) pre-genomic RNA levels and higher transcription efficiency of defective HBV genomes. J Gen Virol. 2015 Oct;96(10):3109-17. doi: 10.1099/jgv.0.000256. Epub 2015 Aug 3. PubMed PMID: 26242411.

 

 

Sankar S, Upadhyay M, Ramamurthy M, Vadivel K, Sagadevan K, Nandagopal B, Vivekanandan P, Sridharan G. Novel Insights on Hantavirus Evolution: The Dichotomy in Evolutionary Pressures Acting on Different Hantavirus Segments. PLoS One. 2015 Jul 20;10(7):e0133407. doi: 10.1371/journal.pone.0133407. eCollection 2015. PubMed PMID: 26193652; PubMed Central PMCID: PMC4508033.

 

 

Samal J, Kandpal M, Vivekanandan P. Hepatitis B "e" antigen-mediated inhibition of HBV replication fitness and transcription efficiency in vitro. Virology. 2015 Oct;484:234-40. doi: 10.1016/j.virol.2015.06.011. Epub 2015 Jun 25. PubMed PMID: 26119876.

 

 

Nirala BK, Perumal V, Gohil NK. Glycated serum albumin stimulates expression of endothelial cell specific molecule-1 in human umbilical vein endothelial cells: Implication in diabetes mediated endothelial dysfunction. Diab Vasc Dis Res. 2015 Jul;12(4):290-7. doi: 10.1177/1479164115583192. Epub 2015 May 11. PubMed PMID: 25963575.

 

 

Misra R, Upadhyay M, Perumal V, Mohanty S. In vitro control release, cytotoxicity assessment and cellular uptake of methotrexate loaded liquid-crystalline folate nanocarrier. Biomed Pharmacother. 2015 Feb;69:102-10. doi: 10.1016/j.biopha.2014.11.012. Epub 2014 Nov 20. PubMed PMID: 25661345.

2014

Upadhyay M, Sharma N, Vivekanandan P. Systematic CpT (ApG) depletion and CpG excess are unique genomic signatures of large DNA viruses infecting invertebrates. PLoS One. 2014 Nov 4;9(11):e111793. doi: 10.1371/journal.pone.0111793. eCollection 2014. PubMed PMID: 25369195; PubMed. Central PMCID: PMC4219779.

 

2013

Upadhyay M, Samal J, Kandpal M, Vasaikar S, Biswas B, Gomes J, Vivekanandan P. CpG dinucleotide frequencies reveal the role of host methylation capabilities in parvovirus evolution. J Virol. 2013 Dec;87(24):13816-24. doi: 10.1128/JVI.02515-13. Epub 2013 Oct 9. PubMed PMID: 24109231; PubMed Central PMCID: PMC3838256.

 

 

Woon JT, Maigne JY, Perumal V, Stringer MD. Magnetic resonance imaging morphology and morphometry of the coccyx in coccydynia. Spine (Phila Pa 1976). 2013 Nov 1;38(23):E1437-45. doi: 10.1097/BRS.0b013e3182a45e07. PubMed PMID: 23917643.

Upadhyay M, Samal J, Kandpal M, Singh OV, Vivekanandan P. The Warburg effect: insights from the past decade. Pharmacol Ther. 2013 Mar;137(3):318-30. doi: 10.1016/j.pharmthera.2012.11.003. Epub 2012 Nov 16. Review. PubMed PMID: 23159371.

 

2012

Woon JT, Perumal V, Maigne JY, Stringer MD. CT morphology and morphometry of the normal adult coccyx. Eur Spine J. 2013 Apr;22(4):863-70. doi: 10.1007/s00586-012-2595-2. Epub 2012 Nov 29. PubMed PMID: 23192732; PubMed Central PMCID: PMC3631051.

 

18: Samal J, Kandpal M, Vivekanandan P. Molecular mechanisms underlying occult hepatitis B virus infection. Clin Microbiol Rev. 2012 Jan;25(1):142-63. doi: 10.1128/CMR.00018-11. Review. PubMed PMID: 22232374; PubMed Central PMCID: PMC3255968.

 

2011

 

Ross HM, Daniel HD, Vivekanandan P, Kannangai R, Yeh MM, Wu TT, Makhlouf HR, Torbenson M. Fibrolamellar carcinomas are positive for CD68. Mod Pathol. 2011 Mar;24(3):390-5. doi: 10.1038/modpathol.2010.207. Epub 2010 Nov 26. PubMed PMID: 21113139; PubMed Central PMCID: PMC3292186.

Vivekanandan P, Torbenson M, Ramakrishna B. Hepatitis B virus-associated hepatocellular carcinoma from India: role of viral genotype and mutations in CTNNB1 (beta-catenin) and TP53 genes. J Gastrointest Cancer. 2011 Mar;42(1):20-5. doi: 10.1007/s12029-010-9222-4. PubMed PMID: 20963515.

 

2010

Vivekanandan P, Singh OV. Molecular methods in the diagnosis and management of chronic hepatitis B. Expert Rev Mol Diagn. 2010 Oct;10(7):921-35. doi: 10.1586/erm.10.75. Review. PubMed PMID: 20964611.

 

 

Vivekanandan P, Daniel H, Yeh MM, Torbenson M. Mitochondrial mutations in hepatocellular carcinomas and fibrolamellar carcinomas. Mod Pathol. 2010 Jun;23(6):790-8. doi: 10.1038/modpathol.2010.51. Epub 2010 Mar 12. PubMed PMID: 20228784; PubMed Central PMCID: PMC2879444.

 

 

Lam M, Torbenson M, Yeh MM, Vivekanandan P, Ferrell L. HFE mutations in alpha-1-antitrypsin deficiency: an examination of cirrhotic explants. Mod Pathol. 2010 May;23(5):637-43. doi: 10.1038/modpathol.2010.42. Epub 2010 Mar 5. PubMed PMID: 20208481.

 

 

Vivekanandan P, Daniel HD, Kannangai R, Martinez-Murillo F, Torbenson M. Hepatitis B virus replication induces methylation of both host and viral DNA. J Virol. 2010 May;84(9):4321-9. doi: 10.1128/JVI.02280-09. Epub 2010 Feb 10. PubMed PMID: 20147412; PubMed Central PMCID: PMC2863779.

 

2009

Balagopal A, Ray SC, De Oca RM, Sutcliffe CG, Vivekanandan P, Higgins Y, Mehta SH, Moore RD, Sulkowski MS, Thomas DL, Torbenson MS. Kupffer cells are depleted with HIV immunodeficiency and partially recovered with antiretroviral immune reconstitution. AIDS. 2009 Nov 27;23(18):2397-404. doi: 10.1097/QAD.0b013e3283324344. PubMed PMID: 19773633; PubMed Central PMCID: PMC3092442.

 

 

Kota J, Chivukula RR, O'Donnell KA, Wentzel EA, Montgomery CL, Hwang HW, Chang TC, Vivekanandan P, Torbenson M, Clark KR, Mendell JR, Mendell JT. Therapeutic microRNA delivery suppresses tumorigenesis in a murine liver cancer model. Cell. 2009 Jun 12;137(6):1005-17. doi: 10.1016/j.cell.2009.04.021. PubMed PMID: 19524505; PubMed Central PMCID: PMC2722880.

 

 

Fenton H, Torbenson M, Vivekanandan P, Yeh MM, Hart J, Ferrell L. Marked iron in liver explants in the absence of major hereditary hemochromatosis gene defects: a risk factor for cardiac failure. Transplantation. 2009 Apr 27;87(8):1256-60.

doi: 10.1097/TP.0b013e31819f2280. PubMed PMID: 19384175.

 

 

Vivekanandan P, Thomas D, Torbenson M. Methylation regulates hepatitis B viral protein expression. J Infect Dis. 2009 May 1;199(9):1286-91. doi: 10.1086/597614. PubMed PMID: 19301974; PubMed Central PMCID: PMC3032270.

 

 

Selaru FM, Olaru AV, Kan T, David S, Cheng Y, Mori Y, Yang J, Paun B, Jin Z, Agarwal R, Hamilton JP, Abraham J, Georgiades C, Alvarez H, Vivekanandan P, Yu W, Maitra A, Torbenson M, Thuluvath PJ, Gores GJ, LaRusso NF, Hruban R, Meltzer SJ. MicroRNA-21 is overexpressed in human cholangiocarcinoma and regulates programmed cell death 4 and tissue inhibitor of metalloproteinase 3. Hepatology. 2009 May;49(5):1595-601. doi: 10.1002/hep.22838. PubMed PMID: 19296468; PubMed Central PMCID: PMC3124086.

 

 

Daniels JA, Torbenson M, Vivekanandan P, Anders RA, Boitnott JK. Hepatitis in common variable immunodeficiency. Hum Pathol. 2009 Apr;40(4):484-8. doi: 10.1016/j.humpath.2008.09.008. Epub 2008 Dec 11. PubMed PMID: 19084266.

Vivekanandan P, Micchelli ST, Torbenson M. Anterior gradient-2 is overexpressed by fibrolamellar carcinomas. Hum Pathol. 2009 Mar;40(3):293-9. doi: 10.1016/j.humpath.2008.08.003. Epub 2008 Oct 29. PubMed PMID: 18973922; PubMed Central PMCID: PMC2746414.

2008

Vivekanandan P, Bissett S, Ijaz S, Teo CG, Sridharan G, Raghuraman S, Daniel HD, Kavitha ML, Daniel D, Chandy GM, Abraham P. Correlation between hepatitis B genotypes, 1896 precore mutation, virus loads and liver dysfunction in an Indian population. Indian J Gastroenterol. 2008 Jul-Aug;27(4):142-7. PubMed PMID: 18974463.

 

Chaerkady R, Harsha HC, Nalli A, Gucek M, Vivekanandan P, Akhtar J, Cole RN, Simmers J, Schulick RD, Singh S, Torbenson M, Pandey A, Thuluvath PJ. A quantitative proteomic approach for identification of potential biomarkers in hepatocellular carcinoma. J Proteome Res. 2008 Oct;7(10):4289-98. doi: 10.1021/pr800197z. Epub 2008 Aug 21. PubMed PMID: 18715028; PubMed Central PMCID: PMC3769105.

 

 

Chaerkady R, Thuluvath PJ, Kim MS, Nalli A, Vivekanandan P, Simmers J, Torbenson M, Pandey A. O Labeling for a Quantitative Proteomic Analysis of Glycoproteins in Hepatocellular Carcinoma. Clin Proteomics. 2008 Jul 18;4(3-4):137-155. PubMed PMID: 20357908; PubMed Central PMCID: PMC2847390.

 

 

Vivekanandan P, Kannangai R, Ray SC, Thomas DL, Torbenson M. Comprehensive genetic and epigenetic analysis of occult hepatitis B from liver tissue samples. Clin Infect Dis. 2008 Apr 15;46(8):1227-36. doi: 10.1086/529437. PubMed PMID: 18444860; PubMed Central PMCID: PMC3140175.

 

 

Vivekanandan P, Singh OV. High-dimensional biology to comprehend hepatocellular carcinoma. Expert Rev Proteomics. 2008 Feb;5(1):45-60. doi: 10.1586/14789450.5.1.45. Review. PubMed PMID: 18282123.

 

 

Vivekanandan P, Torbenson M. Epigenetic instability is rare in fibrolamellar carcinomas but common in viral-associated hepatocellular carcinomas. Mod Pathol. 2008 Jun;21(6):670-5. doi: 10.1038/modpathol.2008.32. Epub 2008 Feb 8. PubMed PMID: 18264082.

 

 

Micchelli ST, Vivekanandan P, Boitnott JK, Pawlik TM, Choti MA, Torbenson M. Malignant transformation of hepatic adenomas. Mod Pathol. 2008 Apr;21(4):491-7. doi: 10.1038/modpathol.2008.8. Epub 2008 Feb 1. PubMed PMID: 18246041.

 

 

Vivekanandan P, Torbenson M. Low frequency of Helicobacter DNA in benign and malignant liver tissues from Baltimore, United States. Hum Pathol. 2008 Feb; 39(2):213-6. Epub 2007 Oct 18. PubMed PMID: 17949788; PubMed Central PMCID: PMC2946621.

 

2007

Kannangai R, Vivekanandan P, Netski D, Mehta S, Kirk GD, Thomas DL, Torbenson M. Liver enzyme flares and occult hepatitis B in persons with chronic hepatitis C infection. J Clin Virol. 2007 Jun;39(2):101-5. Epub 2007 Apr 23. PubMed PMID: 17452002.

 

 

Kannangai R, Vivekanandan P, Martinez-Murillo F, Choti M, Torbenson M. Fibrolamellar carcinomas show overexpression of genes in the RAS, MAPK, PIK3, and xenobiotic degradation pathways. Hum Pathol. 2007 Apr;38(4):639-44. PubMed PMID: 17367606.

 

2006

Perumal V, Wang J, Thuluvath P, Choti M, Torbenson M. Hepatitis C and hepatitis B nucleic acids are present in intrahepatic cholangiocarcinomas from the United States. Hum Pathol. 2006 Sep;37(9):1211-6. Epub 2006 Jul 18. PubMed PMID: 16938527.

 

 

Sicklick JK, Li YX, Jayaraman A, Kannangai R, Qi Y, Vivekanandan P, Ludlow JW, Owzar K, Chen W, Torbenson MS, Diehl AM. Dysregulation of the Hedgehog pathway in human hepatocarcinogenesis. Carcinogenesis. 2006 Apr;27(4):748-57. Epub 2005 Dec 8. PubMed PMID: 16339184.

 

2005

Daniel HD, Abraham P, Raghuraman S, Vivekanandan P, Subramaniam T, Sridharan G. Evaluation of a rapid assay as an alternative to conventional enzyme immunoassays for detection of hepatitis C virus-specific antibodies. J Clin Microbiol. 2005 Apr;43(4):1977-8. PubMed PMID: 15815036; PubMed Central PMCID: PMC1081346.

2004

Vivekanandan P, Abraham P, Sridharan G, Chandy G, Shaji RV, Daniel D, Raghuraman S, Daniel HD, Subramaniam T. High frequency of the 1896 precore mutation in patients and blood donors with hepatitis B virus infection from the Indian subcontinent. Mol Diagn. 2004;8(1):51-6. PubMed PMID: 15230642.

 

 

Vivekanandan P, Abraham P, Sridharan G, Chandy G, Daniel D, Raghuraman S, Daniel HD, Subramaniam T. Distribution of hepatitis B virus genotypes in blood donors and chronically infected patients in a tertiary care hospital in southern India. Clin Infect Dis. 2004 May 1;38(9):e81-6. Epub 2004 Apr 9. PubMed PMID: 15127358.

 

2003

 

Perumal V, Mathai E, Jose J, Gupta S. Prevalence of Chlamydia pneumoniae IgG antibodies in patients with coronary artery disease: a report from an Indian population. Indian Heart J. 2003 Nov-Dec;55(6):667. PubMed PMID: 14989526.

  Patents  

1. Portable device and chip for immuno-magnetic capture and enrichment of Biomarker (Co-inventor)

 

2. On chip immunocapture and fluorescent detection of rare cells in large sample volume (Co-inventor)

 

  Beyond Science  

 

  Contact Us  

Dr. Vivekanandan Perumal

Room - IA - 302,

Kusuma School of Biological Sciences

Block - I

Indian Institute of Technology Delhi (IIT D)

Hauz Khas, New Delhi - 110016

India

Phone Number: 011-26597532 

Email:  vperumal@bioschool.iitd.ac.in

            cmcvivek@yahoo.com
           

DIPANNITA GHOSH
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