Specialization

Genetic and Epigenetic Gene Regulation

Email

vikas.handa@thapar.edu; Date of Joining: 28-12-2009

Professional Information

I am working as Assistant Professor in Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala since December 2009. Prior to that I was associated with Lovely Professional University, Phagwara. I have been awarded PhD in Biotechnology by Centre for Biotechnology, Jawaharlal Nehru University. Then I joined Institut fuer Biochemie, Justus Liebig Universitaet, Giessen, Germany for Post Doctoral research. Then I worked as a Guest Scientist in German Cancer Research Centre (DKFZ), Heidelberg, Germany. My research interests include Epigenetics and Gene regulation. Presently I am working on influence of sequence on DNA methylation propensity in human genome using computational approaches.

Academics

Assistant Professor, Dec 2009- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala Teaching Molecular and Cell Biology, Genetic and Metabolic Engineering, Genomics & Proteomics, Concepts in Biotechnology, Bio-Techniques and Environmental studies to Masters, Bachelor & Graduate classes. I have also been involved in conducting entrance examination for MSc and PhD Biotechnology programmes. I have been regularly guiding MSc and MTech Biotechnology students in short research projects.

Professor & Officiating Head of Department, Feb 2007- Dec 2009 Department of Biotechnology, Lovely Professional University, Phagwara Professor and Officiating Head in Department of Biotechnology In addition to teaching above mentioned courses I also contributed in curriculum development for programmes introduced in the department. I have also supervised Masters and co-supervised MPhil students in research projects.

Guest Scientist, 2005 –2007 Deutches Krebs Forchungs Zentrum (DKFZ), Heidelberg, Germany The project I worked on involved investigating the mechanism of targeted DNA demethylation. Mammalian genome undergoes active DNA demethylation during gametogenesis and early embryogenesis. Recent studies have shown activation of pluripotency marker genes during nuclear reprogramming of differentiated cells via targeted DNA demethylation. Solving the question of targeted demethylation may lead to manipulation of epigenetic state of differentiated cell contributing emphatically in the field of stem cell research.

Stem cell pluripotency marker gene Oct4 is known to undergo active DNA demethylation when differentiated cells are subjected to nuclear reprogramming using oocyte or early embryo extracts. In our laboratory Gadd45a (Growth arrest & DNA damage protein) has been found to be playing key role in active DNA demethylation via Nucleotice Excision Repair (NER) mechanism. NER factors XPG & XPB have been found to be associated with Gadd45a in the process of DNA demethylation. Cell biology & molecular approaches are being employed to find out factors responsible for and hence underlying mechanism of targeting of demethylation activity in the promoter region of Oct4 gene (Barreto G et al, 2007).

Post doctoral research, 2002 – 2004 Institut für Biochemie, Justus-Liebig Universität, Giessen, Germany I studied CpG flanking sequence preference of mammalian de novo methyltransferases and its biological significance. The cytosines in CpG dinucleotide context are found methylated in vertebrates genomes. This epigenetic change plays important role in gene imprinting, X chromosome inactivation, gene regulation, embryonic development and pathogenesis of cancer. The aim of the project was to study effect of flanking bases on CpG methylation using coupled molecular and computational approach. (Handa V & Jeltsch A, 2005)

In parallel I worked on another project on developing Programmable DNA Methyltrasferase for highly specific methylation of DNA. Since DNA methylation leads to silencing of gene expression, these enzymes could be used to repress expression of any target gene by directed methylation in vivo. Using onco genes or genes of viral origin as target, it can be used as therapeutic agent against cancer and viral diseases. The advantage of this method is that DNA-methylation is heritable hence there is no need of life-long therapy involving toxic substances. I also contributed in project on DNA-protein interactions & catalytic mechanism of Dnmt3a (Gowher et al, 2006). I was involved in practical classes of Masters Students and guiding (in part) Masters & PhD students.

PhD, Biotechnology, 1995 - 2001 Centre for Biotechnology, Jawaharlal Nehru University, New Delhi Secured an 8.43 CGPA in 16 credit course-work covering courses on Animal Virology, Application of computers in Biotechnology, Microvax and GCG Package, Research Methodology, Instrumentation and Journal Club in the first two semesters Thesis title: Identification and purification of liver-specific factor(s) that activate human apo(a) gene transcription. The project was to study transcriptional regulation of human apo(a) gene that has been associated with atherosclerosis. This gene is expressed in liver in a tissue specific manner in human and some primates only. A combination of reporter gene assays using 5’ flanking region of the gene and DNA-Protein interaction studies was used to address the problem. 700 bp region upstream of gene was found to be interacting with multiple protein factors resulting in transcriptional activation. (Handa V et al, 2002 & Negi S et al, 2004)

Publications

1. Apoorva, Handa V, Batra S, Arora V (2024) Advancing epigenetic profiling in cervical cancer: machine learning techniques for classifying DNA methylation patterns 3 Biotech 14(11):264 – 303.
2. Sharma V, Lohia N, Handa V, Baranwal M (2017) Amomum subulatum seed extract exhibit antioxidant, cytotoxic and immune-suppressive effect. Indian J Biochem Biophys 54 135-139.
3. Barreto G, Schäfer A, Marhold J, Stach D, Swaminathan SK, Handa V, Döderlein G, Maltry N, Wu W, Lyko F and Niehrs C (2007) Gadd45a promotes epigenetic gene activation by repair-mediated DNA demethylation Nature 445 671-675 [PMID: 17268471]
4. Gowher H, Loutchanwoot P, Vorobjeva O, Handa V, Jurkowska RZ, Jurkowski TP, Jeltsch A (2006) Mutational analysis of the catalytic domain of the murine Dnmt3a DNA-(cytosine C5)-methyltransferase. J Mol Biol 357 928-941 [PMID: 16472822]
5. Handa V and Jeltsch A (2005) Profound flanking sequence preference of dnmt3a and dnmt3b Mammalian DNA methyltransferases shape the human epigenome. J Mol Biol 348 1103-1112 [PMID: 15854647]
6. Handa V and Jeltsch A (2004) Anomalous mobility of PCR products after bisulfite treatment of DNA. Anal Biochem 333 196-198 [PMID: 15351297]
7. Negi S, Singh SK, Pati N, Handa V, Chauhan R and Pati U (2004) A proximal tissue-specific module and a distal negative regulatory module control apolipoprotein(a) gene transcription. Biochem J 379 151-159 [PMID: 14680477]
8. Handa V, Mahboob-ul-hussain, Pati N and Pati U (2002) Multiple liver-specific factors bind to a 64-bp element and activate apo(a) gene. Biochem Biophys Res Commun 292 243-249 [PMID: 11890699]

Junior Research Fellow, 1994-1995

• Department of Biochemistry, Jamia Hamdard University, New Delhi Worked as a Junior Research Fellow in a Department of Biotechnology sponsored project on Characterisation and Modulation of Biosynthetic Pathway of Artemisinin
• M. Sc. Biotechnology, 1992-1994 Centre for Biotechnology, Maharaja Sayajirao University of Baroda, Baroda. A two-year masters program covering the following subjects: Prokaryotic and Eukaryotic Molecular Biology, Genetic Engineering, Biophysics, Biostatistics, Biochemistry, Environmental Biology, Microbiology, Biochemical Engineering, Developmental Biology, Plant Physiology & Plant Tissue-culture and Immunology. Dissertation: Studies on Cytokinin Induced Inhibition of Dormancy Break in Kalanchoe mortagei. Seminar: Protein engineering and its industrial implication Project proposal: Effect of protein splicing on prokaryotic mRNA stability
• B. Sc. (Honours) Chemistry, 1989-1992 Atma Ram Sanatan Dharm College, University of Delhi, New Delhi A three-year bachelors program covering the following subjects: Inorganic Chemistry, Organic Chemistry & Physical Chemistry as main subjects and Mathematics & Physics as subsidiary subjects
• AISSCE XII Grade,1989 Central Board of Secondary Education, Kendriya Vidyalaya, Janakpuri, New Delhi Subjects: Mathematics, Physics, Chemistry, English & Biology
• AISSE X Grade, 1987 Central Board of Secondary Education, Kendriya Vidyalaya, Janakpuri, New Delhi Subjects: Mathematics, Sciences, Social Sciences, Hindi & English

Academic Accomplishments

• Qualified the Joint CSIR-UGC (Council of Scientific & Industrial Research - University Grants Commission) Test for Junior Research Fellowship and Eligibility for Lecturer ship (July 1995)
• Qualified GATE-94 (Graduate Aptitude Test in Engineering) with a score of 96.91 percentile

Participations

1. Developed ‘Self Learning Material’ of  ‘Biostatistics and Computer Applications’ course of Masters programme in Biotechnology for Punjab Technical University, Kapurthala (2014)
2. Co-organized Summer Training Program in Modern Biotechnology at CORE, Thapar Institute of Engineering & Technology (June - July 2014)
3. Delivered lecture in 9th Summer Training Programme in Industrial Biotechnology organized by STEP-TIET (June - July 2014)
4. Selected as Member, Board of Studies for Biotechnology Engineering and Sciences, Punjab Technical University, Kapurthala for two years (June, 2014 onwards)
5. As Member of Jury, Evaluated projects / models in INNOTECH-2014 organized by Pushpa Gujral Science City, Kapurthala in collaboration with Punjab Technical University, Kapurthala (March 2014)
6. Attended a TEQIP-II sponsored National Seminar on Innovation and Entrepreneurship organized by STEP-TIET (Oct 2013)
7. NCSTC, DST funded RISHI project judgment as mentor at Pushpa Gujral Science City, Kapurthala (May 2013)
8. Delivered a lecture, titled ‘Mathematics and Biology’ in a workshop on hands on approach in Mathematics, co-organized by Pushpa Gujral Science City, Kapurthala and NCSTC, DST (March 2013)
9. Attended a TEQIP-II sponsored Three Day Faculty Development Program on ‘MatLab for Chemical Engineers’ held in the Department of Chemical Engineering, Thapar Institute of Engineering & Technology (June 2013)
10. Oral presentation, titled ‘Studies on effect of sequence attributes on DNA methylation' in 2nd international conference BEATS 2012 held in NIT, Jalandhar (2012)
11. Reviewed research article for the journal Enzyme Research (2012)
12. Member of Board of Studies, BTech Biotechnology of Punjab Technical University since 2012
13. Invited Presentation titled ‘Course Content of Cell and Molecular Biology of required in Biotechnology’ in a Workshop on the Curriculum development of B. Tech. Biotechnology Programme, held in SUSCET, Tangori and organized by Punjab Technical University, Kapurthala (23 – 24 Jan 2011)
14. Co-organized National Conference on Emerging Trends in Biopharmaceuticals: Relevance to Human Health in Thapar Institute of Engineering & Technology, Patiala (11th – 13th November, 2010)
15. Attended workshop on Intellectual Property Rights organized in National Institute of Technology, Jalandhar (2008)
16. Attended a Bioinformatics workshop (HUSAR/GCG Sequence Analysis Package) in dkfz, Heidelberg (2005)
17. Attended a symposium titled ‘DNA Methylation – An important signal: Its significance in Biology and Pathogenesis’ organised in Weissenburg, Germany (2004)
18. Presented a poster at the 67th annual meet of society of biological chemists (India) held Jawaharlal Nehru University, New Delhi (1998) on Activation of apo(a) gene transcription by four HepG2 specific factors
19. Attended a workshop on DNA and Protein footprinting, organised at Centre for Cellular & Molecular Biology, Hyderabad (1997)
20. Attended a workshop on Self-Fabricated Instruments, organised by Department of Chemistry, Maitreyi College and Centre for Science Education & Communication, University of Delhi (1991)

Personal Information

• Languages known: English, Hindi and Punjabi
• Born : (24th September 1971) and brought up in India
• Permanent residence :in New Delhi