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Health Sciences profile

Dr Aniruddha Chatterjee

PositionResearch Fellow (supported by the New Zealand Institute for Cancer Research Trust)
DepartmentDepartment of Pathology (DSM)
QualificationsMSc PhD
Research summaryEpigenetic events in disease and phenotype
TeachingPATH 301 Applied Pathology (lecture on epigenetics)
Memberships
  • 2015–present: Affiliate investigator of Maurice Wilkins Centre CoRE, New Zealand
  • 2015–present: Member, Australia and New Zealand Melanoma Trials Group (ANZMTG)
  • 2013–present: Post-doctoral association, University of Otago
  • 2012–present: Staff representative: Otago University Post-graduate Society (OUPS)
  • 2010–present: Genetics Otago, New Zealand
  • 2010–2013: PhD student representative, Graduate Research Services and Liaison committee, University of Otago
  • 2009–2015: Member, National Centre for Growth and Development (Gravida),CoRE

Research

Aims

The main aims are

  1. Documenting epigenetic alterations (DNA methylation and miRNA) in cancer progression (primary to metastasis) and the test the functional consequences of these changes in the laboratory.
  2. Continue to develop tools, statistical methods for accurate analysis of epigenomic datasets from next generation sequencing technologies (NGS).

Two other areas of research

  1. Profiling inter-individual epigenetic variation in humans
  2. Using zebrafish as a model to understand the role of DNA methylation in development and altered phenotype when exposed to environmental cues.

Methodology

  1. Reduced representation bisulfite sequencing (RRBS): Genome-wide sequncing technique that specifically enriches genomic regions with a high density of potential methylation sites and enables investigation of DNA methylation at single-nucleotide resolution.
  2. RNA-Seq: To quantify gene expression and determine differential expression.
  3. microRNA analysis (miRNA): using NanoString, NGS and microarray platfrom.
  4. Methylation-specific PCR and Sequenom: To distinguish methylation difference at single gene (or allele) level.
  5. Computational tools: DMAP (our own development), Fastqc, Bismark, BSMAP, SeqMonk, methylKit, BiSeq, R, IGV, Taxedo package, Dexus, Unix, and Linux script to process NGS data, scan_tcga tools (our own development).

Relevance of these findings

I performed the first genome-wide study to provide single-nucleotide resolution DNA methylation profiles in human neutrophils and showed existence of wide-spread inter-individual variation in epigenetic marks in normal population. This work provides a comprehensive resource for understanding the nature and mechanism of variable phenotypic traits and altered disease susceptibility due to variable DNA methylation patterns and also has broader implications for the selection of DNA methylation based biomarker.

My work highlighted the epigenetic landscape of zebrafish and opened new anevues for using this model to further understand the biology of DNA methylation (such as sex determination mechanism in teleosts, effect of environmental pollutants in alterted methylation and phenotype). The pipeline we developed is being applied to investigate several other research questions (e.g., methylation based marker for Preeclamsia and Myelodysplasia). My recent work enabled detection of abberant DNA methylation pattern in metastastic melanomas. These findings will be useful to understand role of epigenetic events in metastasis and potentially could be expanded to other cancers (such as hepatoblastoma and neuro-endocrine tumours).

Recently in media

Additional details

These are the current research projects available ranging from Honours / Masters to PhD. We warmly encourage prospective postgraduate students to directly contact us to discuss the projects and / or your career goals.

1) Project title: Investigation of genetic and epigenetic signatures of primary and metastatic melanoma. Level: Honours/Masters

2) Project title: Analysis of cancer genome atlas data to identify epigenetic signature of tumour metastatis. Level: Masters

3) Project title: Single cell epigeneomics to investigate circulating tumour cells. Level: Honours / Master’s / PhD

Publications

Chatterjee, A., Rodger, E. J., Stockwell, P. A., Le Mée, G., & Morison, I. M. (2017). Generating multiple base-resolution DNA methylomes using reduced representation bisulfite sequencing. In G. J. Seymour, M. P. Cullinan & N. C. K. Heng (Eds.), Oral biology: Molecular techniques and applications: Methods in molecular biology (Vol. 1537). (2nd ed.) (pp. 279-298). New York, NY: Springer. doi: 10.1007/978-1-4939-6685-1_16

Chatterjee, A., Rodger, E. J., Morison, I. M., Eccles, M. R., & Stockwell, P. A. (2017). Tools and strategies for analysis of genome-wide and gene-specific DNA methylation patterns. In G. J. Seymour, M. P. Cullinan & N. C. K. Heng (Eds.), Oral biology: Molecular techniques and applications: Methods in molecular biology (Vol. 1537). (2nd ed.) (pp. 249-277). New York, NY: Springer. doi: 10.1007/978-1-4939-6685-1_15

Chatterjee, A., Rodger, E. J., & Eccles, M. R. (2017). Epigenetic drivers of tumourigenesis and cancer metastasis. Seminars in Cancer Biology. Advance online publication. doi: 10.1016/j.semcancer.2017.08.004

Rajendiran, A., Chatterjee, A., & Pan, A. (2017). Computational approaches and related tools to identify microRNAs in a species: A bird's eye view. Interdisciplinary Sciences. Advance online publication. doi: 10.1007/s12539-017-0223-x

Chatterjee, A., Stockwell, P. A., Ahn, A., Rodger, E. J., Leichter, A. L., & Eccles, M. R. (2017). Genome-wide methylation sequencing of paired primary and metastatic cell lines identifies common DNA methylation changes and a role for EBF3 as a candidate epigenetic driver of melanoma metastasis. Oncotarget, 8, 6085-6101. doi: 10.18632/oncotarget.14042

Authored Book - Research

Chatterjee, A., & Pan, A. (2012). Genome and proteome composition of Bdellovibrio bacteriovorus: Indications of recent horizontal gene transfer in Bdellovibrio bacteriovorus. Saarbrücken, Germany: Lambert Academic, 112p.

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Chapter in Book - Research

Chatterjee, A., Rodger, E. J., Stockwell, P. A., Le Mée, G., & Morison, I. M. (2017). Generating multiple base-resolution DNA methylomes using reduced representation bisulfite sequencing. In G. J. Seymour, M. P. Cullinan & N. C. K. Heng (Eds.), Oral biology: Molecular techniques and applications: Methods in molecular biology (Vol. 1537). (2nd ed.) (pp. 279-298). New York, NY: Springer. doi: 10.1007/978-1-4939-6685-1_16

Chatterjee, A., Rodger, E. J., Morison, I. M., Eccles, M. R., & Stockwell, P. A. (2017). Tools and strategies for analysis of genome-wide and gene-specific DNA methylation patterns. In G. J. Seymour, M. P. Cullinan & N. C. K. Heng (Eds.), Oral biology: Molecular techniques and applications: Methods in molecular biology (Vol. 1537). (2nd ed.) (pp. 249-277). New York, NY: Springer. doi: 10.1007/978-1-4939-6685-1_15

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Journal - Research Article

Chatterjee, A., Rodger, E. J., & Eccles, M. R. (2017). Epigenetic drivers of tumourigenesis and cancer metastasis. Seminars in Cancer Biology. Advance online publication. doi: 10.1016/j.semcancer.2017.08.004

Chatterjee, A., Stockwell, P. A., Ahn, A., Rodger, E. J., Leichter, A. L., & Eccles, M. R. (2017). Genome-wide methylation sequencing of paired primary and metastatic cell lines identifies common DNA methylation changes and a role for EBF3 as a candidate epigenetic driver of melanoma metastasis. Oncotarget, 8, 6085-6101. doi: 10.18632/oncotarget.14042

Rajendiran, A., Chatterjee, A., & Pan, A. (2017). Computational approaches and related tools to identify microRNAs in a species: A bird's eye view. Interdisciplinary Sciences. Advance online publication. doi: 10.1007/s12539-017-0223-x

Ludgate, J. L., Wright, J., Stockwell, P. A., Morison, I. M., Eccles, M. R., & Chatterjee, A. (2017). A streamlined method for analysing genome-wide DNA methylation patterns from low amounts of FFPE DNA. BMC Medical Genomics, 10, 54. doi: 10.1186/s12920-017-0290-1

Chatterjee, A., Macaulay, E. C., Ahn, A., Ludgate, J. L., Stockwell, P. A., Weeks, R. J., Parry, M. F., Foster, T. J., … Eccles, M. R., & Morison, I. M. (2017). Comparative assessment of DNA methylation patterns between reduced representation bisulfite sequencing and Sequenom EpiTyper methylation analysis. Epigenomics, 9(6), 823-832. doi: 10.2217/epi-2016-0176

Leichter, A. L., Sullivan, M. J., Eccles, M. R., & Chatterjee, A. (2017). MicroRNA expression patterns and signalling pathways in the development and progression of childhood solid tumours. Molecular Cancer, 16(1), 15. doi: 10.1186/s12943-017-0584-0

Macaulay, E. C., Chatterjee, A., Cheng, X., Baguley, B. C., Eccles, M. R., & Morison, I. M. (2017). The genes of life and death: A potential role for placental-specific genes in cancer: Active retrotransposons in the placenta encode unique functional genes that may also be used by cancer cells to promote malignancy. BioEssays. Advance online publication. doi: 10.1002/bies.201700091

Chatterjee, A., Stockwell, P. A., Rodger, E. J., & Morison, I. M. (2016). Genome-scale DNA methylome and transcriptome profiling of human neutrophils. Scientific Data, 3, 160019. doi: 10.1038/sdata.2016.19

Chatterjee, A., Stockwell, P. A., Rodger, E. J., Parry, M. F., & Eccles, M. R. (2016). scan_tcga tools for integrated epigenomic and transcriptomic analysis of tumor subgroups. Epigenomics, 8(10), 1315-1330. doi: 10.2217/epi-2016-0063

Chatterjee, A., Macaulay, E. C., Rodger, E. J., Stockwell, P. A., Parry, M. F., Roberts, H. E., Slatter, T. L., Hung, N. A., Devenish, C. J., & Morison, I. M. (2016). Placental hypomethylation is more pronounced in genomic loci devoid of retroelements. Genes Genomes Genetics, 6, 1911-1921. doi: 10.1534/g3.116.030379

Jones, A. M., Ferguson, P., Gardner, J., Rooker, S., Sutton, T., Ahn, A., Chatterjee, A., … Sarwar, M., Emanuel, P., Kenwright, D., … Eccles, M. R. (2016). NRAS and EPHB6 mutation rates differ in metastatic melanomas of patients in the North Island versus South Island of New Zealand. Oncotarget, 7(27), 41017-41030. doi: 10.18632/oncotarget.9351

Chatterjee, A., Lagisz, M., Rodger, E. J., Zhen, L., Stockwell, P. A., Duncan, E. J., Horsfield, J. A., … Nakagawa, S. (2016). Sex differences in DNA methylation and expression in zebrafish brain: A test of an extended ‘male sex drive’ hypothesis. Gene, 590, 307-316. doi: 10.1016/j.gene.2016.05.042

Chatterjee, A., Leichter, A. L., Fan, V., Tsai, P., Purcell, R. V., Sullivan, M. J., & Eccles, M. R. (2015). A cross comparison of technologies for the detection of microRNAs in clinical FFPE samples of hepatoblastoma patients. Scientific Reports, 5, 10438. doi: 10.1038/srep10438

Chatterjee, A., Stockwell, P. A., Rodger, E. J., Duncan, E. J., Parry, M. F., Weeks, R. J., & Morison, I. M. (2015). Genome-wide DNA methylation map of human neutrophils reveals widespread inter-individual epigenetic variation. Scientific Reports, 5, 17328. doi: 10.1038/srep17328

Leichter, A. L., Purcell, R. V., Sullivan, M. J., Eccles, M. R., & Chatterjee, A. (2015). Multi-platform microRNA profiling of hepatoblastoma patients using formalin fixed paraffin embedded archival samples. GigaScience, 4, 54. doi: 10.1186/s13742-015-0099-9

Stockwell, P. A., Chatterjee, A., Rodger, E. J., & Morison, I. M. (2014). DMAP: Differential methylation analysis package for RRBS and WGBS data. Bioinformatics, 30(13), 1814-1822. doi: 10.1093/bioinformatics/btu126

Rodger, E. J., Chatterjee, A., & Morison, I. M. (2014). 5-hydroxymethylcytosine: A potential therapeutic target in cancer. Epigenomics, 6(5), 503-514. doi: 10.2217/epi.14.39

Chatterjee, A., Ozaki, Y., Stockwell, P. A., Horsfield, J. A., Morison, I. M., & Nakagawa, S. (2013). Mapping the zebrafish brain methylome using reduced representation bisulfite sequencing. Epigenetics, 8(9), 979-989. doi: 10.4161/epi.25797

Laskar, A., Rodger, E. J., Chatterjee, A., & Mandal, C. (2012). Modeling and structural analysis of PA clan serine proteases. BMC Research Notes, 5, 256. doi: 10.1186/1756-0500-5-256

Chatterjee, A., Stockwell, P. A., Rodger, E. J., & Morison, I. M. (2012). Comparison of alignment software for genome-wide bisulphite sequence data. Nucleic Acids Research, 40(10), e79. doi: 10.1093/nar/gks150

Chatterjee, A., Rodger, E. J., Stockwell, P. A., Weeks, R. J., & Morison, I. M. (2012). Technical considerations for reduced representation bisulfite sequencing with multiplexed libraries. Journal of Biomedicine & Biotechnology, 2012, 741542. doi: 10.1155/2012/741542

Laskar, A., Chatterjee, A., Chatterjee, S., & Rodger, E. J. (2012). Three-dimensional molecular modeling of a diverse range of SC clan serine proteases. Molecular Biology International, 2012, 580965. doi: 10.1155/2012/580965

Laskar, A., Rodger, E. J., Chatterjee, A., & Mandal, C. (2011). Modeling and structural analysis of evolutionarily diverse S8 family serine proteases. Bioinformation, 7(5), 239-245.

Chatterjee, A., & Basu, A. (2011). Rubisco: Limitations and re-engineering for a better enzyme. International Research Journal of Plant Science, 2(2), 022-024.

Basu, A., Chatterjee, A., & Kottalil, D. M. (2010). Helicobacter pylori: Revisiting the role of host genetics in susceptibility to infectious diseases. Journal of Computational Intelligence in Bioinformatics, 3(1), 1-9.

Chatterjee, A., & Pan, A. (2010). Horizontal gene transfer: A genomic perspective. Online Journal of BioTechnology Research, 1(4), 167-169.

Laskar, A., Mandal, C. N., & Chatterjee, A. (2010). Protease-inhibitor interactions: A structural insight. International Journal of Biotechnology & Biochemistry, 6(2), 231-258.

Laskar, A., & Chatterjee, A. (2009). Protease: Revisiting the types and potential. Online Journal of BioTechnology Research, 1(1), 55-61.

Chatterjee, A. (2009). Bdellovibrio bacteriovorus: Life cycle and potential as a predatory renaissance. Advanced Biotech, 8(9), 27-29.

Laskar, A., & Chatterjee, A. (2009). Computer aided molecular modeling and its implications. Bioinformatics Trends, 4(1), 85-92.

Chatterjee, A. (2009). John's wort (Hypericum perforatum): A review on pharmacodynamics and therapeutic potential. Herbal Tech Industry, 5(5), 18-22.

Shrivastava, R., Chauhan, U. K., Sarkar, R., & Chatterjee, A. (2009). Observation on the reaction rate kinetics in cellulosic paper waste. Advanced Biotech, 8(7), 21-25.

Shrivastava, R., Sarkar, R., Chatterjee, A., & Khadikar, P. V. (2009). QSAR studies on the action of an algicide from a cyanobacterium: Oscillatoria laetevirens, on photosystem II activity. Advanced Biotech, 8(8), 16-18.

Chatterjee, A., & Sarkar, R. (2008). RNA interference (RNA i): A novel strategy in health care and crop improvement. Advanced Biotech, 7(3), 36-38.

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Journal - Research Other

Eccles, M. R., Chatterjee, A., & Rodger, E. J. (2017). Identifying drivers of metastasis; towards a systematic approach. Translational Cancer Research, 6(Suppl. 7), S1273-S1276. doi: 10.21037/tcr.2017.09.52

Ahn, A., Chatterjee, A., & Eccles, M. R. (2017). The slow cycling phenotype: A growing problem for treatment resistance in melanoma. Molecular Cancer Therapeutics, 16(6), 1002-1009. doi: 10.1158/1535-7163.mct-16-0535

Chatterjee, A., Stockwell, P. A., Horsfield, J. A., Morison, I. M., & Nakagawa, S. (2014). Base-resolution DNA methylation landscape of zebrafish brain and liver [Data in brief]. Genomics Data, 2, 342-344. doi: 10.1016/j.gdata.2014.10.008

Chatterjee, A. (2012). Epigenetic regulation: From mechanism to intervention. Epigenomics, 4(5), 487-490. doi: 10.2217/epi.12.47

Chatterjee, A., & Morison, I. M. (2011). Monozygotic twins: Genes are not the destiny? [Views and challenges]. Bioinformation, 7(7), 369-370.

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