Profile
Research Interest:
Breast Cancer Genomics and Epigenomics; biology of selected cancer related coding and non-coding RNAs; Extracellular Vesicle Biology.
Selected Publications:
- Das P,
Gupta A, Desai KV. JMJD6
orchestrates a transcriptional program in favor of endocrine resistance in ER+
breast cancer cells. Front Endocrinol. 2022, Nov 7: 13
- Biswas A, Mukherjee G, Kondaiah P, Desai KV. Both EZH2 and JMJD6 regulate cell cycle genes in breast cancer. BMC Cancer. 2020 Nov 27;20(1):1159.
- Haque MM and Desai KV. Pathways to Endocrine Therapy Resistance in Breast Cancer. Front. Endocrinol. 2019 10:573.
- Biswas A, Shettar A, Mukherjee G, Kondaiah P, Desai KV. JMJD6 induces HOTAIR, an oncogenic lincRNA, by physically interacting with its proximal promoter. Biochem J. 2018 Jan 15;475(1):355-371
- Lee YF, Miller LD, Chan XB, Black MA, Pang B, Ong CW, Salto-Tellez M, Liu ET, Desai KV. JMJD6 is a driver of cellular proliferation and motility and a marker of poor prognosis in breast cancer. Breast Cancer Res. 2012 May 23;14(3):R85
Research
Minimally invasive biopsy/Liquid biopsy
Monitoring breast cancer progression after diagnosis and its response to treatment, its ability to recur over time, is extremely challenging. Not only are breast tumors highly heterogeneous to begin with, they evolve during the course of treatment and sampling such tumors longitudinally by repeated biopsies within a same patient is not possible. In addition, a biopsy of larger tumors rarely represents its cellular or molecular complexity and such sampling introduces a bias in defining tumor characteristics. One way to address this challenge is to use minimally invasive techniques that involve sampling biofluids such as blood, urine, and/or saliva that is, using liquid biopsy approaches. Such collections also receive better patient compliance allowing for repeated sampling in a longitudinal manner. Most cancers shed cells into circulation, release exosomes and circulating cell free tumor DNA (ccftDNA) that grossly represent the total population of tumor cells. In addition, these contents are amenable to Next Generation Sequencing (NGS)-based analysis. We are interested in tiny extracellular vesicles (EVs/exosomes) and ccftDNA present in breast cancer patient sera. We study their DNA, RNA and protein content by genomic and proteomic approaches. We hope to unravel their contribution to breast cancer biology and understand how they could be used to monitor the disease and/or response to therapy.
Non-coding RNA biology
In our genome, DNA coding for proteins represents only a portion of it. It is evident that the remaining so called junk DNA contains regulatory regions and generates several non-coding RNAs (ncRNAs). These ncRNAs have regulatory roles within the cell and transcriptomics (RNA-seq) data is rapidly establishing their expression profiles across multiple cancers. However, for many lncRNAs, their exact function in tumor development and progression remains unknown. We are using bioinformatic approaches to identify cancer related lncRNAs from sequencing data with the aim of functionalizing them using human and Zebrafish model system.
Jumonji domain containing protein 6 (JMJD6):
We previously showed that JMJD6 associates with poor prognosis and worse survival of breast cancer patients. Exploring the molecular pathways, we discovered that JMJD6 promoted cell proliferation along with another epigenetic regulator EZH2 by physically interacting with the regulatory regions of cell cycle genes such as AURKA and AURKB. Many of the JMJD6 regulated genes are themselves well known cancer targets and drugs against them are in clinical trials. We are concluding our efforts in understanding JMJD6 mediated transcription and its contribution to endocrine therapy resistance in breast cancer.
Projects
- Principle Investigator SERB POWER grant: Interaction of JMJD6 and YBX1 and their impact on breast cancer progression, September 2022-August 2025
- Principal Investigator Department of Health Research, HRD Scheme: Using differential RNA expression in serum exosomes as a tool to understand breast cancer recurrence, March 2019-March 2022
- Principal Investigator TATA trust grant: Enabling diagnosis and treatment of Breast cancer throughout India, July 2018-July 2020
- Principal Investigator (Indian partner) U-Chicago Delhi Centre: Proposal for a Fourth India-UChicago Cancer Research Initiative: Strategic Partnership in Cancer Research between India and the University of Chicago, July 2018-Jun 2019
- Principal Investigator West Bengal DBT grant: A metagene signature indicative of prognosis and/or response to therapy in breast cancer, January 2018-Jan 2021
- Principal Investigator DBT Bio-Care grant: “Mechanism of JMJD6 mediated gene regulation”, July 2013-Jul 2016
- Co-Principal Investigator DBT grant: “Association of gene mutations/polymorphisms with therapeutic efficacy of Metformin in Type 2 Diabetes Mellitus patients of West Bengal, India, July 2013-July 2016
CV
Name: Kartiki V. Desai
Email: kd1@nibmg.ac.in
Present position: Professor
Highest Educational Qualification: Ph.D.
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Year
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Degree
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University
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1999
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Ph.D.
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MRDG, Indian Institute of Science, Bangalore
Thesis adviser: Prof. Paturu Kondaiah
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1992
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M.Sc.
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University of Poona, Pune
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1990
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B.Sc.
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University of Poona, Pune
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Professional Appointments
- Professor, National Institute of Biomedical Genomics, Current
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Research Scientist, Genome Institute of Singapore Oct 2006-Aug 2011
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Research Associate, Division of Johns Hopkins, Singapore Feb 2005-Oct 2006
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Postdoctoral Researcher, National Cancer Institute, NIH, Bethesda Dec 1999-Dec 2004
Professional Memberships
1. Co-opted Council Member, Human Genome Organization (HUGO) 2012 - 2017
2. Review Editor-Frontiers in Cancer Genetics
3. Member- Society, Biomedical Genomics Center 2012-2016
4. Member- Editorial Board, Journal of Genetics since Jan 2018
5. Member- The Technical Expert Committee on Genomic Technologies, DBT, India
6. Member- Governing Board of International Association of Breast Cancer Research (IABCR)
7. Member- STAG Knowledge Generation and Discovery Research, New tools and technologies
Awards and Honors
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Year
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Award
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2002
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Technology Transfer Award
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Center for Cancer Research, NIH
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2004
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Outstanding postdoctoral researcher
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National Cancer Institute, NIH
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2016
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Long term Fellowship (Czech Republic)
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Bilateral Exchange Program, INSA
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2017
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Short-term Fellowship (University of Chicago)
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Dept. Of Health Research, India
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Past Major Projects
1. Principal Investigator A*STAR-JCO grant : “Toward a systems biology framework for estrogen signaling integrating technology, biology and computation “ Jan 2010-September 2012
2. Principal Investigator A*STAR-JCO grant: “Nanosensors for hormone receptor Biology” Jan 2010-November 2011
3. Co-investigator: Singapore Cancer Syndicate: Expansion of National Xenograft Therapeutic Programs for HCC: establishment of cell lines, genomic analysis, and evaluation/identification of drugs used in prevention and/or treatment of HCC November 2006-2007
4. Project Manager: GIS internal grants “Systems Reconstruction of Transcriptional Output by Nuclear Hormone Receptors” Apr 2010 to Apr 2012
5. Project Manager : GIS internal grants: Functional Characterization of Cancer biomarkers Aug 2009- Aug 2011
6. Project Manager : GIS internal grants: Use of the mouse xenograft system as a validation tool for novel oncogenes, tumor suppressors and isolation of cancer stem cells September 2007-Apr 2009
Publications
- Das P,
Gupta A, Desai KV. JMJD6
orchestrates a transcriptional program in favor of endocrine resistance in ER+
breast cancer cells. Front Endocrinol. Nov 7, 2022: 13
- Biswas A, Mukherjee G, Kondaiah P, Desai KV. Both EZH2 and JMJD6 regulate cell cycle genes in breast cancer. BMC Cancer. 2020 Nov 27;20(1):1159.
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Haque MM and Desai KV. Pathways to Endocrine Therapy Resistance in Breast Cancer. Front. Endocrinol. 2019 10:573.
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Biswas A, Shettar A, Mukherjee G, Kondaiah P, Desai KV. JMJD6 induces HOTAIR, an oncogenic lincRNA, by physically interacting with its proximal promoter. Biochem J. 2018 Jan 15;475(1):355-371
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Biswas, A. and Desai, K.V. The LncRNA HOTAIR-expression, regulation and function in cancer Nucleus 2017 60: 155
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Nagarajan N, Bertrand D, Hillmer AM, Zang ZJ, Yao F, Jacques PE, Teo AS, Cutcutache I, Zhang Z, Lee WH, Sia YY, Gao S, Ariyaratne PN, Ho A, Woo XY, Veeravali L, Ong CK, Deng N, Desai KV, Khor CC, Hibberd ML, Shahab A, Rao J, Wu M, Teh M, Zhu F, Chin SY, Pang B, So JB, Bourque G, Soong R, Sung WK, Teh BT,Rozen S, Ruan X, Yeoh KG, Tan PB, Ruan Y. Whole-genome reconstruction and mutational signatures in gastric cancer. Genome Biol. 2012 Dec 13;13(12):R115.
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Lee YF, Miller LD, Chan XB, Black MA, Pang B, Ong CW, Salto-Tellez M, Liu ET, Desai KV*. JMJD6 is a driver of cellular proliferation and motility and a marker of poor prognosis in breast cancer. Breast Cancer Res. 2012 May 23;14(3):R85
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Seo J, Kim SC, Lee HS, Kim JK, Shon HJ, Salleh NL, Desai KV, Lee JH, Kang ES, Kim JS, Choi JK. Genome-wide profiles of H2AX and γ-H2AX differentiate endogenous and exogenous DNA damage hotspots in human cells. Nucleic Acids Res. 2012 Mar 29. Jul;40(13):5965-74
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Soon WW, Miller LD, Black MA, Dalmasso C, Chan XB, Pang B, Ong CW, Salto-Tellez M, Desai KV*, Liu ET. Combined genomic and phenotype screening reveals secretory factor SPINK1 as an invasion and survival factor associated with patient prognosis in breast cancer.EMBO Mol Med. 2011 Aug;3(8):451-64.
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Interrogating Oestrogen Receptor–DNA Interactions using Metallic Nanoparticles and Surface Plasmon Resonance Technique. Khin Moh Moh Aung, Tan YN, Desai KV, Xiaodi Su. Australian Journal of Chemistry 2011 Sept;64( 9):1288 - 129.
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Inaki K, Hillmer AM, Ukil L, Yao F, Woo XY, Vardy LA, Zawack KF, Lee CW,Ariyaratne PN, Chan YS, Desai KV, Bergh J, Hall P, Putti TC, Ong WL, Shahab A,Cacheux-Rataboul V, Karuturi RK, Sung WK, Ruan X, Bourque G, Ruan Y, Liu ET. Transcriptional consequences of genomic structural aberrations in breast cancer. Genome Res. 2011 May;21(5):676-87
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Li Y, Li Y, Wedrén S, Li G, Charn TH, Desai KV, Bonnard C, Czene K, Humphreys K, Darabi H, Einarsdóttir K, Heikkinen T, Aittomäki K, Blomqvist C, Chia KS,Nevanlinna H, Hall P, Liu ET, Liu J. Genetic variation of ESR1 and its co-activator PPARGC1B is synergistic in augmenting the risk of estrogen receptor-positive breast cancer. Breast Cancer Res. 2011 Jan 26;13(1):R10.
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Zhang GJ, Huang MJ, Ang JJ, Liu ET, Desai KV. Self-assembled monolayer-assisted silicon nanowire biosensor for detection of protein-DNA interactions in nuclear extracts from breast cancer cell. Biosens Bioelectron. 2011 Mar 15;26(7):3233-9.
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Liu JJ, Desai KV, Li Yuqing, Shakeela Banu, Lee YK, Qu D, Heikkinen T Aaltonen K, Muranen TA, Kajiji TS, Bonnard C, Aittoma¨ki K, von Smitten K, Blomqvist C, Hopper JL, Southey MC, Brauch H, Chenevix-Trench G, Beesley J, Spurdle AB, Chen X, Cuningham K, Czene K, Hall P, Nevanlinna H, Liu ET. Germ-line variation at a functional p53 binding site increases susceptibility to breast cancer development. HUGO J, 2009 Dec;3(1-4):31-40.
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Fullwood MJ, Liu MH, Pan YF, Liu J, Xu H, Mohamed YB, Orlov YL, Velkov S, Ho A, Mei PH, Chew EG, Huang PY, Welboren WJ, Han Y, Ooi HS, Ariyaratne PN, Vega VB, Luo Y, Tan PY, Choy PY, Wansa KD, Zhao B, Lim KS, Leow SC, Yow JS, Joseph R, Li H, Desai KV, Thomsen JS, Lee YK, Karuturi RK, Herve T, Bourque G, Stunnenberg HG, Ruan X, Cacheux-Rataboul V, Sung WK, Liu ET, Wei CL, Cheung E, Ruan Y. An oestrogen-receptor-alpha-bound human chromatin interactome. Nature. 2009 Nov 5;462(7269):58-64.
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Limaye AM, Desai KV, Chavalmane AK, Kondaiah P. Regulation of mRNAs encoding MMP-9 and MMP-2, and their inhibitors TIMP-1 and TIMP-2 by androgens in the rat ventral prostate. Mol Cell Endocrinol. 2008 Nov 6;294(1-2):10-8.
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Arany PR, Flanders KC, Kobayashi T, Kuo CK, Stuelten C, Desai KV, Tuan R, Rennard SI, Roberts AB. Smad3 deficiency alters key structural elements of the extracellular matrix and the mechanotransduction of wound closure. Proc. Natl. Acad. Sci. 2006 Jun 13;103(24)
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Huang S, Li Y, Chen Y, Podsypanina K, Chamorro M, Olshen AB, Desai KV, Tann A, Petersen D, Green JE, Varmus HE. Changes in gene expression during the development of mammary tumors in MMTV-Wnt-1 transgenic mice.Genome Biol. 2005;6(10):R84.
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Desai KV, Michalowska A, Shih J, Kondaiah P, Ward JM, Green JE. Gene expression profiling identifies a unique androgen-mediated inflammatory/immune signature and a PTEN-mediated apoptotic response specific to the rat ventral prostate. Mol Endocrinol. 2004 Dec;18(12):2895-907
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Utomo A, Jiang X, Furuta S, Yun J, Levin DS, Wang YC, Desai KV, Green JE, Chen PL, Lee WH. Identification of a novel putative non-selenocysteine containing phospholipid hydroperoxide glutathione peroxidase (NPGPx) essential for alleviating oxidative stress generated from polyunsaturated fatty acids in breast cancer cells. J Biol Chem. 2004 Oct 15;279(42):43522-9
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Green JE, Desai KV, Ye Y, Kavanaugh C, Calvo A, Huh JI. Application of gene expression profiling for validating models of human breast cancer. Toxicol Pathol. 2004 Mar-Apr;32 Suppl 1:84-9.
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Fargiano AA, Desai KV, Green JE. Interrogating Mouse Mammary Cancer Models:Insights from Gene Expression Profiling. J Mammary Gland Biol Neoplasia. 2003 Jul;8(3):321-34.
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Goswami MT, Desai KV, Kondaiah P. Comparative functional analysis of rat TGF-beta1 and Xenopus laevis TGF-beta5 promoters suggest differential regulations. J Mol Evol. 2003 Jul;57(1):44-51.
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Kavanaugh CJ, Desai KV, Calvo A, Brown, PH, Couldrey C, Lubet, R Green JE. Pre-Clinical Applications of Transgenic Mouse Mammary Cancer Models. Transgenic Res. 2002 Dec;11(6):617-33
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Desai KV, Kavanaugh CJ, Calvo A, Green JE. Chipping Away at Breast Cancer: insights from microarray studies of human and mouse mammary cancer. Endocr Relat Cancer. 2002 Dec;9(4):207-20
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Shih SC, Robinson GS, Perruzzi CA, Calvo A, Desai K, Green JE, Ali IU, Smith LE, Senger DR. Molecular profiling of angiogenesis markers. Am J Pathol. 2002 Jul;161(1):35-41.
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Desai KV, Xiao N, Wang W, Gangi L, Greene J, Powell JI, Dickson R, Furth P, Hunter K, Kucherlapati R, Simon R, Liu ET, Green JE. Initiating Oncogenic Event Determines Gene Expression Patterns of Human Breast Cancer Models. Proc. Natl. Acad. Sci 2002 May;99(10):6967-72.
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Desai KV, Kondaiah P. Androgen ablation results in differential regulation of transforming growth factor-beta isoforms in rat male accessory sex organs and epididymis. J Mol Endocrinol. 2000 Apr;24(2):253-60.
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Desai KV, Flanders KC, Kondaiah P. Expression of transforming growth factor-beta isoforms in the rat male accessory sex organs and epididymis. Cell Tissue Res. 1998 Nov;294(2):271-7.
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Sumathy K, Desai KV, Kondaiah P. Isolation of transforming growth factor-beta 2 cDNA from a fish, Cyprinus carpio by RT-PCR. Gene. 1997 May 20;191(1):103-7.
BOOK CHAPTER
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Edison T. Liu, Sanket Goel, Kartiki Desai and Mathijs Voorhoeve. Genomic Technologies for Systems Biology. Liu ET, Lauffenberger DA. Systems Biomedicine: Concepts and Perspectives. Elsevier and Academic Press. 2009
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Redox State and Gene Regulation in Breast Cancer. Aritra Gupta, Shayantani Chakraborty, Partha Das, Animesh Chowdhury, and Kartiki V. Desai; Springer Nature Singapore Pte Ltd. 2021; S. Chakraborti et al. (eds.), Handbook of Oxidative Stress in Cancer: Mechanistic Aspects, https://doi.org/10.1007/978-981-15-4501-6_98-1
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Chandra V, Tiwari A, Singh RP, Desai KV. Therapeutic intervention of signaling pathways in colorectal cancer. Colon Cancer Diagnosis and Therapy Vol-3, 143-171, 2022
Patent(s)
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US patent.: US2012/0100144 “A biomarker and treatment for cancer” Inventors: Kartiki V DESAI; Edison LIU; Lance D. MILLER
Lab members
Ph.D. Students (Current)
Partha Das
Aritra Gupta
Sayan Ghorai
Monalisa Mukherjee
Saheli Pramanik
Past Members
Ph.D. : Antara Biswas Master's: Amisha Joshi
Project-linked fellows : Shayantani Chakraborty; Pujoyita; Sugandha Basu
Postdoctoral Fellows : Animesh Chowdhury; Md. Moquitul Haque
