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अखिल भारतीय आयुर्विज्ञान संस्थान, नई दिल्ली
All India Institute Of Medical Sciences, New Delhi

Dr. Subhradip Karmakar

Address: Room no: 3020, Teaching block,

                Department of Biochemistry,

                AIIMS, New Delhi.

Phone: 011-26593314

Email id: This email address is being protected from spambots. You need JavaScript enabled to view it. , This email address is being protected from spambots. You need JavaScript enabled to view it.

Social media links

  1. 1.      https://www.linkedin.com/in/subhradip-karmakar-367b437?trk=hp-identity-name
  2. 2.      https://scholar.google.com/citations?user=v0HVsbwAAAAJ&hl=en

 

Academic Details:

Degree

Subject

University/ Institution

Year

PhD

Biochemistry

AIIMS, New Delhi

2004

MSc

Medical Biochemistry

JIPMER, Pondicherry

1998

BSc(Hons)

Chemistry

Calcutta University

1995

 

Positions held:

Position

Department

University/ Institution

Dates

Assistant Professor

Biochemistry

AIIMS, New Delhi

Since Nov 2014

Staff Scientist

Hem & Oncology

University of Chicago, USA

2011-2014

Research Associate

Geno & Sys Biol

University of Chicago, USA

2009-2011

Sr Post Doc

Genetics

Yale University

2005-2009

 

 

 

Notable Awards and Society Memberships

1)   Best Poster award in “Drug Discovery and Development 2015” held at Hyderabad

2)   Indian National Science Academy(INSA) young scientist award (2005) (Highest level national award for young scientist)

3)   Best Postgraduate in Clinical research award in PhD, 2004

4)   Best poster award, Globin Switching meeting Asilomar CA 2008

5)   Best outgoing Student Award(Honor of Merit) for University 1st Rank in Masters(MS)

6)   Endowment Award in MS for best overall performance

7)    Best Postgraduate Alumni Award (1995-1998) in Dept of Biochemistry, India

8)    (1998,1999) {CSIR National Level Merit Exam for PhD fellowship}

9)   SLET(state level lectureship examination for universities)

10)  Best Oral presentation award, Indian Immunology Society meeting (2001)

 

 

EDITORIAL AND REVIEWED PAPERS

  • Associate Editor: Journal of Biomedical Sciences(http://www.jbiomeds.com)
  • Associate Editor: J of Single Cell Biology(Omics publication group)
  • Associate Editor: Annals of Clinical and Laboratory Research.
  • Journal of Clinical Pathology(http://www.jcp.bmj.com)
  • Journal of Molecular Cell Biology(http://www. jmcb. oxfordjournals.org)
  • Chinese J of Cancer Research
  • Willey Science Advisor

                                               

RESEARCH PRESENTATIONS

  • IACR meeting New Delhi 2016
  • SelectBio conference on NGS, Bangalore, 2015
  • India Association for Cancer Research(IACR), Jaipur, 2015
  • The American Society of Hematology meeting, 2006, Florida

 

  • American Society of Hematology meeting, 2007, Atlanta
  • ENCODE consortium, Bethesda , Maryland 2010,2011

 

 

  • American Urological Association, Annual Meeting; May 14-19, Washington,2011
  • Globin Switching meeting, Asilomar, CA 2008
  • Congress on Reproductive Immunology, Rhodes Island, Greece 2003
  • International Congress on Reproductive Immunology, Opatija, Croatia, 2001

 

 

Research Focus of the Lab

Our Lab is currently engaged in two areas of research.

  1. 1.      Human Trophoblast Biology
  2. 2.      Role of TET protens in Acute Myeloid Leukaemia(AML)
  3. 3.      Blood stem cell biology (Proteomics and Genomics)

Understanding the mechanisms of trophoblast invasion and differentiation and its control by cytokines and hormones:

Trophoblast cells forming the outer trophoectodermal epithelial layer of the developing blastocysts with stem cell like pluripotent properties are pseudo-malignant in nature. These cells invade uterine endometrium and remodel its vasculature to ensure and establish the fetal-maternal unit for blood flow, waste-exchange and cytokine-hormonal cross talks  . Trophoblast invasion is tempo-spatially regulated and both fetal and maternal factors orchestrate this delicate and complicated process. Our lab is actively engaged to understand the molecular mechanisms that drive this process. Using human trophoblast cells isolated from human placenta at term and those from early gestation following terminated pregnancies as well as trophoblast derived cell lines, we address the problems using a systems biology approach.

Currently four members of the lab are addressing the different aspect of this problem. Mr Sunil Kumar Singh Rawat (MSc Biochemistry student) is investigating the role of PPAR alpha transcription factor during trophoblast invasion. Mr Sovon Acharya (MSc Biotechnology student) is investigating the role of TET proteins in trophoblast invasion and differentiation. Dr AnkitaJain(Jr Resident, MD fellow, Biochemistry) is studying role of Glucocorticoid hormones and maternal stress in trophoblast invasion and differentiation. Dr Ashok Ahirwar(Sr Resident)  is investigating the role of CO signalling during trophoblast invasion .

Role of TET proteins in Acute Myeloid Leukaemia(AML)

TET(Ten Eleven Translocase) are dedicated DNA de-methylase that converts 5 Methyl Cytosine to un-methylated Cytosine through an iterative process, thus influencing the epigenetic landscape of the cell. Our lab is interested to know the involvement of this TET proteins in blood cell disorders like AML, MDS and other leukaemia. Previous work done in this lab identified TET2 to be restricted to the hematopoietic compartment with different TET2 transcript  switching during the stem cell lineage commitment. We are actively investigating the various driver mutations of TET2 in AML and its association with its function using both wet/dry lab approach as how it might contribute to the disease biology.

Dr Karthikeyan(SrResident and PhD fellow) is investigating the effect of TET2 hotspot mutations and its effect on global DNA methylation/hydroxymethylation  in AML. Using a multi-pronged approach we are investigating the role of TET2 variants and its likelihood to predispose to cancer by analysing cis-eQTLs.

Dr AshikhSetty (Sr Resident and PhD fellow) is studying the role of TET proteins in RNA hydroxymethylation, its association with disease pathology and to explore the genome wide differential hydroxymethyl signature in AML using TAB-Seq(TET assisted bi-sulphite sequencing)  We also plan to identify and characterizecytosinehydroxylmethyl binding proteins using proteomic approach.

 

List of Lab members (Including technicians and attendants)

  1. 1.      Mr Sunil Singh Rawat(MSc student)
  2. 2.      Mr Sovon Acharya (MSc Biotechnology)
  3. 3.      Dr Ankita Raj (JR and MD student)
  4. 4.      Dr KarthikeyanPethusamy MD (SR and PhD student)
  5. 5.      Dr AshikhSeethy (SR and PhD student)
  6. 6.      Dr Ashok Ahirwar (SR)
  7. 7.      Dr Ruby Dhar (Independent WoSA Fellow)
  8. 8.      Sunil Kandpal (Lab techie)

Positions Available

JRF -01 (On TET-ology)

SRF- 01 (Developing algorithms for variant calling)

Summer trainee -01

Key publications:

1)      ReducedDOCK4 expression leads to erythroid dysplasia in myelodysplastic syndromes  PNAS (USA), October  2015

2)      Guoqiang Li1*, Weimin Ci1*, Subhradip Karmakar2*et.al. (*equal contributions) Cancer Cell(March 20th2014)

3)      SubhradipKarmakar* Cell Based Immunotherapy: As a promising Futuristic solution to effective cancer therapy .Single Cell Biology2014, 3: 105 (* corresponding author)

4)      L Liu*, SubhradipKarmakar*, R Dhar, M Mahajan, A Choudhury, S Weissman, BS Pace (*equal contributions), 8 (11), e78253; PLoS One2013(November )

5)      An integrated encyclopedia of DNA elements in human genome. vol. 489 Pg : 57-74. doi:10.1038/nature11247 (ENCODE Consortium) Nature 2012

6)      ChIP-Seq guidelines and practices of ENCODE and modENCODEconsortia.Sep;22(9):1813-31(ENCODE Consortium) Genome Res. 2012

7)      M.McNerney, C.Brown,X.Wang, SubhradipKarmakar, C Bandlamudi,S Yu, Kevin P White.  (doi:10.1182/blood-2012-04-426965 Dec 3) Blood 2012

8)      A User's guide to the encyclopedia of DNA elements(ENCODE) Apr;9(4):e1001046. Epub 2011 Apr 19. (ENCODE Consortium)PLoS Biol. 2011

9)      SubhradipKarmakar, Milind Mahajan, Vincent Schulz,GokulBoyapatyandShermanWeissman  (31 Aug 2010)doi:10.1038/emboj.2010.204 Article) EMBO Journal 2010

10)  Mahajan MC, SubhradipKarmakar, NewburgerPE, Krause DS, Weissman SM. Oct;37(10):1143-1156.e3. ExpHematology 2009

11)  Mahajan MC, SubhradipKarmakar,Weissman SM.  Nov 1;102(4):801-10. JCell Biochemistry 2007

12)  SubhradipKarmakar, Das C. Dec;64(1-2):9-29.JReprodImmunol 2004

13)  SubhradipKarmakar, Dhar R, Das C.. 2004 Dec 31;279(53):55297-307. Epub Sep 23. J BiolChem 2004

13)Dhar R, SubhradipKarmakar, Sriraman R, Talwar GP, Das C. May;51(5):358-63. Am J ReprodImmunol 2004

14)Subhradip Karmakar, Das C. Oct;48(4):210-9.Am J ReprodImmunol 2002

 

Funding agencies:

  • DST early career
  • AIIMS intramural
  • DST-extramural

 

1.      Dr. KarthikeyanPethusamy, MD - Senior Resident

 

Dr. Karthikeyan completed his M.D in Biochemistry from Maulana Azad Medical College, New Delhi and MBBS from Kanyakumari Government Medical College, Tamil Nadu. Currently he is working on the effect of TET-2 protein in the pathogenesis of Acute Myeloid Leukemia.

 

2.   Dr. Ashok Kumar Ahirwar M.D. - Senior Resident

 

Dr. Ashok Kumar Ahirwar has completed his MBBS from GMC, Bhopal (MP) in 2011 and MD in Biochemistry from Lady Hardinge Medical College, New Delhi in 2014. He is currently working as Senior Resident in the Department of Biochemistry, AIIMS, New Delhi. His current area of research is Insulin Resistance and Endothelial dysfunction in Metabolic Syndrome, Diabetes Mellitus, Hypertension, dyslipidemia and obesity associated co-morbidities. Also working on the adipokines profile of adipocytes in obesity. He is also working on the field of Endocrinology to study the effect of Thyroid hormones (T3, T4, TSH) on Insulin resistance and adipokines profile in obesity. Also working on  carbon mono-oxide (CO) signaling on trophoblast invasion in humans under the guidance of Dr. SubhradipKarmakar. He has got ICMR MD/MS thesis grant. He won the best poster award in AMBICON, Bhubaneswar 2012.

His recent publications are-

1) Ahirwar AK, Jain A, Goswami B, Bhatnagar MK, Bhatacharjee J. Imbalance between protective (adiponectin) and prothrombotic (Plasminogen Activator Inhibitor-1) adipokines in metabolic syndrome. Diab Met Syndr: Clin Res Rev (2014);8(3):152-5.

 2) Ahirwar AK, Jain A, Singh A Goswami B, Bhatnagar MK, Bhatacharjee J. The study of markers of endothelial dysfunction in metabolic syndrome. HormMolBiolClin Invest; 2015(3).

3) Ahirwar AK, Keshri PK, Agarwal S, Jain A, Ahirwar P, Prabhakar N, Jain N, Goswami B, Bhatnagar MK, Bhatacharjee J. The Study of Insulin Resistance in the Pathogenesis of Metabolic Syndrome. Journal of Medical Erudite. 2015;3(1):1-3.

4)

Dr. Ashok Kumar Ahirwar has completed his MBBS from GMC, Bhopal (MP) in 2011 and MD in Biochemistry from Lady Hardinge Medical College, New Delhi in 2014. He is currently working as Senior Resident in the Department of Biochemistry, AIIMS, New Delhi. His current area of research is Insulin Resistance and Endothelial dysfunction in Metabolic Syndrome, Diabetes Mellitus, Hypertension, dyslipidemia and obesity associated co-morbidities. Also working on the adipokines profile of adipocytes in obesity. He is also working on the field of Endocrinology to study the effect of Thyroid hormones (T3, T4, TSH) on Insulin resistance and adipokines profile in obesity. Also working on  carbon mono-oxide (CO) signaling on trophoblast invasion in humans under the guidance of Dr. SubhradipKarmakar. He has got ICMR MD/MS thesis grant. He won the best poster award in AMBICON, Bhubaneswar 2012.

His recent publications are-

1) Ahirwar AK, Jain A, Goswami B, Bhatnagar MK, Bhatacharjee J. Imbalance between protective (adiponectin) and prothrombotic (Plasminogen Activator Inhibitor-1) adipokines in metabolic syndrome. Diab Met Syndr: Clin Res Rev (2014);8(3):152-5.

 2) Ahirwar AK, Jain A, Singh A Goswami B, Bhatnagar MK, Bhatacharjee J. The study of markers of endothelial dysfunction in metabolic syndrome. HormMolBiolClin Invest; 2015(3).

3) Ahirwar AK, Keshri PK, Agarwal S, Jain A, Ahirwar P, Prabhakar N, Jain N, Goswami B, Bhatnagar MK, Bhatacharjee J. The Study of Insulin Resistance in the Pathogenesis of Metabolic Syndrome. Journal of Medical Erudite. 2015;3(1):1-3.

4) Bherwani S,Saumya AS,Ahirwar AK,Sandhya AS,Prajapat B,Patel S,Singh R,Ghotekar LH. The association of folic acid deficiency and diabetic nephropathy in patients with type 2 diabetes mellitus.EndocrMetab Immune Disord Drug Targets. 2016.

5) Prabhakar N, Agrawal A, Jain N, Ahirwar AK. Effect of perinatal asphyxia on level of thyroid hormones in term neonates. International Journal of Contemporary Pediatrics. 2016 Jul;3(3):882-6.

 

3. Dr AshikhSeethy MD Senior Resident and PhD Scholar

 

AshikhSeethy completed his MBBS from MOSC Medical College, Cochin in 2013 and MD in Biochemistry from Maulana Azad Medical College, New Delhi in 2016. During MD, he studied the role of tight junction protein- Claudin-6 in breast cancer cells and its regulation by CpG island methylation and hydroxymethylation. He was awarded the best oral paper presentation at the International Conference on Stem Cells and Cancer (ICSCC-2015) and the award presentation price at the National Level AMBICON-2015. He had won post graduate quiz competitions in Biochemistry at North Zone AMBICON (2014), National Level AMBICON (2014, 2015) and ACBICON (2015). He was also acknowledged as a reviewer of the text book "Biochemistry"-8th ed, by LubertStryer. His current interest is in the role of TET mediated base modifications in tumorigenesis.

   4. Dr. Ankita Raj, Junior Resident

 She joined Department of Biochemistry in July 2015 as MD student. She has completed her MBBS from S.V.S Medical College, Mahbubnagar, Telangana. She is doing her MD Thesis under guidance of Dr. SubhradipKarmakar. Her current area of research is in “Role of cortisol on Human trophoblast cell invasion and differentiation”

 

5.Mr Sunil Singh, M.Sc. student

 

Mr. Sunil Singh, currently pursuing his M.Sc. in Biochemistry, AIIMS. He completed his graduation in Biochemistry from Deshbandhu College (University of Delhi). His M.Sc. thesis title is “Role of Peroxisome Proliferator Activated Receptor alpha (PPAR-α) in Human Trophoblast Invasion”

 

 

 

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