Rumela Chakrabarti, Ph.D.

faculty photo
Graduate Group Affiliations

Contact information
BS (Zoology)
National Institute of Immunology, New Delhi, India, 2000.
MS (Genetics)
University of Pune, India, 2001.
PhD (Cellular & Molecular Biology)
Kent State University, 2007.
Permanent link
> Perelman School of Medicine   > Faculty   > Details

Description of Research Expertise

1. We seek to determine how cell intrinsic function of transcription factors dictating cell fate affect normal mammary stem/progenitor cells in mammary gland development as well as cancer stem cells in breast cancer.

2. Unlike other organs such as skin and intestine, mammary gland stem cell niche still remain elusive. Our laboratory is interested in identifying the stem cell niche cells in normal mammary gland as well as in breast cancer. Particularly, we are interested in understanding function and mechanism of how cells such as macrophages, fibroblasts and endothelial cells affect stem cells in normal tissue development and in disease such as breast cancer. We will use mouse genetics, lineage tracing, 2-photon microscopy, in vitro co-culture assays, bioinformatics and other molecular biology assays to determine the functions of microenvironment on stem cells in normal development of breast and in breast cancer.

3. It is known that the behavior of the initial transformed cells after oncogenic insult can dictate the fate of the tumor cells during disease progression. However, cell-of-origin of breast cancer is still poorly understood. We aim to characterize the cell of origin/tumor initiating cells in different subtypes of breast cancer using powerful tools like lineage tracing, whole mount mammary gland 3-D imaging and mouse genetics.

4. Determine how epigenetic modification such as histone modification and/or DNA methylation control fate of normal stem cells and cancer stem cells.

Selected Publications

Kumar Sushil, Srivastav Ratnesh Kumar, Wilkes David W, Ross Taylor, Kim Sabrina, Kowalski Jules, Chatla Srinivas, Zhang Qing, Nayak Anupma, Guha Manti, Fuchs Serge Y, Thomas Christoforos, Chakrabarti Rumela: Estrogen-dependent DLL1-mediated Notch signaling promotes luminal breast cancer. [PMID 30442981] Oncogene 38(12): 2092-2107, Mar 2019.

Aref-Eshghi Erfan, Bend Eric G, Colaiacovo Samantha, Caudle Michelle, Chakrabarti Rana, Napier Melanie, Brick Lauren, Brady Lauren, Carere Deanna Alexis, Levy Michael A, Kerkhof Jennifer, Stuart Alan, Saleh Maha, Beaudet Arthur L, Li Chumei, Kozenko Maryia, Karp Natalya, Prasad Chitra, Siu Victoria Mok, Tarnopolsky Mark A, Ainsworth Peter J, Lin Hanxin, Rodenhiser David I, Krantz Ian D, Deardorff Matthew A, Schwartz Charles E, Sadikovic Bekim: Diagnostic Utility of Genome-wide DNA Methylation Testing in Genetically Unsolved Individuals with Suspected Hereditary Conditions. [PMID 30929737] American journal of human genetics 104(4): 685-700, Apr 2019.

Singh Snahlata, Elenio Emily, Leu Nicolae A, Romano Rose-Anne, Vaughan Andrew E, DeRiso Jennifer, Surendran Kameswaran, Chakrabarti Rumela: A new Elf5 BAC transgenic mouse model for tracing Elf5 cell lineages in adult tissues. [PMID 31002388 ] FEBS letters 593(10): 1030-1039, May 2019.

Singh Snahlata, Chakrabarti Rumela: Consequences of EMT-Driven Changes in the Immune Microenvironment of Breast Cancer and Therapeutic Response of Cancer Cells. [PMID 31075939] Journal of clinical medicine 8(5), May 2019.

Guha, M., Srinivasan, S., Raman, P., Jiang, Y., Kaufman, B. A., Taylor, D., Dong, D., Chakrabarti, R., Picard, M., Carstens, R. P., Kijima, Y., Feldman, M., Avadhani, N. G.: Aggressive triple negative breast cancers have unique molecular signature on the basis of mitochondrial genetic and functional defects [PMID 29309924] Biochim Biophys Acta 1864(4 Pt A): 1060-1071, 2018.

Chakrabarti Rumela, Celià-Terrassa Toni, Kumar Sushil, Hang Xiang, Wei Yong, Choudhury Abrar, Hwang Julie, Peng Jia, Nixon Briana, Grady John J, DeCoste Christina, Gao Jie, van Es Johan H, Li Ming O, Aifantis Iannis, Clevers Hans, Kang Yibin: Notch ligand Dll1 mediates cross-talk between mammary stem cells and the macrophageal niche. [PMID 29773667] Science (New York, N.Y.) 360(6396), 06 2018.

Kumar Sushil, Wilkes David W, Samuel Nina, Blanco Mario Andres, Nayak Anupma, Alicea-Torres Kevin, Gluck Christian, Sinha Satrajit, Gabrilovich Dmitry, Chakrabarti Rumela: DeltaNp63-driven recruitment of myeloid-derived suppressor cells promotes metastasis in triple-negative breast cancer. [PMID 30295647] The Journal of clinical investigation 128(11): 5095-5109, Nov 2018.

Celia-Terrassa, T., Liu, D. D., Choudhury, A., Hang, X., Wei, Y., Zamalloa, J., Alfaro-Aco, R., Chakrabarti, R., Jiang, Y. Z., Koh, B. I., Smith, H. A., DeCoste, C., Li, J. J., Shao, Z. M., Kang, Y.: Normal and cancerous mammary stem cells evade interferon-induced constraint through the miR-199a-LCOR axis [PMID 28530657] Nat Cell Biol 19(6): 711-723, 2017.

Chakrabarti R, Kang Y: Transplantable mouse tumor models of breast cancer metastasis. [PMID 25636479] Methods in molecular biology (Clifton, N.J.) 1267: 367-80, 2015.

Mathias RA, Greco TM, Oberstein A, Budayeva HG, Chakrabarti R, Rowland EA, Kang Y, Shenk T, Cristea IM: Sirtuin 4 is a lipoamidase regulating pyruvate dehydrogenase complex activity.[PMID 25525879] Cell 159(7): 1615-25, Dec 2014.

Cicchini M, Chakrabarti R, Kongara S, Price S, Nahar R, Lozy F, Zhong H, Vazquez A, Kang Y, Karantza V: Autophagy regulator BECN1 suppresses mammary tumorigenesis driven by WNT1 activation and following parity. [PMID 25483966 ] Autophagy 10(11): 2036-52, 2014.

Chakrabarti R, Wei Y, Hwang J, Hang X, Andres Blanco M, Choudhury A, Tiede B, Romano RA, DeCoste C, Mercatali L, Ibrahim T, Amadori D, Kannan N, Eaves CJ, Sinha S, Kang Y: DeltaNp63 promotes stem cell activity in mammary gland development and basal-like breast cancer by enhancing Fzd7 expression and Wnt signalling.[PMID 25241036 ] Nature cell biology 16(10): 1004-15, 1-13, Oct 2014.

Wan L, Lu X, Yuan S, Wei Y, Guo F, Shen M, Yuan M, Chakrabarti R, Hua Y, Smith HA, Blanco MA, Chekmareva M, Wu H, Bronson RT, Haffty BG, Xing Y, Kang Y: MTDH-SND1 interaction is crucial for expansion and activity of tumor-initiating cells in diverse oncogene- and carcinogen-induced mammary tumors. [PMID 24981741] Cancer cell 26(1): 92-105, Jul 2014.

Chakrabarti R, Hwang J, Andres Blanco M, Wei Y, Lukačišin M, Romano RA, Smalley K, Liu S, Yang Q, Ibrahim T, Mercatali L, Amadori D, Haffty BG, Sinha S, Kang Y: Elf5 inhibits the epithelial-mesenchymal transition in mammary gland development and breast cancer metastasis by transcriptionally repressing Snail2. [PMID 23086238] Nature cell biology 14(11): 1212-22, Nov 2012.

Chakrabarti R, Wei Y, Romano RA, DeCoste C, Kang Y, Sinha S: Elf5 regulates mammary gland stem/progenitor cell fate by influencing notch signaling.[PMID 22523003] Stem cells (Dayton, Ohio) 30(7): 1496-508, Jul 2012.

Yusuf D, Butland SL, Swanson MI, Bolotin E, Ticoll A, Cheung WA, Zhang XY, Dickman CT, Fulton DL, Lim JS, Schnabl JM, Ramos OH, Vasseur-Cognet M, de Leeuw CN, Simpson EM, Ryffel GU, Lam EW, Kist R, Wilson MS, Marco-Ferreres R, Brosens JJ, Beccari LL, Bovolenta P, Benayoun BA, Monteiro LJ, Schwenen HD, Grontved L, Wederell E, Mandrup S, Veitia RA, Chakravarthy H, Hoodless PA, Mancarelli MM, Torbett BE, Banham AH, Reddy SP, Cullum RL, Liedtke M, Tschan MP, Vaz M, Rizzino A, Zannini M, Frietze S, Farnham PJ, Eijkelenboom A, Brown PJ, Laperrière D, Leprince D, de Cristofaro T, Prince KL, Putker M, del Peso L, Camenisch G, Wenger RH, Mikula M, Rozendaal M, Mader S, Ostrowski J, Rhodes SJ, Van Rechem C, Boulay G, Olechnowicz SW, Breslin MB, Lan MS, Nanan KK, Wegner M, Hou J, Mullen RD, Colvin SC, Noy PJ, Webb CF, Witek ME, Ferrell S, Daniel JM, Park J, Waldman SA, Peet DJ, Taggart M, Jayaraman PS, Karrich JJ, Blom B, Vesuna F, O'Geen H, Sun Y, Gronostajski RM, Woodcroft MW, Hough MR, Chen E, Europe-Finner GN, Karolczak-Bayatti M, Bailey J, Hankinson O, Raman V, LeBrun DP, Biswal S, Harvey CJ, DeBruyne JP, Hogenesch JB, Hevner RF, Héligon C, Luo XM, Blank MC, Millen KJ, Sharlin DS, Forrest D, Dahlman-Wright K, Zhao C, Mishima Y, Sinha S, Chakrabarti R, Portales-Casamar E, Sladek FM, Bradley PH, Wasserman WW: The transcription factor encyclopedia. [PMID 22458515] Genome biology 13(3): R24, 2012.

Escamilla-Hernandez R, Chakrabarti R, Romano RA, Smalley K, Zhu Q, Lai W, Halfon MS, Buck MJ, Sinha S: Genome-wide search identifies Ccnd2 as a direct transcriptional target of Elf5 in mouse mammary gland.[PMID 20831799] BMC molecular biology 11: 68, 2010.

Chakrabarti R, Shepardson S, Karmakar M, Trdan R, Walker J, Shandilya R, Stewart D, Vijayaraghavan S, Hoeh W: Extra-mitochondrial localization and likely reproductive function of a female-transmitted cytochrome c oxidase subunit II protein. [PMID 19469787] Development, growth & differentiation 51(5): 511-9, Jun 2009.

Choi YS, Chakrabarti R, Escamilla-Hernandez R, Sinha S: Elf5 conditional knockout mice reveal its role as a master regulator in mammary alveolar development: failure of Stat5 activation and functional differentiation in the absence of Elf5.[PMID 19269284] Developmental biology 329(2): 227-41, May 2009.

Chakrabarti R, Walker JM, Chapman EG, Shepardson SP, Trdan RJ, Curole JP, Watters GT, Stewart DT, Vijayaraghavan S, Hoeh WR: Reproductive function for a C-terminus extended, male-transmitted cytochrome c oxidase subunit II protein expressed in both spermatozoa and eggs. [PMID 17950289] FEBS letters 581(27): 5213-9, Nov 2007.

Chakrabarti R, Cheng L, Puri P, Soler D, Vijayaraghavan S: Protein phosphatase PP1 gamma 2 in sperm morphogenesis and epididymal initiation of sperm motility. [PMID 17589781] Asian journal of andrology 9(4): 445-52, Jul 2007.

Vijayaraghavan S, Chakrabarti R, Myers K: Regulation of sperm function by protein phosphatase PP1gamma2. [PMID 17566266] Society of Reproduction and Fertility supplement 63: 111-21, 2007.

Chakrabarti R, Kline D, Lu J, Orth J, Pilder S, Vijayaraghavan S: Analysis of Ppp1cc-null mice suggests a role for PP1gamma2 in sperm morphogenesis. [PMID 17301292] Biology of reproduction 76(6): 992-1001, Jun 2007.

Chakrabarti R, Walker JM, Stewart DT, Trdan RJ, Vijayaraghavan S, Curole JP, Hoeh WR: Presence of a unique male-specific extension of C-terminus to the cytochrome c oxidase subunit II protein coded by the male-transmitted mitochondrial genome of Venustaconcha ellipsiformis (Bivalvia: Unionoidea). [PMID 16414043] FEBS letters 580(3): 862-6, Feb 2006.

Huang Z, Somanath PR, Chakrabarti R, Eddy EM, Vijayaraghavan S: Changes in intracellular distribution and activity of protein phosphatase PP1gamma2 and its regulating proteins in spermatozoa lacking AKAP4. [PMID 15385410] Biology of reproduction 72(2): 384-92, Feb 2005.

back to top
Last updated: 08/05/2019
The Trustees of the University of Pennsylvania