My work focuses around bioinformatics and data analysis for the lab. I am currently working on analyzing ChIP-seq and RNA-seq data, along with performing DNA motif-oriented analysis to investigate DNA-binding mechanisms of RelA. In my spare time, I enjoy playing and listening to music, playing and watching sports, and experiencing the variety of cuisines that Los Angeles has to offer.
My current research focuses on how inflammation impacts early B lymphopoiesis and upstream hematopoiesis in aging. By using quantitative muti-color flow cytometry analysis, in vivo bone marrow chimera experiments, mathematical modeling, and single-cell transcriptomic profiling, we can pin down the stage that is substantially impacted by the activation of inflammatory signaling and the discrepancy between cell-surface marker and transcriptomic profiles between developmental stages. My hobbies include film/digital photography and cooking.
Warsaw Fellowship, Jul. 2018, University of California, Los Angeles, CA, United States
Top Poster Award, Jun. 2018, Immunology, Inflammation, Infection, and Transplantation research theme retreat, David Geffen School of Medicine, University of California, Los Angeles, CA, United States
Sidney C. Rittenberg Award, Dec. 2015, University of California, Los Angeles, CA, United States
Koushik Roy, Simon Mitchell, Yi Liu, Sho Ohta, Yu-Sheng Lin, Marie Oliver Metzig, Stephen L Nutt and Alexander Hoffmann, A Regulatory Circuit Controlling the Dynamics of NFκB cRel Transitions B Cells from Proliferation to Plasma Cell Differentiation, Immunity, Immunity. 2019 Mar 19;50(3):616-628
Riku Fagerlund, Marcelo Behar, Karen T. Fortmann, Y. Eason Lin, Jesse D. Vargas, and Alexander Hoffmann, Anatomy of a negative feedback loop: the case of IκBα, J R Soc Interface. 2015 Sep 6;12(110):0262
Tsung-Feng Wu, Tony Minghung Yen, Yuanyuan Han, Yu-Jui Chiu, Eason Y.-S. Lin and Yu-Hwa Lo, A light-sheet microscope compatible with mobile devices for label-free intracellular imaging and biosensing, Lab Chip. 2014 Sep 7;14(17):3341-8
My research aims to investigate factors influencing B cell activation with subsequent proliferation and differentiation. Specifically, I study B cell population dynamics and NFκB regulation associated with immunological disease such as B cell lymphoma. I am particularly interested in induced pathways that affect inflammatory and immune responses. My hobbies include surfing, basketball, hiking, volunteering and traveling.
UT Southwestern Summer Undergraduate Research Fellowship (2019)
UCLA Biochemistry College Honors (2016-present)
Dean’s Honors List (2016-present)
IFC Academic Merit Scholarship Recipient (2018)
Alan MacMorran Memorial Scholarship Award (2017)
My work aims at understanding how macrophages are able to distinguish different stimuli to elicit stimuli-specific responses. Particularly, I am interested in how macrophages differentiate between different ligands by documenting the NF-kB dynamics of these cells in response to stimulation with various ligands. Specific aims of my work focus on measuring NF-kB dynamics in response to both PAMPs and DAMPs recognized by TLR4 and characterizing how tolerance induced by pre-exposure effects NF-kB dynamics in macrophages. During my free time, I enjoy hiking on the various trails in the Los Angeles area.
I am investigating how combinatorial and temporal codes generated by the innate immune signaling network act together to determine stimulus-specific macrophage responses.
1: Sun C*, Luecke S*, Bodda C, Jønsson KL, Cai Y, Zhang BC, Jensen SB, Nordentoft I, Jensen JM, Jakobsen MR, Paludan SR. Cellular Requirements for Sensing and Elimination of Incoming HSV-1 DNA and Capsids. J Interferon Cytokine Res. 2019 Mar 11. doi: 10.1089/jir.2018.0141. *CS and SLcontributed equally
2: Chitadze G, Flüh C, Quabius ES, Freitag-Wolf S, Peters C, Lettau M, Bhat J, Wesch D, Oberg HH, Luecke S, Janssen O, Synowitz M, Held-Feindt J, Kabelitz D. In-depth immunophenotyping of patients with glioblastoma multiforme: Impact of steroid treatment. Oncoimmunology. 2017 Aug 8;6(11):e1358839. doi: 10.1080/2162402X.2017.1358839.
3: Luecke S, Holleufer A, Christensen MH, Jønsson KL, Boni GA, Sørensen LK, Johannsen M, Jakobsen MR, Hartmann R, Paludan SR. cGAS is activated by DNA in a length-dependent manner. EMBO Rep. 2017 Oct;18(10):1707-1715. doi: 10.15252/embr.201744017.
4: Ogunjimi B, Zhang SY, Sørensen KB, Skipper KA, Carter-Timofte M, Kerner G, Luecke S, Prabakaran T, Cai Y, Meester J, Bartholomeus E, Bolar NA, Vandeweyer G, Claes C, Sillis Y, Lorenzo L, Fiorenza RA, Boucherit S, Dielman C, Heynderickx S, Elias G, Kurotova A, Auwera AV, Verstraete L, Lagae L, Verhelst H, Jansen A, Ramet J, Suls A, Smits E, Ceulemans B, Van Laer L, Plat Wilson G, Kreth J, Picard C, Von Bernuth H, Fluss J, Chabrier S, Abel L, Mortier G, Fribourg S, Mikkelsen JG, Casanova JL, Paludan SR, Mogensen TH. Inborn errors in RNA polymerase III underlie severe varicella zoster virus infections. J Clin Invest. 2017 Sep 1;127(9):3543-3556. doi: 10.1172/JCI92280.
5: Luecke S, Paludan SR. Molecular requirements for sensing of intracellular microbial nucleic acids by the innate immune system. Cytokine. 2017 Oct; 98:4-14. doi: 10.1016/j.cyto.2016.10.003. Review.
6: Christensen MH, Jensen SB, Miettinen JJ, Luecke S, Prabakaran T, Reinert LS, Mettenleiter T, Chen ZJ, Knipe DM, Sandri-Goldin RM, Enquist LW, Hartmann R, Mogensen TH, Rice SA, Nyman TA, Matikainen S, Paludan SR. HSV-1 ICP27 targets the TBK1-activated STING signalsome to inhibit virus-induced type I IFN expression. EMBO J. 2016 Jul 1;35(13):1385-99. doi: 10.15252/embj.201593458.
7: Chitadze G, Lettau M, Luecke S, Wang T, Janssen O, Fürst D, Mytilineos J, Wesch D, Oberg HH, Held-Feindt J, Kabelitz D. NKG2D- and T-cell receptor-dependent lysis of malignant glioma cell lines by human γδ T cells: Modulation by temozolomide and A disintegrin and metalloproteases 10 and 17 inhibitors. Oncoimmunology. 2015 Dec 10;5(4):e1093276.
8: Luecke S, Paludan SR. Innate recognition of alphaherpesvirus DNA. Adv Virus Res. 2015;92:63-100. doi: 10.1016/bs.aivir.2014.11.003. Review.
My research aims to use mathematical modeling in the context of high cell-to-cell variability to elucidate the network behavior of the NFκB system for applications in therapeutics. Specific aims of my project include developing novel methods for quantitatively fitting math models to single-cell data, identifying key stimulus-specific NFκB dynamics, pinpointing crucial sources of molecular noise that diminish NFκB information encoding, and understanding the mechanisms for decoding NFκB dynamics into stimulus-specific gene expression. I am particularly passionate about advocating for mental health awareness in graduate education. My hobbies include yoga and photography.
UCLA Grad Slam – Audience Choice Award (2019) (Talk Title: Deciphering the Immune System Code – VIDEO HERE)
UCLA Cellular and Molecular Biology Trainee (2018-present)
NSF Graduate Research Fellowship Program (GRFP) – Honorable Mention (2018)
NFκB is a key regulator of B cell activation with subsequent proliferation and differentiation. cRel is necessary for B cell proliferation and RelA is necessary for B cell differentiation. Misregulated NFκB is associated with immunological disease such as B cell lymphoma.We have developed an integrated system of single cell microscopy tracking and dye dilution analysis tool to quantitatively study B cell population dynamics in terms of cell biological parameters at the single cell level. I am interested to study what is the role of dimer and the dynamic to the B cell fate decision at single cell level and population level.
Boyer/Parvin Postdoctoral Award, Recognizing Excellence in Postdoctoral Research, UCLA, 2019
Best Presentation, Preventive Medicine: Current Perspective, India, 2014
Best Presentation, CSIR-Indian Institute of Chemical Biology on Immunology day, India, 2014
Best Poster, International Symposium on Molecular Signaling, India, 2013
Best Poster, Society of Biological Chemist Symposium, India, 2012
16. Roy K*, Mitchell S*,Liu Y, Ohta S, Lin YS, Metzig MO, Nutt SL, Hoffmann A. A Regulatory Circuit Controlling the Dynamics of NFκB cRel Transitions B Cells from Proliferation to Plasma Cell Differentiation. Immunity. 2019 Mar 19;50(3):616-628. (*Equal contribution)
15. Mitchell S*, Roy K*, Zangle TA, Hoffmann A. Non-genetic origins of cell-to-cell variability in B-lymphocyte proliferation. Proceedings of the National Academy of Sciences, USA (2018), Mar 7. pii: 201715639. doi: 10.1073/pnas.1715639115. (*Equal contribution)
14. Roy K, Shokhirev M, Mitchell S, Hoffmann A. Deriving quantitative cell biological information from dye-dilution lymphocyte proliferation experiments. Methods in Molecular Biology (2018), 2018;1707:81-94
13. Roy K, Mazumder A, Ghosh P, Naiya G, Ghosh B, Roy S. A Peptide-based Synthetic Transcription Factor Selectively Activates Transcription in a Mammalian Cell. Chemical Communications, 2018, 54(13):1611-1614
12. Roy K*, Mandloi S*, Chakrabarti S, Roy S. Cholesterol Corrects Altered Conformation of MHC-II Protein in Leishmania donovani Infected Macrophages: Implication in Therapy. PLOS Neglected Tropical Diseases, 2016 May 23;10(5):e0004710. (*Equal contribution)
11. Ghosh M*, Roy K*, Das Mukherjee D, Chakrabarti G, Roy Choudhury K, Roy S. Leishmania donovani infection enhances lateral mobility of macrophage membrane protein which is reversed by liposomal cholesterol. PLOS Neglected Tropical Diseases, 2014 Dec4;8(12):e3367. (*Equal contribution)
10. Dhar A, Mallick S, Ghosh P, Maiti A, Ahmed I, Bhattacharya S, Mandal T, Manna A, Roy K, Singh S, Nayak DK, Wilder PT, Markowitz J, Weber D, Ghosh MK, Chattopadhyay S, Guha R, Konar A, Bandyopadhyay S, Roy S. Simultaneous Inhibition of Key Growth Pathways in Melanoma Cells and Tumor Regression by a Designed Bidentate Constrained Helical Peptide. Biopolymers-Peptide Science, 2014 Apr; 101(4):344-58.
9. Roy K, Naskar K, Ghosh M, Roy S. Class II MHC/peptide interaction in Leishmania donovani infection: implications in vaccine design. Journal of Immunology, 2014, 192(12):5873-80.
8. Roy K, Ghosh M, Pal TK, Chakrabarti S, Roy S. Cholesterol lowering drug may influence cellular immune response by altering MHC II function. Journal of Lipid Research, 2013, 54(11):3106-15.
(F1000 Faculty: recommended)
7. Ghosh M, Roy K, Roy S. Immunomodulatory effects of antileishmanial drugs. Journal of Antimicrobial Chemotherapy, 2013, 68(12):2834-8.
6. Ghosh M, Solanki AK, Roy K, Dhoke RR, Ashish, Roy S. Carrier protein influences immunodominance hierarchy: implication in vaccine design. Vaccine, 2013, 31(41):4682-8.
5. Mondal S, Bardhan R, Mondal B, Dey A, Mukhopadhyay SS, Roy S, Guha R, Roy K. Synthesis, characterization and in vitro cytotoxicity assessment of hydroxyapatite from different bioresources for tissue engineering application. Bulletin of Material Science, 2012, 35(4), 683-691.
4. Roy S, Ghosh P, Roy NS, Mazumder A, Roy K, Manna AK, Mallick S, Ahmed I. Peptide based Molecules as Protein-Protein Interaction Inhibitors: Tools for Chemical Genetics and Therapy. Current Chemical Biology, 2012, 6(2):145-163. (Review)
3. Mazumder A, Maiti A, Roy K, Roy S. A synthetic peptide mimic of λ-Cro shows sequence-specific binding in vitro and in vivo. ACS Chemical Biology, 2012, 15;7(6):1084-94.
2. Sen S, Roy K, Mukherjee S, Mukhopadhyay R, Roy S. Restoration of IFNγR subunit assembly, IFNγ signaling and parasite clearance in Leishmania donovani infected macrophages: role of membrane cholesterol. PLoS Pathogen, 2011, September 7(9), e1002229.
1. Raha P, Chattopadhyay S, Mukherjee S, Chattopadhyay R, Roy K, Roy S. Alternative sigma factors in the free state are equilibrium mixtures of open and compact conformations. Biochemistry, 2010, 49, 9809–9819.
My research is focused on understanding the mechanisms underlying the activation of gene transcription by NFκB RelA subunit. This is done by elucidating specific attributes of RelA that contribute to its ability to activate and regulate inflammatory gene expression programs by employing a panel of RelA mutations and examining their impact on transcription. By using biochemical analysis, mathematical model-aided analysis approach, RNA and ChIP-seq analyses, we find specialized, non-overlapping functions in DNA binding and transcriptional activation in RelA. My hobbies include playing beach volleyball, badminton, baking, and volunteering for Buddhist temple events.
MIMG Warsaw Fellowship, 2017-2018
Sidney Rittenberg Award, 2015
Fortmann KT, Lewis RD, Ngo KA, Fagerlund R, Hoffmann A. 2015. “A Regulated, Ubiquitin-Independent Degron in IκBα.” Journal of Molecular Biology. PMID: 26191773
Tsui R, Kearns JD, Lynch C, Vu D, Ngo KA, Basak S, Ghosh G, Hoffmann A. 2015. “IκBβ enhances the generation of the low-affinity NFκB/RelA homodimer.” Nature Communications. PMID: 25946967.
Almaden JV, Tsui R, Liu YC, Birnbaum H, Shokhirev MN, Ngo KA, Davis-Turak JC, Otero D, Basak S, Rickert RC, Hoffmann A. 2014. “A pathway switch directs BAFF signaling to distinct NFκB transcription factors in maturing and proliferating B cells”. Cell Reports. PMID: 25497099