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Deepshika Ramanan


The Ramanan lab is interested in studying the impact of breastfeeding on maternal and offspring immunity. A mother’s microbiota, diet, exposure to infections, and other environmental factors are crucial for a newborn’s early development and long-term immune health. But it remains unclear exactly how these maternal factors influence a person’s susceptibility to autoimmune disorders such as inflammatory bowel disease later on. Studying the underlying biological mechanisms will help us better understand the causes of autoimmune and inflammatory diseases and enable researchers to develop interventions to prevent and treat them. How the maternal immune system changes during pregnancy and breastfeeding is also poorly understood. Studying the ways immune cells function during these crucial times, especially in the intestine and the mammary glands, will help advance our understanding of women’s health. Using a combination of single-cell techniques, metabolomics, and metagenomics in mouse models, and human tissues our team is interested in understanding how immune cell changes during pregnancy and breastfeeding influences both maternal health and offspring immunity for multiple generations.

Select Publications

  • Ramanan D, Pratama A, Zhu Y, Venezia O, Sassone-Corsi M, Chowdhary K, Galvan-Pena S, Sefik E, Brown C, Gelineau A, Mathis D, Benoist C. (2023) Regulatory T cells in the face of the microbiota. Nature Reviews Immunology
  • Ramanan D, Chowdhary K, Candeias SM, Sassone-Corsi M, Mathis D, Benoist C. (2023) Homeostatic, repertoire and transcriptional relationships between colon T regulatory cell subsets. PNAS 12;120(50):e2311566120 (Preprint at bioRxiv May 2023)
  • Chowdhary K, Leon J, Ramanan D, Mathis D, Benoist C. (2023) An interwoven network of transcription factors, with divergent influences from Foxp3, underlies Treg diversity. Preprint at bioRxiv
  • Wu M, Zheng W, Song X, Bao B, Wang Y, Ramanan D, Yang D, Li R, Macbeth JC, Do EA, Andrade WA, Yang T, Cho H, Gazzaniga FS, Ilves M, Coronado D, Thompson C, Hang S, Chiu IM, Moffitt JR, Hsiao A, Mekalanos JJ, Benoist C, Kasper DL. (2023) Microbiome induced complement synthesized in the gut protects against enteric infections. Preprint at bioRxiv
  • Sassone-Corsi M, Azriel S, Simon A, Ramanan D, Ortiz-Lopez A, Chen F, Yissachar N, Mathis D, Benoist C. (2022) Sequestration of gut pathobionts in intraluminal casts, a mechanism to avoid dysregulated T cell activation by pathobionts. PNAS. 11;119(41):e2209624119
  • Yan Y, Ramanan D, Rozenberg M, McGovern K, Rastelli D, Vijaykumar B, Yaghi O, Voisin T, Mosaheb M, Chiu I, Itzkovitz S, Rao M, Mathis D, Benoist C. (2021) Neuron-produced IL6 is at the center of a microbiota-neuron-Treg triangle in the gut. Immunity. 54(3):499-513.
  • Ramanan D, Sefik E, Galván-Peña S, Wu M, Yang L, Yang Z, Kostic A, Golovkina TV, Kasper DL, Mathis D, Benoist C. (2020) An Immunologic Mode of Multigenerational Transmission Governs a Gut Treg Setpoint. Cell. S0092-8674(20)30493-1.
  • DiSpirito JR*, Zemmour D*, Ramanan D, Cho J, Zilionis R, Klein AM, Benoist C, Mathis D. (2018) Molecular Diversification of Regulatory T cells in Nonlymphoid Tissues. Science Immunology. 3(27):eaat5861. *co-first authors
  • Wong SY*, Coffre M*, Ramanan D*, Hines MJ, Gomez LE, Peters LA, Schadt EE, Koralov SB, Cadwell K. (2018) B Cell Defects Observed in Nod2 Kockout Mice Are a Consequence of a Dock2 Mutation Frequently Found in Inbred Strains. Journal of Immunology. 201(5):1442-1451. *co-first authors.
  • Ramanan D*, Bowcutt R*, Lee SC, Tang MS, Kurtz ZD, Ding Y, Honda K, Gause WC, Blaser MJ, Bonneau RA, Lim YA, Loke P, Cadwell K. (2016) Helminth infection promotes colonization resistance via type 2 immunity. Science. 352(6285):608-12. *co-first authors.
  • Ramanan D, Cadwell K. (2016) Intrinsic defense mechanisms of the intestinal epithelium. Cell Host and Microbe. 19(4):434-41.
  • Ramanan D, Tang MS, Bowcutt R, Loke P, Cadwell K. (2014) Bacterial sensor Nod2 prevents inflammation of the small intestine by restricting the expansion of the commensal Bacteroides vulgatus. Immunity. 41(2):311- 324.
  • Marchiando AM, Ramanan D, Ding Y, Gomez LE, Hubbard-Lucey VM, Maurer K, Wang C, Ziel, JW, Rooijen NV, Nunez G, Finlay BB, Mysorekar IU, Cadwell K. (2013) Atg16L1 deficiency enhances resistance to an enteric bacterial infection. Cell Host and Microbe. 14(2):216-24.
  • Zhang Z, Wu Y, Wang Z, Dunning FM, Rehfuss J, Ramanan D, Chapman ER, Jackson MB. (2010) Release mode of large and small dense-core vesicles specified by different synaptotagmin isoforms in PC12 cells. Mol Biol Cell. 22(13):2324-36.


Deepshika “Shika” Ramanan, PhD, is an Assistant professor at the NOMIS Center for Immunobiology and Microbial Pathogenesis at the Salk Institute. Her area of interests include maternal transfer of immunity, and the impact of breastmilk on offspring immune health, particularly infection and autoimmunity. Her lab also studies how maternal immunity can be transferred for multiple generations, and how the maternal immune system changes during pregnancy and breastfeeding. Ramanan earned her B.Sc. at Winona State University and PhD in immunology and inflammation at New York University. She completed her postdoctoral fellowship at Harvard Medical School and has received numerous awards including the Damon Runyon Dale F. Frey Breakthrough Scientist Award and STAT Wunderkind Award.

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