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Understanding and engineering microbe-immune interactions
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Research
Our work focuses on understanding and engineering the interactions between commensal skin bacteria and the immune system.
Mechanisms of skin microbe-immune crosstalk
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Commensal microbes are critical for immune education. Skin bacteria, including Staphylococcus epidermidis and Corynebacterium species, can generate specific T cell responses, simply by colonizing the skin. However, commensal microbiota are not invasive and live outside our epithelial barriers. So, how are they seen by the immune system? And how do different bacteria drive distinct T cell outcomes?
We use a combination of bacterial genetics and in vivo immune profiling in mice to define the mechanisms of microbe-immune communication. We are also developing genetic tools to enable investigation of currently intractable commensal skin bacteria
Immunologic output of microbial communities
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Commensal bacteria live within a complex ecosystem of other microbes. How does microbial ecology impact the host immune response? And how do immune responses to different commensal bacteria synergize or antagonize?
These have been challenging questions because it is difficult to follow the immune responses to multiple members of a microbial community simultaneously. We are developing tools that allow us to define the combinatorial T cell responses to skin microbial communities.
Engineering commensal-based therapeutics
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Immune modulation is critical to the treatment of human diseases. We have shown that commensal S. epidermidis can be engineered to elicit tumor-specific CD8+ T cells. Colonization of mice with these bacteria can cure established mouse tumors when given in combination with immune checkpoint blockade. Our goal is to mine and engineer skin commensal bacteria for novel immune-modulating behaviors, in order to develop live immunotherapies.
People
erin chen
Y. Erin Chen
Principal Investigator
erinchen at yeclab dot org
I am an Assistant Professor at MIT Biology, Core Faculty at the Broad Institute, and Attending Dermatologist at MGH. I completed my MD-PhD in the Harvard-MIT HST program. My PhD in the laboratory of Michael Laub focused on how bacteria use kinase and phosphatase pathways to generate complex behaviors, such as asymmetric cell division. I then completed my Dermatology residency at UCSF and joined Michael Fischbach's laboratory to work on how skin commensal bacteria interact with the immune system. We discovered that we could rewire one of these commensal-immune interactions to generate anti-cancer T cells. In my lab, we continue to dissect the mechanisms of commensal-immune crosstalk and use these insights to engineer novel therapies. I have been the recipient of the Dermatology Foundation Research Award, the AP Giannini Postdoctoral Fellowship, and the HHMI Hanna H. Gray Fellowship.
ana vergara
Ana Vergara
Administrative Assistant
vergara at broadinstitute dot org
I grew up in Asunción, Paraguay but went to college in Boston and got my degree in Politics, Philosophy and Economics. Upon graduation, I went back to Paraguay to work for the Ministry of Public Works and Communications as a monitoring and evaluation assistant for water and sanitation projects. In October 2022, I returned to Boston and started working at Broad Institute as an administrative assistant.
caleb staudinger
Caleb Staudinger
Lab Manager
cstaudin at broadinstitute dot org
I grew up in upstate New York before attending Carnegie Mellon University, where I graduated with a degree in Biological Sciences. I have since worked as a research technician at Boston Children's Hospital in the study of thrombosis and hemostasis and as a lab manager in the study of glycobiology and immunology at Florida International University. In the YEC Lab, I am the lab manager. I am also in charge of collaborative technology development for microbe-host interactions and commensal-based vaccine platforms.
kevin lenzi
Kevin Lenzi
Graduate student / MIT Bio
lenzi at broadinstitute dot org
I grew up in Massachusetts and went to Northeastern university where I graduated with degrees in Cell and Molecular Biology and Philosophy. While at Northeastern, I worked in gene editing, cancer, and immunology through two co-ops at Tango Therapeutics and Vor Biopharma, and as an undergraduate researcher in Arlene Sharpe's laboratory at Harvard Medical School. I started my PhD in biology at MIT in fall 2022, and I joined the YEC lab in spring 2023. I am interested in investigating the cellular mechanisms by which cytotoxic T cells are activated by certain skin commensal microbes. Outside of lab, I like to bake, watch movies and sports, and travel.
will owens
William Owens
Graduate student / MIT Bio
owens at broadinstitute dot org
After surviving 18 years in Florida, I attended the University of Florida where I received my degrees in Microbiology and Computer Science and researched cancer epigenomics in the lab of Dr. Michael Kladde. After college, I worked as a SynBio RA at Octant, where I developed new transcriptional reporters and led a collaboration with the English Lab at the University of Utah. I entered the MIT Biology PhD program in Fall of 2022 and joined the YEC Lab in Spring 2023. I am interested in studying the dynamics of complex skin communities and the mechanisms by which some microbes interface with the immune system. In my free time, I enjoy reading, writing, weightlifting, and programming.
dorcas li
Duojia (Dorcas) Li
Graduate student / MIT Bio
liduojia at broadinstitute dot org
I grew up in China and went to college at the University of Michigan, where I graduated with a degree in Molecular, Cellular, and Developmental Biology. During my time as an undergraduate and technician, I was part of the Yamashita Lab, studying the regulation of ribosomal DNA expression in Drosophila and exploring how its copy number instability might contribute to karyotype evolution. In fall 2022, I started grad school at MIT Biology, and in spring 2023, I joined the YEC Lab. Here, my research is centered around how skin commensal bacteria influence the generation of T cell memory and the properties of this immune memory. In my free time, I enjoy singing, baking, hiking, and playing tennis.
caroline kim
Caroline Kim
Graduate student / MIT Bio
kimcarol at broadinstitute dot org
I am originally from LA and went to school at the University of Chicago where I majored in biochemistry. As an undergraduate researcher I studied nuclear receptor crosstalk in hormonally-driven breast cancers. After graduating in 2018, I worked in Dr. Bruce Spiegelman's lab at Dana Farber Cancer Institute studying the physiology and biochemistry of the exercise hormone irisin. I entered the MIT Biology PhD program in fall 2022 and joined the YEC lab in spring 2023. In the YEC lab, I am interested in characterizing how skin commensal microbes communicate with host immune cells across an intact skin barrier. In my free time I enjoy reading, hiking, and playing volleyball.
caroline kim
Soumya Kannan
Postdoc
skannan at broadinstitute dot org
I am currently a Junior Fellow at the Harvard Society of Fellows. I obtained my bachelor's degree at Caltech in bioengineering and was subsequently a Fulbright scholar at the Technical University of Denmark in the Department of Biotechnology and Biomedicine. I completed my PhD in biological engineering at MIT in Feng Zhang's lab at the Broad Institute, where I studied the origins of CRISPR-Cas systems from ancestral RNA-guided nucleases encoded in mobile elements, biochemical diversity in CRISPR-Cas systems, and applications of RNA-guided systems for genome and transcriptome editing. In my free time, I play and coach water polo, and enjoy reading.
caroline kim
Emilia Lim
Graduate student / MIT Bio
limemili at broadinstitute dot org
I grew up in San Francisco and graduated from the University of Chicago where I majored in biochemistry and first developed an interest in exploring the mechanisms of bacterial communication. I entered the MIT Biology PhD program in fall of 2023 and joined the lab in spring 2024. In the YEC lab, I am interested in exploring how complex commensal communities can impact the dynamics of immune responses and the different mechanisms for host-commensal interactions. In my free time, I enjoy reading, cooking, and trying lots of new food.
nkazi nchinda
Nkazi Nchinda
MD-PhD Student / HST
nnchinda at broadinstitute dot org
I grew up outside Milwaukee and graduated from Harvard College where I studied Biomedical Engineering and Sociology. Following graduation, I studied Epidemiology at the University of Oxford, researching how new HIV strains emerge and evolve in UNAIDS key populations. After an additional year studying Public Policy, I started an MD-PhD in the Harvard-MIT HST program in Fall 2023. In the YEC lab, I'm excited to explore how commensals can drive and decrease antigen competition. Outside of the lab, you'll find me baking cakes, planning dinner parties, or staring wistfully into space on the way home.
nkazi nchinda
Shivali Verma
Graduate student / MIT Bio
sverma at broadinstitute dot org
I grew up in Bangalore, India and completed my undergraduate degree in Biology and Computer Science at Columbia University. As an undergrad, I worked on tissue resident memory T cell generation and early life immune development in Dr. Donna Farber's Lab. After graduating, I worked at Gentibio as an Associate Scientist, where I developed novel engineered regulatory T cells and CAR-regulatory T cells as a cellular therapy against Inflammatory Bowel Disease. I started my PhD in Biology at MIT in Fall of 2024 and joined the YEC Lab in Spring 2025. In the YEC Lab, I am interested in understanding how skin commensals can generate long-lived immune memory populations without triggering inflammation. Outside of lab, I enjoy painting, playing volleyball, going on nature walks, and feeding my boba addiction.
nkazi nchinda
Jessie Liu
Research Associate
liujessi at broadinstitute dot org
I grew up in New York before attending the University of Toronto where I completed a specialist program in Molecular Genetics. As an undergraduate student, I studied atherosclerosis in different genetically engineered mouse models in Dr. Minna Woo's lab and investigated host metabolic genes affecting resistance to microsporidia in a microsporidia/C. elegans model system in Dr. Aaron Reinke's lab. I joined the YEC lab in winter of 2025 where I am the lab tech. Outside of lab, I enjoy exploring and photographing the city, watercolor painting, and listening to music.
nkazi nchinda
Wendy Geng
Undergraduate / MIT UROP
wgeng at broadinstitute dot org
I am from Texas and am currently a biochemistry undergraduate at MIT. I've studied the gut microbiota and done research on cancer neuropathy in the past, which is what sparked my interest in commensal bacteria and immunology. In the YEC lab, I work under Will, and I am broadly interested in discovering what about commensals can influence the immune system. In my free time, I enjoy playing tennis, thrifting, and going to farmers markets.
nkazi nchinda
Monica Pan
Undergraduate / MIT UROP
rpan at broadinstitute dot org
I grew up in Michigan and am currently pursuing a Biology major at MIT. I lived near a large forest in Michigan, and was also raised on a farm by my grandparents in China for several years before coming back to America, which gave me a deep appreciation for nature and sparked my fascination with living organisms. In high school, I was involved with Science Olympiad, miRcore, tutoring, and played for my school's tennis team. Outside of school, I studied mitochondrial lipid metabolism in the Greenberg Lab at Wayne State University, and conducted biochemical research on fungal pathogens through the Summer Science Program. In the YEC lab, I work as an undergraduate researcher under the guidance of Caroline Kim, and I am interested in studying the mechanisms by which commensal skin microbes influence T-cell responses in the immune system. In my free time, I enjoy running, painting, gardening, and going on walks.
nkazi nchinda
Elizabeth Negron
MSRP student
enegron at broadinstitute dot org
I was born and raised in San Antonio Texas where I currently attend the University of Texas at San Antonio as a Microbiology/Immunology major in my 3rd year. As an undergraduate researcher I studied the phenotypic abilities of a gastrointestinal commensal fungi and will shift to C. difficile. I will be joining the YEC Lab for 10 weeks through the MIT BSG-MSRP-Bio program for the summer of 2025. Here I will be contributing to a project with Dorcas Li. In this project I will be working with bacterial commensals and their effect on the memory of T cells, and the development of regulatory T cells during neonatal colonization. Outside of Lab, I like to work out, bake, hike, and create art when I have time.
Alumni
caroline kim
Grace Ginder
MSRP student
Current Position:
PhD student at Duke University
Publications
Please see a full list of publications here: https://www.ncbi.nlm.nih.gov/myncbi/yiyin.chen.1/bibliography/public/
  • Chen, Y.E., Bousbaine, D., Veinbachs, A., Atabakhsh, K., Dimas, A., Yu, V.K., Zhao, A., Enright, N.J., Nagashima, K., Belkaid, Y., Fischbach, M.A. Engineered skin bacteria induce antitumor T cell responses against melanoma. Science. 2023 Apr 14;380(6641):203-210. doi: 10.1126/science.abp9563. Epub 2023 Apr 13. PMID: 37053311.
  • Chen, Y.E., Bouladoux, N., Hurabielle, C., Mattke, A.M., Belkaid, Y., Fischbach, M.A. Decoding commensal-host communication through genetic engineering of Staphylococcus epidermidis. BioRxiv 664656 [preprint]. Available from: https://doi.org/10.1101/664656.
  • Lima-Junior, D.S., Krishnamurthy, S.R., Bouladoux, N., Collins, N., Han, S.-J., Chen, E.Y., Constantinides, M.G., Link, V.M., Lim, A.I., Enamorado, M., et al. (2021). Endogenous retroviruses promote homeostatic and inflammatory responses to the microbiota. Cell 184, 3794-3811.e19.
  • Constantinides, M.G., Link, V.M., Tamoutounour, S., Wong, A.C., Perez-Chaparro, P.J., Han, S.-J., Chen, Y.E., Li, K., Farhat, S., Weckel, A., et al. (2019). MAIT cells are imprinted by the microbiota in early life and promote tissue repair. Science 366, eaax6624.
  • Chen, Y.E., Fischbach, M.A., and Belkaid, Y. (2018). Skin microbiota–host interactions. Nature 553, 427–436.
  • Ridaura, V.K., Bouladoux, N., Claesen, J., Chen, Y.E., Byrd, A.L., Constantinides, M.G., Merrill, E.D., Tamoutounour, S., Fischbach, M.A., and Belkaid, Y. (2018). Contextual control of skin immunity and inflammation by Corynebacterium. J. Exp. Med. 215, 785–799.
  • Ji, Z., Chen, Y.E., Kumar, R., Taylor, M., Njauw, C.-N.J., Miao, B., Frederick, D.T., Wargo, J.A., Flaherty, K.T., Jönsson, G., et al. (2015). MITF Modulates Therapeutic Resistance through EGFR Signaling. J. Invest. Dermatol. 135, 1863–1872.
  • Chen, Y.E., Gerstle, T., Verma, K., Treiser, M., Kimball, A., and Orgill, D. (2014). Management of Hidradenitis Suppurativa Wounds with an Internal Vacuum-Assisted Closure Device. Plast. Reconstr. Surg. 133.
  • Ji, Z., Kumar, R., Taylor, M., Rajadurai, A., Marzuka-Alcalá, A., Chen, Y.E., Njauw, C.-N.J., Flaherty, K., Jönsson, G., and Tsao, H. (2013). Vemurafenib Synergizes with Nutlin-3 to Deplete Survivin and Suppress Melanoma Viability and Tumor Growth. Clin. Cancer Res. Off. J. Am. Assoc. Cancer Res. 19, 4383–4391.
  • Chen, Y.E., and Tsao, H. (2013). The skin microbiome: Current perspectives and future challenges. J. Am. Acad. Dermatol. 69, 143–155.e3.
  • Chen, Y.E., Gerstle, T.L., Liang, F., and Lee, B.T. (2012). Use of a novel laser projection grid to assess symmetry in breast surgery. Plast. Reconstr. Surg. 130, 231e-233e.
  • Jonas, K.*, Chen, Y.E.*, and Laub, M.T. (2011). Modularity of the bacterial cell cycle enables independent spatial and temporal control of DNA replication. Curr. Biol. CB 21, 1092–1101.
  • Chen, Y.E.*, Tropini, C.*, Jonas, K., Tsokos, C.G., Huang, K.C., and Laub, M.T. (2011). Spatial gradient of protein phosphorylation underlies replicative asymmetry in a bacterium. Proc. Natl. Acad. Sci. 108, 1052–1057.
  • Gora, K.G., Tsokos, C.G., Chen, Y.E., Srinivasan, B.S., Perchuk, B.S., and Laub, M.T. (2010). A Cell-Type-Specific Protein-Protein Interaction Modulates Transcriptional Activity of a Master Regulator in Caulobacter crescentus. Mol. Cell 39, 455–467.
  • Chen, Y.E., Tsokos, C.G., Biondi, E.G., Perchuk, B.S., and Laub, M.T. (2009). Dynamics of Two Phosphorelays Controlling Cell Cycle Progression in Caulobacter crescentus. J. Bacteriol. 191, 7417–7429.
  • Lapidos, K.A., Chen, Y.E., Earley, J.U., Heydemann, A., Huber, J.M., Chien, M., Ma, A., and McNally, E.M. (2004). Transplanted hematopoietic stem cells demonstrate impaired sarcoglycan expression after engraftment into cardiac and skeletal muscle. J. Clin. Invest. 114, 1577–1585.
Contact
The YEC Lab opened in January 2023 at the Broad Institute in Cambridge, MA.
We are recruiting research technicians, graduate students, and postdoctoral scholars who are curious, ambitious, and passionate about microbiology and immunology.
We welcome scientists of all backgrounds and aim to build a community of inclusion and respect.
Reach out to me via email:
erinchen at yeclab dot org
Y. Erin Chen
Principal Investigator