Moffitt Laboratory
@MoffittLab
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A research group passionate about developing genomic microscopy methods to illuminate microbe-host interactions. @BostonChildrens @harvardmed | moffittlab.bsky
Boston, MA
Joined April 2023
Proud to announce our new technique for tracking relative B cell clonality in situ with B Cell Receptor MERFISH (BCR-MERFISH)! Congratulations to Evan Yang and our colleagues in the Carroll laboratory! Check out our bioRxiv: 1/9
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Yesterday our first grad student -- DR. Rosalind Xu -- had her official PhD hooding ceremony in @HarvardCCB! A massive congratulations to her and all of the other freshly minted PhDs!
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As plasma cells play fundamental roles in tissue behavior in health and disease, we are excited to see the wide range of questions that BCR-MERFISH will now allow us and others to address! 9/9.
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To our surprise, we found that some plasma cell clones form patches of co-occurring clones along the gut, suggesting, perhaps, that there is local production of IgA specific to a subset of the microbiome! 8/9
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Plasma cells modulate the microbiome by secreting IgA, and different plasma cell clones secrete IgA that targets different bacteria. But how these cells are distributed along the gut is not clear. Excitingly, BCR-MERFISH can now measure this distribution. 7/9
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Importantly, BCR-MERFISH labels not only the Clone ID, but also the transcriptome of all surrounding cell types in the same slice, placing unique clones within their tissue contexts with single-cell resolution! 6/9
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To test BCR-MERFISH, we profiled V gene usage in plasma B cells in the mouse ileum, defined B cell clones via the VH and VKVL gene choice within individual B cells, and showed that the usage of these genes agreed with BCR-sequencing. 5/9
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However, MERFISH has been unable to discriminate B cells based on the BCR sequence because of the high degree of homology between V, D, and J genes. Evan solved this problem with a homology-aware probe design and encoding approach to produce a technique we call BCR-MERFISH! 4/9
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However, some cell types - such as plasma B cells – may only differ in their expression of a single transcript, the B cell receptor (BCR). Yet, it is the sequence of this receptor, generated through V(D)J recombination, that sets their antigen specificity! 3/9.
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Multiplexed FISH methods such as #MERFISH can image 1000s of unique RNA transcripts within single cells, and in turn define a massive diversity of cell types and states within intact tissues. 2/9.
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Interested in connecting single-cell biology to tissue level behaviors? I have the Keystone meeting for you! Short-talk abstracts are due on Feb 11th. Registration continues to April 17th.
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What a pleasure to see our bacterial-MERFISH work out in @ScienceMagazine this week! Congratulations to the talented team that led this effort--Ari, Yuanyou, and Nana!
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What a pleasure to see this work online! .Excellent work by our own Brianna Watson! And an amazing collaboration with Biplab Paul and Alan Mullen!.
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Wow, our first graduate student just passed her defense! A MASSIVE congratulations to Dr. Rosalind Xu!
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Whether it is specialization in biofilms, the dynamics of antibiotic-resistant persisters, or complex communication in commensal communities, we anticipate bacterial-MERFISH will be a powerful tool for a wide range of questions! Excited to see this technique out! 12/12.
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Remarkably, B. theta adapts its gene expression to different niches in the colon. For example, when near the host mucus layer, B. theta upregulates a rich diversity of genes associated with the harvest of mucus polysaccharides (PULs)! 11/12
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Most bacteria live in complex, spatially structured environments not well approximated by a culture flask. To illustrate the ability of bacterial-MERFISH to profile bacterial gene expression in such environments, we characterized B. theta expression in the colon of mice. 10/12
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The results were a shock! The E. coli transcriptome is extensively organized. We identified and classified a diversity of patterns and found that elements of the proteome organization and the genome organization shape the organization of the transcriptome. 9/12
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Even though bacteria are small, there is a growing appreciation that different mRNAs can be localized to different sub-cellular regions with important functional consequences. So next we charted the organization of the E. coli transcriptome with bacterial-MERFISH. 8/12
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This heterogeneous response taught us two things. First, the required levels of essential genes during growth arises from coordinated transcriptional bursts. Second, when starved, E. coli explores many different sugars--not in our medium--before settling on xylose. 7/12
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