Bryan Bryson

Computational Immunologist - Boston, Massachusetts (US) job with Ragon Institute of MGH, MIT, & Harvard | 12849577 The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard in Cambridge MA, together with the Departmen

The @ragoninstitute.bsky.social is launching a new faculty search for a computational immunologist! Applications are open now and reviewed on a rolling basis. Please share broadly with your networks! #immunosky

www.nature.com/naturecareer...

Thanks to our many collaborators at the @ragoninstitute.bsky.social and across the broader community and our funders #tbsky #tuberculosis

Congrats especially to Owen and Rachel, the two fearless graduate students who led this work -- y'all are the best <3

We're excited! This study supports the concept that there are multiple ways to transfer proteins from the phagosome to the cytosol, and that Mtb specifically takes advantage of this.

2. For those of you who know Mtb, you'll know that Mtb mutants lacking the virulence lipid, PDIM, partially phenocopy ESX-1 mutants. We asked if PDIM mutants have a similar MHC-I phenotype. They didn't! This argues there is a specific role for the ESX-1 secretion system in MHC-I presentation

So, we were stuck. Our data point to a role for ESX-1 in presentation but was it the secretion system or some other response that is downstream of ESX-1? So we did 2 experiments

1. We did discovery MS with macrophages infected with an ESX-1 mutant and asked if we could see Mtb-derived peptides. No!

We examined the role of newly identified host pore-forming proteins (MPEG-1) to define their role in presentation of Mtb-derived peptides, and they were dispensable.

OK, so ESX-1 controls galectin recruitment to the phagosome. Can we figure out a way to restore galectin positivity to the phagosome of an ESX-1 mutant? Yes, we used some previously identified small molecules and restored galectin positivity, but it did not rescue presentation.

We first tested an antigen expression hypothesis -- is the loss of presentation of Mtb-derived peptides on MHC-I explained by loss of expression of these antigens in the ESX-1 mutant in macrophages? No! If anything, we see elevated gene expression in the mutant.

ESX-1 activity controls a lot in phagocytes, and we had previously demonstrated that the loss of presentation we saw was independent of interferon production. We still had a lot left to explore, and this preprint does just that.

Bar graph showing CD69 positivity on an EsxJ-specific T cell clone following co-culture with macrophages (mock infected, WT infected, ESX-1 mutant infected).

In our previous paper, we showed that loss of ESX-1 disrupts presentation of Mtb-derived peptides on MHC-I using immunopeptidomics. Here, we first corroborated those findings using a T cell clone specific for one of the peptides we saw by MS.

Happy to share our newest preprint on antigen presentation of Mtb-derived peptides on MHC-I: www.biorxiv.org/cgi/content/...

This is a follow up to our previous paper where we applied immunopeptidomics to understand MHC-I presentation by Mtb-infected cells: elifesciences.org/articles/84070

Last, a major thanks to our funders and excellent collaborators!

Please reach out if there's anything in the paper that interests you!

We think this work is important because:
1. It helps us think about species differences in new ways
2. It highlights a metabolic gate in Mtb-host interactions
3. It may help resolve long-standing challenges in translating concepts from mouse studies to humans

There's a lot more in the paper than I'm including in this summary so I encourage you to take a read!

Microscopy images of Mtb within human macrophages that have been treated with different inhibitors of TAG synthesis. White arrows point to where lipid inclusions become detectable in human macrophages.

So we took a step back and realized that in our hands human macrophages have more lipid droplets (LDs) at baseline than murine macrophages, so we tested the hypothesis that human LDs regulated the ability of Mtb to acquire and store lipids. Inhibition of host TAG synthesis did the trick (partially)!

We spent a full year trying to break the phenotype (macrophage culture media, macrophage and Mtb mutants) or small molecule perturbations (initially focusing on well-characterized species differences). TL, DR: these perturbations didn't do all that much

Microscopy images examining lipids in green, Mtb and nuclei. The image looks at Mtb in human or mouse macrophages using two different lipid probes.

Many of these Mtb genes were associated with lipid metabolism, so we orthogonally validated these observations by tracking Mtb acquisition and storage of lipids using established techniques and found that Mtb readily forms intracellular lipid inclusions in mouse but not human macrophages

Volcano plot examining the log2 fold change and adjusted p value of Mtb gene expression between human and mouse macrophages.

Here in work led by postdoc Jonathan Padilla-Gomez, we asked that question using an vitro model of Mtb infection of either primary human or mouse macrophages. To our surprise, we found many differentially expressed Mtb genes across host environments

We often use mouse and human macrophages interchangeably to study Mtb-host interactions, but an open question in the field is how (if at all) different species impose unique stresses on intracellular Mtb

Systems analysis reveals alternate metabolic states adopted by Mycobacterium tuberculosis across species Mycobacterium tuberculosis (Mtb) persists within macrophages, yet how different host species shape bacterial state remains poorly understood. Here, we directly compared the intracellular transcriptome...

Excited to share our lab's newest preprint (strap in if you're excited about metabolism, species differences, or Mtb gene expression): www.biorxiv.org/content/10.1...

Thanks friends!

And importantly -- thank you to Owen, Forest White and our many amazing collaborators!

Please get in touch if you want to chat more or have questions!

And watch this space for the next two chapters of the Mtb-MHC saga (coming soon, they are very very exciting)

We're super excited! These are needle in the haystack measurements out of the BL3 that Owen executed beautifully. These studies also provide us a path to antigen discovery and vaccine optimization in human cells. And it's generalizable -- we can definitely extend to other pathogens!

TL, DR:
(1) Type VII secretion system substrates strike again -- enriched for presentation on MHC-II.
(2) Lysosomal targeting enhances presentation on MHC-II by multiple orders of magnitude.
(3) Coexpression of natural heterodimeric pairs can enhance presentation of Mtb-derived peptides.

Here, we apply immunopeptidomics in primary human phagocytes to identify Mtb peptides presented by infected cells on MHC-II and then optimize mRNA vaccines encoding these antigens.

Immunopeptidomics can inform the design of mRNA vaccines for the delivery of Mycobacterium tuberculosis MHC class II antigens MHC class II immunopeptidomics in human phagocytes infected with Mycobacterium tuberculosis enables vaccine immunogen design and optimization.

Excited to share our newest manuscript on antigen discovery and vaccine design for tuberculosis lead by Owen Leddy (everyone hiring new faculty in a few years, remember this name!)

www.science.org/doi/10.1126/... #TBsky

TL, DR:
(1) Type VII secretion system substrates strike again -- enriched for presentation on MHC-II.
(2) Lysosomal targeting enhances presentation on MHC-II by multiple orders of magnitude.
(3) Coexpression of natural heterodimeric pairs can enhance presentation of Mtb-derived peptides.

Here, we apply immunopeptidomics in primary human phagocytes to identify Mtb peptides presented by infected cells on MHC-II and then optimize mRNA vaccines encoding these antigens.

Congrats to the Carpenter Lab on this exciting study!

I might now sound like a broken record, but check the abstract!!!

Let’s go type 7 secretion system substrates! #tuberculosis #tbsky

Happy to see more data pointing to an important role for type 7 secretion substrates in TB protective immunity