Ryan Flynn
@raflynn5.bsky.social
RNA, Glycans, Space, Renewable Energy, and all technologies making lives more interesting.
PI at Boston Children’s Hospital SCP
Assistant Professor at Harvard SCRB
PI at Boston Children’s Hospital SCP
Assistant Professor at Harvard SCRB
Lab organized a pretty good costume
October 31, 2025 at 6:07 PM
Lab organized a pretty good costume
Finally, DNASE1L3 has been previously established as regulating dsDNA levels in the plasma and loss can result in auto-Abs to dsDNA. Interestingly, in vitro, DNASE1L3 could cleave csDNA from B cells in patients with inactivating mutations in the enzyme we see csDNA accumulates on B cells and T cells
October 7, 2025 at 1:22 PM
Finally, DNASE1L3 has been previously established as regulating dsDNA levels in the plasma and loss can result in auto-Abs to dsDNA. Interestingly, in vitro, DNASE1L3 could cleave csDNA from B cells in patients with inactivating mutations in the enzyme we see csDNA accumulates on B cells and T cells
We found that csDNA is not restricted to cultured cells, but in health donors, B cells and monocytes had clear csDNA accumulation while T cells and NK cells did not.
October 7, 2025 at 1:22 PM
We found that csDNA is not restricted to cultured cells, but in health donors, B cells and monocytes had clear csDNA accumulation while T cells and NK cells did not.
Protein proximity labeling and mass spec (pPL-MS) defined the local proteomes of csDNA revealing certain membrane domains enriched in addition to some csRBPs and glycoRNAs.
October 7, 2025 at 1:22 PM
Protein proximity labeling and mass spec (pPL-MS) defined the local proteomes of csDNA revealing certain membrane domains enriched in addition to some csRBPs and glycoRNAs.
Inhibitor and enzyme treatment experiments demonstrated that healthy mitochondria and heparan sulfate were needed to maintain csDNA on the surface of living cells
October 7, 2025 at 1:22 PM
Inhibitor and enzyme treatment experiments demonstrated that healthy mitochondria and heparan sulfate were needed to maintain csDNA on the surface of living cells
Wanting a simpler assay to integrate this, we reasoned that the Tn5 enzyme used for ATAC-seq should be able to transpose surface-exposed DNA if applied to intact, living cells. Indeed this was possible and dye-coupled oligos enabled imaging of the csDNA on cells.
October 7, 2025 at 1:22 PM
Wanting a simpler assay to integrate this, we reasoned that the Tn5 enzyme used for ATAC-seq should be able to transpose surface-exposed DNA if applied to intact, living cells. Indeed this was possible and dye-coupled oligos enabled imaging of the csDNA on cells.
We first realized DNA (in addition to RNA) could be liberated from the cell surface using trypsin - this DNA was oxidized and when sequenced enriched for mitochondrial reads
October 7, 2025 at 1:22 PM
We first realized DNA (in addition to RNA) could be liberated from the cell surface using trypsin - this DNA was oxidized and when sequenced enriched for mitochondrial reads
rPAL-seq was applied to 13 cell lines - showing that unlike the bulk small RNA expression, glycoRNA enrichment was able to classify the cells based on their tissue of origin.
October 6, 2025 at 1:36 PM
rPAL-seq was applied to 13 cell lines - showing that unlike the bulk small RNA expression, glycoRNA enrichment was able to classify the cells based on their tissue of origin.
Lead by postdoc in the lab Ruiqi Ge and in collaboration with Bob Coffey’s lab, we are happy to share rPAL-seq for rapid and sensitive sequencing based profiling of glycoRNAs @biorxivpreprint.bsky.social www.biorxiv.org/content/10.1...
October 6, 2025 at 1:36 PM
Lead by postdoc in the lab Ruiqi Ge and in collaboration with Bob Coffey’s lab, we are happy to share rPAL-seq for rapid and sensitive sequencing based profiling of glycoRNAs @biorxivpreprint.bsky.social www.biorxiv.org/content/10.1...
We defined the chemical moiety causing this stimulation to be the core RNA modification of acp3U, which we had previously found to be a covalent linker between RNA and N-glycans (Xie et al. Cell 2024). We confirmed this with chemical synthesis RNAs containing only 1 acp3U.
August 6, 2025 at 3:36 PM
We defined the chemical moiety causing this stimulation to be the core RNA modification of acp3U, which we had previously found to be a covalent linker between RNA and N-glycans (Xie et al. Cell 2024). We confirmed this with chemical synthesis RNAs containing only 1 acp3U.
This effect was also true on the surface of apoptotic material which is normally cleared via efferocytosis in an immune silent process. Loss of N-glycans on this material triggers innate immune cells.
August 6, 2025 at 3:36 PM
This effect was also true on the surface of apoptotic material which is normally cleared via efferocytosis in an immune silent process. Loss of N-glycans on this material triggers innate immune cells.
We found that de-N-glycosylation of purified small RNA using PNGaseF causes the RNA to be immunostimulatory to both mouse and human macrophages
August 6, 2025 at 3:36 PM
We found that de-N-glycosylation of purified small RNA using PNGaseF causes the RNA to be immunostimulatory to both mouse and human macrophages
RNA N-glycosylation enables immune evasion and homeostatic efferocytosis by chemically caging acp3U. Excited to report this work lead by Vinnie @vinnieviruses.bsky.social and in collaboration with @vijayrathinam.bsky.social in @nature.com www.nature.com/articles/s41...
August 6, 2025 at 3:36 PM
RNA N-glycosylation enables immune evasion and homeostatic efferocytosis by chemically caging acp3U. Excited to report this work lead by Vinnie @vinnieviruses.bsky.social and in collaboration with @vijayrathinam.bsky.social in @nature.com www.nature.com/articles/s41...
It was an exciting week for the Flynn Lab - our first PhD student has successfully defended his thesis: congrats to Dr. Jonathan Perr! @harvardmcb.bsky.social @bostonchildrens.bsky.social
May 8, 2025 at 2:10 PM
It was an exciting week for the Flynn Lab - our first PhD student has successfully defended his thesis: congrats to Dr. Jonathan Perr! @harvardmcb.bsky.social @bostonchildrens.bsky.social
Excited to share Benson’s and Maria’s work in collab w/Kostas Tzelepis: we found the nucleolar protein NPM1 is a marker of AML and can be targeted therapeutically
connecting ‘cell surface RNA biology’ to cancer biology
@natbiotech.nature.com
www.nature.com/articles/s41...
connecting ‘cell surface RNA biology’ to cancer biology
@natbiotech.nature.com
www.nature.com/articles/s41...
April 23, 2025 at 11:44 AM
Excited to share Benson’s and Maria’s work in collab w/Kostas Tzelepis: we found the nucleolar protein NPM1 is a marker of AML and can be targeted therapeutically
connecting ‘cell surface RNA biology’ to cancer biology
@natbiotech.nature.com
www.nature.com/articles/s41...
connecting ‘cell surface RNA biology’ to cancer biology
@natbiotech.nature.com
www.nature.com/articles/s41...
A nearly 9 year effort to design and implement new CLIP-based technologies to define multimeric protein assemblies on RNA.
Enables ‘watching’ of RNP assemblies inside living cells
Special congrats to Luca Ducoli, Brian Zarnegar, and Paul Khavari @nature.com
www.nature.com/articles/s41...
Enables ‘watching’ of RNP assemblies inside living cells
Special congrats to Luca Ducoli, Brian Zarnegar, and Paul Khavari @nature.com
www.nature.com/articles/s41...
March 26, 2025 at 5:40 PM
A nearly 9 year effort to design and implement new CLIP-based technologies to define multimeric protein assemblies on RNA.
Enables ‘watching’ of RNP assemblies inside living cells
Special congrats to Luca Ducoli, Brian Zarnegar, and Paul Khavari @nature.com
www.nature.com/articles/s41...
Enables ‘watching’ of RNP assemblies inside living cells
Special congrats to Luca Ducoli, Brian Zarnegar, and Paul Khavari @nature.com
www.nature.com/articles/s41...
Had a great time visiting @duke-university.bsky.social to share our recent work on #glycoRNA and #csRBPs and the broader ideas of cell surface RNA biology. Thanks to Kate Meyer for hosting and fun talking to Gladfelter, Boyce, Horner, and Chory labs as well as students at lunch!
March 3, 2025 at 1:59 PM
Had a great time visiting @duke-university.bsky.social to share our recent work on #glycoRNA and #csRBPs and the broader ideas of cell surface RNA biology. Thanks to Kate Meyer for hosting and fun talking to Gladfelter, Boyce, Horner, and Chory labs as well as students at lunch!
congrats to Brendan Floyd, postdoc in @carolynbertozzi.bskyverified.social lab on his exciting work "mapping the nanoscale organization of the human cell surface proteome"
High resolution, High Effort, and Creative Analytics produce new views of the cell surface
www.biorxiv.org/content/10.1...
High resolution, High Effort, and Creative Analytics produce new views of the cell surface
www.biorxiv.org/content/10.1...
February 18, 2025 at 4:31 PM
congrats to Brendan Floyd, postdoc in @carolynbertozzi.bskyverified.social lab on his exciting work "mapping the nanoscale organization of the human cell surface proteome"
High resolution, High Effort, and Creative Analytics produce new views of the cell surface
www.biorxiv.org/content/10.1...
High resolution, High Effort, and Creative Analytics produce new views of the cell surface
www.biorxiv.org/content/10.1...
Welcoming Maggie Zhang to the lab as our newest graduate student from the Chemical Biology program here at HMS
February 6, 2025 at 2:31 PM
Welcoming Maggie Zhang to the lab as our newest graduate student from the Chemical Biology program here at HMS
Happy to welcome Ruiqi Ge as a new (a bit delayed as he joined us in November) postdoc in the lab!
February 4, 2025 at 2:37 PM
Happy to welcome Ruiqi Ge as a new (a bit delayed as he joined us in November) postdoc in the lab!
January 25, 2025 at 6:48 PM
Finally, we used MS (DIA+DDA) to characterize the O-glycans on RNA from cells and colon organoids which have way more sialoglycoRNA than cultured cells. Interestingly in the context of Ulcerative Colitis, organoids derived from inflamed regions of the colon had higher levels of sialylated glycoRNA.
August 30, 2024 at 12:57 PM
Finally, we used MS (DIA+DDA) to characterize the O-glycans on RNA from cells and colon organoids which have way more sialoglycoRNA than cultured cells. Interestingly in the context of Ulcerative Colitis, organoids derived from inflamed regions of the colon had higher levels of sialylated glycoRNA.
We established an optimized enzymatic strategy using Galactose Oxidase to label N- and O-linked glycoRNA to complement rPAL which is dependent on the presence of sialic acid.
August 30, 2024 at 12:56 PM
We established an optimized enzymatic strategy using Galactose Oxidase to label N- and O-linked glycoRNA to complement rPAL which is dependent on the presence of sialic acid.