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Article ; Online: Mapping proteolytic neo-N termini at the surface of living cells.

Weeks, Amy M / Byrnes, James R / Lui, Irene / Wells, James A

Proceedings of the National Academy of Sciences of the United States of America

2021 Volume 118, Issue 8

Abstract: N terminomics is a powerful strategy for profiling proteolytic neo-N termini, but its application to cell surface proteolysis has been limited by the low relative abundance of plasma membrane proteins. Here we apply plasma membrane-targeted subtiligase ... ...

Abstract	N terminomics is a powerful strategy for profiling proteolytic neo-N termini, but its application to cell surface proteolysis has been limited by the low relative abundance of plasma membrane proteins. Here we apply plasma membrane-targeted subtiligase variants (subtiligase-TM) to efficiently and specifically capture cell surface N termini in live cells. Using this approach, we sequenced 807 cell surface N termini and quantified changes in their abundance in response to stimuli that induce proteolytic remodeling of the cell surface proteome. To facilitate exploration of our datasets, we developed a web-accessible Atlas of Subtiligase-Captured Extracellular N Termini (ASCENT; http://wellslab.org/ascent). This technology will facilitate greater understanding of extracellular protease biology and reveal neo-N termini biomarkers and targets in disease.
MeSH term(s)	Cell Membrane/metabolism ; HEK293 Cells ; Humans ; Mutation ; Peptide Mapping/methods ; Peptide Synthases/genetics ; Peptide Synthases/metabolism ; Protein Processing, Post-Translational ; Proteolysis ; Subtilisins/genetics ; Subtilisins/metabolism
Chemical Substances	Subtilisins (EC 3.4.21.-) ; Peptide Synthases (EC 6.3.2.-) ; subtiligase (EC 6.3.2.-)
Language	English
Publishing date	2021-02-04
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2018809118
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Article: Photoproximity Labeling from Single Catalyst Sites Allows Calibration and Increased Resolution for Carbene Labeling of Protein Partners In Vitro and on Cells.

Bartholow, Thomas G / Burroughs, Paul W W / Elledge, Susanna K / Byrnes, James R / Kirkemo, Lisa L / Garda, Virginia / Leung, Kevin K / Wells, James A

ACS central science

2023 Volume 10, Issue 1, Page(s) 199–208

Abstract: ... Rodriguez-Rivera, F. P.; Parker, D. L.; Hett, E. C.; Fadeyi, O. O.; Oslund, R. C.; MacMillan, D. W. C. ...

Abstract	The cell surface proteome (surfaceome) plays a pivotal role in virtually all extracellular biology, and yet we are only beginning to understand the protein complexes formed in this crowded environment. Recently, a high-resolution approach (μMap) was described that utilizes multiple iridium-photocatalysts attached to a secondary antibody, directed to a primary antibody of a protein of interest, to identify proximal neighbors by light-activated conversion of a biotin-diazirine to a highly reactive carbene followed by LC/MS (Geri, J. B.; Oakley, J. V.; Reyes-Robles, T.; Wang, T.; McCarver, S. J.; White, C. H.; Rodriguez-Rivera, F. P.; Parker, D. L.; Hett, E. C.; Fadeyi, O. O.; Oslund, R. C.; MacMillan, D. W. C.
Language	English
Publishing date	2023-12-26
Publishing country	United States
Document type	Journal Article
ISSN	2374-7943
ISSN	2374-7943
DOI	10.1021/acscentsci.3c01473
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Article: Site-specific proximity labeling at single residue resolution for identification of protein partners

Bartholow, Thomas G / Burroughs, Paul / Elledge, Susanna K / Byrnes, James R / Kirkemo, Lisa L / Garda, Virginia / Leung, Kevin K / Wells, James A

bioRxiv : the preprint server for biology

2023

Abstract: ... E. C., Fadeyi, O. O., Oslund, R. C., and MacMillan, D. W. C. (2020) ...

Abstract	The cell surface proteome, or surfaceome, is encoded by more than 4000 genes, but we are only beginning to understand the complexes they form. Rapid proximity labeling around specific membrane targets allows for capturing weak and transient interactions expected in the crowded and dynamic environment of the surfaceome. Recently, a high-resolution approach called μMap has been described (Geri, J. B., Oakley, J. V., Reyes-Robles, T., Wang, T., McCarver, S. J., White, C. H., Rodriguez-Rivera, F. P., Parker, D. L., Hett, E. C., Fadeyi, O. O., Oslund, R. C., and MacMillan, D. W. C. (2020)
Language	English
Publishing date	2023-07-27
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.07.27.550738
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Article ; Online: PVRL2 Suppresses Antitumor Immunity through PVRIG- and TIGIT-independent Pathways.

Yang, Jiuling / Wang, Li / Byrnes, James R / Kirkemo, Lisa L / Driks, Hannah / Belair, Cassandra D / Aguilar, Oscar A / Lanier, Lewis L / Wells, James A / Fong, Lawrence / Blelloch, Robert

Cancer immunology research

2024 , Page(s) OF1–OF17

Abstract: Poliovirus receptor-related 2 (PVRL2, also known as nectin-2 or CD112) is believed to act as an immune checkpoint protein in cancer; however, most insight into its role is inferred from studies on its known receptor, poliovirus receptor (PVR)-related ... ...

Abstract	Poliovirus receptor-related 2 (PVRL2, also known as nectin-2 or CD112) is believed to act as an immune checkpoint protein in cancer; however, most insight into its role is inferred from studies on its known receptor, poliovirus receptor (PVR)-related immunoglobulin domain protein (PVRIG, also known as CD112R). Here, we study PVRL2 itself. PVRL2 levels were found to be high in tumor cells and tumor-derived exosomes. Deletion of PVRL2 in multiple syngeneic mouse models of cancer showed a dramatic reduction in tumor growth that was immune dependent. This effect was even greater than that seen with deletion of PD-L1. PVRL2 was shown to function by suppressing CD8+ T and natural killer cells in the tumor microenvironment. The loss of PVRL2 suppressed tumor growth even in the absence of PVRIG. In contrast, PVRIG loss showed no additive effect in the absence of PVRL2. T-cell immunoreceptor with Ig and ITIM domains (TIGIT) blockade combined with PVRL2 deletion resulted in a near complete block in tumor growth. This effect was not recapitulated by the combined deletion of PVRL2 with its paralog, PVR, which is the ligand for TIGIT. These data uncover PVRL2 as a distinct inhibitor of the antitumor immune response with functions beyond that of its known receptor PVRIG. Moreover, the data provide a strong rationale for combinatorial targeting of PVRL2 and TIGIT for cancer immunotherapy.
Language	English
Publishing date	2024-04-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	2732489-8
ISSN	2326-6074 ; 2326-6066
ISSN (online)	2326-6074
ISSN	2326-6066
DOI	10.1158/2326-6066.CIR-23-0722
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Article: Advocacy for Change: An Osteopathic Review of Traumatic Brain Injury Among Combat Veterans.

Pendlebury, Gehan A / Oro, Peter / Haynes, William / Byrnes, Thomas R / Keane, James / Goldstein, Leonard

Cureus

2022 Volume 14, Issue 5, Page(s) e25051

Abstract: As a "signature injury" of the Iraq and Afghanistan wars, traumatic brain injury (TBI) remains a major health concern among military service members. Traumatic brain injury is associated with a wide range of symptoms which may be cognitive, emotional, ... ...

Abstract	As a "signature injury" of the Iraq and Afghanistan wars, traumatic brain injury (TBI) remains a major health concern among military service members. Traumatic brain injury is associated with a wide range of symptoms which may be cognitive, emotional, psychological, biochemical, and social in nature. Mild TBI (mTBI) ranks as the most common traumatic brain injury among veterans. Due to the absence of specific symptoms, mTBI diagnosis may be challenging in acute settings. Repetitive traumatic brain injury during combat deployments can lead to devastating chronic neurodegenerative diseases and other major life disruptions. Many cases of TBI remain undetected in veterans and may lead to long-term adverse comorbidities such as post-traumatic stress disorder (PTSD), suicide, alcohol disorders, psychiatric diagnoses, and service-related somatic dysfunctions. Veterans with TBI are almost twice as likely to die from suicide in comparison to veterans without a history of TBI. Veterans diagnosed with TBI experience significant comorbid conditions and thus advocacy for improved care is justified and necessary. Given the complexity and variation in the symptomatology of TBI, a personalized, multimodal approach is warranted in the evaluation and treatment of veterans with TBI and other associated conditions. As such, this review provides a broad overview of treatment options, with an emphasis on advocacy and osteopathic integration in the standard of care for veterans.
Language	English
Publishing date	2022-05-16
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2747273-5
ISSN	2168-8184
ISSN	2168-8184
DOI	10.7759/cureus.25051
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Article: Direct Identification of Proteolytic Cleavages on Living Cells Using a Glycan-Tethered Peptide Ligase.

Schaefer, Kaitlin / Lui, Irene / Byrnes, James R / Kang, Emily / Zhou, Jie / Weeks, Amy M / Wells, James A

ACS central science

2022 Volume 8, Issue 10, Page(s) 1447–1456

Abstract: Proteolytic cleavage of cell surface proteins triggers critical processes including cell-cell interactions, receptor activation, and shedding of signaling proteins. Consequently, dysregulated extracellular proteases contribute to malignant cell ... ...

Abstract	Proteolytic cleavage of cell surface proteins triggers critical processes including cell-cell interactions, receptor activation, and shedding of signaling proteins. Consequently, dysregulated extracellular proteases contribute to malignant cell phenotypes including most cancers. To understand these effects, methods are needed that identify proteolyzed membrane proteins within diverse cellular contexts. Herein we report a proteomic approach, called cell surface N-terminomics, to broadly identify precise cleavage sites (neo-N-termini) on the surface of living cells. First, we functionalized the engineered peptide ligase, called stabiligase, with an N-terminal nucleophile that enables covalent attachment to naturally occurring glycans. Upon the addition of a biotinylated peptide ester, glycan-tethered stabiligase efficiently tags extracellular neo-N-termini for proteomic analysis. To demonstrate the versatility of this approach, we identified and characterized 1532 extracellular neo-N-termini across a panel of different cell types including primary immune cells. The vast majority of cleavages were not identified by previous proteomic studies. Lastly, we demonstrated that single oncogenes,
Language	English
Publishing date	2022-10-11
Publishing country	United States
Document type	Journal Article
ISSN	2374-7943
ISSN	2374-7943
DOI	10.1021/acscentsci.2c00899
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Article ; Online: Identifying and antagonizing the interactions between layilin and glycosylated collagens.

Glasgow, Jeff E / Byrnes, James R / Barbee, Susannah D / Moreau, Joshua M / Rosenblum, Michael D / Wells, James A

Cell chemical biology

2022 Volume 29, Issue 4, Page(s) 597–604.e7

Abstract: Layilin is a small type I transmembrane receptor thought to bridge extracellular ligands with the cytoskeleton through its intracellular interactions with the scaffolding protein talin. Recent bulk- and single-cell RNA sequencing experiments have ... ...

Abstract	Layilin is a small type I transmembrane receptor thought to bridge extracellular ligands with the cytoskeleton through its intracellular interactions with the scaffolding protein talin. Recent bulk- and single-cell RNA sequencing experiments have repeatedly found layilin to be highly upregulated in key T cell sub-populations in multiple disease states, suggesting its importance to the adaptive immune response. Despite this prevalence, little is known about layilin's precise role in mediating extracellular interactions or how these interactions can be modulated in disease states. Here we take advantage of layilin's dependence on calcium ions to discover its interactions with highly glycosylated type II, IV, V, and VI collagens. Toward exploring layilin's role in disease, we exploited the Ca
MeSH term(s)	Carrier Proteins/metabolism ; Ligands ; Membrane Glycoproteins/genetics ; Talin/metabolism
Chemical Substances	Carrier Proteins ; Ligands ; Membrane Glycoproteins ; Talin
Language	English
Publishing date	2022-02-01
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	2451-9448
ISSN (online)	2451-9448
DOI	10.1016/j.chembiol.2022.01.003
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Article ; Online: Hypoxia Is a Dominant Remodeler of the Effector T Cell Surface Proteome Relative to Activation and Regulatory T Cell Suppression.

Byrnes, James R / Weeks, Amy M / Shifrut, Eric / Carnevale, Julia / Kirkemo, Lisa / Ashworth, Alan / Marson, Alexander / Wells, James A

Molecular & cellular proteomics : MCP

2022 Volume 21, Issue 4, Page(s) 100217

Abstract: Immunosuppressive factors in the tumor microenvironment (TME) impair T cell function and limit the antitumor immune response. T cell surface receptors and surface proteins that influence interactions and function in the TME are proven targets for cancer ... ...

Abstract	Immunosuppressive factors in the tumor microenvironment (TME) impair T cell function and limit the antitumor immune response. T cell surface receptors and surface proteins that influence interactions and function in the TME are proven targets for cancer immunotherapy. However, how the entire surface proteome remodels in primary human T cells in response to specific suppressive factors in the TME remains to be broadly and systematically characterized. Here, using a reductionist cell culture approach with primary human T cells and stable isotopic labeling with amino acids in cell culture-based quantitative cell surface capture glycoproteomics, we examined how two immunosuppressive TME factors, regulatory T cells (Tregs) and hypoxia, globally affect the activated CD8
MeSH term(s)	CD8-Positive T-Lymphocytes ; Humans ; Hypoxia ; Proteome ; T-Lymphocytes, Regulatory ; Tumor Microenvironment
Chemical Substances	Proteome
Language	English
Publishing date	2022-02-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	2075924-1
ISSN	1535-9484 ; 1535-9476
ISSN (online)	1535-9484
ISSN	1535-9476
DOI	10.1016/j.mcpro.2022.100217
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Zs.A 5599: Show issues

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Article ; Online: Cell-surface tethered promiscuous biotinylators enable comparative small-scale surface proteomic analysis of human extracellular vesicles and cells.

Kirkemo, Lisa L / Elledge, Susanna K / Yang, Jiuling / Byrnes, James R / Glasgow, Jeff E / Blelloch, Robert / Wells, James A

eLife

2022 Volume 11

Abstract: Characterization of cell surface proteome differences between cancer and healthy cells is a valuable approach for the identification of novel diagnostic and therapeutic targets. However, selective sampling of surface proteins for proteomics requires ... ...

Abstract	Characterization of cell surface proteome differences between cancer and healthy cells is a valuable approach for the identification of novel diagnostic and therapeutic targets. However, selective sampling of surface proteins for proteomics requires large samples (>10e6 cells) and long labeling times. These limitations preclude analysis of material-limited biological samples or the capture of rapid surface proteomic changes. Here, we present two labeling approaches to tether exogenous peroxidases (APEX2 and HRP) directly to cells, enabling rapid, small-scale cell surface biotinylation without the need to engineer cells. We used a novel lipidated DNA-tethered APEX2 (DNA-APEX2), which upon addition to cells promoted cell agnostic membrane-proximal labeling. Alternatively, we employed horseradish peroxidase (HRP) fused to the glycan-binding domain of wheat germ agglutinin (WGA-HRP). This approach yielded a rapid and commercially inexpensive means to directly label cells containing common N-Acetylglucosamine (GlcNAc) and sialic acid glycans on their surface. The facile WGA-HRP method permitted high surface coverage of cellular samples and enabled the first comparative surface proteome characterization of cells and cell-derived small extracellular vesicles (EVs), leading to the robust quantification of 953 cell and EV surface annotated proteins. We identified a newly recognized subset of EV-enriched markers, as well as proteins that are uniquely upregulated on Myc oncogene-transformed prostate cancer EVs. These two cell-tethered enzyme surface biotinylation approaches are highly advantageous for rapidly and directly labeling surface proteins across a range of material-limited sample types.
MeSH term(s)	Extracellular Vesicles ; Horseradish Peroxidase ; Humans ; Male ; Proteome/analysis ; Proteomics ; Wheat Germ Agglutinins
Chemical Substances	Proteome ; Wheat Germ Agglutinins ; Horseradish Peroxidase (EC 1.11.1.-)
Language	English
Publishing date	2022-03-08
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.73982
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Article ; Online: Modular cytokine receptor-targeting chimeras for targeted degradation of cell surface and extracellular proteins.

Pance, Katarina / Gramespacher, Josef A / Byrnes, James R / Salangsang, Fernando / Serrano, Juan-Antonio C / Cotton, Adam D / Steri, Veronica / Wells, James A

Nature biotechnology

2022 Volume 41, Issue 2, Page(s) 273–281

Abstract: Targeted degradation of cell surface and extracellular proteins via lysosomal delivery is an important means to modulate extracellular biology. However, these approaches have limitations due to lack of modularity, ease of development, restricted tissue ... ...

Abstract	Targeted degradation of cell surface and extracellular proteins via lysosomal delivery is an important means to modulate extracellular biology. However, these approaches have limitations due to lack of modularity, ease of development, restricted tissue targeting and applicability to both cell surface and extracellular proteins. We describe a lysosomal degradation strategy, termed cytokine receptor-targeting chimeras (KineTACs), that addresses these limitations. KineTACs are fully genetically encoded bispecific antibodies consisting of a cytokine arm, which binds its cognate cytokine receptor, and a target-binding arm for the protein of interest. We show that KineTACs containing the cytokine CXCL12 can use the decoy recycling receptor, CXCR7, to target a variety of target proteins to the lysosome for degradation. Additional KineTACs were designed to harness other CXCR7-targeting cytokines, CXCL11 and vMIPII, and the interleukin-2 (IL-2) receptor-targeting cytokine IL-2. Thus, KineTACs represent a general, modular, selective and simple genetically encoded strategy for inducing lysosomal delivery of extracellular and cell surface targets with broad or tissue-specific distribution.
MeSH term(s)	Cell Membrane ; Interleukin-2 ; Receptors, Cytokine/chemistry ; Receptors, Cytokine/metabolism ; Signal Transduction ; Proteolysis ; Proteolysis Targeting Chimera ; Chemokine CXCL12/chemistry
Chemical Substances	Interleukin-2 ; Receptors, Cytokine ; Proteolysis Targeting Chimera ; Chemokine CXCL12
Language	English
Publishing date	2022-09-22
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1311932-1
ISSN	1546-1696 ; 1087-0156
ISSN (online)	1546-1696
ISSN	1087-0156
DOI	10.1038/s41587-022-01456-2
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