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Article ; Online: A New Paradigm in Catalase Research.

Fujiki, Yukio / Bassik, Michael C

2021 Volume 31, Issue 3, Page(s) 148–151

Abstract: Recent findings provide evidence for dynamic and highly regulated dual subcellular localization of catalase, a hydrogen peroxide ( ... ...

Abstract	Recent findings provide evidence for dynamic and highly regulated dual subcellular localization of catalase, a hydrogen peroxide (H
MeSH term(s)	Catalase/metabolism ; Cytosol/metabolism ; Hydrogen Peroxide/metabolism ; Oxidative Stress ; Peroxisomes/metabolism
Chemical Substances	Hydrogen Peroxide (BBX060AN9V) ; Catalase (EC 1.11.1.6)
Language	English
Publishing date	2021-01-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	30122-x
ISSN	1879-3088 ; 0962-8924
ISSN (online)	1879-3088
ISSN	0962-8924
DOI	10.1016/j.tcb.2020.12.006
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Article ; Online: Pathogenic or benign?

Du, Peter P / Liu, Katherine / Bassik, Michael C / Hess, Gaelen T

Nature biotechnology

2022 Volume 40, Issue 6, Page(s) 834–836

MeSH term(s)	Genetic Predisposition to Disease ; Humans ; Mutation
Language	English
Publishing date	2022-05-13
Publishing country	United States
Document type	Journal Article ; Comment
ZDB-ID	1311932-1
ISSN	1546-1696 ; 1087-0156
ISSN (online)	1546-1696
ISSN	1087-0156
DOI	10.1038/s41587-022-01333-y
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Article: A Genome-Wide CRISPR Screen Identifies Sortilin as the Receptor Responsible for Galectin-1 Lysosomal Trafficking.

Donnelly, Justin / Kamber, Roarke A / Wisnovsky, Simon / Roberts, David S / Peltan, Egan L / Bassik, Michael C / Bertozzi, Carolyn R

bioRxiv : the preprint server for biology

2024

Abstract: Galectins are a family of mammalian glycan-binding proteins that have been implicated as regulators of myriad cellular processes including cell migration, apoptosis, and immune modulation. Several members of this family, such as galectin-1, exhibit both ... ...

Abstract	Galectins are a family of mammalian glycan-binding proteins that have been implicated as regulators of myriad cellular processes including cell migration, apoptosis, and immune modulation. Several members of this family, such as galectin-1, exhibit both cell-surface and intracellular functions. Interestingly, galectin-1 can be found in the endomembrane system, nucleus, or cytosol, as well as on the cell surface. The mechanisms by which galectin-1 traffics between cellular compartments, including its unconventional secretion and internalization processes, are poorly understood. Here, we determined the pathways by which exogenous galectin-1 enters cells and explored its capacity as a delivery vehicle for protein and siRNA therapeutics. We used a galectin-1-toxin conjugate, modelled on antibody-drug conjugates, as a selection tool in a genome-wide CRISPR screen. We discovered that galectin-1 interacts with the endosome-lysosome trafficking receptor sortilin in a glycan-dependent manner, which regulates galectin-1 trafficking to the lysosome. Further, we show that this pathway can be exploited for delivery of a functional siRNA. This study sheds light on the mechanisms by which galectin-1 is internalized by cells and suggests a new strategy for intracellular drug delivery via galectin-1 conjugation.
Language	English
Publishing date	2024-01-03
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.01.03.574113
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Article ; Online: A BORC-dependent molecular pathway for vesiculation of cell corpse phagolysosomes.

Fazeli, Gholamreza / Levin-Konigsberg, Roni / Bassik, Michael C / Stigloher, Christian / Wehman, Ann M

Current biology : CB

2023 Volume 33, Issue 4, Page(s) 607–621.e7

Abstract: Phagocytic clearance is important to provide cells with metabolites and regulate immune responses, but little is known about how phagolysosomes finally resolve their phagocytic cargo of cell corpses, cell debris, and pathogens. While studying the ... ...

Abstract	Phagocytic clearance is important to provide cells with metabolites and regulate immune responses, but little is known about how phagolysosomes finally resolve their phagocytic cargo of cell corpses, cell debris, and pathogens. While studying the phagocytic clearance of non-apoptotic polar bodies in C. elegans, we previously discovered that phagolysosomes tubulate into small vesicles to facilitate corpse clearance within 1.5 h. Here, we show that phagolysosome vesiculation depends on amino acid export by the solute transporter SLC-36.1 and the activation of TORC1. We demonstrate that downstream of TORC1, BLOC-1-related complex (BORC) is de-repressed by Ragulator through the BORC subunit BLOS-7. In addition, the BORC subunit SAM-4 is needed continuously to recruit the small GTPase ARL-8 to the phagolysosome for tubulation. We find that disrupting the regulated GTP-GDP cycle of ARL-8 reduces tubulation by kinesin-1, delays corpse clearance, and mislocalizes ARL-8 away from lysosomes. We also demonstrate that mammalian phagocytes use BORC to promote phagolysosomal degradation, confirming the conserved importance of TOR and BORC. Finally, we show that HOPS is required after tubulation for the rapid degradation of cargo in small phagolysosomal vesicles, suggesting that additional rounds of lysosome fusion occur. Thus, by observing single phagolysosomes over time, we identified the molecular pathway regulating phagolysosome vesiculation that promotes efficient resolution of phagocytosed cargos.
MeSH term(s)	Animals ; Apoptosis ; Caenorhabditis elegans/metabolism ; Caenorhabditis elegans Proteins/genetics ; Caenorhabditis elegans Proteins/metabolism ; Lysosomes/metabolism ; Mammals ; Mechanistic Target of Rapamycin Complex 1/metabolism ; Phagocytosis ; Phagosomes/metabolism ; Multiprotein Complexes
Chemical Substances	Caenorhabditis elegans Proteins ; Mechanistic Target of Rapamycin Complex 1 (EC 2.7.11.1) ; Multiprotein Complexes
Language	English
Publishing date	2023-01-17
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1071731-6
ISSN	1879-0445 ; 0960-9822
ISSN (online)	1879-0445
ISSN	0960-9822
DOI	10.1016/j.cub.2022.12.041
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Article: SLC12A9 is a lysosome-detoxifying ammonium - chloride co-transporter.

Levin-Konigsberg, Roni / Mitra, Koushambi / Nigam, AkshatKumar / Spees, Kaitlyn / Hivare, Pravin / Liu, Katherine / Kundaje, Anshul / Krishnan, Yamuna / Bassik, Michael C

bioRxiv : the preprint server for biology

2023

Abstract: Ammonia is a ubiquitous, toxic by-product of cell metabolism. Its high membrane permeability and proton affinity causes ammonia to accumulate inside acidic lysosomes in its poorly membrane-permeant form: ammonium ( ... ...

Abstract	Ammonia is a ubiquitous, toxic by-product of cell metabolism. Its high membrane permeability and proton affinity causes ammonia to accumulate inside acidic lysosomes in its poorly membrane-permeant form: ammonium (NH
Language	English
Publishing date	2023-05-22
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.05.22.541801
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Article ; Online: High-throughput discovery and characterization of viral transcriptional effectors in human cells.

Ludwig, Connor H / Thurm, Abby R / Morgens, David W / Yang, Kevin J / Tycko, Josh / Bassik, Michael C / Glaunsinger, Britt A / Bintu, Lacramioara

Cell systems

2023 Volume 14, Issue 6, Page(s) 482–500.e8

Abstract: Viruses encode transcriptional regulatory proteins critical for controlling viral and host gene expression. Given their multifunctional nature and high sequence divergence, it is unclear which viral proteins can affect transcription and which specific ... ...

Abstract	Viruses encode transcriptional regulatory proteins critical for controlling viral and host gene expression. Given their multifunctional nature and high sequence divergence, it is unclear which viral proteins can affect transcription and which specific sequences contribute to this function. Using a high-throughput assay, we measured the transcriptional regulatory potential of over 60,000 protein tiles across ∼1,500 proteins from 11 coronaviruses and all nine human herpesviruses. We discovered hundreds of transcriptional effector domains, including a conserved repression domain in all coronavirus Spike homologs, dual activation-repression domains in viral interferon regulatory factors (VIRFs), and an activation domain in six herpesvirus homologs of the single-stranded DNA-binding protein that we show is important for viral replication and late gene expression in Kaposi's sarcoma-associated herpesvirus (KSHV). For the effector domains we identified, we investigated their mechanisms via high-throughput sequence and chemical perturbations, pinpointing sequence motifs essential for function. This work massively expands viral protein annotations, serving as a springboard for studying their biological and health implications and providing new candidates for compact gene regulation tools.
MeSH term(s)	Humans ; Herpesvirus 8, Human/genetics ; Herpesvirus 8, Human/metabolism ; Virus Replication/genetics ; Gene Expression Regulation
Language	English
Publishing date	2023-06-22
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2854138-8
ISSN	2405-4720 ; 2405-4712
ISSN (online)	2405-4720
ISSN	2405-4712
DOI	10.1016/j.cels.2023.05.008
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Article ; Online: Direct mapping of ligandable tyrosines and lysines in cells with chiral sulfonyl fluoride probes.

Chen, Ying / Craven, Gregory B / Kamber, Roarke A / Cuesta, Adolfo / Zhersh, Serhii / Moroz, Yurii S / Bassik, Michael C / Taunton, Jack

Nature chemistry

2023 Volume 15, Issue 11, Page(s) 1616–1625

Abstract: Advances in chemoproteomic technology have revealed covalent interactions between small molecules and protein nucleophiles, primarily cysteine, on a proteome-wide scale. Most chemoproteomic screening approaches are indirect, relying on competition ... ...

Abstract	Advances in chemoproteomic technology have revealed covalent interactions between small molecules and protein nucleophiles, primarily cysteine, on a proteome-wide scale. Most chemoproteomic screening approaches are indirect, relying on competition between electrophilic fragments and a minimalist electrophilic probe with inherently limited proteome coverage. Here we develop a chemoproteomic platform for direct electrophile-site identification based on enantiomeric pairs of clickable arylsulfonyl fluoride probes. Using stereoselective site modification as a proxy for ligandability in intact cells, we identify 634 tyrosines and lysines within functionally diverse protein sites, liganded by structurally diverse probes. Among multiple validated sites, we discover a chiral probe that modifies Y228 in the MYC binding site of the epigenetic regulator WDR5, as revealed by a high-resolution crystal structure. A distinct chiral probe stimulates tumour cell phagocytosis by covalently modifying Y387 in the recently discovered immuno-oncology target APMAP. Our work provides a deep resource of ligandable tyrosines and lysines for the development of covalent chemical probes.
MeSH term(s)	Lysine/chemistry ; Proteome/chemistry ; Tyrosine ; Binding Sites
Chemical Substances	Lysine (K3Z4F929H6) ; Proteome ; sulfuryl fluoride (64B59K7U6Q) ; Tyrosine (42HK56048U)
Language	English
Publishing date	2023-07-17
Publishing country	England
Document type	Journal Article
ZDB-ID	2464596-5
ISSN	1755-4349 ; 1755-4330
ISSN (online)	1755-4349
ISSN	1755-4330
DOI	10.1038/s41557-023-01281-3
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Article ; Online: Co-transcriptional genome surveillance by HUSH is coupled to termination machinery.

Spencley, Andrew L / Bar, Shiran / Swigut, Tomek / Flynn, Ryan A / Lee, Cameron H / Chen, Liang-Fu / Bassik, Michael C / Wysocka, Joanna

Molecular cell

2023 Volume 83, Issue 10, Page(s) 1623–1639.e8

Abstract: The HUSH complex recognizes and silences foreign DNA such as viruses, transposons, and transgenes without prior exposure to its targets. Here, we show that endogenous targets of the HUSH complex fall into two distinct classes based on the presence or ... ...

Abstract	The HUSH complex recognizes and silences foreign DNA such as viruses, transposons, and transgenes without prior exposure to its targets. Here, we show that endogenous targets of the HUSH complex fall into two distinct classes based on the presence or absence of H3K9me3. These classes are further distinguished by their transposon content and differential response to the loss of HUSH. A de novo genomic rearrangement at the Sox2 locus induces a switch from H3K9me3-independent to H3K9me3-associated HUSH targeting, resulting in silencing. We further demonstrate that HUSH interacts with the termination factor WDR82 and-via its component MPP8-with nascent RNA. HUSH accumulates at sites of high RNAPII occupancy including long exons and transcription termination sites in a manner dependent on WDR82 and CPSF. Together, our results uncover the functional diversity of HUSH targets and show that this vertebrate-specific complex exploits evolutionarily ancient transcription termination machinery for co-transcriptional chromatin targeting and genome surveillance.
MeSH term(s)	Gene Silencing ; Transcription Factors/metabolism ; Transcription, Genetic ; Genome/genetics ; RNA
Chemical Substances	Transcription Factors ; RNA (63231-63-0)
Language	English
Publishing date	2023-05-09
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2023.04.014
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Article ; Online: Genome-scale CRISPR screening reveals that C3aR signaling is critical for rapid capture of fungi by macrophages.

Cohen, Allison / Jeng, Edwin E / Voorhies, Mark / Symington, Jane / Ali, Nebat / Rodriguez, Rosa A / Bassik, Michael C / Sil, Anita

PLoS pathogens

2022 Volume 18, Issue 9, Page(s) e1010237

Abstract: The fungal pathogen Histoplasma capsulatum (Hc) invades, replicates within, and destroys macrophages. To interrogate the molecular mechanisms underlying this interaction, we conducted a host-directed CRISPR-Cas9 screen and identified 361 genes that ... ...

Abstract	The fungal pathogen Histoplasma capsulatum (Hc) invades, replicates within, and destroys macrophages. To interrogate the molecular mechanisms underlying this interaction, we conducted a host-directed CRISPR-Cas9 screen and identified 361 genes that modify macrophage susceptibility to Hc infection, greatly expanding our understanding of host gene networks targeted by Hc. We identified pathways that have not been previously implicated in Hc interaction with macrophages, including the ragulator complex (involved in nutrient stress sensing), glycosylation enzymes, protein degradation machinery, mitochondrial respiration genes, solute transporters, and the ER membrane complex (EMC). The highest scoring protective hits included the complement C3a receptor (C3aR), a G-protein coupled receptor (GPCR) that recognizes the complement fragment C3a. Although it is known that complement components react with the fungal surface, leading to opsonization and release of small peptide fragments such as C3a, a role for C3aR in macrophage interactions with fungi has not been elucidated. We demonstrated that whereas C3aR is dispensable for macrophage phagocytosis of bacteria and latex beads, it is critical for optimal macrophage capture of pathogenic fungi, including Hc, the ubiquitous fungal pathogen Candida albicans, and the causative agent of Valley Fever Coccidioides posadasii. We showed that C3aR localizes to the early phagosome during Hc infection where it coordinates the formation of actin-rich membrane protrusions that promote Hc capture. We also showed that the EMC promotes surface expression of C3aR, likely explaining its identification in our screen. Taken together, our results provide new insight into host processes that affect Hc-macrophage interactions and uncover a novel and specific role for C3aR in macrophage recognition of fungi.
MeSH term(s)	Actins ; Receptors, Complement/metabolism ; Macrophages/metabolism ; Histoplasma/genetics ; Histoplasma/metabolism ; Receptors, G-Protein-Coupled/metabolism ; Histoplasmosis ; Peptide Fragments
Chemical Substances	complement C3a receptor ; Actins ; Receptors, Complement ; Receptors, G-Protein-Coupled ; Peptide Fragments
Language	English
Publishing date	2022-09-29
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2205412-1
ISSN	1553-7374 ; 1553-7374
ISSN (online)	1553-7374
ISSN	1553-7374
DOI	10.1371/journal.ppat.1010237
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Article ; Online: Identification of orphan ligand-receptor relationships using a cell-based CRISPRa enrichment screening platform.

Siepe, Dirk H / Henneberg, Lukas T / Wilson, Steven C / Hess, Gaelen T / Bassik, Michael C / Zinn, Kai / Garcia, K Christopher

eLife

2022 Volume 11

Abstract: Secreted proteins, which include cytokines, hormones, and growth factors, are extracellular ligands that control key signaling pathways mediating cell-cell communication within and between tissues and organs. Many drugs target secreted ligands and their ... ...

Abstract	Secreted proteins, which include cytokines, hormones, and growth factors, are extracellular ligands that control key signaling pathways mediating cell-cell communication within and between tissues and organs. Many drugs target secreted ligands and their cell surface receptors. Still, there are hundreds of secreted human proteins that either have no identified receptors ('orphans') or are likely to act through cell surface receptors that have not yet been characterized. Discovery of secreted ligand-receptor interactions by high-throughput screening has been problematic, because the most commonly used high-throughput methods for protein-protein interaction (PPI) screening are not optimized for extracellular interactions. Cell-based screening is a promising technology for the deorphanization of ligand-receptor interactions, because multimerized ligands can enrich for cells expressing low affinity cell surface receptors, and such methods do not require purification of receptor extracellular domains. Here, we present a proteo-genomic cell-based CRISPR activation (CRISPRa) enrichment screening platform employing customized pooled cell surface receptor sgRNA libraries in combination with a magnetic bead selection-based enrichment workflow for rapid, parallel ligand-receptor deorphanization. We curated 80 potentially high-value orphan secreted proteins and ultimately screened 20 secreted ligands against two cell sgRNA libraries with targeted expression of all single-pass (TM1) or multi-pass transmembrane (TM2+) receptors by CRISPRa. We identified previously unknown interactions in 12 of these screens, and validated several of them using surface plasmon resonance and/or cell binding assays. The newly deorphanized ligands include three receptor protein tyrosine phosphatase (RPTP) ligands and a chemokine-like protein that binds to killer immunoglobulin-like receptors (KIRs). These new interactions provide a resource for future investigations of interactions between the human-secreted and membrane proteomes.
MeSH term(s)	Humans ; Ligands ; Proteome/metabolism ; Clustered Regularly Interspaced Short Palindromic Repeats ; Receptors, Cell Surface/metabolism ; Protein Binding/physiology ; Cytokines/metabolism ; Hormones ; Immunoglobulins/metabolism
Chemical Substances	Ligands ; Proteome ; Receptors, Cell Surface ; Cytokines ; Hormones ; Immunoglobulins
Language	English
Publishing date	2022-09-30
Publishing country	England
Document type	Journal Article ; 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.81398
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