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Article ; Online: Ligandability of E3 Ligases for Targeted Protein Degradation Applications.

Belcher, Bridget P / Ward, Carl C / Nomura, Daniel K

2021 Volume 62, Issue 3, Page(s) 588–600

Abstract: Targeted protein degradation (TPD) using proteolysis targeting chimeras (PROTACs) and molecular glue degraders has arisen as a powerful therapeutic modality for eliminating disease-causing proteins from cells. PROTACs and molecular glue degraders employ ... ...

Abstract	Targeted protein degradation (TPD) using proteolysis targeting chimeras (PROTACs) and molecular glue degraders has arisen as a powerful therapeutic modality for eliminating disease-causing proteins from cells. PROTACs and molecular glue degraders employ heterobifunctional or monovalent small molecules, respectively, to chemically induce the proximity of target proteins with E3 ubiquitin ligases to ubiquitinate and degrade specific proteins via the proteasome. Whereas TPD is an attractive therapeutic strategy for expanding the druggable proteome, only a relatively small number of E3 ligases out of the >600 E3 ligases encoded by the human genome have been exploited by small molecules for TPD applications. Here we review the existing E3 ligases that have thus far been successfully exploited for TPD and discuss chemoproteomics-enabled covalent screening strategies for discovering new E3 ligase recruiters. We also provide a chemoproteomic map of reactive cysteines within hundreds of E3 ligases that may represent potential ligandable sites that can be pharmacologically interrogated to uncover additional E3 ligase recruiters.
MeSH term(s)	Humans ; Ubiquitin-Protein Ligases/metabolism ; Proteolysis ; Proteins/metabolism ; Proteasome Endopeptidase Complex/metabolism ; Ubiquitination
Chemical Substances	Ubiquitin-Protein Ligases (EC 2.3.2.27) ; Proteins ; Proteasome Endopeptidase Complex (EC 3.4.25.1)
Language	English
Publishing date	2021-09-02
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/acs.biochem.1c00464
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Article ; Online: NHS-Esters As Versatile Reactivity-Based Probes for Mapping Proteome-Wide Ligandable Hotspots.

Ward, Carl C / Kleinman, Jordan I / Nomura, Daniel K

ACS chemical biology

2017 Volume 12, Issue 6, Page(s) 1478–1483

Abstract: Most of the proteome is considered undruggable, oftentimes hindering translational efforts for drug discovery. Identifying previously unknown druggable hotspots in proteins would enable strategies for pharmacologically interrogating these sites with ... ...

Abstract	Most of the proteome is considered undruggable, oftentimes hindering translational efforts for drug discovery. Identifying previously unknown druggable hotspots in proteins would enable strategies for pharmacologically interrogating these sites with small molecules. Activity-based protein profiling (ABPP) has arisen as a powerful chemoproteomic strategy that uses reactivity-based chemical probes to map reactive, functional, and ligandable hotspots in complex proteomes, which has enabled inhibitor discovery against various therapeutic protein targets. Here, we report an alkyne-functionalized N-hydroxysuccinimide-ester (NHS-ester) as a versatile reactivity-based probe for mapping the reactivity of a wide range of nucleophilic ligandable hotspots, including lysines, serines, threonines, and tyrosines, encompassing active sites, allosteric sites, post-translational modification sites, protein interaction sites, and previously uncharacterized potential binding sites. Surprisingly, we also show that fragment-based NHS-ester ligands can be made to confer selectivity for specific lysine hotspots on specific targets including Dpyd, Aldh2, and Gstt1. We thus put forth NHS-esters as promising reactivity-based probes and chemical scaffolds for covalent ligand discovery.
MeSH term(s)	Aldehyde Dehydrogenase, Mitochondrial/metabolism ; Alkynes/chemistry ; Binding Sites ; Esters/chemistry ; Glutathione Transferase/metabolism ; Humans ; Ligands ; Lysine/metabolism ; Molecular Probes/chemistry ; Proteome/metabolism ; Succinimides
Chemical Substances	Alkynes ; Esters ; Ligands ; Molecular Probes ; Proteome ; Succinimides ; ALDH2 protein, human (EC 1.2.1.3) ; Aldehyde Dehydrogenase, Mitochondrial (EC 1.2.1.3) ; glutathione S-transferase T1 (EC 2.5.1.-) ; Glutathione Transferase (EC 2.5.1.18) ; Lysine (K3Z4F929H6) ; N-hydroxysuccinimide (MJE3791M4T)
Language	English
Publishing date	2017-05-01
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ISSN	1554-8937
ISSN (online)	1554-8937
DOI	10.1021/acschembio.7b00125
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Article ; Online: Activity-based protein profiling for mapping and pharmacologically interrogating proteome-wide ligandable hotspots.

Roberts, Allison M / Ward, Carl C / Nomura, Daniel K

Current opinion in biotechnology

2017 Volume 43, Page(s) 25–33

Abstract: Despite the completion of human genome sequencing efforts nearly 15 years ago that brought with it the promise of genome-based discoveries that would cure human diseases, most protein targets that control human diseases have remained largely untranslated, ...

Abstract	Despite the completion of human genome sequencing efforts nearly 15 years ago that brought with it the promise of genome-based discoveries that would cure human diseases, most protein targets that control human diseases have remained largely untranslated, in-part because they represent difficult protein targets to drug. In addition, many of these protein targets lack screening assays or accessible binding pockets, making the development of small-molecule modulators very challenging. Here, we discuss modern methods for activity-based protein profiling-based chemoproteomic strategies to map 'ligandable' hotspots in proteomes using activity and reactivity-based chemical probes to allow for pharmacological interrogation of these previously difficult targets. We will showcase several recent examples of how these technologies have been used to develop highly selective small-molecule inhibitors against disease-related protein targets.
MeSH term(s)	Animals ; Biomarkers/analysis ; Biomarkers/metabolism ; Drug Design ; Humans ; Protein Array Analysis ; Proteins/analysis ; Proteins/metabolism ; Proteome/analysis ; Proteome/metabolism
Chemical Substances	Biomarkers ; Proteins ; Proteome
Language	English
Publishing date	2017-02
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	1052045-4
ISSN	1879-0429 ; 0958-1669
ISSN (online)	1879-0429
ISSN	0958-1669
DOI	10.1016/j.copbio.2016.08.003
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Article: Role of Long Non-coding RNAs in Reprogramming to Induced Pluripotency

Kanwal, Shahzina / Guo, Xiangpeng / Ward, Carl / Volpe, Giacomo / Qin, Baoming / Esteban, Miguel A / Bao, Xichen

Genomics, proteomics & bioinformatics. 2020 Feb., v. 18, no. 1

2020

Abstract: The generation of induced pluripotent stem cells through somatic cell reprogramming requires a global reorganization of cellular functions. This reorganization occurs in a multi-phased manner and involves a gradual revision of both the epigenome and ... ...

Abstract	The generation of induced pluripotent stem cells through somatic cell reprogramming requires a global reorganization of cellular functions. This reorganization occurs in a multi-phased manner and involves a gradual revision of both the epigenome and transcriptome. Recent studies have shown that the large-scale transcriptional changes observed during reprogramming also apply to long non-coding RNAs (lncRNAs), a type of traditionally neglected RNA species that are increasingly viewed as critical regulators of cellular function. Deeper understanding of lncRNAs in reprogramming may not only help to improve this process but also have implications for studying cell plasticity in other contexts, such as development, aging, and cancer. In this review, we summarize the current progress made in profiling and analyzing the role of lncRNAs in various phases of somatic cell reprogramming, with emphasis on the re-establishment of the pluripotency gene network and X chromosome reactivation.
Keywords	bioinformatics ; epigenome ; genes ; genomics ; plasticity ; proteomics ; somatic cells ; transcription (genetics) ; transcriptome
Language	English
Dates of publication	2020-02
Size	p. 16-25.
Publishing place	Elsevier B.V.
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	2240213-5
ISSN	2210-3244 ; 1672-0229
ISSN (online)	2210-3244
ISSN	1672-0229
DOI	10.1016/j.gpb.2019.06.003
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Article ; Online: In Vitro Screening Platforms for Identifying Autophagy Modulators in Mammalian Cells.

Seranova, Elena / Ward, Carl / Chipara, Miruna / Rosenstock, Tatiana R / Sarkar, Sovan

Methods in molecular biology (Clifton, N.J.)

2019 Volume 1880, Page(s) 389–428

Abstract: Autophagy is a vital homeostatic pathway essential for cellular survival and human health. It primarily functions as an intracellular degradation process for the turnover of aggregation-prone proteins and unwanted organelles. Dysregulation of autophagy ... ...

Abstract	Autophagy is a vital homeostatic pathway essential for cellular survival and human health. It primarily functions as an intracellular degradation process for the turnover of aggregation-prone proteins and unwanted organelles. Dysregulation of autophagy underlying diverse human diseases reduces cell viability, whereas stimulation of autophagy is cytoprotective in a number of transgenic disease models including neurodegenerative disorders. Thus, therapeutic exploitation of autophagy is considered a potential treatment strategy in certain human diseases, and therefore, chemical inducers of autophagy have tremendous biomedical relevance. In this review, we describe the in vitro screening platforms to identify autophagy modulators in mammalian cells using various methodologies including fluorescence and high-content imaging, flow cytometry, fluorescence and luminescence detection by microplate reader, immunoblotting, and immunofluorescence. The commonly used autophagy reporters in these screening platforms are either based on autophagy marker like LC3 or autophagy substrate such as aggregation-prone proteins or p62/SQSTM1. The reporters and assays for monitoring autophagy are evolving over time to become more sensitive in measuring autophagic flux with the capability of high-throughput applications for drug discovery. Here we highlight these developments and also describe the stringent secondary autophagy assays for characterizing the autophagy modulators arising from the primary screen. Since autophagy is implicated in myriad human physiological and pathological conditions, these technologies will enable identifying novel chemical modulators or genetic regulators of autophagy that will be of biomedical and fundamental importance to human health.
MeSH term(s)	Animals ; Autophagy/physiology ; Autophagy-Related Proteins/metabolism ; Biological Assay/instrumentation ; Biological Assay/methods ; Cell Culture Techniques/instrumentation ; Cell Culture Techniques/methods ; Cell Line ; Flow Cytometry/instrumentation ; Flow Cytometry/methods ; Genes, Reporter/genetics ; Humans ; Luminescent Proteins/chemistry ; Luminescent Proteins/genetics ; Microscopy, Fluorescence/instrumentation ; Microscopy, Fluorescence/methods ; Microtubule-Associated Proteins ; Sequestosome-1 Protein/metabolism ; Transfection/instrumentation ; Transfection/methods
Chemical Substances	Autophagy-Related Proteins ; Luminescent Proteins ; Microtubule-Associated Proteins ; Sequestosome-1 Protein
Language	English
Publishing date	2019-01-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-8873-0_26
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Article ; Online: Improving prime editing with an endogenous small RNA-binding protein.

Yan, Jun / Oyler-Castrillo, Paul / Ravisankar, Purnima / Ward, Carl C / Levesque, Sébastien / Jing, Yangwode / Simpson, Danny / Zhao, Anqi / Li, Hui / Yan, Weihao / Goudy, Laine / Schmidt, Ralf / Solley, Sabrina C / Gilbert, Luke A / Chan, Michelle M / Bauer, Daniel E / Marson, Alexander / Parsons, Lance R / Adamson, Britt

Nature

2024 Volume 628, Issue 8008, Page(s) 639–647

Abstract: Prime editing enables the precise modification of genomes through reverse transcription of template sequences appended to the 3' ends of CRISPR-Cas guide ... ...

Abstract	Prime editing enables the precise modification of genomes through reverse transcription of template sequences appended to the 3' ends of CRISPR-Cas guide RNAs
MeSH term(s)	Humans ; CRISPR-Cas Systems/genetics ; Gene Editing/methods ; K562 Cells ; Poly U/genetics ; Poly U/metabolism ; RNA Polymerase III/metabolism ; RNA, Guide, CRISPR-Cas Systems/genetics ; RNA, Guide, CRISPR-Cas Systems/metabolism ; RNA-Binding Proteins/metabolism
Chemical Substances	Poly U (27416-86-0) ; RNA Polymerase III (EC 2.7.7.6) ; RNA, Guide, CRISPR-Cas Systems ; RNA-Binding Proteins
Language	English
Publishing date	2024-04-03
Publishing country	England
Document type	Journal Article
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-024-07259-6
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Zs.A 26: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article: Global Profiling of the Lysine Crotonylome in Different Pluripotent States

Lv, Yuan / Bu, Chen / Meng, Jin / Ward, Carl / Volpe, Giacomo / Hu, Jieyi / Jiang, Mengling / Guo, Lin / Chen, Jiekai / Esteban, Miguel A / Bao, Xichen / Cheng, Zhongyi

Genomics, proteomics & bioinformatics. 2021 Jan. 27,

2021

Abstract: Pluripotent stem cells (PSCs) can be expanded in vitro in different culture conditions, resulting in a spectrum of cell states with distinct properties. Understanding how PSCs transition from one state to another, ultimately leading to lineage-specific ... ...

Abstract	Pluripotent stem cells (PSCs) can be expanded in vitro in different culture conditions, resulting in a spectrum of cell states with distinct properties. Understanding how PSCs transition from one state to another, ultimately leading to lineage-specific differentiation, is important for developmental biology and regenerative medicine. Although there is significant information regarding gene expression changes controlling these transitions, less is known about post-translational modifications of proteins. Protein crotonylation is a newly discovered post-translational modification where lysine residues are modified with a crotonyl group. Here, we employed affinity purification of crotonylated peptides and liquid chromatography-tandem mass spectrometry (LC–MS/MS) to systematically profile protein crotonylation in mouse PSCs in different states including ground, metastable, and primed states, as well as metastable PSCs undergoing early pluripotency exit. We successfully identified 3628 high-confidence crotonylated sites in 1426 proteins. These crotonylated proteins are enriched for factors involved in functions/processes related to pluripotency such as RNA biogenesis, central carbon metabolism, and proteasome function. Moreover, we found that increasing the cellular levels of crotonyl-coenzyme A (crotonyl-CoA) through crotonic acid treatment promotes proteasome activity in metastable PSCs and delays their differentiation, consistent with previous observations showing that enhanced proteasome activity helps to sustain pluripotency. Our atlas of protein crotonylation will be valuable for further studies of pluripotency regulation and may also provide insights into the role of metabolism in other cell fate transitions.
Keywords	RNA ; acid treatment ; biogenesis ; bioinformatics ; carbon metabolism ; gene expression ; genomics ; liquid chromatography ; lysine ; medicine ; mice ; peptides ; post-translational modification ; proteasome endopeptidase complex ; proteomics ; tandem mass spectrometry
Language	English
Dates of publication	2021-0127
Publishing place	Elsevier B.V.
Document type	Article
Note	NAL-AP-2-clean ; Pre-press version
ZDB-ID	2240213-5
ISSN	2210-3244 ; 1672-0229
ISSN (online)	2210-3244
ISSN	1672-0229
DOI	10.1016/j.gpb.2021.01.004
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Article ; Online: Formaldehyde regulates

Pham, Vanha N / Bruemmer, Kevin J / Toh, Joel D W / Ge, Eva J / Tenney, Logan / Ward, Carl C / Dingler, Felix A / Millington, Christopher L / Garcia-Prieto, Carlos A / Pulos-Holmes, Mia C / Ingolia, Nicholas T / Pontel, Lucas B / Esteller, Manel / Patel, Ketan J / Nomura, Daniel K / Chang, Christopher J

Science (New York, N.Y.)

2023 Volume 382, Issue 6670, Page(s) eabp9201

Abstract: One-carbon metabolism is an essential branch of cellular metabolism that intersects with epigenetic regulation. In this work, we show how formaldehyde (FA), a one-carbon unit derived from both endogenous sources and environmental exposure, regulates one- ... ...

Abstract	One-carbon metabolism is an essential branch of cellular metabolism that intersects with epigenetic regulation. In this work, we show how formaldehyde (FA), a one-carbon unit derived from both endogenous sources and environmental exposure, regulates one-carbon metabolism by inhibiting the biosynthesis of
MeSH term(s)	Animals ; Mice ; Carbon/metabolism ; Epigenesis, Genetic/drug effects ; Protein Isoforms/antagonists & inhibitors ; Protein Isoforms/metabolism ; S-Adenosylmethionine/antagonists & inhibitors ; S-Adenosylmethionine/metabolism ; Formaldehyde/metabolism ; Formaldehyde/toxicity ; Environmental Exposure ; Methionine Adenosyltransferase/antagonists & inhibitors ; Methionine Adenosyltransferase/genetics ; Methionine Adenosyltransferase/metabolism ; Cysteine/metabolism ; Humans ; Hep G2 Cells
Chemical Substances	Carbon (7440-44-0) ; Protein Isoforms ; S-Adenosylmethionine (7LP2MPO46S) ; Formaldehyde (1HG84L3525) ; Mat1a protein, mouse (EC 2.5.1.6) ; Methionine Adenosyltransferase (EC 2.5.1.6) ; Cysteine (K848JZ4886) ; MAT1A protein, human (EC 2.5.1.6)
Language	English
Publishing date	2023-11-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.abp9201
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Zs.A 27: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 77: Show issues

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Article ; Online: Ectopic expression of meiotic cohesin generates chromosome instability in cancer cell line.

Boukaba, Abdelhalim / Liu, Jian / Ward, Carl / Wu, Qiongfang / Arnaoutov, Alexei / Liang, Jierong / Pugacheva, Elena M / Dasso, Mary / Lobanenkov, Victor / Esteban, Miguel / Strunnikov, Alexander V

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

2022 Volume 119, Issue 40, Page(s) e2204071119

Abstract: Many tumors express meiotic genes that could potentially drive somatic chromosome instability. While germline cohesin subunits SMC1B, STAG3, and REC8 are widely expressed in many cancers, messenger RNA and protein for RAD21L subunit are expressed at very ...

Abstract	Many tumors express meiotic genes that could potentially drive somatic chromosome instability. While germline cohesin subunits SMC1B, STAG3, and REC8 are widely expressed in many cancers, messenger RNA and protein for RAD21L subunit are expressed at very low levels. To elucidate the potential of meiotic cohesins to contribute to genome instability, their expression was investigated in human cell lines, predominately in DLD-1. While the induction of the REC8 complex resulted in a mild mitotic phenotype, the expression of the RAD21L complex produced an arrested but viable cell pool, thus providing a source of DNA damage, mitotic chromosome missegregation, sporadic polyteny, and altered gene expression. We also found that genomic binding profiles of ectopically expressed meiotic cohesin complexes were reminiscent of their corresponding specific binding patterns in testis. Furthermore, meiotic cohesins were found to localize to the same sites as BORIS/CTCFL, rather than CTCF sites normally associated with the somatic cohesin complex. These findings highlight the existence of a germline epigenomic memory that is conserved in cells that normally do not express meiotic genes. Our results reveal a mechanism of action by unduly expressed meiotic cohesins that potentially links them to aneuploidy and chromosomal mutations in affected cells.
MeSH term(s)	Cell Cycle Proteins/genetics ; Cell Cycle Proteins/metabolism ; Cell Line ; Chromosomal Instability/genetics ; Chromosomal Proteins, Non-Histone ; Chromosome Segregation ; DNA-Binding Proteins/metabolism ; Ectopic Gene Expression ; Humans ; Male ; Meiosis/genetics ; Neoplasms/genetics ; Nuclear Proteins/metabolism ; Phosphoproteins/metabolism ; RNA, Messenger ; Cohesins
Chemical Substances	CTCFL protein, human ; Cell Cycle Proteins ; Chromosomal Proteins, Non-Histone ; DNA-Binding Proteins ; Nuclear Proteins ; Phosphoproteins ; RNA, Messenger ; STAG3 protein, human
Language	English
Publishing date	2022-09-30
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural ; 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.2204071119
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Article ; Online: Role of Long Non-coding RNAs in Reprogramming to Induced Pluripotency.

Kanwal, Shahzina / Guo, Xiangpeng / Ward, Carl / Volpe, Giacomo / Qin, Baoming / Esteban, Miguel A / Bao, Xichen

Genomics, proteomics & bioinformatics

2020 Volume 18, Issue 1, Page(s) 16–25

Abstract	The generation of induced pluripotent stem cells through somatic cell reprogramming requires a global reorganization of cellular functions. This reorganization occurs in a multi-phased manner and involves a gradual revision of both the epigenome and transcriptome. Recent studies have shown that the large-scale transcriptional changes observed during reprogramming also apply to long non-coding RNAs (lncRNAs), a type of traditionally neglected RNA species that are increasingly viewed as critical regulators of cellular function. Deeper understanding of lncRNAs in reprogramming may not only help to improve this process but also have implications for studying cell plasticity in other contexts, such as development, aging, and cancer. In this review, we summarize the current progress made in profiling and analyzing the role of lncRNAs in various phases of somatic cell reprogramming, with emphasis on the re-establishment of the pluripotency gene network and X chromosome reactivation.
MeSH term(s)	Animals ; Cellular Reprogramming/genetics ; Humans ; Induced Pluripotent Stem Cells/cytology ; Induced Pluripotent Stem Cells/metabolism ; Induced Pluripotent Stem Cells/physiology ; RNA, Long Noncoding/genetics ; RNA, Long Noncoding/physiology ; Transcriptome ; X Chromosome
Chemical Substances	RNA, Long Noncoding
Language	English
Publishing date	2020-05-21
Publishing country	China
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2240213-5
ISSN	2210-3244 ; 1672-0229
ISSN (online)	2210-3244
ISSN	1672-0229
DOI	10.1016/j.gpb.2019.06.003
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