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Article ; Online: New Approaches for Targeting PCSK9: Small-Interfering Ribonucleic Acid and Genome Editing.

Oostveen, Reindert F / Khera, Amit V / Kathiresan, Sekar / Stroes, Erik S G / Fitzgerald, Kevin / Harms, Matthew J / Oakes, Benjamin L / Kastelein, John J P

Arteriosclerosis, thrombosis, and vascular biology

2023 Volume 43, Issue 7, Page(s) 1081–1092

Abstract: There is overwhelming clinical and genetic evidence supporting the concept that low-density-lipoprotein cholesterol should be as low as possible for as long as possible in patients at very high cardiovascular risk. Despite the wide availability of ... ...

Abstract	There is overwhelming clinical and genetic evidence supporting the concept that low-density-lipoprotein cholesterol should be as low as possible for as long as possible in patients at very high cardiovascular risk. Despite the wide availability of effective lipid-lowering therapies, the majority of patients still fail to reach guideline-based lipid goals. Advances in novel approaches targeting PCSK9 (proprotein convertase subtilisin/kexin type 9) through small-interfering RNA and genome editing hold the potential to bridge this gap, by offering long-acting alternatives, which may overcome adherence and other challenges in the current chronic care model. In this review, we discuss the history of targeting PCSK9 with the use of mRNA and small-interfering ribonucleic acid. We also shed light on targeting PCSK9 with genome editing, including discussion of the VERVE-101 clustered regularly interspaced short palindromic repeats-base editing medicine currently being evaluated in a clinical trial and others in development.
MeSH term(s)	Humans ; Proprotein Convertase 9/genetics ; Gene Editing ; Cholesterol, LDL ; RNA, Small Interfering/genetics
Chemical Substances	PCSK9 protein, human (EC 3.4.21.-) ; Proprotein Convertase 9 (EC 3.4.21.-) ; Cholesterol, LDL ; RNA, Small Interfering
Language	English
Publishing date	2023-06-01
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	1221433-4
ISSN	1524-4636 ; 1079-5642
ISSN (online)	1524-4636
ISSN	1079-5642
DOI	10.1161/ATVBAHA.122.317963
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Article ; Online: Analysis of Adverse Events and Intravenous Iron Infusion Formulations in Adults With and Without Prior Infusion Reactions.

Arastu, Asad H / Elstrott, Benjamin K / Martens, Kylee L / Cohen, Jonathan L / Oakes, Michael H / Rub, Zhoe T / Aslan, Joseph J / DeLoughery, Thomas G / Shatzel, Joseph

JAMA network open

2022 Volume 5, Issue 3, Page(s) e224488

Abstract: Importance: Although iron deficiency is common, it remains unclear which iron repletion strategy is associated with the lowest rate of infusion-related adverse events, and how patients with history of infusion reaction should be managed.: Objective: ... ...

Abstract	Importance: Although iron deficiency is common, it remains unclear which iron repletion strategy is associated with the lowest rate of infusion-related adverse events, and how patients with history of infusion reaction should be managed. Objective: To evaluate rates of infusion reactions among 4 commonly used intravenous iron repletion strategies and determine how readministration was managed in patients with history of reaction. Design, setting, and participants: This cohort study included all patients receiving intravenous iron infusion from January 1, 2015, to September 7, 2021, at 6 centers in Portland, Oregon. Participants included a total of 12 237 patients with iron deficiency, not restricted by etiology. Statistical analysis was performed from September to October 2021. Exposures: Type of intravenous iron formulation and concurrent administration of diphenhydramine, epinephrine, famotidine, and/or hydrocortisone, used as surrogate maker of infusion reaction. Main outcomes and measures: Incidence of adverse events, including severe events requiring epinephrine, stratified by type of iron formulation, and in patients who received premedication or with history of infusion-related reaction receiving subsequent doses. Results: Among 35 737 unique iron infusions (12 237 patients [9480 (77.5%) women; 717 (5.9%) Black; 10 250 (83.7%) White; mean (SD) age of 51 (20) years]), comprising 22 309 iron sucrose doses, 9067 iron dextran total doses (1771 preceded by test dose, 56 test doses alone), 3147 ferumoxytol doses, and 1214 ferric carboxymaltose doses, incidence of adverse events was 3.9% (n = 1389; 95% CI, 3.7%-4.1%). Rate of infusion events differed among iron formulations: 4.3% (n = 970; 95% CI, 4.1%-4.6%) iron sucrose, 3.8% (n = 345, 95% CI: 3.4%-4.2%) iron dextran (test and full doses or test dose alone), 1.8% (n = 57; 95% CI, 1.4%-2.3%) ferumoxytol, and 1.4% (n = 17, 95% CI, 0.8%-2.3%) ferric carboxymaltose (P < .001). Severe adverse events were exceedingly rare with only 2 documented epinephrine administrations, both associated with iron dextran. Incidence of adverse events among those who received premedication was 23-fold higher compared with those who did not (38.6% vs 1.7%, χ21 = 7324.8; P < .001). Among 873 patients with history of infusion reaction who underwent readministration, the majority received the same formulation, which was associated with significantly higher reaction rate particularly if premedication was administered (68% [95% CI, 64%-72%] vs 32% [95% CI, 26%-41%], respectively), compared with those who received an alternate formulation (21% [95% CI, 11%-35%] vs 5% [95% CI, 2%-12%], respectively) (P < .001). Conclusions and relevance: These data, and the preponderance of published evidence, suggest that intravenous iron is generally well tolerated with exceedingly low risk of severe reaction, use of premedication and test doses are unnecessary, and that optimal prevention and management of infusion-related reactions warrant further study.
MeSH term(s)	Administration, Intravenous ; Adult ; Cohort Studies ; Female ; Ferrosoferric Oxide/adverse effects ; Humans ; Infusions, Intravenous ; Iron/adverse effects ; Male ; Middle Aged
Chemical Substances	Iron (E1UOL152H7) ; Ferrosoferric Oxide (XM0M87F357)
Language	English
Publishing date	2022-03-01
Publishing country	United States
Document type	Journal Article
ISSN	2574-3805
ISSN (online)	2574-3805
DOI	10.1001/jamanetworkopen.2022.4488
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Author Correction: Circularly permuted and PAM-modified Cas9 variants broaden the targeting scope of base editors.

Huang, Tony P / Zhao, Kevin T / Miller, Shannon M / Gaudelli, Nicole M / Oakes, Benjamin L / Fellmann, Christof / Savage, David F / Liu, David R

Nature biotechnology

2019 Volume 37, Issue 7, Page(s) 820

Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

Abstract	An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Language	English
Publishing date	2019-06-11
Publishing country	United States
Document type	Published Erratum
ZDB-ID	1311932-1
ISSN	1546-1696 ; 1087-0156
ISSN (online)	1546-1696
ISSN	1087-0156
DOI	10.1038/s41587-019-0168-1
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Article ; Online: A high areal capacity lithium-sulfur battery cathode prepared by site-selective vapor infiltration of hierarchical carbon nanotube arrays.

Carter, Rachel / Davis, Benjamin / Oakes, Landon / Maschmann, Matthew R / Pint, Cary L

Nanoscale

2017 Volume 9, Issue 39, Page(s) 15018–15026

Abstract: The widespread use of melt infiltration has to date restricted sulfur-carbon cathode architectures to only host materials processed as bulk powders with no site control of sulfur deposits. Here, we combine structurally designed hierarchical carbon ... ...

Abstract	The widespread use of melt infiltration has to date restricted sulfur-carbon cathode architectures to only host materials processed as bulk powders with no site control of sulfur deposits. Here, we combine structurally designed hierarchical carbon nanotube (CNT) arrays with site-selective vapor phase sulfur infiltration to produce thick electrodes with controlled sulfur loading and high areal performance. Our results illustrate the critical role structural hierarchy plays in sustaining electrical connectivity to enable high utilization of the sulfur embedded in thick electrodes with high gravimetric loading. Here, a primary large-diameter CNT population provides robust conductive trunks that branch into a secondary small-diameter and high-surface-area CNT population capable of giving rapid electrical access to coated sulfur. Site-selective vapor phase sulfur infiltration, based on the capillary effect, controllably targets loading of one or both of the CNT populations to facilitate gravimetric loading from 60 wt% to 70 wt% sulfur. With the high areal loading of 6 mg cm
Language	English
Publishing date	2017-10-12
Publishing country	England
Document type	Journal Article
ZDB-ID	2515664-0
ISSN	2040-3372 ; 2040-3364
ISSN (online)	2040-3372
ISSN	2040-3364
DOI	10.1039/c7nr02368e
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Article ; Online: Comprehensive deletion landscape of CRISPR-Cas9 identifies minimal RNA-guided DNA-binding modules.

Shams, Arik / Higgins, Sean A / Fellmann, Christof / Laughlin, Thomas G / Oakes, Benjamin L / Lew, Rachel / Kim, Shin / Lukarska, Maria / Arnold, Madeline / Staahl, Brett T / Doudna, Jennifer A / Savage, David F

Nature communications

2021 Volume 12, Issue 1, Page(s) 5664

Abstract: Proteins evolve through the modular rearrangement of elements known as domains. Extant, multidomain proteins are hypothesized to be the result of domain accretion, but there has been limited experimental validation of this idea. Here, we introduce a ... ...

Abstract	Proteins evolve through the modular rearrangement of elements known as domains. Extant, multidomain proteins are hypothesized to be the result of domain accretion, but there has been limited experimental validation of this idea. Here, we introduce a technique for genetic minimization by iterative size-exclusion and recombination (MISER) for comprehensively making all possible deletions of a protein. Using MISER, we generate a deletion landscape for the CRISPR protein Cas9. We find that the catalytically-dead Streptococcus pyogenes Cas9 can tolerate large single deletions in the REC2, REC3, HNH, and RuvC domains, while still functioning in vitro and in vivo, and that these deletions can be stacked together to engineer minimal, DNA-binding effector proteins. In total, our results demonstrate that extant proteins retain significant modularity from the accretion process and, as genetic size is a major limitation for viral delivery systems, establish a general technique to improve genome editing and gene therapy-based therapeutics.
MeSH term(s)	CRISPR-Associated Protein 9/genetics ; CRISPR-Associated Protein 9/metabolism ; CRISPR-Associated Protein 9/ultrastructure ; CRISPR-Cas Systems/genetics ; Cell Line, Tumor ; Cryoelectron Microscopy ; DNA/metabolism ; Gene Editing/methods ; Humans ; Protein Interaction Domains and Motifs/genetics ; RNA, Guide, CRISPR-Cas Systems/metabolism ; Single Molecule Imaging
Chemical Substances	RNA, Guide, CRISPR-Cas Systems ; DNA (9007-49-2) ; CRISPR-Associated Protein 9 (EC 3.1.-) ; Cas9 endonuclease Streptococcus pyogenes (EC 3.1.-)
Language	English
Publishing date	2021-09-27
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-021-25992-8
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Article ; Online: Protein engineering of Cas9 for enhanced function.

Oakes, Benjamin L / Nadler, Dana C / Savage, David F

Methods in enzymology

2014 Volume 546, Page(s) 491–511

Abstract: CRISPR/Cas systems act to protect the cell from invading nucleic acids in many bacteria and archaea. The bacterial immune protein Cas9 is a component of one of these CRISPR/Cas systems and has recently been adapted as a tool for genome editing. Cas9 is ... ...

Abstract	CRISPR/Cas systems act to protect the cell from invading nucleic acids in many bacteria and archaea. The bacterial immune protein Cas9 is a component of one of these CRISPR/Cas systems and has recently been adapted as a tool for genome editing. Cas9 is easily targeted to bind and cleave a DNA sequence via a complementary RNA; this straightforward programmability has gained Cas9 rapid acceptance in the field of genetic engineering. While this technology has developed quickly, a number of challenges regarding Cas9 specificity, efficiency, fusion protein function, and spatiotemporal control within the cell remain. In this work, we develop a platform for constructing novel proteins to address these open questions. We demonstrate methods to either screen or select active Cas9 mutants and use the screening technique to isolate functional Cas9 variants with a heterologous PDZ domain inserted within the protein. As a proof of concept, these methods lay the groundwork for the future construction of diverse Cas9 proteins. Straightforward and accessible techniques for genetic editing are helping to elucidate biology in new and exciting ways; a platform to engineer new functionalities into Cas9 will help forge the next generation of genome-modifying tools.
MeSH term(s)	Amino Acid Sequence ; Bacteria/chemistry ; Bacteria/enzymology ; Bacteria/genetics ; Bacteria/metabolism ; Base Sequence ; CRISPR-Associated Proteins/chemistry ; CRISPR-Associated Proteins/genetics ; CRISPR-Associated Proteins/metabolism ; CRISPR-Cas Systems ; Deoxyribonuclease I/chemistry ; Deoxyribonuclease I/genetics ; Deoxyribonuclease I/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutation ; PDZ Domains ; Protein Conformation ; Protein Engineering/methods ; Streptococcus pyogenes/chemistry ; Streptococcus pyogenes/enzymology ; Streptococcus pyogenes/genetics ; Streptococcus pyogenes/metabolism
Chemical Substances	CRISPR-Associated Proteins ; Deoxyribonuclease I (EC 3.1.21.1)
Language	English
Publishing date	2014
Publishing country	United States
Document type	Journal Article
ISSN	1557-7988 ; 0076-6879
ISSN (online)	1557-7988
ISSN	0076-6879
DOI	10.1016/B978-0-12-801185-0.00024-6
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Comprehensive deletion landscape of CRISPR-Cas9 identifies minimal RNA-guided DNA-binding modules

Arik Shams / Sean A. Higgins / Christof Fellmann / Thomas G. Laughlin / Benjamin L. Oakes / Rachel Lew / Shin Kim / Maria Lukarska / Madeline Arnold / Brett T. Staahl / Jennifer A. Doudna / David F. Savage

Nature Communications, Vol 12, Iss 1, Pp 1-

2021 Volume 11

Abstract: Proteins evolve through the modular rearrangement of domains. Here the authors introduce MISER, a minimization by iterative size-exclusion and recombination method to make all possible deletions of a protein, uncovering functions for Cas9 domains ... ...

Abstract	Proteins evolve through the modular rearrangement of domains. Here the authors introduce MISER, a minimization by iterative size-exclusion and recombination method to make all possible deletions of a protein, uncovering functions for Cas9 domains involved in DNA binding.
Keywords	Science ; Q
Language	English
Publishing date	2021-09-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Circularly permuted and PAM-modified Cas9 variants broaden the targeting scope of base editors.

Huang, Tony P / Zhao, Kevin T / Miller, Shannon M / Gaudelli, Nicole M / Oakes, Benjamin L / Fellmann, Christof / Savage, David F / Liu, David R

Nature biotechnology

2019 Volume 37, Issue 6, Page(s) 626–631

Abstract: Base editing requires that the target sequence satisfy the protospacer adjacent motif requirement of the Cas9 domain and that the target nucleotide be located within the editing window of the base editor. To increase the targeting scope of base editors, ... ...

Abstract	Base editing requires that the target sequence satisfy the protospacer adjacent motif requirement of the Cas9 domain and that the target nucleotide be located within the editing window of the base editor. To increase the targeting scope of base editors, we engineered six optimized adenine base editors (ABEmax variants) that use SpCas9 variants compatible with non-NGG protospacer adjacent motifs. To increase the range of target bases that can be modified within the protospacer, we use circularly permuted Cas9 variants to produce four cytosine and four adenine base editors with an editing window expanded from ~4-5 nucleotides to up to ~8-9 nucleotides and reduced byproduct formation. This set of base editors improves the targeting scope of cytosine and adenine base editing.
MeSH term(s)	Adenine/chemistry ; CRISPR-Associated Protein 9/genetics ; CRISPR-Cas Systems/genetics ; Cytosine/chemistry ; Gene Editing/methods ; Humans ; Nucleotides/chemistry ; Nucleotides/genetics ; Plasmids/chemistry ; Plasmids/genetics
Chemical Substances	Nucleotides ; Cytosine (8J337D1HZY) ; CRISPR-Associated Protein 9 (EC 3.1.-) ; Adenine (JAC85A2161)
Language	English
Publishing date	2019-05-20
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1311932-1
ISSN	1546-1696 ; 1087-0156
ISSN (online)	1546-1696
ISSN	1087-0156
DOI	10.1038/s41587-019-0134-y
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Article ; Online: Electrically Conductive Hierarchical Carbon Nanotube Networks with Tunable Mechanical Response.

Davis, Benjamin F / Yan, Xingyi / Muralidharan, Nitin / Oakes, Landon / Pint, Cary L / Maschmann, Matthew R

ACS applied materials & interfaces

2016 Volume 8, Issue 41, Page(s) 28004–28011

Abstract: Small diameter carbon nanotube (CNTs) are synthesized directly from a parent CNT forest using a floating catalyst chemical vapor deposition (CVD) method. To support a new CNT generation from an existing forest, an alumina coating was applied to the CNT ... ...

Abstract	Small diameter carbon nanotube (CNTs) are synthesized directly from a parent CNT forest using a floating catalyst chemical vapor deposition (CVD) method. To support a new CNT generation from an existing forest, an alumina coating was applied to the CNT forest using atomic layer deposition (ALD). The new generation of small diameter CNTs (8 nm average) surround the first generation, filling the interstitial regions. The hierarchical forests exhibit a 5-10-fold increase in stiffness, and the two generations are electrically addressable in spite of the interfacial alumina layer between them. This work enables the design of complex CNT architectures with hierarchical features that bring tailored properties such as high specific surface area and robust mechanical properties that can benefit a range of applications.
Language	English
Publishing date	2016-10-11
Publishing country	United States
Document type	Journal Article
ISSN	1944-8252
ISSN (online)	1944-8252
DOI	10.1021/acsami.6b10726
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Article ; Online: Erythrocytosis and thromboembolic events in transgender individuals receiving gender-affirming testosterone.

Oakes, Michael / Arastu, Asad / Kato, Catherine / Somers, Julia / Holly, Hannah D / Elstrott, Benjamin K / Dy, Geolani W / Kohs, Tia C L / Patel, Rishi R / McCarty, Owen J T / DeLoughery, Thomas G / Milano, Christina / Raghunathan, Vikram / Shatzel, Joseph J

Thrombosis research

2021 Volume 207, Page(s) 96–98

Abstract: Erythrocytosis is a well-recognized consequence of exogenous testosterone, however its prevalence and contributions to thrombosis remain unknown in the context of gender-affirming hormonal therapy. We undertook a retrospective study of transgender and ... ...

Abstract	Erythrocytosis is a well-recognized consequence of exogenous testosterone, however its prevalence and contributions to thrombosis remain unknown in the context of gender-affirming hormonal therapy. We undertook a retrospective study of transgender and non-binary (TGNB) adults receiving exogenous testosterone. In the retrospective sample, 923 transgender individuals receiving testosterone were identified with 519 having documented pre- and post-testosterone hemoglobin and hematocrit (Hgb/Hct). The mean peak Hgb/Hct was 15.7 g/dL, and 47.0%. Mean time-to-peak Hgb/Hct was 31.2 months; 7.8% developed a hemoglobin >17.5 g/dL, whereas 20% developed a hematocrit of >50%. Testosterone dose reduction occurred in 42% of patients with erythrocytosis and 4.8% underwent phlebotomy. Thromboembolic events occurred in 0.9%, of which 80% had developed erythrocytosis by either Hgb or Hct, including two cases each of superficial and calf vein thrombosis as well as one ischemic stroke. We then performed an analysis of 14,294,784 hospitalizations from the 2016-17 US National Inpatient Sample (NIS), which identified 4141 admissions involving transgender individuals. Of those, seven had erythrocytosis with one concurrent venous thromboembolic event. Hematocrit >50% occurs in up to 20% of transgender individuals receiving testosterone. Despite the high incidence of erythrocytosis, thromboembolic events and hospitalizations involving erythrocytosis were uncommon.
Language	English
Publishing date	2021-09-20
Publishing country	United States
Document type	Letter
ZDB-ID	121852-9
ISSN	1879-2472 ; 0049-3848
ISSN (online)	1879-2472
ISSN	0049-3848
DOI	10.1016/j.thromres.2021.09.005
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