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Article ; Online: The history of genome editing: advances from the interface of chemistry & biology.

Matsumoto, Daisuke / Nomura, Wataru

Chemical communications (Cambridge, England)

2023 Volume 59, Issue 50, Page(s) 7676–7684

Abstract: Genome editing had a long history before the appearance of CRISPR. Although a decade has passed since the initial use of CRISPR with mammalian cells, the first attempts at gene editing occurred in the 1980's. Subsequently, many researchers tried to ... ...

Abstract	Genome editing had a long history before the appearance of CRISPR. Although a decade has passed since the initial use of CRISPR with mammalian cells, the first attempts at gene editing occurred in the 1980's. Subsequently, many researchers tried to develop methods to edit specific genes. Here, we review the history of genome editing and improvements in genome editing tools. In the last two decades, genome editing tools have been applied in basic sciences, the bio-industry, and therapeutics. We provide examples in which genome editing tools have been applied to various tasks. Recently, new CRISPR-Cas techniques, such as base and prime editing and anti-CRISPR proteins, have attracted considerable interest. Accordingly, these topics are also reviewed.
MeSH term(s)	Animals ; Gene Editing/methods ; CRISPR-Cas Systems/genetics ; Biology ; Mammals/genetics
Language	English
Publishing date	2023-06-20
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	1472881-3
ISSN	1364-548X ; 1359-7345 ; 0009-241X
ISSN (online)	1364-548X
ISSN	1359-7345 ; 0009-241X
DOI	10.1039/d3cc00559c
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Article ; Online: Effects of social activity participation and trust in the community on the transition of frailty classification in late-stage older adults: a 4-year prospective cohort study.

Takatori, Katsuhiko / Matsumoto, Daisuke

BMJ open

2023 Volume 13, Issue 5, Page(s) e072243

Abstract: Objectives: In Japan, frailty is a major risk factor for requiring long-term care, especially among older adults aged 75 years or older (ie, late-stage older adults). Both physical and social factors (eg, social activities, social support and community ... ...

Abstract	Objectives: In Japan, frailty is a major risk factor for requiring long-term care, especially among older adults aged 75 years or older (ie, late-stage older adults). Both physical and social factors (eg, social activities, social support and community trust) are protective factors against frailty. However, few longitudinal studies have examined reversible change or stage improvement in frailty. This study investigated social activity participation and trust in the community that may affect the transition of late-stage older adults' frailty status. Design: A mail-based survey was used to analyse the improvement or deterioration of frailty status (categorised as frailty, pre-frailty and robust) over a 4-year period. Binomial and multinomial logistic regression analyses were conducted; the transition in frailty classification was the dependent variable, while a change in social activity participation and the degree of trust in the community were the independent variables. Setting: Ikoma City, Nara Prefecture, Japan. Participants: 4249 community-dwelling older adults, aged ≥75 years, not requiring long-term care who completed a follow-up questionnaire from April to May 2016. Results: Adjusting for confounding factors, no significant social factors were detected regarding improvement in frailty. However, an increase in exercise-based social participation was an improvement factor in the pre-frailty group (OR 2.43 (95% CI 1.08 to 5.45)). Conversely, a decrease in community-based social activity was a risk factor in the deterioration from pre-frailty to frailty (OR 0.46 (95% CI 0.22 to 0.93)). In the robust group, increased community-based social activity (OR 1.38 (95% CI 1.00 to 1.90)) was a protective factor against frailty, whereas decreased community trust was a risk factor (OR 1.87 (95% CI 1.38 to 2.52)). Conclusions: No social factors had a significant influence on the improvement of frailty in late-stage older adults. However, the promotion of exercise-based social participation was found to be important for improvement in the pre-frailty state. Trial registration number: UMIN000025621.
MeSH term(s)	Aged ; Humans ; Frailty ; Frail Elderly ; Social Participation ; Prospective Studies ; Trust ; Geriatric Assessment ; Independent Living
Language	English
Publishing date	2023-05-04
Publishing country	England
Document type	Journal Article
ZDB-ID	2599832-8
ISSN	2044-6055 ; 2044-6055
ISSN (online)	2044-6055
ISSN	2044-6055
DOI	10.1136/bmjopen-2023-072243
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Article: Reconceptualization of Proximal Nail Fold Reconstruction: Skin Grafting over the Nail Plate.

Hara, Runa / Matsumoto, Daisuke / Funabashi, Hitomi

Plastic and reconstructive surgery. Global open

2023 Volume 11, Issue 6, Page(s) e5047

Abstract: The structure of the periungual area is complicated, resulting in historically difficult morphological reconstruction after trauma or cancer resection. There is also no established standard for its reconstruction; thus, we aimed to use a full-thickness ... ...

Abstract	The structure of the periungual area is complicated, resulting in historically difficult morphological reconstruction after trauma or cancer resection. There is also no established standard for its reconstruction; thus, we aimed to use a full-thickness skin graft (FTSG) over the nail plate. Three patients with Bowen disease on their proximal nail fold (PNF) underwent excision with a 2-mm margin preserving the nail matrix, and a temporary wound dressing was applied. The FTSG was harvested from the ipsilateral ulnar wrist joint and placed over the skin defect, including the nail plate. Initially, the FTSG seemed to have shrunken; however, after 3 months, it extended and the PNF had a good color and texture match. Remarkably, the FTSG adhered to the nail plate, and the complex PNF structure appeared well reconstructed. Occasionally, a local flap is used; however, it is limited to small defects and causes a deformity of the periungual structure. In this study, the reconstructed PNF showed good results. We presumed that the bridging phenomenon caused graft survival on the nail plate, and that the presence of stem cells near the nail matrix caused graft extension and eponychium and cuticle regeneration. Specifically, the acquisition of sufficient raw surface around the nail plate and wound preparation after excision resulted in the former, and the nail matrix preservation after excision contributed to the latter. This surgical technique is simple and can therefore be considered a remarkably effective method for periungual area reconstruction to date.
Language	English
Publishing date	2023-06-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	2851682-5
ISSN	2169-7574 ; 2169-7574
ISSN (online)	2169-7574
ISSN	2169-7574
DOI	10.1097/GOX.0000000000005047
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Article ; Online: Molecular Switch Engineering for Precise Genome Editing.

Matsumoto, Daisuke / Nomura, Wataru

Bioconjugate chemistry

2021 Volume 32, Issue 4, Page(s) 639–648

Abstract: Genome editing technology commenced in 1996 with the discovery of the first zinc-finger nuclease. Application of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) associated protein 9 (Cas9) technology to genome editing of mammalian cells ...

Abstract	Genome editing technology commenced in 1996 with the discovery of the first zinc-finger nuclease. Application of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) associated protein 9 (Cas9) technology to genome editing of mammalian cells allowed researchers to use genome editing more easily and cost-effectively. However, one of the technological problems that remains to be solved is "off-target effects", which are unexpected mutations in nontarget DNA. One significant improvement in genome editing technology has been achieved with molecular/protein engineering. The key to this engineering is a "switch" to control function. In this review, we discuss recent efforts to design novel "switching" systems for precise editing using genome editing tools.
MeSH term(s)	CRISPR-Cas Systems ; DNA/genetics ; Gene Editing ; Genetic Engineering ; Nucleic Acid Hybridization ; Proteolysis ; RNA/genetics
Chemical Substances	RNA (63231-63-0) ; DNA (9007-49-2)
Language	English
Publishing date	2021-04-07
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1024041-x
ISSN	1520-4812 ; 1043-1802
ISSN (online)	1520-4812
ISSN	1043-1802
DOI	10.1021/acs.bioconjchem.1c00088
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Article ; Online: Social factors associated with reversing frailty progression in community-dwelling late-stage elderly people: An observational study.

Takatori, Katsuhiko / Matsumoto, Daisuke

PloS one

2021 Volume 16, Issue 3, Page(s) e0247296

Abstract: Frailty is considered to be a complex concept based mainly on physical vulnerability, but also vulnerabilities in mental/psychological and social aspects. Frailty can be reversible with appropriate intervention; however, factors that are important in ... ...

Abstract	Frailty is considered to be a complex concept based mainly on physical vulnerability, but also vulnerabilities in mental/psychological and social aspects. Frailty can be reversible with appropriate intervention; however, factors that are important in recovering from frailty have not been clarified. The aim of the present study was to identify factors that help an individual reverse frailty progression and characteristics of individuals that have recovered from frailty. Community-dwelling people aged ≥75 years who responded to the Kihon Checklist (KCL) were enrolled in the study. The KCL consists of 25 yes/no questions in 7 areas: daily-life related activities, motor functions, nutritional status, oral functions, homebound, cognitive functions, and depressed mood. The number of social activities, degree of trust in the community, degree of interaction with neighbors, and subjective age were also evaluated. Frailty was assessed based on the number of checked items: 0-3 for robust, 4-7 for pre-frailty, and ≥8 for frailty. A total of 5050 participants were included for statistical analysis. At the time of the baseline survey in 2016, 18.7% (n = 942) of respondents had frailty, and the follow-up survey showed that the recovery rate from frailty within 2 years (median 24 months) was 31.8% (n = 300). Multiple logistic regression analysis showed that exercise-based social participation (odds ratio [OR] 2.0, 95% confidence interval [CI] 1.2-3.4; P<0.01) and self-rated health (OR 1.2, CI 1.0-1.5; P = 0.02) were related to reversing frailty progression. Principal component analysis indicated that the main factors constituting the first principal component (contribution rate, 18.3%) included items related to social capital, such as interaction with neighbors, trust in the community, and number of social participation activities. Our results demonstrate that exercise-based social participation and high self-rated health have associations with reversing frailty progression. Individuals that recovered from frailty are characterized by high individual-level social capital components (i.e., trust in community, interaction with neighbors, and social participation).
MeSH term(s)	Aged ; Aged, 80 and over ; Cognition ; Depression/psychology ; Female ; Follow-Up Studies ; Frail Elderly/psychology ; Frailty/psychology ; Humans ; Independent Living/psychology ; Japan ; Male ; Social Factors
Language	English
Publishing date	2021-03-03
Publishing country	United States
Document type	Clinical Trial ; Journal Article ; Observational Study
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0247296
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Article ; Online: Regional Differences in Disability Incidence among Japanese Adults Aged 75 Years and Older: A 4-Year Prospective Cohort Study.

Matsumoto, Daisuke / Takatori, Katsuhiko

International journal of environmental research and public health

2021 Volume 18, Issue 13

Abstract: The present prospective study investigated the regional differences and trajectories of new-onset disabilities among older adults in the districts within a city in Japan. We analyzed data from 5050 Japanese residents aged ≥75 years old (men/women: 2512/ ... ...

Abstract	The present prospective study investigated the regional differences and trajectories of new-onset disabilities among older adults in the districts within a city in Japan. We analyzed data from 5050 Japanese residents aged ≥75 years old (men/women: 2512/2538) who completed the Kihon Checklist (a self-reported questionnaire on frailty) and a questionnaire on medical history and social capital in Ikoma city in 2015. The incidence of disability was determined using the new certification of long-term care insurance and was followed-up on 4 years after the primary outcome. A Cox proportional hazards regression model was used to determine the factors related to the risk of incident disability. During the 4-year follow-up period, 567 participants (11.2%) were newly certified to have a disability. The disability incidence rate ranged from 8.1% to 14.6%, depending on the district. After adjustment for the covariates of: older, women, stroke, prefrail, frail, participation in multiple social activities (hazard ratio [HR] = 0.72, 95% confidence interval [CI] = 0.56-0.91), and one of the districts (HR = 1.67, 95% CI = 1.06-2.61) were significantly associated with disability incidence. The findings of this longitudinal study suggest that there could be a regional difference in disability incidence among older adults in Japan. Thus, community-based approaches should be designed to prevent disability in older adults.
MeSH term(s)	Aged ; Female ; Frail Elderly ; Humans ; Incidence ; Independent Living ; Japan/epidemiology ; Longitudinal Studies ; Male ; Prospective Studies
Language	English
Publishing date	2021-06-24
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2175195-X
ISSN	1660-4601 ; 1661-7827
ISSN (online)	1660-4601
ISSN	1661-7827
DOI	10.3390/ijerph18136791
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Article: SpCas9-HF1 enhances accuracy of cell cycle-dependent genome editing by increasing HDR efficiency, and by reducing off-target effects and indel rates.

Matsumoto, Daisuke / Matsugi, Erina / Kishi, Kanae / Inoue, Yuto / Nigorikawa, Kiyomi / Nomura, Wataru

Molecular therapy. Nucleic acids

2024 Volume 35, Issue 1, Page(s) 102124

Abstract: In genome editing, it is important to avoid off-target mutations so as to reduce unexpected side effects, especially for therapeutic applications. Recently, several high-fidelity versions of SpCas9 have been developed to reduce off-target mutations. In ... ...

Abstract	In genome editing, it is important to avoid off-target mutations so as to reduce unexpected side effects, especially for therapeutic applications. Recently, several high-fidelity versions of SpCas9 have been developed to reduce off-target mutations. In addition to reducing off-target effects, highly efficient intended target gene correction is also essential to rescue protein functions that have been disrupted by single nucleotide polymorphisms. Homology-directed repair (HDR) corrects genes precisely using a DNA template. Our recent development of cell cycle-dependent genome editing has shown that regulation of Cas9 activation with an anti-CRISPR-Cdt1 fusion protein increases HDR efficiency and reduces off-target effects. In this study, to apply high-fidelity SpCas9 variants to cell cycle-dependent genome editing, we evaluated anti-CRISPR inhibition of high-fidelity SpCas9s. In addition, HDR efficiency of high-fidelity SpCas9s was addressed, identifying eSpCas9, SpCas9-HF1, and LZ3 Cas9 as promising candidates. Although eSpCas9 and LZ3 Cas9 showed decreased HDR efficiency in cell cycle-dependent genome editing, SpCas9-HF1 successfully achieved increased HDR efficiency and few off-target effects when co-expressed with an AcrIIA4-Cdt1 fusion.
Language	English
Publishing date	2024-01-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	2662631-7
ISSN	2162-2531
ISSN	2162-2531
DOI	10.1016/j.omtn.2024.102124
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Article ; Online: Cas9‐Geminin and Cdt1‐fused anti‐CRISPR protein synergistically increase editing accuracy

Matsumoto, Daisuke / Kishi, Kanae / Matsugi, Erina / Inoue, Yuto / Nigorikawa, Kiyomi / Nomura, Wataru

FEBS Letters. 2023 Apr., v. 597, no. 7 p.985-994

2023

Abstract: Genome editing with CRISPR‐Cas9, particularly for therapeutic purposes, should be accomplished via the homology‐directed repair (HDR) pathway, which exhibits greater precision than other pathways. However, one of the issues to be solved is that genome ... ...

Abstract	Genome editing with CRISPR‐Cas9, particularly for therapeutic purposes, should be accomplished via the homology‐directed repair (HDR) pathway, which exhibits greater precision than other pathways. However, one of the issues to be solved is that genome editing efficiency with HDR is generally low. A Streptococcus pyogenes Cas9 (SpyCas9) fusion with human Geminin (Cas9‐Gem) reportedly increases HDR efficiency slightly. In contrast, we found that regulation of SpyCas9 activity with an anti‐CRISPR protein (AcrIIA4) fused to Chromatin licensing and DNA replication factor 1 (Cdt1) significantly increases HDR efficiency and reduces off‐target effects. Here, another anti‐CRISPR protein, AcrIIA5, was applied, and the combined use of Cas9‐Gem and Anti‐CRISPR+Cdt1 showed synergistic enhancement of HDR efficiency. The method may be applicable to various anti‐CRISPR/CRISPR‐Cas combinations.
Keywords	CRISPR-Cas systems ; DNA replication ; Streptococcus pyogenes ; chromatin ; genome ; humans ; therapeutics
Language	English
Dates of publication	2023-04
Size	p. 985-994.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	212746-5
ISSN	1873-3468 ; 0014-5793
ISSN (online)	1873-3468
ISSN	0014-5793
DOI	10.1002/1873-3468.14608
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Patterns of premenstrual syndrome in collegiate women: A cross-sectional study.

Morino, Saori / Hirata, Hinako / Matsumoto, Daisuke / Yokota, Isao / Aoyama, Tomoki

Medicine

2022 Volume 101, Issue 35, Page(s) e30186

Abstract: Premenstrual syndrome (PMS) has a wide variety of symptoms. The classification of these symptoms into several patterns is useful for more effective tailor-made treatment. Therefore, our study aimed to examine the patterns of PMS by analyzing multiple ... ...

Abstract	Premenstrual syndrome (PMS) has a wide variety of symptoms. The classification of these symptoms into several patterns is useful for more effective tailor-made treatment. Therefore, our study aimed to examine the patterns of PMS by analyzing multiple factors to identify the characteristics of each pattern. This is a cross-sectional study. A total of 165 women (18.9 ± 1.0 years) were investigated by using of questionnaire about PMS, nutrition, physical activity, and other lifestyle traits. Then, the factor analysis was performed to classify the premenstrual symptoms, that is, the pattern of PMS. Additionally, logistic regression analysis was performed to identify the characteristics of each pattern, adjusted for age, body mass index, sleep duration, and caffeine intake. As the result, PMS was classified into 3 patterns. The type related to psychological symptoms such as depression, physiological symptoms, such as abdominal pain, and intermingled type, were labeled as affected, somatic, and mixed types, respectively. From the result of logistic regression analysis, self-rating depression scale scoring was marginally associated with affective type (odds ratio [OR]: 1.08, 95% confidence interval [CI]: 0.99-1.16), physical activity was significantly associated with the mixed type (OR: 1.13, 95% CI: 1.00-1.28), and physical activity (OR: 1.20, 95% CI: 1.05-1.36) and some nutrients (OR: 0.56-1.00) were significantly associated with the somatic type. Understanding PMS and management of these complicated symptoms has been difficult. From the results of this study, the complicated symptoms were categorized into simpler patterns. Our findings may contribute to the understanding and possible management adjusted for each categorized case of PMS.
MeSH term(s)	Caffeine ; Cross-Sectional Studies ; Female ; Humans ; Premenstrual Syndrome/epidemiology ; Risk Factors ; Universities
Chemical Substances	Caffeine (3G6A5W338E)
Language	English
Publishing date	2022-09-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	80184-7
ISSN	1536-5964 ; 0025-7974
ISSN (online)	1536-5964
ISSN	0025-7974
DOI	10.1097/MD.0000000000030186
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Article: Ureterocele prolapse eliciting unusual patient behavior to control intermittent voiding.

Nishio, Hidenori / Mizuno, Kentaro / Matsumoto, Daisuke / Yasui, Takahiro / Hayashi, Yutaro

Urology case reports

2022 Volume 46, Page(s) 102295

Abstract: Ureterocele prolapse, an unusual but distinctive finding, may cause voiding difficulty. A 6-year-old male patient was referred to our hospital after his mother discovered that he tapped his lower abdomen when his urinary stream was interrupted during ... ...

Abstract	Ureterocele prolapse, an unusual but distinctive finding, may cause voiding difficulty. A 6-year-old male patient was referred to our hospital after his mother discovered that he tapped his lower abdomen when his urinary stream was interrupted during voiding. Voiding cystourethrography indicated a ureterocele prolapse causing the intermittency of voiding; therefore, transvesicoscopic ureteral reimplantation with ureterocelectomy was performed and the voiding consequently improved. However, this condition would not have been diagnosed had the unusual voiding behavior gone unnoticed. Therefore, diagnosing congenital bladder obstructions could be challenging if a patient adapts to a voiding difficulty.
Language	English
Publishing date	2022-11-30
Publishing country	United States
Document type	Case Reports
ZDB-ID	2745459-9
ISSN	2214-4420
ISSN	2214-4420
DOI	10.1016/j.eucr.2022.102295
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