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Article ; Online: A mechanism for the tissue specificity in BAP1 cancer syndrome.

Machida, Yuichi J

2022 Volume 8, Issue Suppl 6, Page(s) S621–S624

Language	English
Publishing date	2022-01-15
Publishing country	China
Document type	Editorial ; Comment
ZDB-ID	2901601-0
ISSN	2219-6803 ; 2218-676X
ISSN (online)	2219-6803
ISSN	2218-676X
DOI	10.21037/tcr.2019.06.41
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Article ; Online: DNA-protein crosslinks from environmental exposure: Mechanisms of formation and repair.

Kojima, Yusuke / Machida, Yuichi J

Environmental and molecular mutagenesis

2020 Volume 61, Issue 7, Page(s) 716–729

Abstract: Many environmental carcinogens cause DNA damage, which can result in mutations and other alterations in genomic DNA if not repaired promptly. Because of the bulkiness of the lesions, DNA-protein crosslinks (DPCs) are one of the types of toxic DNA damage ... ...

Abstract	Many environmental carcinogens cause DNA damage, which can result in mutations and other alterations in genomic DNA if not repaired promptly. Because of the bulkiness of the lesions, DNA-protein crosslinks (DPCs) are one of the types of toxic DNA damage with potentially deleterious consequences. Despite the importance of DPCs, how cells remove these complex DNA adducts has been incompletely understood. However, major progress in the DPC repair field over the past 5 years now supports the view that cells are equipped with multiple mechanisms to cope with DPCs. Here, we first provide an overview of environmental substances that induce DPCs, describing the sources of exposure and mechanisms of DPC formation. We then review current models of DPC repair and discuss their significance for environmental carcinogens.
MeSH term(s)	Animals ; DNA/drug effects ; DNA/genetics ; DNA Repair/drug effects ; DNA Repair/genetics ; DNA-Binding Proteins/genetics ; Environmental Exposure/adverse effects ; Humans
Chemical Substances	DNA-Binding Proteins ; DNA (9007-49-2)
Language	English
Publishing date	2020-07-09
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	639145-x
ISSN	1098-2280 ; 0893-6692
ISSN (online)	1098-2280
ISSN	0893-6692
DOI	10.1002/em.22381
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Article ; Online: Functions and evolution of FAM111 serine proteases

Allison L. Welter / Yuichi J. Machida

Frontiers in Molecular Biosciences, Vol

2022 Volume 9

Abstract: Proteolysis plays fundamental and regulatory roles in diverse cellular processes. The serine protease FAM111A (FAM111 trypsin-like peptidase A) emerged recently as a protease involved in two seemingly distinct processes: DNA replication and antiviral ... ...

Abstract	Proteolysis plays fundamental and regulatory roles in diverse cellular processes. The serine protease FAM111A (FAM111 trypsin-like peptidase A) emerged recently as a protease involved in two seemingly distinct processes: DNA replication and antiviral defense. FAM111A localizes to nascent DNA and plays a role at the DNA replication fork. At the fork, FAM111A is hypothesized to promote DNA replication at DNA-protein crosslinks (DPCs) and protein obstacles. On the other hand, FAM111A has also been identified as a host restriction factor for mutants of SV40 and orthopoxviruses. FAM111A also has a paralog, FAM111B, a serine protease with unknown cellular functions. Furthermore, heterozygous missense mutations in FAM111A and FAM111B cause distinct genetic disorders. In this review, we discuss possible models that could explain how FAM111A can function as a protease in both DNA replication and antiviral defense. We also review the consequences of FAM111A and FAM111B mutations and explore possible mechanisms underlying the diseases. Additionally, we propose a possible explanation for what drove the evolution of FAM111 proteins and discuss why some species have two FAM111 proteases. Altogether, studies of FAM111 proteases in DNA repair, antiviral defense, and genetic diseases will help us elucidate their functions and the regulatory mechanisms.
Keywords	FAM111A ; FAM111B ; protease ; viral replication ; Kenny-Caffey Syndrome (KCS) ; POIKTMP ; Biology (General) ; QH301-705.5
Subject code	612
Language	English
Publishing date	2022-12-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
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Article ; Online: Dimerization-dependent serine protease activity of FAM111A prevents replication fork stalling at topoisomerase 1 cleavage complexes.

Palani, Sowmiya / Machida, Yuka / Alvey, Julia R / Mishra, Vandana / Welter, Allison L / Cui, Gaofeng / Bragantini, Benoît / Botuyan, Maria Victoria / Cong, Anh T Q / Mer, Georges / Schellenberg, Matthew J / Machida, Yuichi J

Nature communications

2024 Volume 15, Issue 1, Page(s) 2064

Abstract: FAM111A, a serine protease, plays roles in DNA replication and antiviral defense. Missense mutations in the catalytic domain cause hyper-autocleavage and are associated with genetic disorders with developmental defects. Despite the enzyme's biological ... ...

Abstract	FAM111A, a serine protease, plays roles in DNA replication and antiviral defense. Missense mutations in the catalytic domain cause hyper-autocleavage and are associated with genetic disorders with developmental defects. Despite the enzyme's biological significance, the molecular architecture of the FAM111A serine protease domain (SPD) is unknown. Here, we show that FAM111A is a dimerization-dependent protease containing a narrow, recessed active site that cleaves substrates with a chymotrypsin-like specificity. X-ray crystal structures and mutagenesis studies reveal that FAM111A dimerizes via the N-terminal helix within the SPD. This dimerization induces an activation cascade from the dimerization sensor loop to the oxyanion hole through disorder-to-order transitions. Dimerization is essential for proteolytic activity in vitro and for facilitating DNA replication at DNA-protein crosslink obstacles in cells, while it is dispensable for autocleavage. These findings underscore the role of dimerization in FAM111A's function and highlight the distinction in its dimerization dependency between substrate cleavage and autocleavage.
MeSH term(s)	Dimerization ; Serine Endopeptidases/metabolism ; Proteolysis ; Serine Proteases ; DNA Replication ; Serine
Chemical Substances	Serine Endopeptidases (EC 3.4.21.-) ; Serine Proteases (EC 3.4.-) ; Serine (452VLY9402)
Language	English
Publishing date	2024-03-07
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-46207-w
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Article: Frailty and sarcopenia in older kidney transplant recipients: a cross-sectional study.

Kosoku, Akihiro / Iwai, Tomoaki / Kabei, Kazuya / Nishide, Shunji / Machida, Yuichi / Uchida, Junji

European geriatric medicine

2023 Volume 14, Issue 4, Page(s) 861–868

Abstract: ... of the Cardiovascular Health Study (J-CHS) criteria and the Kihon Checklist (KCL) and that of sarcopenia based ... sarcopenia, and secondly, to determine the concurrent validity of the KCL with the revised J-CHScriteria ... to February 2019. The diagnosis of frailty was assessed using the revised J-CHS criteria and the KCL ...

Abstract	Purpose: The aging of the kidney transplant population is accelerating, and measures against geriatric syndromes including frailty and sarcopenia, which elevate the risk of needing long-term care and even death, are being considered important. Recently, both the frailty and sarcopenia criteria for Asians were revised based on various research reports and clinical experiences. The purpose of this study is twofold: firstly, to investigate the prevalence of frailty based on the revised Japanese version of the Cardiovascular Health Study (J-CHS) criteria and the Kihon Checklist (KCL) and that of sarcopenia based on the Asian Working Group for Sarcopenia (AWGS) 2019 as well as the relationship between frailty and sarcopenia, and secondly, to determine the concurrent validity of the KCL with the revised J-CHScriteria in older kidney transplant recipients. Methods: This study was a single-center cross-sectional investigation carried out on older kidney transplant recipients who visited our hospital from August 2017 to February 2019. The diagnosis of frailty was assessed using the revised J-CHS criteria and the KCL. The diagnosis of sarcopenia was made by low skeletal muscle mass and either low physical performance or low muscle strength based on the AWGS 2019. To examine the relationship between frailty and sarcopenia, categorical variables were compared using chi-squared test and continuous variables Mann-Whitney U test. Spearman's correlation analysis was used to investigate the correlation between the KCL score and the revised J-CHS score. The concurrent validity of the KCL for estimating frailty based on the revised J-CHS criteria was evaluated using the receiver operating characteristics (ROC) curve analysis. Results: A total of 100 older kidney transplant recipients were enrolled in this study. The median age was 67, 63 (63%) were males, and the median time after transplant was 95 months. The prevalence of frailty based on the revised J-CHS criteria and the KCL, and sarcopenia based on the AWGS 2019 was 15%, and 19%, and 16% respectively. Sarcopenia was significantly associated with frailty based on the KCL (p = 0.016), while not with frailty based on the revised J-CHS criteria (p = 0.11). The KCL score significantly correlated with the revised J-CHS score (p < 0.001). The area under the ROC curve was 0.91. Conclusion: Frailty and sarcopenia are interrelated complex geriatric syndromes that are risk factors for adverse health outcomes. In older kidney transplant recipients, frailty and sarcopenia were highly prevalent and frequently co-existed. Furthermore, the KCL was verified as a useful tool for frailty screening in these patient. Easy identification of patients with frailty, which is reversible, can help clinicians institute appropriate corrective measures for kidney transplant recipients to improve transplant outcomes.
MeSH term(s)	Male ; Aged ; Humans ; Female ; Sarcopenia/diagnosis ; Sarcopenia/epidemiology ; Frailty/diagnosis ; Frailty/epidemiology ; Cross-Sectional Studies ; Kidney Transplantation/adverse effects ; Syndrome ; Geriatric Assessment
Language	English
Publishing date	2023-05-23
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2556794-9
ISSN	1878-7657 ; 1878-7649
ISSN (online)	1878-7657
ISSN	1878-7649
DOI	10.1007/s41999-023-00803-z
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Article ; Online: Daprodustat for Post-Transplant Anemia in Renal Transplant Recipients.

Machida, Yuichi / Iwai, Tomoaki / Kabei, Kazuya / Naganuma, Toshihide / Uchida, Junji

Transplantation proceedings

2024 Volume 56, Issue 3, Page(s) 534–539

Abstract: Background: Daprodustat, a hypoxia-inducible factor prolyl hydroxylase inhibitor, has been reported to be effective in treating conservative renal failure and renal anemia in patients undergoing dialysis. However, its effects on post-transplant anemia ... ...

Abstract	Background: Daprodustat, a hypoxia-inducible factor prolyl hydroxylase inhibitor, has been reported to be effective in treating conservative renal failure and renal anemia in patients undergoing dialysis. However, its effects on post-transplant anemia have not yet been reported. This study aimed to determine whether daprodustat may be a useful treatment for post-transplant anemia. Materials: Excluding 5 cases in which the drug was discontinued due to side effects, 21 post-transplant patients treated with daprodustat for ≥12 months and available for follow-up were analyzed. Changes in hemoglobin levels, iron metabolism, estimated glomerular filtration rate, and low-density lipoprotein levels were evaluated over 1 year. Results: The average hemoglobin level was 10.1 g/dL before treatment, and after 1, 2, 3, 6, 9, and 12 months, these had increased significantly to 10.9, 11.2, 11.9, 12.3, 12.3, and 12.6, respectively. Ferritin levels were significantly lower throughout the 12-month study period. Transferrin saturation was significantly lower than before treatment during the first 6 months, with no significant differences after that. The participants' estimated glomerular filtration rate and low-density lipoprotein cholesterol levels did not change significantly throughout the treatment. Conclusion: Daprodustat significantly increased hemoglobin levels was easily dose-adjusted and was relatively safe for continuous use over 1 year. It was also effective in patients who had responded inadequately to erythropoiesis-stimulating agents. Therefore, we conclude that daprodustat may be a useful treatment for post-transplant anemia.
MeSH term(s)	Humans ; Kidney Transplantation/adverse effects ; Anemia/drug therapy ; Anemia/etiology ; Male ; Female ; Middle Aged ; Glycine/analogs & derivatives ; Glycine/therapeutic use ; Hemoglobins/metabolism ; Hemoglobins/analysis ; Glomerular Filtration Rate ; Adult ; Barbiturates/therapeutic use ; Aged ; Transplant Recipients ; Treatment Outcome
Chemical Substances	Glycine (TE7660XO1C) ; Hemoglobins ; GSK1278863 ; Barbiturates
Language	English
Publishing date	2024-02-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	82046-5
ISSN	1873-2623 ; 0041-1345
ISSN (online)	1873-2623
ISSN	0041-1345
DOI	10.1016/j.transproceed.2024.01.016
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Article ; Online: Intra-S phase checkpoint kinase Chk1 dissociates replication proteins Treslin and TopBP1 through multiple mechanisms during replication stress.

Kelly, Rebecca L / Huehls, Amelia M / Venkatachalam, Annapoorna / Huntoon, Catherine J / Machida, Yuichi J / Karnitz, Larry M

The Journal of biological chemistry

2022 Volume 298, Issue 4, Page(s) 101777

Abstract: Replication stress impedes DNA polymerase progression causing activation of the ataxia telangiectasia and Rad3-related signaling pathway, which promotes the intra-S phase checkpoint activity through phosphorylation of checkpoint kinase 1 (Chk1). Chk1 ... ...

Abstract	Replication stress impedes DNA polymerase progression causing activation of the ataxia telangiectasia and Rad3-related signaling pathway, which promotes the intra-S phase checkpoint activity through phosphorylation of checkpoint kinase 1 (Chk1). Chk1 suppresses replication origin firing, in part, by disrupting the interaction between the preinitiation complex components Treslin and TopBP1, an interaction that is mediated by TopBP1 BRCT domain-binding to two cyclin-dependent kinase (CDK) phosphorylation sites, T968 and S1000, in Treslin. Two nonexclusive models for how Chk1 regulates the Treslin-TopBP1 interaction have been proposed in the literature: in one model, these proteins dissociate due to a Chk1-induced decrease in CDK activity that reduces phosphorylation of the Treslin sites that bind TopBP1 and in the second model, Chk1 directly phosphorylates Treslin, resulting in dissociation of TopBP1. However, these models have not been formally examined. We show here that Treslin T968 phosphorylation was decreased in a Chk1-dependent manner, while Treslin S1000 phosphorylation was unchanged, demonstrating that T968 and S1000 are differentially regulated. However, CDK2-mediated phosphorylation alone did not fully account for Chk1 regulation of the Treslin-TopBP1 interaction. We also identified additional Chk1 phosphorylation sites on Treslin that contributed to disruption of the Treslin-TopBP1 interaction, including S1114. Finally, we showed that both of the proposed mechanisms regulate origin firing in cancer cell line models undergoing replication stress, with the relative roles of each mechanism varying among cell lines. This study demonstrates that Chk1 regulates Treslin through multiple mechanisms to promote efficient dissociation of Treslin and TopBP1 and furthers our understanding of Treslin regulation during the intra-S phase checkpoint.
MeSH term(s)	Ataxia Telangiectasia Mutated Proteins/metabolism ; Carrier Proteins/metabolism ; Cell Line ; Checkpoint Kinase 1/metabolism ; DNA Replication/physiology ; Phosphorylation ; Stress, Physiological
Chemical Substances	Carrier Proteins ; Ataxia Telangiectasia Mutated Proteins (EC 2.7.11.1) ; Checkpoint Kinase 1 (EC 2.7.11.1)
Language	English
Publishing date	2022-02-26
Publishing country	United States
Document type	Journal Article
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2022.101777
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Article ; Online: FAM111A protects replication forks from protein obstacles via its trypsin-like domain.

Kojima, Yusuke / Machida, Yuka / Palani, Sowmiya / Caulfield, Thomas R / Radisky, Evette S / Kaufmann, Scott H / Machida, Yuichi J

Nature communications

2020 Volume 11, Issue 1, Page(s) 1318

Abstract: Persistent protein obstacles on genomic DNA, such as DNA-protein crosslinks (DPCs) and tight nucleoprotein complexes, can block replication forks. DPCs can be removed by the proteolytic activities of the metalloprotease SPRTN or the proteasome in a ... ...

Abstract	Persistent protein obstacles on genomic DNA, such as DNA-protein crosslinks (DPCs) and tight nucleoprotein complexes, can block replication forks. DPCs can be removed by the proteolytic activities of the metalloprotease SPRTN or the proteasome in a replication-coupled manner; however, additional proteolytic mechanisms may exist to cope with the diversity of protein obstacles. Here, we show that FAM111A, a PCNA-interacting protein, plays an important role in mitigating the effect of protein obstacles on replication forks. This function of FAM111A requires an intact trypsin-like protease domain, the PCNA interaction, and the DNA-binding domain that is necessary for protease activity in vivo. FAM111A, but not SPRTN, protects replication forks from stalling at poly(ADP-ribose) polymerase 1 (PARP1)-DNA complexes trapped by PARP inhibitors, thereby promoting cell survival after drug treatment. Altogether, our findings reveal a role of FAM111A in overcoming protein obstacles to replication forks, shedding light on cellular responses to anti-cancer therapies.
MeSH term(s)	Camptothecin/pharmacology ; Cell Cycle Checkpoints/drug effects ; Cell Line, Tumor ; DNA Damage ; DNA Replication ; DNA Topoisomerases, Type I/metabolism ; DNA, Single-Stranded/metabolism ; Humans ; Mutation/genetics ; Poly(ADP-ribose) Polymerase Inhibitors/pharmacology ; Poly(ADP-ribose) Polymerases/metabolism ; Protein Binding/drug effects ; Protein Domains ; Receptors, Virus/chemistry ; Receptors, Virus/genetics ; Receptors, Virus/metabolism ; Trypsin/chemistry
Chemical Substances	DNA, Single-Stranded ; FAM111A protein, human ; Poly(ADP-ribose) Polymerase Inhibitors ; Receptors, Virus ; Poly(ADP-ribose) Polymerases (EC 2.4.2.30) ; Trypsin (EC 3.4.21.4) ; DNA Topoisomerases, Type I (EC 5.99.1.2) ; Camptothecin (XT3Z54Z28A)
Language	English
Publishing date	2020-03-12
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-020-15170-7
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Article ; Online: FAM111A protects replication forks from protein obstacles via its trypsin-like domain

Yusuke Kojima / Yuka Machida / Sowmiya Palani / Thomas R. Caulfield / Evette S. Radisky / Scott H. Kaufmann / Yuichi J. Machida

Nature Communications, Vol 11, Iss 1, Pp 1-

2020 Volume 14

Abstract: DNA-protein crosslinks represent obstacles on genomic DNA that can hamper progression of replication forks. Here, the authors reveal that FAM111A, a PCNA-interacting protein, plays part in mitigating the effect of protein obstacles on replication forks. ...

Abstract	DNA-protein crosslinks represent obstacles on genomic DNA that can hamper progression of replication forks. Here, the authors reveal that FAM111A, a PCNA-interacting protein, plays part in mitigating the effect of protein obstacles on replication forks.
Keywords	Science ; Q
Language	English
Publishing date	2020-03-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: FAM111A protects replication forks from protein obstacles via its trypsin-like domain

Yusuke Kojima / Yuka Machida / Sowmiya Palani / Thomas R. Caulfield / Evette S. Radisky / Scott H. Kaufmann / Yuichi J. Machida

Nature Communications, Vol 11, Iss 1, Pp 1-

2020 Volume 14

Abstract	DNA-protein crosslinks represent obstacles on genomic DNA that can hamper progression of replication forks. Here, the authors reveal that FAM111A, a PCNA-interacting protein, plays part in mitigating the effect of protein obstacles on replication forks.
Keywords	Science ; Q
Language	English
Publishing date	2020-03-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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