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Carreño A, Guerrero-Yagüe R, Casal E, Mendoza R, Corchero JL. Tuning plasmid DNA amounts for cost-effective transfections of mammalian cells: when less is more. Appl Microbiol Biotechnol 2024; 108:98. [PMID: 38212965 PMCID: PMC10784393 DOI: 10.1007/s00253-024-13003-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 12/29/2023] [Accepted: 01/04/2024] [Indexed: 01/13/2024]
Abstract
Transient gene expression (TGE) in mammalian cells is a well-known approach to the fast expression of recombinant proteins. The human cell line HEK (human embryonic kidney) 293F is widely used in this field, due to its adaptability to grow in suspension to high cell densities in serum-free media, amenability to transfection, and production of recombinant proteins in satisfactory quantities for functional and structural analysis. Amounts of plasmid DNA (pDNA) required in transfections for TGE remain high (usually 1 µg pDNA/mL, or even higher), representing a noticeable proportion of the overall cost. Thus, there is an economic need to reduce amounts of coding pDNA in TGE processes. In this work, amounts of both pDNA and transfecting agent used for TGE in HEK 293F cells have been explored in order to reduce them without compromising (or even improving) the productivity of the process in terms of protein yield. In our hands, minimal polyethyleneimine (PEI) cytotoxicity and optimum protein yields were obtained when transfecting at 0.5 µg pDNA/mL (equal to 0.5 µg pDNA/million cells) and a DNA-to-PEI ratio of 1:3, a trend confirmed for several unrelated recombinant proteins. Thus, carefully tuning pDNA and transfecting agent amounts not only reduces the economic costs but also results in higher recombinant protein yields. These results surely have a direct application and interest for the biopharmaceutical industry, always concerned in increasing productivity while decreasing economic costs. KEY POINTS: • Mammalian cells are widely used to produce recombinant proteins in short times. • Tuning DNA and transfecting agent are of great interest to optimize economic costs. • Reducing DNA and transfecting agent amounts result in higher protein yields.
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Affiliation(s)
- Aida Carreño
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
- Institut de Ciència de Materials de Barcelona, ICMAB-CSIC, Campus UAB, 08193, Bellaterra, Spain
| | - Rubén Guerrero-Yagüe
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
- Gene Therapy for Neurometabolic Disorders, Edifici H, Institute of Neurosciences (INc) & Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Enriqueta Casal
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
- Alderley Analytical Ltd. Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK
| | - Rosa Mendoza
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, 08193, Bellaterra, Barcelona, Spain
| | - José Luis Corchero
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
- CIBER de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, 08193, Bellaterra, Barcelona, Spain.
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
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Tian H, Zhai Y, Sun S, Zhang W, Zhao Z. The transcription factor HMGB2 indirectly regulates APRIL expression and Gd-IgA1 production in patients with IgA nephropathy. Ren Fail 2024; 46:2338931. [PMID: 38622929 DOI: 10.1080/0886022x.2024.2338931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/31/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND IgA nephropathy (IgAN) is the most common primary glomerulonephritis worldwide. Proliferation-inducing ligand (APRIL) was identified as an important cause of glycosylation deficiency of IgA1 (Gd-IgA1), which can 'trigger' IgAN. Our previous study indicated that high migration group protein B2 (HMGB2) in peripheral blood mononuclear cells from patients with IgAN was associated with disease severity, but the underlying mechanism remains unclear. MATERIALS AND METHODS The location of HMGB2 was identified by immunofluorescence. qRT-PCR and Western blotting were used to measure HMGB2, HMGA1, and APRIL expression. Gd-IgA1 levels were detected by enzyme-linked immunosorbent assay (ELISA). In addition, we used DNA pull-down, protein profiling, and transcription factor prediction software to identify proteins bound to the promoter region of the APRIL gene. RNA interference and coimmunoprecipitation (Co-IP) were used to verify the relationships among HMGB2, high mobility group AT-hook protein 1 (HMGA1), and APRIL. RESULTS HMGB2 expression was greater in IgAN patients than in HCs and was positively associated with APRIL expression in B cells. DNA pull-down and protein profiling revealed that HMGB2 and HMGA1 bound to the promoter region of the APRIL gene. The expression levels of HMGA1, APRIL, and Gd-IgA1 were downregulated after HMGB2 knockdown. Co-IP indicated that HMGB2 binds to HMGA1. The Gd-IgA1 concentration in the supernatant was reduced after HMGA1 knockdown. HMGA1 binding sites were predicted in the promoter region of the APRIL gene. CONCLUSION HMGB2 expression is greater in IgAN patients than in healthy controls; it promotes APRIL expression by interacting with HMGA1, thereby inducing Gd-IgA1 overexpression and leading to IgAN.
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Affiliation(s)
- Huijuan Tian
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- The Renal Research Institution of Zhengzhou University, Zhengzhou, China
| | - Yaling Zhai
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- The Renal Research Institution of Zhengzhou University, Zhengzhou, China
| | - Shuaigang Sun
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- The Renal Research Institution of Zhengzhou University, Zhengzhou, China
| | - Wenhui Zhang
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- The Renal Research Institution of Zhengzhou University, Zhengzhou, China
| | - Zhanzheng Zhao
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- The Renal Research Institution of Zhengzhou University, Zhengzhou, China
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Michels KB, Binder AM. Impact of folic acid supplementation on the epigenetic profile in healthy unfortified individuals - a randomized intervention trial. Epigenetics 2024; 19:2293410. [PMID: 38096372 PMCID: PMC10730197 DOI: 10.1080/15592294.2023.2293410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 12/05/2023] [Indexed: 12/18/2023] Open
Abstract
Folate is an essential mediator in one-carbon metabolism, which provides methyl groups for DNA synthesis and methylation. The availability of active methyl groups can be influenced by the uptake of folic acid. We conducted a randomized intervention trial to test the influence of folic acid supplementation on DNA methylation in an unfortified population in Germany. A total of 16 healthy male volunteers (age range 23-61 y) were randomized to receive either 400 μg (n = 9) or 800 μg (n = 7) folic acid supplements daily for 8 weeks. Infinium Human Methylation 450K BeadChip Microarrays were used to assay site-specific DNA methylation across the genome. Microarray analyses were conducted on PBL DNA. We estimated several epigenetic clocks and mean DNA methylation across all autosomal probes on the array. AgeAccel was estimated as the residual variation in each metric. In virtually all participants, both serum and red blood cell (RBC) folate increased successively throughout the trial period. Participants with a larger increase in RBC folate had a larger increase in DNAmAge AgeAccel (Spearman Rho: 0.56, p-value = 0.03). No notable changes in the methylome resulting from the folic acid supplementation emerged. In this population with adequate folate levels derived from diet, an increase in RBC folate had a modest impact on the epigenetic clock predicting chronologic age.
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Affiliation(s)
- Karin B. Michels
- Institute for Prevention and Cancer Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA, USA
| | - Alexandra M. Binder
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA, USA
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
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Pekkarinen M, Nordfors K, Uusi-Mäkelä J, Kytölä V, Hartewig A, Huhtala L, Rauhala M, Urhonen H, Häyrynen S, Afyounian E, Yli-Harja O, Zhang W, Helen P, Lohi O, Haapasalo H, Haapasalo J, Nykter M, Kesseli J, Rautajoki KJ. Aberrant DNA methylation distorts developmental trajectories in atypical teratoid/rhabdoid tumors. Life Sci Alliance 2024; 7:e202302088. [PMID: 38499326 PMCID: PMC10948937 DOI: 10.26508/lsa.202302088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 03/06/2024] [Accepted: 03/06/2024] [Indexed: 03/20/2024] Open
Abstract
Atypical teratoid/rhabdoid tumors (AT/RTs) are pediatric brain tumors known for their aggressiveness and aberrant but still unresolved epigenetic regulation. To better understand their malignancy, we investigated how AT/RT-specific DNA hypermethylation was associated with gene expression and altered transcription factor binding and how it is linked to upstream regulation. Medulloblastomas, choroid plexus tumors, pluripotent stem cells, and fetal brain were used as references. A part of the genomic regions, which were hypermethylated in AT/RTs similarly as in pluripotent stem cells and demethylated in the fetal brain, were targeted by neural transcriptional regulators. AT/RT-unique DNA hypermethylation was associated with polycomb repressive complex 2 and linked to suppressed genes with a role in neural development and tumorigenesis. Activity of the several NEUROG/NEUROD pioneer factors, which are unable to bind to methylated DNA, was compromised via the suppressed expression or DNA hypermethylation of their target sites, which was also experimentally validated for NEUROD1 in medulloblastomas and AT/RT samples. These results highlight and characterize the role of DNA hypermethylation in AT/RT malignancy and halted neural cell differentiation.
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Affiliation(s)
- Meeri Pekkarinen
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Kristiina Nordfors
- https://ror.org/033003e23 Tampere Center for Child Health Research, Tays Cancer Center, Tampere University and Tampere University Hospital, Tampere, Finland
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- Unit of Pediatric Hematology and Oncology, Tampere University Hospital, Tampere, Finland
| | - Joonas Uusi-Mäkelä
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Ville Kytölä
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Anja Hartewig
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Laura Huhtala
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Minna Rauhala
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- https://ror.org/033003e23 Department of Neurosurgery, Tays Cancer Centre, Tampere University Hospital and Tampere University, Tampere, Finland
| | - Henna Urhonen
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Sergei Häyrynen
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Ebrahim Afyounian
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Olli Yli-Harja
- https://ror.org/033003e23 Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- Institute for Systems Biology, Seattle, WA, USA
| | - Wei Zhang
- Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, USA
| | - Pauli Helen
- https://ror.org/033003e23 Department of Neurosurgery, Tays Cancer Centre, Tampere University Hospital and Tampere University, Tampere, Finland
| | - Olli Lohi
- https://ror.org/033003e23 Tampere Center for Child Health Research, Tays Cancer Center, Tampere University and Tampere University Hospital, Tampere, Finland
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- https://ror.org/033003e23 Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Hannu Haapasalo
- https://ror.org/033003e23 Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- https://ror.org/031y6w871 Fimlab Laboratories Ltd, Tampere University Hospital, Tampere, Finland
| | - Joonas Haapasalo
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- https://ror.org/033003e23 Department of Neurosurgery, Tays Cancer Centre, Tampere University Hospital and Tampere University, Tampere, Finland
- https://ror.org/031y6w871 Fimlab Laboratories Ltd, Tampere University Hospital, Tampere, Finland
| | - Matti Nykter
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Juha Kesseli
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Kirsi J Rautajoki
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- https://ror.org/033003e23 Tampere Institute for Advanced Study, Tampere University, Tampere, Finland
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Feng Y, Zhao X, Ruan Z, Li Z, Mo H, Lu F, Shi D. Zinc improves the developmental ability of bovine in vitro fertilization embryos through its antioxidative action. Theriogenology 2024; 221:47-58. [PMID: 38554613 DOI: 10.1016/j.theriogenology.2024.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 03/18/2024] [Accepted: 03/22/2024] [Indexed: 04/02/2024]
Abstract
Zinc, an essential trace mineral, exerts a pivotal influence in various biological processes. Through zinc concentration analysis, we found that the zinc concentration in the bovine embryo in vitro culture (IVC) medium was significantly lower than that in bovine follicular fluid. Therefore, this study explored the impact of zinc sulfate on IVC bovine embryo development and investigated the underlying mechanism. The results revealed a significant decline in zygote cleavage and blastocyst development rates when zinc deficiency was induced using zinc chelator N, N, N', N'-Tetrakis (2-pyridylmethyl) ethylenediamine (TPEN) in culture medium during embryo in vitro culture. The influence of zinc-deficiency was time-dependent. Conversely, supplementing 0.8 μg/mL zinc sulfate to culture medium (CM) increased the cleavage and blastocyst formation rate significantly. Moreover, this supplementation reduced reactive oxygen species (ROS) levels, elevated the glutathione (GSH) levels in blastocysts, upregulated the mRNA expression of antioxidase-related genes, and activated the Nrf2-Keap1-ARE signaling pathways. Furthermore, 0.8 μg/mL zinc sulfate enhanced mitochondrial membrane potential, maintained DNA stability, and enhanced the quality of bovine (in vitro fertilization) IVF blastocysts. In conclusion, the addition of 0.8 μg/mL zinc sulfate to CM could enhance the antioxidant capacity, activates the Nrf2-Keap1-ARE signaling pathways, augment mitochondrial membrane potential, and stabilizes DNA, ultimately improving blastocyst quality and in vitro bovine embryo development.
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Affiliation(s)
- Yun Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Guangxi University, Nanning, 530005, China
| | - Xin Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Guangxi University, Nanning, 530005, China; Reproductive Medicine Center, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530003, China
| | - Ziyun Ruan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Guangxi University, Nanning, 530005, China
| | - Zhengda Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Guangxi University, Nanning, 530005, China
| | - Hongfang Mo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Guangxi University, Nanning, 530005, China
| | - Fenghua Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Guangxi University, Nanning, 530005, China.
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Guangxi University, Nanning, 530005, China.
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Huerta-Venegas PI, Raya-González J, Ruíz-Herrera LF, López-Bucio J. PHYTOCHROME A controls the DNA damage response and cell death tolerance within the Arabidopsis root meristem. Plant Cell Environ 2024; 47:1513-1525. [PMID: 38251425 DOI: 10.1111/pce.14831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 11/21/2023] [Accepted: 01/11/2024] [Indexed: 01/23/2024]
Abstract
The DNA damage response avoids mutations into dividing cells. Here, we analysed the role of photoreceptors on the restriction of root growth imposed by genotoxic agents and its relationship with cell viability and performance of meristems. Comparison of root growth of Arabidopsis WT, phyA-211, phyB-9, and phyA-211phyB-9 double mutants unveiled a critical role for phytochrome A (PhyA) in protecting roots from genotoxic stress, regeneration and cell replenishment in the meristematic zone. PhyA was located on primary root tips, where it influences genes related to the repair of DNA, including ERF115 and RAD51. Interestingly, phyA-211 mutants treated with zeocin failed to induce the expression of the repressor of cell cycle MYB3R3, which correlated with expression of the mitotic cyclin CycB1, suggesting that PhyA is required for safeguarding the DNA integrity during cell division. Moreover, the growth of the primary roots of PhyA downstream component HY5 and root growth analyses in darkness suggest that cell viability and DNA damage responses within root meristems may act independently from light and photomorphogenesis. These data support novel roles for PhyA as a key player for stem cell niche maintenance and DNA damage responses, which are critical for proper root growth.
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Affiliation(s)
- Pedro Iván Huerta-Venegas
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
| | - Javier Raya-González
- Facultad de Químico Farmacobiología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
| | - León Francisco Ruíz-Herrera
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
| | - José López-Bucio
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
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Kaja E, Vijande D, Kowalczyk J, Michalak M, Gapiński J, Kobras C, Rolfe P, Stracy M. Comparing Mfd- and UvrD-dependent models of transcription coupled DNA repair in live Escherichia coli using single-molecule tracking. DNA Repair (Amst) 2024; 137:103665. [PMID: 38513450 DOI: 10.1016/j.dnarep.2024.103665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 02/16/2024] [Accepted: 03/01/2024] [Indexed: 03/23/2024]
Abstract
During transcription-coupled DNA repair (TCR) the detection of DNA damage and initiation of nucleotide excision repair (NER) is performed by translocating RNA polymerases (RNAP), which are arrested upon encountering bulky DNA lesions. Two opposing models of the subsequent steps of TCR in bacteria exist. In the first model, stalled RNAPs are removed from the damage site by recruitment of Mfd which dislodges RNAP by pushing it forwards before recruitment of UvrA and UvrB. In the second model, UvrD helicase backtracks RNAP from the lesion site. Recent studies have proposed that both UvrD and UvrA continuously associate with RNAP before damage occurs, which forms the primary damage sensor for NER. To test these two models of TCR in living E. coli, we applied super-resolution microscopy (PALM) combined with single particle tracking to directly measure the mobility and recruitment of Mfd, UvrD, UvrA, and UvrB to DNA during ultraviolet-induced DNA damage. The intracellular mobilities of NER proteins in the absence of DNA damage showed that most UvrA molecules could in principle be complexed with RNAP, however, this was not the case for UvrD. Upon DNA damage, Mfd recruitment to DNA was independent of the presence of UvrA, in agreement with its role upstream of this protein in the TCR pathway. In contrast, UvrD recruitment to DNA was strongly dependent on the presence of UvrA. Inhibiting transcription with rifampicin abolished Mfd DNA-recruitment following DNA damage, whereas significant UvrD, UvrA, and UvrB recruitment remained, consistent with a UvrD and UvrA performing their NER functions independently of transcribing RNAP. Together, although we find that up to ∼8 UvrD-RNAP-UvrA complexes per cell could potentially form in the absence of DNA damage, our live-cell data is not consistent with this complex being the primary DNA damage sensor for NER.
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Affiliation(s)
- Elżbieta Kaja
- Molecular Biophysics Division, Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznańskiego 2, Poznan 61-614, Poland; Chair and Department of Medical Chemistry and Laboratory Medicine, Poznan University of Medical Sciences, Rokietnicka 8, 60-806 Poznan, Poland.
| | - Donata Vijande
- Molecular Biophysics Division, Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznańskiego 2, Poznan 61-614, Poland
| | - Justyna Kowalczyk
- Molecular Biophysics Division, Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznańskiego 2, Poznan 61-614, Poland
| | - Michał Michalak
- Molecular Biophysics Division, Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznańskiego 2, Poznan 61-614, Poland
| | - Jacek Gapiński
- Molecular Biophysics Division, Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznańskiego 2, Poznan 61-614, Poland
| | - Carolin Kobras
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Philippa Rolfe
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Mathew Stracy
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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Zhang S, Qiu B, Lv B, Yang G, Tao Y, Hu Y, Li K, Yu X, Tang C, Du J, Jin H, Huang Y. Endogenous sulfur dioxide deficiency as a driver of cardiomyocyte senescence through abolishing sulphenylation of STAT3 at cysteine 259. Redox Biol 2024; 71:103124. [PMID: 38503216 PMCID: PMC10963856 DOI: 10.1016/j.redox.2024.103124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 03/21/2024] Open
Abstract
OBJECTIVE Cardiomyocyte senescence is an important contributor to cardiovascular diseases and can be induced by stressors including DNA damage, oxidative stress, mitochondrial dysfunction, epigenetic regulation, etc. However, the underlying mechanisms for the development of cardiomyocyte senescence remain largely unknown. Sulfur dioxide (SO2) is produced endogenously by aspartate aminotransferase 2 (AAT2) catalysis and plays an important regulatory role in the development of cardiovascular diseases. The present study aimed to explore the effect of endogenous SO2 on cardiomyocyte senescence and the underlying molecular mechanisms. APPROACH AND RESULTS We interestingly found a substantial reduction in the expression of AAT2 in the heart of aged mice in comparison to young mice. AAT2-knockdowned cardiomyocytes exhibited reduced SO2 content, elevated expression levels of Tp53, p21Cip/Waf, and p16INk4a, enhanced SA-β-Gal activity, and elevated level of γ-H2AX foci. Notably, supplementation with a SO2 donor ameliorated the spontaneous senescence phenotype and DNA damage caused by AAT2 deficiency in cardiomyocytes. Mechanistically, AAT2 deficiency suppressed the sulphenylation of signal transducer and activator of transcription 3 (STAT3) facilitated its nuclear translocation and DNA-binding capacity. Conversely, a mutation in the cysteine (Cys) 259 residue of STAT3 blocked SO2-induced STAT3 sulphenylation and subsequently prevented the inhibitory effect of SO2 on STAT3-DNA-binding capacity, DNA damage, and cardiomyocyte senescence. Additionally, cardiomyocyte (cm)-specific AAT2 knockout (AAT2cmKO) mice exhibited a deterioration in cardiac function, cardiomegaly, and cardiac aging, whereas supplementation with SO2 donors mitigated the cardiac aging and remodeling phenotypes in AAT2cmKO mice. CONCLUSION Downregulation of the endogenous SO2/AAT2 pathway is a crucial pathogenic mechanism underlying cardiomyocyte senescence. Endogenous SO2 modifies STAT3 by sulphenylating Cys259, leading to the inhibition of DNA damage and the protection against cardiomyocyte senescence.
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Affiliation(s)
- Shangyue Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, 100034, China
| | - Bingquan Qiu
- Department of Pediatrics, Peking University First Hospital, Beijing, 100034, China
| | - Boyang Lv
- Department of Pediatrics, Peking University First Hospital, Beijing, 100034, China
| | - Guosheng Yang
- Laboratory Animal Facility, Peking University First Hospital, Beijing, 100034, China
| | - Yinghong Tao
- Laboratory Animal Facility, Peking University First Hospital, Beijing, 100034, China
| | - Yongyan Hu
- Laboratory Animal Facility, Peking University First Hospital, Beijing, 100034, China
| | - Kun Li
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Xiaoqi Yu
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Chaoshu Tang
- Department of Physiology and Pathophysiology, Peking University Health Science Center, Beijing, 100191, China
| | - Junbao Du
- Department of Pediatrics, Peking University First Hospital, Beijing, 100034, China; State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, 100191, China
| | - Hongfang Jin
- Department of Pediatrics, Peking University First Hospital, Beijing, 100034, China; State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, 100191, China.
| | - Yaqian Huang
- Department of Pediatrics, Peking University First Hospital, Beijing, 100034, China.
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9
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Sun S, Han X, Jin R, Jiao J, Wang J, Niu S, Yang Z, Wu D, Wang Y. Generation of CRISPR-edited birch plants without DNA integration using Agrobacterium-mediated transformation technology. Plant Sci 2024; 342:112029. [PMID: 38354755 DOI: 10.1016/j.plantsci.2024.112029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/16/2024]
Abstract
CRISPR/Cas9 system has emerged as a powerful tool in genome editing; however, generation of CRISPR-edited DNA-free plants is still challenging. In this study, Betula platyphylla (birch) was used to build a method to generate CRISPR-edited plant without foreign DNA integration using Agrobacterium-mediated transformation (CPDAT method). This technique utilizes transient genetic transformation to introduce T-DNA coding gRNA and Cas9 into birch cells, and T-DNA will express to synthesize gRNA and Cas9 protein, which will form a complex to cleave the target DNA site. The genome may be mutated due to DNA repair, and these mutations will be preserved and accumulated not dependent on whether T-DNA is integrated into the genome or not. After transient transformation, birch plants were cut into explants to induce adventitious buds without antibiotic selection pressure. Each adventitious bud can be considered as an independent potentially CRISPR-edited line for mutation detection. CRISPR-edited birch plants without foreign DNA integration are further selected by screening CRISPR-edited lines without T-DNA integration. Among 65 randomly chosen independent lines, the mutation rate was 80.00% including 40.00% of lines with both alleles mutated. In addition, 5 lines out of 65 studied lines (7.69%) were CRISPR-edited birch plants without DNA integration. In conclusion, this innovative method presents a novel strategy for generating CRISPR-edited birch plants, thereby significantly enhancing the efficiency of generating common CRISPR-edited plants. These findings offer considerable potential to develop plant genome editing techniques further.
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Affiliation(s)
- Shilin Sun
- College of Forestry, Shenyang Agricultural University, Shenyang 110866, China; Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang 110866, China
| | - Xue Han
- College of Forestry, Shenyang Agricultural University, Shenyang 110866, China; Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang 110866, China
| | - Ruoxuan Jin
- College of Forestry, Shenyang Agricultural University, Shenyang 110866, China; Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang 110866, China
| | - Junbo Jiao
- College of Forestry, Shenyang Agricultural University, Shenyang 110866, China; Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang 110866, China
| | - Jingwen Wang
- College of Forestry, Shenyang Agricultural University, Shenyang 110866, China; Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang 110866, China
| | - Siyuan Niu
- College of Forestry, Shenyang Agricultural University, Shenyang 110866, China; Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang 110866, China
| | - Ziyao Yang
- College of Forestry, Shenyang Agricultural University, Shenyang 110866, China; Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang 110866, China
| | - Di Wu
- College of Forestry, Shenyang Agricultural University, Shenyang 110866, China; Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang 110866, China
| | - Yucheng Wang
- College of Forestry, Shenyang Agricultural University, Shenyang 110866, China; Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang 110866, China.
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10
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Cho JE, Shaltz S, Yakovleva L, Shuman S, Jinks-Robertson S. Deletions initiated by the vaccinia virus TopIB protein in yeast. DNA Repair (Amst) 2024; 137:103664. [PMID: 38484460 PMCID: PMC10994728 DOI: 10.1016/j.dnarep.2024.103664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 02/14/2024] [Accepted: 03/01/2024] [Indexed: 04/06/2024]
Abstract
The type IB topoisomerase of budding yeast (yTop1) generates small deletions in tandem repeats through a sequential cleavage mechanism and larger deletions with random endpoints through the nonhomologous end-joining (NHEJ) pathway. Vaccinia virus Top1 (vTop1) is a minimized version of the eukaryal TopIB enzymes and uniquely has a strong consensus cleavage sequence: the pentanucleotide (T/C)CCTTp↓. To define the relationship between the position of TopIB cleavage and mutagenic outcomes, we expressed vTop1 in yeast top1Δ strains containing reporter constructs with a single CCCTT site, tandem CCCTT sites, or CCCTT sites separated by 42 bp. vTop1 cleavage at a single CCCTT site was associated with small, NHEJ-dependent deletions. As observed with yTop1, vTop1 generated 5-bp deletions at tandem CCCTT sites. In contrast to yTop1-initiated deletions, however, 5-bp deletions associated with vTop1 expression were not affected by the level of ribonucleotides in genomic DNA. vTop1 expression was associated with a 47-bp deletion when CCCTT sites were separated by 42 bp. Unlike yTop1-initiated large deletions, the vTop1-mediated 47-bp deletion did not require NHEJ, consistent with a model in which re-ligation of enzyme-associated double-strand breaks is catalyzed by vTop1.
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Affiliation(s)
- Jang Eun Cho
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Samantha Shaltz
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Lyudmila Yakovleva
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sue Jinks-Robertson
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA.
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11
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Liu N, Niu M, Luo S, Lv L, Quan X, Wang C, Meng Z, Yuan J, Xu Q, Liu Y. Rosamultin ameliorates radiation injury via promoting DNA injury repair and suppressing oxidative stress in vitro and in vivo. Chem Biol Interact 2024; 393:110938. [PMID: 38484825 DOI: 10.1016/j.cbi.2024.110938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 02/19/2024] [Accepted: 02/29/2024] [Indexed: 03/23/2024]
Abstract
Radiotherapy remains the preferred treatment option for cancer patients with the advantages of broad indications and significant therapeutic effects. However, ionizing radiation can also damage normal tissues. Unfortunately, there are few anti-radiation damage drugs available on the market for radiotherapy patients. Our previous study showed that rosamultin had antioxidant and hepatoprotective activities. However, its anti-radiation activity has not been evaluated. Irradiating small intestinal epithelial cells and mice with whole-body X-rays radiation were used to evaluate the in vitro and in vivo effects of rosamultin, respectively. Intragastric administration of rosamultin improved survival, limited leukocyte depletion, and reduced damage to the spleen and small intestine in irradiated mice. Rosamultin reversed the downregulation of the apoptotic protein BCL-2 and the upregulation of BAX in irradiated mouse small intestine tissue and in irradiation-induced small intestinal epithelial cells. DNA-PKcs antagonists reversed the promoting DNA repair effects of rosamulin. Detailed mechanistic studies revealed that rosamultin promoted Translin-associated protein X (TRAX) into the nucleus. Knockdown of TRAX reduced the protective effect of rosamultin against DNA damage. In addition, rosamultin reduced irradiation-induced oxidative stress through promoting Nrf2/HO-1 signaling pathway. To sum up, in vitro and in vivo experiments using genetic knockdown and pharmacological activation demonstrated that rosamultin exerts radioprotection via the TRAX/NHEJ and Nrf2/HO pathways.
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Affiliation(s)
- Ning Liu
- College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, 215123, China; Institute of Chinese Medicine Innovation and Translation, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Mengxin Niu
- College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, 215123, China; Institute of Chinese Medicine Innovation and Translation, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Saiyan Luo
- College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, 215123, China; Institute of Chinese Medicine Innovation and Translation, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Lijuan Lv
- College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, 215123, China; Institute of Chinese Medicine Innovation and Translation, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Xiaoxiao Quan
- Scientific Experimental Center of Guangxi University of Chinese Medicine, Nanning, China
| | - Chang Wang
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Medical College of Soochow University, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Zhiyun Meng
- Beijing Institute of Radiation Medicine, 100850, China
| | - Jingquan Yuan
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Medical College of Soochow University, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Qiongming Xu
- College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, 215123, China; Institute of Chinese Medicine Innovation and Translation, Soochow University, Suzhou, Jiangsu, 215123, China.
| | - Yanli Liu
- College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, 215123, China; Institute of Chinese Medicine Innovation and Translation, Soochow University, Suzhou, Jiangsu, 215123, China.
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12
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Mizuguchi M, Kyan N, Nishimata S, Nabeshima Y, Obita T. Enzymatic activity of cGAS in the presence of three types of DNAs: limited cGAS stimulation by single-stranded HIV-1 SL2 DNA. Biosci Rep 2024; 44:BSR20240269. [PMID: 38530250 PMCID: PMC10994814 DOI: 10.1042/bsr20240269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/04/2024] [Accepted: 03/25/2024] [Indexed: 03/27/2024] Open
Abstract
Cyclic GMP-AMP (cGAMP) synthase (cGAS) is activated by binding to DNA. Activated cGAS produces 2'3'-cGAMP, which subsequently binds to the adaptor protein STING (stimulator of interferon genes). This interaction triggers the cGAS/STING signaling pathway, leading to the production of type I interferons. Three types of DNA, namely double-stranded DNA longer than 40 base pairs, a 70-nucleotide single-stranded HIV-1 DNA known as SL2, and Y-form DNA with unpaired guanosine trimers (G3 Y-form DNA), induce interferon production by activating cGAS/STING signaling. However, the extent of cGAS activation by each specific DNA type remains unclear. The comparison of cGAS stimulation by various DNAs is crucial for understanding the mechanisms underlying cGAS-mediated type I interferon production in the innate immune response. Here, we revealed that cGAS produces 2'3'-cGAMP at a significantly lower rate in the presence of single-stranded SL2 DNA than in the presence of double-stranded DNA or G3 Y-form DNA. Furthermore, the guanine-to-cytosine mutations and the deletion of unpaired guanosine trimers significantly reduced the 2'3'-cGAMP production rate and the binding of cGAS to Y-form DNA. These studies will provide new insights into the cGAS-mediated DNA-sensing in immune response.
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Affiliation(s)
- Mineyuki Mizuguchi
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Niko Kyan
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Suzuka Nishimata
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Yuko Nabeshima
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Takayuki Obita
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
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13
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Bagheri N, Chamorro A, Idili A, Porchetta A. PAM-Engineered Toehold Switches as Input-Responsive Activators of CRISPR-Cas12a for Sensing Applications. Angew Chem Int Ed Engl 2024; 63:e202319677. [PMID: 38284432 DOI: 10.1002/anie.202319677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/28/2024] [Accepted: 01/29/2024] [Indexed: 01/30/2024]
Abstract
The RNA-programmed CRISPR effector protein Cas12a has emerged as a powerful tool for gene editing and molecular diagnostics. However, additional bio-engineering strategies are required to achieve control over Cas12a activity. Here, we show that Toehold Switch DNA hairpins, presenting a rationally designed locked protospacer adjacent motif (PAM) in the loop, can be used to control Cas12a in response to molecular inputs. Reconfiguring the Toehold Switch DNA from a hairpin to a duplex conformation through a strand displacement reaction provides an effective means to modulate the accessibility of the PAM, thereby controlling the binding and cleavage activities of Cas12a. Through this approach, we showcase the potential to trigger downstream Cas12a activity by leveraging proximity-based strand displacement reactions in response to target binding. By utilizing the trans-cleavage activity of Cas12a as a signal transduction method, we demonstrate the versatility of our approach for sensing applications. Our system enables rapid, one-pot detection of IgG antibodies and small molecules with high sensitivity and specificity even within complex matrices. Besides the bioanalytical applications, the switchable PAM-engineered Toehold Switches serve as programmable tools capable of regulating Cas12a-based targeting and DNA processing in response to molecular inputs and hold promise for a wide array of biotechnological applications.
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Affiliation(s)
- Neda Bagheri
- Department of Sciences and Chemical Technologies, University of Rome, Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Alejandro Chamorro
- Department of Sciences and Chemical Technologies, University of Rome, Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Andrea Idili
- Department of Sciences and Chemical Technologies, University of Rome, Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Alessandro Porchetta
- Department of Sciences and Chemical Technologies, University of Rome, Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy
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14
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Padmanaban S, Lambacher NJ, Tesmer VM, Zhang J, Shibuya H, Nandakumar J. Caenorhabditis elegans telomere-binding proteins TEBP-1 and TEBP-2 adapt the Myb module to dimerize and bind telomeric DNA. Proc Natl Acad Sci U S A 2024; 121:e2316651121. [PMID: 38588418 DOI: 10.1073/pnas.2316651121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 02/17/2024] [Indexed: 04/10/2024] Open
Abstract
Protecting chromosome ends from misrecognition as double-stranded (ds) DNA breaks is fundamental to eukaryotic viability. The protein complex shelterin prevents a DNA damage response at mammalian telomeres. Mammalian shelterin proteins TRF1 and TRF2 and their homologs in yeast and protozoa protect telomeric dsDNA. N-terminal homodimerization and C-terminal Myb-domain-mediated dsDNA binding are two structural hallmarks of end protection by TRF homologs. Yet our understanding of how Caenorhabditis elegans protects its telomeric dsDNA is limited. Recently identified C. elegans proteins TEBP-1 (also called DTN-1) and TEBP-2 (also called DTN-2) are functional homologs of TRF proteins, but how they bind DNA and whether or how they dimerize is not known. TEBP-1 and TEBP-2 harbor three Myb-containing domains (MCDs) and no obvious dimerization domain. We demonstrate biochemically that only the third MCD binds DNA. We solve the X-ray crystal structure of TEBP-2 MCD3 with telomeric dsDNA to reveal the structural mechanism of telomeric dsDNA protection in C. elegans. Mutagenesis of the DNA-binding site of TEBP-1 and TEBP-2 compromises DNA binding in vitro, and increases DNA damage signaling, lengthens telomeres, and decreases brood size in vivo. Via an X-ray crystal structure, biochemical validation of the dimerization interface, and SEC-MALS analysis, we demonstrate that MCD1 and MCD2 form a composite dimerization module that facilitates not only TEBP-1 and TEBP-2 homodimerization but also heterodimerization. These findings provide fundamental insights into C. elegans telomeric dsDNA protection and highlight how different eukaryotes have evolved distinct strategies to solve the chromosome end protection problem.
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Affiliation(s)
- Shilpa Padmanaban
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110
| | - Nils J Lambacher
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden 41390
| | - Valerie M Tesmer
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Jingjing Zhang
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden 41390
| | - Hiroki Shibuya
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden 41390
- Laboratory for Gametogenesis, RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - Jayakrishnan Nandakumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
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15
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Brangulis K, Akopjana I, Drunka L, Matisone S, Zelencova-Gopejenko D, Bhattacharya S, Bogans J, Tars K. Members of the paralogous gene family 12 from the Lyme disease agent Borrelia burgdorferi are non-specific DNA-binding proteins. PLoS One 2024; 19:e0296127. [PMID: 38626020 DOI: 10.1371/journal.pone.0296127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 12/06/2023] [Indexed: 04/18/2024] Open
Abstract
Lyme disease is the most prevalent vector-borne infectious disease in Europe and the USA. Borrelia burgdorferi, as the causative agent of Lyme disease, is transmitted to the mammalian host during the tick blood meal. To adapt to the different encountered environments, Borrelia has adjusted the expression pattern of various, mostly outer surface proteins. The function of most B. burgdorferi outer surface proteins remains unknown. We determined the crystal structure of a previously uncharacterized B. burgdorferi outer surface protein BBK01, known to belong to the paralogous gene family 12 (PFam12) as one of its five members. PFam12 members are shown to be upregulated as the tick starts its blood meal. Structural analysis of BBK01 revealed similarity to the coiled coil domain of structural maintenance of chromosomes (SMC) protein family members, while functional studies indicated that all PFam12 members are non-specific DNA-binding proteins. The residues involved in DNA binding were identified and probed by site-directed mutagenesis. The combination of SMC-like proteins being attached to the outer membrane and exposed to the environment or located in the periplasm, as observed in the case of PFam12 members, and displaying the ability to bind DNA, represents a unique feature previously not observed in bacteria.
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Affiliation(s)
| | - Inara Akopjana
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Laura Drunka
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | | | | | - Janis Bogans
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Kaspars Tars
- Latvian Biomedical Research and Study Centre, Riga, Latvia
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16
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Visalli MA, Nale Lovett DJ, Kornfeind EM, Herrington H, Xiao YT, Lee D, Plair P, Wilder SG, Garza BK, Young A, Visalli RJ. Mutagenesis and functional analysis of the varicella-zoster virus portal protein. J Virol 2024; 98:e0060323. [PMID: 38517165 PMCID: PMC11019927 DOI: 10.1128/jvi.00603-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 03/01/2024] [Indexed: 03/23/2024] Open
Abstract
Herpesviruses replicate by cleaving concatemeric dsDNA into single genomic units that are packaged through an oligomeric portal present in preformed procapsids. In contrast to what is known about phage portal proteins, details concerning herpesvirus portal structure and function are not as well understood. A panel of 65 Varicella-Zoster virus (VZV) recombinant portal proteins with five amino acid in-frame insertions were generated by random transposon mutagenesis of the VZV portal gene, ORF54. Subsequently, 65 VZVLUC recombinant viruses (TNs) were generated via recombineering. Insertions were mapped to predicted portal domains (clip, wing, stem, wall, crown, and β-hairpin tunnel-loop) and recombinant viruses were characterized for plaque morphology, replication kinetics, pORF54 expression, and classified based on replication in non-complementing (ARPE19) or complementing (ARPE54C50) cell lines. The N- and C-termini were tolerant to insertion mutagenesis, as were certain clip sub-domains. The majority of mutants mapping to the wing, wall, β-hairpin tunnel loop, and stem domains were lethal. Elimination of the predicted ORF54 start codon revealed that the first 40 amino acids of the N-terminus were not required for viral replication. Stop codon insertions in the C-terminus showed that the last 100 amino acids were not required for viral replication. Lastly, a putative protease cleavage site was identified in the C-terminus of pORF54. Cleavage was likely orchestrated by a viral protease; however, processing was not required for DNA encapsidation and viral replication. The panel of recombinants should prove valuable in future studies to dissect mammalian portal structure and function.IMPORTANCEThough nucleoside analogs and a live-attenuated vaccine are currently available to treat some human herpesvirus family members, alternate methods of combating herpesvirus infection could include blocking viral replication at the DNA encapsidation stage. The approval of Letermovir provided proof of concept regarding the use of encapsidation inhibitors to treat herpesvirus infections in the clinic. We propose that small-molecule compounds could be employed to interrupt portal oligomerization, assembly into the capsid vertex, or affect portal function/dynamics. Targeting portal at any of these steps would result in disruption of viral DNA packaging and a decrease or absence of mature infectious herpesvirus particles. The oligomeric portals of herpesviruses are structurally conserved, and therefore, it may be possible to find a single compound capable of targeting portals from one or more of the herpesvirus subfamilies. Drug candidates from such a series would be effective against viruses resistant to the currently available antivirals.
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Affiliation(s)
- Melissa A. Visalli
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia, USA
| | - Dakota J. Nale Lovett
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia, USA
| | - Ellyn M. Kornfeind
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia, USA
| | - Haley Herrington
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia, USA
| | - Yi Tian Xiao
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia, USA
| | - Daniel Lee
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia, USA
| | - Patience Plair
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia, USA
| | - S. Garrett Wilder
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia, USA
| | - Bret K. Garza
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia, USA
| | - Ashton Young
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia, USA
| | - Robert J. Visalli
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia, USA
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17
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Bellamri M, Yao L, Tomar R, Vartanian V, Rizzo CJ, Stone MP, Groopman JD, Lloyd RS, Turesky RJ. Mass Spectrometry-Based Method to Measure Aflatoxin B 1 DNA Adducts in Formalin-Fixed Paraffin-Embedded Tissues. Chem Res Toxicol 2024; 37:633-642. [PMID: 38498000 DOI: 10.1021/acs.chemrestox.4c00005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Aflatoxin B1 (AFB1) is a potent human liver carcinogen produced by certain molds, particularly Aspergillus flavus and Aspergillus parasiticus, which contaminate peanuts, corn, rice, cottonseed, and ground and tree nuts, principally in warm and humid climates. AFB1 undergoes bioactivation in the liver to produce AFB1-exo-8,9-epoxide, which forms the covalently bound cationic AFB1-N7-guanine (AFB1-N7-Gua) DNA adduct. This adduct is unstable and undergoes base-catalyzed opening of the guanine imidazolium ring to form two ring-opened diastereomeric 8,9-dihydro-8-(2,6-diamino-4-oxo-3,4-dihydropyrimid-5-yl-formamido)-9-hydroxy-aflatoxin B1 (AFB1-FapyGua) adducts. The AFB1 formamidopyrimidine (Fapy) adducts induce G → T transversion mutations and are likely responsible for the carcinogenic effects of AFB1. Quantitative liquid chromatography-mass spectrometry (LC-MS) methods have shown that AFB1-N7-Gua is eliminated in rodent and human urine, whereas ring-opened AFB1-FapyGua adducts persist in rodent liver. However, fresh frozen biopsy tissues are seldom available for biomonitoring AFB1 DNA adducts in humans, impeding research advances in this potent liver carcinogen. In contrast, formalin-fixed paraffin-embedded (FFPE) specimens used for histopathological analysis are often accessible for molecular studies. However, ensuring nucleic acid quality presents a challenge due to incomplete reversal of formalin-mediated DNA cross-links, which can preclude accurate quantitative measurements of DNA adducts. In this study, employing ion trap or high-resolution accurate Orbitrap mass spectrometry, we demonstrate that ring-opened AFB1-FapyGua adducts formed in AFB1-exposed newborn mice are stable to the formalin fixation and DNA de-cross-linking retrieval processes. The AFB1-FapyGua adducts can be detected at levels comparable to those in a match of fresh frozen liver. Orbitrap MS2 measurements can detect AFB1-FapyGua at a quantification limit of 4.0 adducts per 108 bases when only 0.8 μg of DNA is assayed on the column. Thus, our breakthrough DNA retrieval technology can be adapted to screen for AFB1 DNA adducts in FFPE human liver specimens from cohorts at risk of this potent liver carcinogen.
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Affiliation(s)
| | | | - Rachana Tomar
- Department of Chemistry, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Vladimir Vartanian
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Carmelo J Rizzo
- Department of Chemistry, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Michael P Stone
- Department of Chemistry, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - John D Groopman
- Department of Environmental Health and Engineering, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland 21205, United States
| | - R Stephen Lloyd
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, Oregon 97239, United States
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18
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Jin C, Einig E, Xu W, Kollampally RB, Schlosser A, Flentje M, Popov N. The dimeric deubiquitinase USP28 integrates 53BP1 and MYC functions to limit DNA damage. Nucleic Acids Res 2024; 52:3011-3030. [PMID: 38227944 DOI: 10.1093/nar/gkae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 12/21/2023] [Accepted: 01/04/2024] [Indexed: 01/18/2024] Open
Abstract
DNA replication is a major source of endogenous DNA damage in tumor cells and a key target of cellular response to genotoxic stress. DNA replication can be deregulated by oncoproteins, such as transcription factor MYC, aberrantly activated in many human cancers. MYC is stringently regulated by the ubiquitin system - for example, ubiquitination controls recruitment of the elongation factor PAF1c, instrumental in MYC activity. Curiously, a key MYC-targeting deubiquitinase USP28 also controls cellular response to DNA damage via the mediator protein 53BP1. USP28 forms stable dimers, but the biological role of USP28 dimerization is unknown. We show here that dimerization limits USP28 activity and restricts recruitment of PAF1c by MYC. Expression of monomeric USP28 stabilizes MYC and promotes PAF1c recruitment, leading to ectopic DNA synthesis and replication-associated DNA damage. USP28 dimerization is stimulated by 53BP1, which selectively binds USP28 dimers. Genotoxic stress diminishes 53BP1-USP28 interaction, promotes disassembly of USP28 dimers and stimulates PAF1c recruitment by MYC. This triggers firing of DNA replication origins during early response to genotoxins and exacerbates DNA damage. We propose that dimerization of USP28 prevents ectopic DNA replication at transcriptionally active chromatin to maintain genome stability.
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Affiliation(s)
- Chao Jin
- Department of Medical Oncology and Pulmonology, University Hospital Tübingen, Otfried-Müller-Str 14, 72076 Tübingen, Germany
- DFG Cluster of Excellence 2180 'Image-guided and Functionally Instructed Tumor Therapies' (iFIT), University of Tübingen, Tübingen, Germany
| | - Elias Einig
- Department of Medical Oncology and Pulmonology, University Hospital Tübingen, Otfried-Müller-Str 14, 72076 Tübingen, Germany
- DFG Cluster of Excellence 2180 'Image-guided and Functionally Instructed Tumor Therapies' (iFIT), University of Tübingen, Tübingen, Germany
| | - Wenshan Xu
- Department of Radiation Oncology, University Hospital Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany
| | - Ravi Babu Kollampally
- Department of Medical Oncology and Pulmonology, University Hospital Tübingen, Otfried-Müller-Str 14, 72076 Tübingen, Germany
- DFG Cluster of Excellence 2180 'Image-guided and Functionally Instructed Tumor Therapies' (iFIT), University of Tübingen, Tübingen, Germany
| | - Andreas Schlosser
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of Würzburg, Josef-Schneider-Str 2, 97080 Würzburg, Germany
| | - Michael Flentje
- Department of Radiation Oncology, University Hospital Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany
| | - Nikita Popov
- Department of Medical Oncology and Pulmonology, University Hospital Tübingen, Otfried-Müller-Str 14, 72076 Tübingen, Germany
- DFG Cluster of Excellence 2180 'Image-guided and Functionally Instructed Tumor Therapies' (iFIT), University of Tübingen, Tübingen, Germany
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19
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Madakashira BP, Magnani E, Ranjan S, Sadler KC. DNA hypomethylation activates Cdk4/6 and Atr to induce DNA replication and cell cycle arrest to constrain liver outgrowth in zebrafish. Nucleic Acids Res 2024; 52:3069-3087. [PMID: 38321933 PMCID: PMC11014291 DOI: 10.1093/nar/gkae031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 12/12/2023] [Accepted: 01/16/2024] [Indexed: 02/08/2024] Open
Abstract
Coordinating epigenomic inheritance and cell cycle progression is essential for organogenesis. UHRF1 connects these functions during development by facilitating maintenance of DNA methylation and cell cycle progression. Here, we provide evidence resolving the paradoxical phenotype of uhrf1 mutant zebrafish embryos which have activation of pro-proliferative genes and increased number of hepatocytes in S-phase, but the liver fails to grow. We uncover decreased Cdkn2a/b and persistent Cdk4/6 activation as the mechanism driving uhrf1 mutant hepatocytes into S-phase. This induces replication stress, DNA damage and Atr activation. Palbociclib treatment of uhrf1 mutants prevented aberrant S-phase entry, reduced DNA damage, and rescued most cellular and developmental phenotypes, but it did not rescue DNA hypomethylation, transposon expression or the interferon response. Inhibiting Atr reduced DNA replication and increased liver size in uhrf1 mutants, suggesting that Atr activation leads to dormant origin firing and prevents hepatocyte proliferation. Cdkn2a/b was downregulated pro-proliferative genes were also induced in a Cdk4/6 dependent fashion in the liver of dnmt1 mutants, suggesting DNA hypomethylation as a mechanism of Cdk4/6 activation during development. This shows that the developmental defects caused by DNA hypomethylation are attributed to persistent Cdk4/6 activation, DNA replication stress, dormant origin firing and cell cycle inhibition.
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20
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Wang C, Chu C, Guo Z, Zhan X. Structures and dynamics of Rpd3S complex bound to nucleosome. Sci Adv 2024; 10:eadk7678. [PMID: 38598631 PMCID: PMC11006229 DOI: 10.1126/sciadv.adk7678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 03/07/2024] [Indexed: 04/12/2024]
Abstract
The Rpd3S complex plays a pivotal role in facilitating local histone deacetylation in the transcribed regions to suppress intragenic transcription initiation. Here, we present the cryo-electron microscopy structures of the budding yeast Rpd3S complex in both its apo and three nucleosome-bound states at atomic resolutions, revealing the exquisite architecture of Rpd3S to well accommodate a mononucleosome without linker DNA. The Rpd3S core, containing a Sin3 Lobe and two NB modules, is a rigid complex and provides three positive-charged anchors (Sin3_HCR and two Rco1_NIDs) to connect nucleosomal DNA. In three nucleosome-bound states, the Rpd3S core exhibits three distinct orientations relative to the nucleosome, assisting the sector-shaped deacetylase Rpd3 to locate above the SHL5-6, SHL0-1, or SHL2-3, respectively. Our work provides a structural framework that reveals a dynamic working model for the Rpd3S complex to engage diverse deacetylation sites.
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Affiliation(s)
- Chengcheng Wang
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
- Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Chen Chu
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
- Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Zhouyan Guo
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
- Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Xiechao Zhan
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
- Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
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21
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Aman R, Syed MM, Saleh A, Melliti F, Gundra S, Wang Q, Marsic T, Mahas A, Mahfouz M. Peptide nucleic acid-assisted generation of targeted double-stranded DNA breaks with T7 endonuclease I. Nucleic Acids Res 2024; 52:3469-3482. [PMID: 38421613 PMCID: PMC11014363 DOI: 10.1093/nar/gkae148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/14/2024] [Accepted: 02/18/2024] [Indexed: 03/02/2024] Open
Abstract
Gene-editing technologies have revolutionized biotechnology, but current gene editors suffer from several limitations. Here, we harnessed the power of gamma-modified peptide nucleic acids (γPNAs) to facilitate targeted, specific DNA invasion and used T7 endonuclease I (T7EI) to recognize and cleave the γPNA-invaded DNA. Our data show that T7EI can specifically target PNA-invaded linear and circular DNA to introduce double-strand breaks (DSBs). Our PNA-Guided T7EI (PG-T7EI) technology demonstrates that T7EI can be used as a programmable nuclease capable of generating single or multiple specific DSBs in vitro under a broad range of conditions and could be potentially applied for large-scale genomic manipulation. With no protospacer adjacent motif (PAM) constraints and featuring a compact protein size, our PG-T7EI system will facilitate and expand DNA manipulations both in vitro and in vivo, including cloning, large-fragment DNA assembly, and gene editing, with exciting applications in biotechnology, medicine, agriculture, and synthetic biology.
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Affiliation(s)
- Rashid Aman
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Muntjeeb M Syed
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Ahmed Saleh
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Firdaws Melliti
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Sivakrishna Rao Gundra
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Qiaochu Wang
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Tin Marsic
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Ahmed Mahas
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
- Department of Genetics, Harvard University, Boston, MA 02115, USA
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
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22
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Tatsukawa K, Sakamoto R, Kawasoe Y, Kubota Y, Tsurimoto T, Takahashi T, Ohashi E. Resection of DNA double-strand breaks activates Mre11-Rad50-Nbs1- and Rad9-Hus1-Rad1-dependent mechanisms that redundantly promote ATR checkpoint activation and end processing in Xenopus egg extracts. Nucleic Acids Res 2024; 52:3146-3163. [PMID: 38349040 PMCID: PMC11014350 DOI: 10.1093/nar/gkae082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 01/21/2024] [Accepted: 01/29/2024] [Indexed: 04/14/2024] Open
Abstract
Sensing and processing of DNA double-strand breaks (DSBs) are vital to genome stability. DSBs are primarily detected by the ATM checkpoint pathway, where the Mre11-Rad50-Nbs1 (MRN) complex serves as the DSB sensor. Subsequent DSB end resection activates the ATR checkpoint pathway, where replication protein A, MRN, and the Rad9-Hus1-Rad1 (9-1-1) clamp serve as the DNA structure sensors. ATR activation depends also on Topbp1, which is loaded onto DNA through multiple mechanisms. While different DNA structures elicit specific ATR-activation subpathways, the regulation and mechanisms of the ATR-activation subpathways are not fully understood. Using DNA substrates that mimic extensively resected DSBs, we show here that MRN and 9-1-1 redundantly stimulate Dna2-dependent long-range end resection and ATR activation in Xenopus egg extracts. MRN serves as the loading platform for ATM, which, in turn, stimulates Dna2- and Topbp1-loading. Nevertheless, MRN promotes Dna2-mediated end processing largely independently of ATM. 9-1-1 is dispensable for bulk Dna2 loading, and Topbp1 loading is interdependent with 9-1-1. ATR facilitates Mre11 phosphorylation and ATM dissociation. These data uncover that long-range end resection activates two redundant pathways that facilitate ATR checkpoint signaling and DNA processing in a vertebrate system.
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Affiliation(s)
- Kensuke Tatsukawa
- Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Reihi Sakamoto
- Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yoshitaka Kawasoe
- Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yumiko Kubota
- Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Toshiki Tsurimoto
- Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Tatsuro S Takahashi
- Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Eiji Ohashi
- Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
- Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga 526-0829, Japan
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23
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Collins J, Osheroff N. Gyrase and Topoisomerase IV: Recycling Old Targets for New Antibacterials to Combat Fluoroquinolone Resistance. ACS Infect Dis 2024; 10:1097-1115. [PMID: 38564341 PMCID: PMC11019561 DOI: 10.1021/acsinfecdis.4c00128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 03/14/2024] [Accepted: 03/18/2024] [Indexed: 04/04/2024]
Abstract
Beyond their requisite functions in many critical DNA processes, the bacterial type II topoisomerases, gyrase and topoisomerase IV, are the targets of fluoroquinolone antibacterials. These drugs act by stabilizing gyrase/topoisomerase IV-generated DNA strand breaks and by robbing the cell of the catalytic activities of these essential enzymes. Since their clinical approval in the mid-1980s, fluoroquinolones have been used to treat a broad spectrum of infectious diseases and are listed among the five "highest priority" critically important antimicrobial classes by the World Health Organization. Unfortunately, the widespread use of fluoroquinolones has been accompanied by a rise in target-mediated resistance caused by specific mutations in gyrase and topoisomerase IV, which has curtailed the medical efficacy of this drug class. As a result, efforts are underway to identify novel antibacterials that target the bacterial type II topoisomerases. Several new classes of gyrase/topoisomerase IV-targeted antibacterials have emerged, including novel bacterial topoisomerase inhibitors, Mycobacterium tuberculosis gyrase inhibitors, triazaacenaphthylenes, spiropyrimidinetriones, and thiophenes. Phase III clinical trials that utilized two members of these classes, gepotidacin (triazaacenaphthylene) and zoliflodacin (spiropyrimidinetrione), have been completed with positive outcomes, underscoring the potential of these compounds to become the first new classes of antibacterials introduced into the clinic in decades. Because gyrase and topoisomerase IV are validated targets for established and emerging antibacterials, this review will describe the catalytic mechanism and cellular activities of the bacterial type II topoisomerases, their interactions with fluoroquinolones, the mechanism of target-mediated fluoroquinolone resistance, and the actions of novel antibacterials against wild-type and fluoroquinolone-resistant gyrase and topoisomerase IV.
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Affiliation(s)
- Jessica
A. Collins
- Department
of Biochemistry, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232, United States
| | - Neil Osheroff
- Department
of Biochemistry, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232, United States
- Department
of Medicine (Hematology/Oncology), Vanderbilt
University School of Medicine, Nashville, Tennessee 37232, United States
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24
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Hadži S, Živič Z, Kovačič M, Zavrtanik U, Haeserts S, Charlier D, Plavec J, Volkov AN, Lah J, Loris R. Fuzzy recognition by the prokaryotic transcription factor HigA2 from Vibrio cholerae. Nat Commun 2024; 15:3105. [PMID: 38600130 PMCID: PMC11006873 DOI: 10.1038/s41467-024-47296-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 03/22/2024] [Indexed: 04/12/2024] Open
Abstract
Disordered protein sequences can exhibit different binding modes, ranging from well-ordered folding-upon-binding to highly dynamic fuzzy binding. The primary function of the intrinsically disordered region of the antitoxin HigA2 from Vibrio cholerae is to neutralize HigB2 toxin through ultra-high-affinity folding-upon-binding interaction. Here, we show that the same intrinsically disordered region can also mediate fuzzy interactions with its operator DNA and, through interplay with the folded helix-turn-helix domain, regulates transcription from the higBA2 operon. NMR, SAXS, ITC and in vivo experiments converge towards a consistent picture where a specific set of residues in the intrinsically disordered region mediate electrostatic and hydrophobic interactions while "hovering" over the DNA operator. Sensitivity of the intrinsically disordered region to scrambling the sequence, position-specific contacts and absence of redundant, multivalent interactions, point towards a more specific type of fuzzy binding. Our work demonstrates how a bacterial regulator achieves dual functionality by utilizing two distinct interaction modes within the same disordered sequence.
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Affiliation(s)
- San Hadži
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- Centre for Structural Biology, VIB, Pleinlaan 2, 1050, Brussels, Belgium
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Zala Živič
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Matic Kovačič
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova, 19, 1000, Ljubljana, Slovenia
| | - Uroš Zavrtanik
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Sarah Haeserts
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- Centre for Structural Biology, VIB, Pleinlaan 2, 1050, Brussels, Belgium
| | - Daniel Charlier
- Research group of Microbiology, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova, 19, 1000, Ljubljana, Slovenia
| | - Alexander N Volkov
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- Centre for Structural Biology, VIB, Pleinlaan 2, 1050, Brussels, Belgium
- Jean Jeener NMR Centre, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Jurij Lah
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia.
| | - Remy Loris
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.
- Centre for Structural Biology, VIB, Pleinlaan 2, 1050, Brussels, Belgium.
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25
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Beck C, Krusche J, Notaro A, Walter A, Kränkel L, Vollert A, Stemmler R, Wittmann J, Schaller M, Slavetinsky C, Mayer C, De Castro C, Peschel A. Wall teichoic acid substitution with glucose governs phage susceptibility of Staphylococcus epidermidis. mBio 2024; 15:e0199023. [PMID: 38470054 PMCID: PMC11005348 DOI: 10.1128/mbio.01990-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 02/20/2024] [Indexed: 03/13/2024] Open
Abstract
The species- and clone-specific susceptibility of Staphylococcus cells for bacteriophages is governed by the structures and glycosylation patterns of wall teichoic acid (WTA) glycopolymers. The glycosylation-dependent phage-WTA interactions in the opportunistic pathogen Staphylococcus epidermidis and in other coagulase-negative staphylococci (CoNS) have remained unknown. We report a new S. epidermidis WTA glycosyltransferase TagE whose deletion confers resistance to siphoviruses such as ΦE72 but enables binding of otherwise unbound podoviruses. S. epidermidis glycerolphosphate WTA was found to be modified with glucose in a tagE-dependent manner. TagE is encoded together with the enzymes PgcA and GtaB providing uridine diphosphate-activated glucose. ΦE72 transduced several other CoNS species encoding TagE homologs, suggesting that WTA glycosylation via TagE is a frequent trait among CoNS that permits interspecies horizontal gene transfer. Our study unravels a crucial mechanism of phage-Staphylococcus interaction and horizontal gene transfer, and it will help in the design of anti-staphylococcal phage therapies.IMPORTANCEPhages are highly specific for certain bacterial hosts, and some can transduce DNA even across species boundaries. How phages recognize cognate host cells remains incompletely understood. Phages infecting members of the genus Staphylococcus bind to wall teichoic acid (WTA) glycopolymers with highly variable structures and glycosylation patterns. How WTA is glycosylated in the opportunistic pathogen Staphylococcus epidermidis and in other coagulase-negative staphylococci (CoNS) species has remained unknown. We describe that S. epidermidis glycosylates its WTA backbone with glucose, and we identify a cluster of three genes responsible for glucose activation and transfer to WTA. Their inactivation strongly alters phage susceptibility patterns, yielding resistance to siphoviruses but susceptibility to podoviruses. Many different CoNS species with related glycosylation genes can exchange DNA via siphovirus ΦE72, suggesting that glucose-modified WTA is crucial for interspecies horizontal gene transfer. Our finding will help to develop antibacterial phage therapies and unravel routes of genetic exchange.
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Affiliation(s)
- Christian Beck
- Cluster of Excellence “Controlling Microbes to Fight Infections (CMFI)”, University of Tübingen, Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Janes Krusche
- Cluster of Excellence “Controlling Microbes to Fight Infections (CMFI)”, University of Tübingen, Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Anna Notaro
- Department of Agricultural Sciences, University of Naples, Naples, Italy
| | - Axel Walter
- Cluster of Excellence “Controlling Microbes to Fight Infections (CMFI)”, University of Tübingen, Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Organismic Interactions/Glycobiology, University of Tübingen, Tübingen, Germany
| | - Lara Kränkel
- Cluster of Excellence “Controlling Microbes to Fight Infections (CMFI)”, University of Tübingen, Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Anneli Vollert
- Electron-Microscopy, Department of Dermatology, University Hospital Tübingen, Tübingen, Germany
| | - Regine Stemmler
- Cluster of Excellence “Controlling Microbes to Fight Infections (CMFI)”, University of Tübingen, Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Johannes Wittmann
- Leibniz Institute, DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Martin Schaller
- Electron-Microscopy, Department of Dermatology, University Hospital Tübingen, Tübingen, Germany
| | - Christoph Slavetinsky
- Cluster of Excellence “Controlling Microbes to Fight Infections (CMFI)”, University of Tübingen, Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
- Pediatric Surgery and Urology, University Children's Hospital Tübingen, University of Tübingen, Tübingen, Germany
| | - Christoph Mayer
- Cluster of Excellence “Controlling Microbes to Fight Infections (CMFI)”, University of Tübingen, Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Organismic Interactions/Glycobiology, University of Tübingen, Tübingen, Germany
| | | | - Andreas Peschel
- Cluster of Excellence “Controlling Microbes to Fight Infections (CMFI)”, University of Tübingen, Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
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26
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Kock KH, Kimes PK, Gisselbrecht SS, Inukai S, Phanor SK, Anderson JT, Ramakrishnan G, Lipper CH, Song D, Kurland JV, Rogers JM, Jeong R, Blacklow SC, Irizarry RA, Bulyk ML. DNA binding analysis of rare variants in homeodomains reveals homeodomain specificity-determining residues. Nat Commun 2024; 15:3110. [PMID: 38600112 PMCID: PMC11006913 DOI: 10.1038/s41467-024-47396-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 03/29/2024] [Indexed: 04/12/2024] Open
Abstract
Homeodomains (HDs) are the second largest class of DNA binding domains (DBDs) among eukaryotic sequence-specific transcription factors (TFs) and are the TF structural class with the largest number of disease-associated mutations in the Human Gene Mutation Database (HGMD). Despite numerous structural studies and large-scale analyses of HD DNA binding specificity, HD-DNA recognition is still not fully understood. Here, we analyze 92 human HD mutants, including disease-associated variants and variants of uncertain significance (VUS), for their effects on DNA binding activity. Many of the variants alter DNA binding affinity and/or specificity. Detailed biochemical analysis and structural modeling identifies 14 previously unknown specificity-determining positions, 5 of which do not contact DNA. The same missense substitution at analogous positions within different HDs often exhibits different effects on DNA binding activity. Variant effect prediction tools perform moderately well in distinguishing variants with altered DNA binding affinity, but poorly in identifying those with altered binding specificity. Our results highlight the need for biochemical assays of TF coding variants and prioritize dozens of variants for further investigations into their pathogenicity and the development of clinical diagnostics and precision therapies.
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Affiliation(s)
- Kian Hong Kock
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
- Program in Biological and Biomedical Sciences, Harvard University, Cambridge, MA, USA
| | - Patrick K Kimes
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Stephen S Gisselbrecht
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - Sachi Inukai
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - Sabrina K Phanor
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - James T Anderson
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - Gayatri Ramakrishnan
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
- Boston Bangalore Biosciences Beginnings Program, Harvard University, Cambridge, MA, USA
| | - Colin H Lipper
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Dongyuan Song
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jesse V Kurland
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - Julia M Rogers
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
- Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA, USA
| | - Raehoon Jeong
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
- Bioinformatics and Integrative Genomics Graduate Program, Harvard University, Cambridge, MA, USA
| | - Stephen C Blacklow
- Program in Biological and Biomedical Sciences, Harvard University, Cambridge, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA
- Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA, USA
| | - Rafael A Irizarry
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA.
- Program in Biological and Biomedical Sciences, Harvard University, Cambridge, MA, USA.
- Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA, USA.
- Bioinformatics and Integrative Genomics Graduate Program, Harvard University, Cambridge, MA, USA.
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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27
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Marshall PR, Davies J, Zhao Q, Liau WS, Lee Y, Basic D, Periyakaruppiah A, Zajaczkowski EL, Leighton LJ, Madugalle SU, Musgrove M, Kielar M, Brueckner AM, Gong H, Ren H, Walsh A, Kaczmarczyk L, Jackson WS, Chen A, Spitale RC, Bredy TW. DNA G-Quadruplex Is a Transcriptional Control Device That Regulates Memory. J Neurosci 2024; 44:e0093232024. [PMID: 38418220 PMCID: PMC11007313 DOI: 10.1523/jneurosci.0093-23.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/14/2024] [Accepted: 02/20/2024] [Indexed: 03/01/2024] Open
Abstract
The conformational state of DNA fine-tunes the transcriptional rate and abundance of RNA. Here, we report that G-quadruplex DNA (G4-DNA) accumulates in neurons, in an experience-dependent manner, and that this is required for the transient silencing and activation of genes that are critically involved in learning and memory in male C57/BL6 mice. In addition, site-specific resolution of G4-DNA by dCas9-mediated deposition of the helicase DHX36 impairs fear extinction memory. Dynamic DNA structure states therefore represent a key molecular mechanism underlying memory consolidation.One-Sentence Summary: G4-DNA is a molecular switch that enables the temporal regulation of the gene expression underlying the formation of fear extinction memory.
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Affiliation(s)
- Paul R Marshall
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
- Genome Sciences and Cancer Division & Eccles Institute of Neuroscience, John Curtin School of Medical Research, Australian National University, Canberra 2601, Australia
| | - Joshua Davies
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Qiongyi Zhao
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Wei-Siang Liau
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Yujin Lee
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Dean Basic
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Ambika Periyakaruppiah
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Esmi L Zajaczkowski
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Laura J Leighton
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Sachithrani U Madugalle
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Mason Musgrove
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Marcin Kielar
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Arie Maeve Brueckner
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Hao Gong
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Haobin Ren
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Alexander Walsh
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Lech Kaczmarczyk
- Department of Biomedical and Clinical Sciences (BKV), Division of Neurobiology (NEURO), Linköping University, Linköping 581 83, Sweden
| | - Walker S Jackson
- Department of Biomedical and Clinical Sciences (BKV), Division of Neurobiology (NEURO), Linköping University, Linköping 581 83, Sweden
| | - Alon Chen
- Neurobiology of Stress Laboratory, Department Brain Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, California 92697
| | - Timothy W Bredy
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
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28
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Lu J, Guo Y, Yin J, Chen J, Wang Y, Wang GG, Song J. Structure-guided functional suppression of AML-associated DNMT3A hotspot mutations. Nat Commun 2024; 15:3111. [PMID: 38600075 PMCID: PMC11006857 DOI: 10.1038/s41467-024-47398-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 03/26/2024] [Indexed: 04/12/2024] Open
Abstract
DNA methyltransferases DNMT3A- and DNMT3B-mediated DNA methylation critically regulate epigenomic and transcriptomic patterning during development. The hotspot DNMT3A mutations at the site of Arg822 (R882) promote polymerization, leading to aberrant DNA methylation that may contribute to the pathogenesis of acute myeloid leukemia (AML). However, the molecular basis underlying the mutation-induced functional misregulation of DNMT3A remains unclear. Here, we report the crystal structures of the DNMT3A methyltransferase domain, revealing a molecular basis for its oligomerization behavior distinct to DNMT3B, and the enhanced intermolecular contacts caused by the R882H or R882C mutation. Our biochemical, cellular, and genomic DNA methylation analyses demonstrate that introducing the DNMT3B-converting mutations inhibits the R882H-/R882C-triggered DNMT3A polymerization and enhances substrate access, thereby eliminating the dominant-negative effect of the DNMT3A R882 mutations in cells. Together, this study provides mechanistic insights into DNMT3A R882 mutations-triggered aberrant oligomerization and DNA hypomethylation in AML, with important implications in cancer therapy.
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Affiliation(s)
- Jiuwei Lu
- Department of Biochemistry, University of California, Riverside, CA, USA
| | - Yiran Guo
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, USA
| | - Jiekai Yin
- Environmental Toxicology Graduate Program, University of California, Riverside, CA, USA
| | - Jianbin Chen
- Department of Biochemistry, University of California, Riverside, CA, USA
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, CA, USA
- Department of Chemistry, University of California, Riverside, CA, USA
| | - Gang Greg Wang
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA.
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, USA.
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA.
| | - Jikui Song
- Department of Biochemistry, University of California, Riverside, CA, USA.
- Environmental Toxicology Graduate Program, University of California, Riverside, CA, USA.
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29
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Kuang W, Zhao Y, Li J, Deng Z. Structure-function analysis of the ATPase domain of African swine fever virus topoisomerase. mBio 2024; 15:e0308623. [PMID: 38411066 PMCID: PMC11005426 DOI: 10.1128/mbio.03086-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/05/2024] [Indexed: 02/28/2024] Open
Abstract
Type II topoisomerase utilizes the energy from ATP hydrolysis to alter DNA topology during genome replication and transcription. The ATPase domain of this enzyme is required for ATP hydrolysis and plays a crucial role in coupling DNA binding and ATP turnover with the DNA strand passage reaction. The African swine fever virus (ASFV) specifically encodes a topoisomerase II (topo II), which is critical for viral replication and an attractive target for antiviral development. Here, we present a high-resolution crystal structure of the ASFV topo II ATPase domain complexed with the substrate analog AMPPNP. Structural comparison reveals that the ASFV topo II ATPase domain shares a conserved overall structure with its homologs from eukaryotes and prokaryotes but also has three characteristic regions, including the intra-molecular interface formed by the ATP-lid and QTK loop as well as helix α9, the K-loop in the transducer domain, and the antennae-like α-helix at the ATP binding domain. Mutating the key residues within these three regions impairs or abolishes the basal and DNA-stimulated ATPase activities and reduces or eliminates the relaxation activity of the holoenzyme. Our data indicate that all three regions are functionally important for the ATPase and relaxation activities and strongly suggest that ATP hydrolysis, DNA binding, and strand passage are highly coupled and managed by the allosteric coordination of multiple domains of the type II topoisomerase. Moreover, we find a promising druggable pocket in the dimeric interface of the ASFV topo II ATPase domain, which will benefit future anti-ASFV drug development. IMPORTANCE The ATPase domain of type II topoisomerase provides energy by hydrolyzing ATP and coordinates with the DNA-binding/cleavage domain to drive and control DNA transport. The precise molecular mechanisms of how these domains respond to DNA binding and ATP hydrolysis signals and communicate with each other remain elusive. We determine the first high-resolution crystal structure of the ATPase domain of African swine fever virus (ASFV) topo II in complex with AMPPNP and biochemically investigate its function in ATPase and DNA relaxation activities. Importantly, we find that mutations at three characteristic regions of the ASFV ATPase domain produce parallel effects on the basal/DNA-stimulated ATPase and relaxation activities, implying the tight coupling of the ATP hydrolysis and strand passage process. Therefore, our data provide important implications for understanding the strand passage mechanism of the type II topoisomerase and the structural basis for developing ATPase domain-targeting antivirals against ASFV.
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Affiliation(s)
- Wenhua Kuang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Antiviral Research, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Yan Zhao
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Antiviral Research, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jinyue Li
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Antiviral Research, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Zengqin Deng
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Antiviral Research, Chinese Academy of Sciences, Wuhan, Hubei, China
- Hubei Jiangxia Laboratory, Wuhan, Hubei, China
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30
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Ma D, Ojha P, Yu AD, Araujo MS, Luo W, Keefer E, Díaz MM, Wu M, Joiner WJ, Abruzzi KC, Rosbash M. Timeless noncoding DNA contains cell-type preferential enhancers important for proper Drosophila circadian regulation. Proc Natl Acad Sci U S A 2024; 121:e2321338121. [PMID: 38568969 PMCID: PMC11009632 DOI: 10.1073/pnas.2321338121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 03/05/2024] [Indexed: 04/05/2024] Open
Abstract
To address the contribution of transcriptional regulation to Drosophila clock gene expression and to behavior, we generated a series of CRISPR-mediated deletions within two regions of the circadian gene timeless (tim), an intronic E-box region and an upstream E-box region that are both recognized by the key transcription factor Clock (Clk) and its heterodimeric partner Cycle. The upstream deletions but not an intronic deletion dramatically impact tim expression in fly heads; the biggest upstream deletion reduces peak RNA levels and tim RNA cycling amplitude to about 15% of normal, and there are similar effects on tim protein (TIM). The cycling amplitude of other clock genes is also strongly reduced, in these cases due to increases in trough levels. These data underscore the important contribution of the upstream E-box enhancer region to tim expression and of TIM to clock gene transcriptional repression in fly heads. Surprisingly, tim expression in clock neurons is only modestly affected by the biggest upstream deletion and is similarly affected by a deletion of the intronic E-box region. This distinction between clock neurons and glia is paralleled by a dramatically enhanced accessibility of the intronic enhancer region within clock neurons. This distinctive feature of tim chromatin was revealed by ATAC-seq (assay for transposase-accessible chromatin with sequencing) assays of purified neurons and glia as well as of fly heads. The enhanced cell type-specific accessibility of the intronic enhancer region explains the resilience of clock neuron tim expression and circadian behavior to deletion of the otherwise more prominent upstream tim E-box region.
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Affiliation(s)
- Dingbang Ma
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai201210, China
- Shanghai Key Laboratory of Aging Studies, Shanghai201210, China
| | - Pranav Ojha
- HHMI, Brandeis University, Waltham, MA02453
- Department of Biology, Brandeis University, Waltham, MA02453
| | - Albert D. Yu
- HHMI, Brandeis University, Waltham, MA02453
- Department of Biology, Brandeis University, Waltham, MA02453
| | - Maisa S. Araujo
- Laboratory of Entomology, Fiocruz Rondônia and Programa de Pós-Graduação em Biologia Experimental/Programa Nacional de Pós-Doutorado, Federal University Foundation of Rondônia, Porto Velho76801-974, Brazil
| | - Weifei Luo
- Guangxi Academy of Sciences, Nanning530003, China
| | - Evelyn Keefer
- HHMI, Brandeis University, Waltham, MA02453
- Department of Biology, Brandeis University, Waltham, MA02453
| | - Madelen M. Díaz
- The Miami Project to Cure Paralysis, Department of Neurosurgery, University of Miami Miller School of Medicine, Miami, FL33136
| | - Meilin Wu
- Department of Pharmacology, University of California, San Diego, La Jolla, CA92093
| | - William J. Joiner
- Department of Pharmacology, University of California, San Diego, La Jolla, CA92093
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA92093
| | - Katharine C. Abruzzi
- HHMI, Brandeis University, Waltham, MA02453
- Department of Biology, Brandeis University, Waltham, MA02453
| | - Michael Rosbash
- HHMI, Brandeis University, Waltham, MA02453
- Department of Biology, Brandeis University, Waltham, MA02453
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31
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Chen Y, He S, Lian H, Liu G, Liu B, Wei X. Microfluidic Immunosensing Platform Based on a Rolling Circle Amplification-Assisted DNA Dendrimer Probe for Portable and Sensitive Detection of Allergen-Specific IgE. Anal Chem 2024; 96:5625-5632. [PMID: 38556980 DOI: 10.1021/acs.analchem.4c00255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The robust point-of-care platform for sensitive, multiplexed, and affordable detection of allergen-specific IgE (sIgE) is an urgent demand in component-resolved diagnostics. Here, we developed a microfluidic immunosensing platform based on a rolling circle amplification-assisted DNA dendrimer probe for sensitive detection of multiple sIgEs. The versatile multichannel microfluidic whole blood analytical device integrates cell filtration, recombinant antigen-modified magnetic enrichment, and DNA dendrimer probe-amplified signal transduction for portable on-chip analysis. Three sIgEs against common oyster allergens were simultaneously detected in blood samples by simple smartphone-based imaging without any pretreatment. The quantitative detection of multiple allergen-specific antibodies on the platform was achieved with limits of detection of less than 50 pg/mL, exhibiting superior sensitivity compared to most point-of-care testing. The detection results of 55 serum samples and 4 whole blood samples were 100% consistent with the ELISA results, confirming the accuracy and stability of our platform. Additionally, the reversible combination of hexahistidine6-tag and Ni-IMAC magbead was elegantly utilized on the immunosensing platform for desired reversibility. With the advantages of general applicability, high sensitivity, and reversibility, the DNA dendrimer-based microfluidic immunosensing platform provides great potential for the portable detection of immune proteins as a point-of-care platform in disease diagnostics and biological analysis.
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Affiliation(s)
- Yiyu Chen
- College of Materials Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Shan He
- College of Materials Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Huiting Lian
- College of Materials Science and Engineering, Huaqiao University, Xiamen 361021, China
- Key Laboratory of Molecular Designing and Green Conversions, Huaqiao University, Xiamen 361021, China
| | - Guangming Liu
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Bin Liu
- College of Materials Science and Engineering, Huaqiao University, Xiamen 361021, China
- Key Laboratory of Molecular Designing and Green Conversions, Huaqiao University, Xiamen 361021, China
- Xiamen Key Laboratory of Optoelectronic Materials and Advanced Manufacturing, Huaqiao University, Xiamen 361021, China
| | - Xiaofeng Wei
- College of Materials Science and Engineering, Huaqiao University, Xiamen 361021, China
- Key Laboratory of Molecular Designing and Green Conversions, Huaqiao University, Xiamen 361021, China
- Xiamen Key Laboratory of Optoelectronic Materials and Advanced Manufacturing, Huaqiao University, Xiamen 361021, China
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32
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Wu Y, Liu P, Chen W, Bai S, Chen S, Chen J, Xu X, Xia J, Wu Y, Lai J, Sun C, Lao Z, Wan X, Wu Z. Microwave hyperthermia enhances radiosensitization by decreasing DNA repair efficiency and inducing oxidative stress in PC3 prostatic adenocarcinoma cells. Int J Hyperthermia 2024; 41:2335201. [PMID: 38583875 DOI: 10.1080/02656736.2024.2335201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024] Open
Abstract
PURPOSE Radiotherapy (RT) is the primary treatment for prostate cancer (PCa); however, the emergence of castration-resistant prostate cancer (CRPC) often leads to treatment failure and cancer-related deaths. In this study, we aimed to explore the use of microwave hyperthermia (MW-HT) to sensitize PCa to RT and investigate the underlying molecular mechanisms. METHODS We developed a dedicated MW-HT heating setup, created an in vitro and in vivo MW-HT + RT treatment model for CRPC. We evaluated PC3 cell proliferation using CCK-8, colony experiments, DAPI staining, comet assay and ROS detection method. We also monitored nude mouse models of PCa during treatment, measured tumor weight, and calculated the tumor inhibition rate. Western blotting was used to detect DNA damage repair protein expression in PC3 cells and transplanted tumors. RESULTS Compared to control, PC3 cell survival and clone formation rates decreased in RT + MW-HT group, demonstrating significant increase in apoptosis, ROS levels, and DNA damage. Lower tumor volumes and weights were observed in treatment groups. Ki-67 expression level was reduced in all treatment groups, with significant decrease in RT + MW-HT groups. The most significant apoptosis induction was confirmed in RT + MW-HT group by TUNEL staining. Protein expression levels of DNA-PKcs, ATM, ATR, and P53/P21 signaling pathways significantly decreased in RT + MW-HT groups. CONCLUSION MW-HT + RT treatment significantly inhibited DNA damage repair by downregulating DNA-PKcs, ATM, ATR, and P53/P21 signaling pathways, leading to increased ROS levels, aggravate DNA damage, apoptosis, and necrosis in PC3 cells, a well-established model of CRPC.
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Affiliation(s)
- Yajun Wu
- Department of TCM Pharmacy, Zhejiang Hospital, Hangzhou, China
| | - Pengyuan Liu
- Department of Oncology, Zhejiang Hospital, Hangzhou, China
- Department of Radiation Oncology, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wendy Chen
- Nanjing Drum Tower Hospital Group Suqian Hospital, Suqian, China
| | - Shiting Bai
- Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Sisi Chen
- Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jianglin Chen
- Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Xiaogang Xu
- Zhejiang Provincial Key Lab of Geriatrics and Geriatrics Institute of Zhejiang Province, Department of Geriatrics, Zhejiang Hospital, Hangzhou, China
| | - Jindan Xia
- Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yufei Wu
- ACS (International) Singapore, Singapore, Singapore
| | - Jianjun Lai
- Department of Radiation Oncology, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chuan Sun
- Zhejiang Provincial Key Lab of Geriatrics and Geriatrics Institute of Zhejiang Province, Department of Geriatrics, Zhejiang Hospital, Hangzhou, China
| | - Zhenghong Lao
- Department of Oncology, People's Hospital of Deqing County, Huzhou City, China
| | - Xiaoqing Wan
- Department of TCM Pharmacy, Zhejiang Hospital, Hangzhou, China
| | - Zhibing Wu
- Department of Oncology, Zhejiang Hospital, Hangzhou, China
- Department of Radiation Oncology, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, China
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33
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Kazakova A, Frydrych I, Jakubcová N, Pokorný J, Lišková B, Gurská S, Džubák P, Hajdúch M, Urban M. Novel triterpenoid pyrones, phthalimides and phthalates are selectively cytotoxic in CCRF-CEM cancer cells - Synthesis, potency, and mitochondrial mechanism of action. Eur J Med Chem 2024; 269:116336. [PMID: 38520761 DOI: 10.1016/j.ejmech.2024.116336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 03/13/2024] [Accepted: 03/14/2024] [Indexed: 03/25/2024]
Abstract
A series of triterpenoid pyrones was synthesized and subsequently modified to introduce phthalimide or phthalate moieties into the triterpenoid skeleton. These compounds underwent in vitro cytotoxicity screening, revealing that a subset of six compounds exhibited potent activity, with IC50 values in the low micromolar range. Further biological evaluations, including Annexin V and propidium iodide staining experiment revealed, that all compounds induce selective apoptosis in cancer cells. Measurements of mitochondrial potential, cell cycle analysis, and the expression of pro- and anti-apoptotic proteins confirmed, that apoptosis was mediated via the mitochondrial pathway. These findings were further supported by cell cycle modulation and DNA/RNA synthesis studies, which indicated a significant increase in cell accumulation in the G0/G1 phase and a marked reduction in S-phase cells, alongside a substantial inhibition of DNA synthesis. The activation of caspase-3 and the cleavage of PARP, coupled with a decrease in the expression of Bcl-2 and Bcl-XL proteins, underscored the induction of apoptosis through the mitochondrial pathway. Given their high activity and pronounced effect on mitochondria function, trifluoromethyl pyrones 1f and 2f, and dihydrophthalimide 2h have been selected for further development.
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Affiliation(s)
- Anna Kazakova
- Department of Organic Chemistry, Faculty of Science, Palacký University Olomouc, 17. listopadu 1192/12, 771 46, Olomouc, Czech Republic
| | - Ivo Frydrych
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University Olomouc, Hněvotínská 1333/5, 779 00, Olomouc, Czech Republic
| | - Nikola Jakubcová
- Department of Organic Chemistry, Faculty of Science, Palacký University Olomouc, 17. listopadu 1192/12, 771 46, Olomouc, Czech Republic; Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University Olomouc, Hněvotínská 1333/5, 779 00, Olomouc, Czech Republic
| | - Jan Pokorný
- Department of Organic Chemistry, Faculty of Science, Palacký University Olomouc, 17. listopadu 1192/12, 771 46, Olomouc, Czech Republic; Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University Olomouc, Hněvotínská 1333/5, 779 00, Olomouc, Czech Republic
| | - Barbora Lišková
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University Olomouc, Hněvotínská 1333/5, 779 00, Olomouc, Czech Republic
| | - Soňa Gurská
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University Olomouc, Hněvotínská 1333/5, 779 00, Olomouc, Czech Republic
| | - Petr Džubák
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University Olomouc, Hněvotínská 1333/5, 779 00, Olomouc, Czech Republic; Laboratory of Experimental Medicine, University Hospital, Hněvotínská 1333/5, Olomouc, 779 00, Czech Republic
| | - Marián Hajdúch
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University Olomouc, Hněvotínská 1333/5, 779 00, Olomouc, Czech Republic; Laboratory of Experimental Medicine, University Hospital, Hněvotínská 1333/5, Olomouc, 779 00, Czech Republic
| | - Milan Urban
- Department of Organic Chemistry, Faculty of Science, Palacký University Olomouc, 17. listopadu 1192/12, 771 46, Olomouc, Czech Republic; Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University Olomouc, Hněvotínská 1333/5, 779 00, Olomouc, Czech Republic.
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Ren P, Tong X, Li J, Jiang H, Liu S, Li X, Lai M, Yang W, Rong Y, Zhang Y, Jin J, Ma Y, Pan W, Fan HY, Zhang S, Zhang YL. CRL4 DCAF13 E3 ubiquitin ligase targets MeCP2 for degradation to prevent DNA hypermethylation and ensure normal transcription in growing oocytes. Cell Mol Life Sci 2024; 81:165. [PMID: 38578457 PMCID: PMC10997554 DOI: 10.1007/s00018-024-05185-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/23/2024] [Accepted: 02/27/2024] [Indexed: 04/06/2024]
Abstract
The DNA methylation is gradually acquired during oogenesis, a process sustained by successful follicle development. However, the functional roles of methyl-CpG-binding protein 2 (MeCP2), an epigenetic regulator displaying specifical binding with methylated DNA, remains unknown in oogenesis. In this study, we found MeCP2 protein was highly expressed in primordial and primary follicle, but was almost undetectable in secondary follicles. However, in aged ovary, MeCP2 protein is significantly increased in both oocyte and granulosa cells. Overexpression of MeCP2 in growing oocyte caused transcription dysregulation, DNA hypermethylation, and genome instability, ultimately leading to follicle growth arrest and apoptosis. MeCP2 is targeted by DCAF13, a substrate recognition adaptor of the Cullin 4-RING (CRL4) E3 ligase, and polyubiquitinated for degradation in both cells and oocytes. Dcaf13-null oocyte exhibited an accumulation of MeCP2 protein, and the partial rescue of follicle growth arrest induced by Dcaf13 deletion was observed following MeCP2 knockdown. The RNA-seq results revealed that large amounts of genes were regulated by the DCAF13-MeCP2 axis in growing oocytes. Our study demonstrated that CRL4DCAF13 E3 ubiquitin ligase targets MeCP2 for degradation to ensure normal DNA methylome and transcription in growing oocytes. Moreover, in aged ovarian follicles, deceased DCAF13 and DDB1 protein were observed, indicating a potential novel mechanism that regulates ovary aging.
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Affiliation(s)
- Peipei Ren
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Hangzhou, China
| | - Xiaomei Tong
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Hangzhou, China
| | - Junjian Li
- College of Life and Environmental Science, Wenzhou University, Wenzhou, China
| | - Huifang Jiang
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Hangzhou, China
| | - Siya Liu
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Hangzhou, China
| | - Xiang Li
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Hangzhou, China
| | - Mengru Lai
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Hangzhou, China
| | - Weijie Yang
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Hangzhou, China
| | - Yan Rong
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Hangzhou, China
| | - Yingyi Zhang
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Hangzhou, China
| | - Jiamin Jin
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Hangzhou, China
| | - Yerong Ma
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Hangzhou, China
| | - Weiwei Pan
- Department of Cell Biology, College of Medicine, Jiaxing University, Jiaxing, 314001, China
| | - Heng-Yu Fan
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Hangzhou, China
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Songying Zhang
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China.
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Hangzhou, China.
| | - Yin-Li Zhang
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China.
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Hangzhou, China.
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Fried W, Tyagi M, Minakhin L, Chandramouly G, Tredinnick T, Ramanjulu M, Auerbacher W, Calbert M, Rusanov T, Hoang T, Borisonnik N, Betsch R, Krais JJ, Wang Y, Vekariya UM, Gordon J, Morton G, Kent T, Skorski T, Johnson N, Childers W, Chen XS, Pomerantz RT. Discovery of a small-molecule inhibitor that traps Polθ on DNA and synergizes with PARP inhibitors. Nat Commun 2024; 15:2862. [PMID: 38580648 PMCID: PMC10997755 DOI: 10.1038/s41467-024-46593-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 03/04/2024] [Indexed: 04/07/2024] Open
Abstract
The DNA damage response (DDR) protein DNA Polymerase θ (Polθ) is synthetic lethal with homologous recombination (HR) factors and is therefore a promising drug target in BRCA1/2 mutant cancers. We discover an allosteric Polθ inhibitor (Polθi) class with 4-6 nM IC50 that selectively kills HR-deficient cells and acts synergistically with PARP inhibitors (PARPi) in multiple genetic backgrounds. X-ray crystallography and biochemistry reveal that Polθi selectively inhibits Polθ polymerase (Polθ-pol) in the closed conformation on B-form DNA/DNA via an induced fit mechanism. In contrast, Polθi fails to inhibit Polθ-pol catalytic activity on A-form DNA/RNA in which the enzyme binds in the open configuration. Remarkably, Polθi binding to the Polθ-pol:DNA/DNA closed complex traps the polymerase on DNA for more than forty minutes which elucidates the inhibitory mechanism of action. These data reveal a unique small-molecule DNA polymerase:DNA trapping mechanism that induces synthetic lethality in HR-deficient cells and potentiates the activity of PARPi.
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Affiliation(s)
- William Fried
- Molecular and Computational Biology, Department of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Mrityunjay Tyagi
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Leonid Minakhin
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Gurushankar Chandramouly
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Taylor Tredinnick
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Mercy Ramanjulu
- Recombination Therapeutics, Pennsylvania Biotechnology Center, Doylestown, PA, 18902, USA
| | - William Auerbacher
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Marissa Calbert
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA
- Fels Cancer Institute for Personalized Medicine, Philadelphia, PA, USA
| | - Timur Rusanov
- Department of Pharmacology and Regenerative Medicine, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | | | | | - Robert Betsch
- Nuclear Dynamics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - John J Krais
- Nuclear Dynamics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Yifan Wang
- Nuclear Dynamics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Umeshkumar M Vekariya
- Fels Cancer Institute for Personalized Medicine, Philadelphia, PA, USA
- Department of Cancer and Cellular Biology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - John Gordon
- Fels Cancer Institute for Personalized Medicine, Philadelphia, PA, USA
| | - George Morton
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, PA, USA
| | - Tatiana Kent
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Tomasz Skorski
- Fels Cancer Institute for Personalized Medicine, Philadelphia, PA, USA
- Department of Cancer and Cellular Biology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Neil Johnson
- Nuclear Dynamics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Wayne Childers
- Recombination Therapeutics, Pennsylvania Biotechnology Center, Doylestown, PA, 18902, USA
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, PA, USA
| | - Xiaojiang S Chen
- Molecular and Computational Biology, Department of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA, USA
- Recombination Therapeutics, Pennsylvania Biotechnology Center, Doylestown, PA, 18902, USA
| | - Richard T Pomerantz
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA.
- Recombination Therapeutics, Pennsylvania Biotechnology Center, Doylestown, PA, 18902, USA.
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36
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Jiang L, Liu X, Liang X, Dai S, Wei H, Guo M, Chen Z, Xiao D, Chen Y. Structural characterization of the DNA binding mechanism of retinoic acid-related orphan receptor gamma. Structure 2024; 32:467-475.e3. [PMID: 38309263 DOI: 10.1016/j.str.2024.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/15/2023] [Accepted: 01/08/2024] [Indexed: 02/05/2024]
Abstract
Retinoic acid-related orphan receptor gamma (RORγ) plays critical roles in regulating various biological processes and has been linked to immunodeficiency disorders and cancers. DNA recognition is essential for RORγ to exert its functions. However, the underlying mechanism of the DNA binding by RORγ remains unclear. In this study, we present the crystal structure of the complex of RORγ1 DNA-binding domain (RORγ1-DBD)/direct repeat DNA element DR2 at 2.3 Å resolution. We demonstrate that RORγ1-DBD binds the DR2 motif as a homodimer, with the C-terminal extension (CTE) region of RORγ1-DBD contributing to the DNA recognition and the formation of dimeric interface. Further studies reveal that REV-ERB-DBD and RXR-DBD, also bind the DR2 site as a homodimer, while NR4A2-DBD binds DR2 as a monomer. Our research uncovers a binding mechanism of RORγ1 to the DR2 site and provides insights into the biological functions of RORγ1 and the broader RORs subfamily.
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Affiliation(s)
- Longying Jiang
- Department of Pathology, NHC Key Laboratory of Cancer Proteomics, State Local Joint Engineering Laboratory for Anticancer Drugs, Department of Oncology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xueke Liu
- Department of Pathology, NHC Key Laboratory of Cancer Proteomics, State Local Joint Engineering Laboratory for Anticancer Drugs, Department of Oncology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xujun Liang
- Department of Pathology, NHC Key Laboratory of Cancer Proteomics, State Local Joint Engineering Laboratory for Anticancer Drugs, Department of Oncology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shuyan Dai
- Department of Pathology, NHC Key Laboratory of Cancer Proteomics, State Local Joint Engineering Laboratory for Anticancer Drugs, Department of Oncology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hudie Wei
- Department of Pathology, NHC Key Laboratory of Cancer Proteomics, State Local Joint Engineering Laboratory for Anticancer Drugs, Department of Oncology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ming Guo
- Department of Pathology, NHC Key Laboratory of Cancer Proteomics, State Local Joint Engineering Laboratory for Anticancer Drugs, Department of Oncology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhuchu Chen
- Department of Pathology, NHC Key Laboratory of Cancer Proteomics, State Local Joint Engineering Laboratory for Anticancer Drugs, Department of Oncology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Desheng Xiao
- Department of Pathology, NHC Key Laboratory of Cancer Proteomics, State Local Joint Engineering Laboratory for Anticancer Drugs, Department of Oncology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Yongheng Chen
- Department of Pathology, NHC Key Laboratory of Cancer Proteomics, State Local Joint Engineering Laboratory for Anticancer Drugs, Department of Oncology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.
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37
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Wei X, Xu H, Zhou M, Zhou Q, Li M, Liu Y. Chemically modified microRNA delivery via DNA tetrahedral frameworks for dental pulp regeneration. J Nanobiotechnology 2024; 22:150. [PMID: 38575923 DOI: 10.1186/s12951-024-02393-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 03/10/2024] [Indexed: 04/06/2024] Open
Abstract
Dental pulp regeneration is a promising strategy for addressing tooth disorders. Incorporating this strategy involves the fundamental challenge of establishing functional vascular networks using dental pulp stem cells (DPSCs) to support tissue regeneration. Current therapeutic approaches lack efficient and stable methods for activating DPSCs. In the study, we used a chemically modified microRNA (miRNA)-loaded tetrahedral-framework nucleic acid nanostructure to promote DPSC-mediated angiogenesis and dental pulp regeneration. Incorporating chemically modified miR-126-3p into tetrahedral DNA nanostructures (miR@TDNs) represents a notable advancement in the stability and efficacy of miRNA delivery into DPSCs. These nanostructures enhanced DPSC proliferation, migration, and upregulated angiogenesis-related genes, enhancing their paracrine signaling effects on endothelial cells. This enhanced effect was substantiated by improvements in endothelial cell tube formation, migration, and gene expression. Moreover, in vivo investigations employing matrigel plug assays and ectopic dental pulp transplantation confirmed the potential of miR@TDNs in promoting angiogenesis and facilitating dental pulp regeneration. Our findings demonstrated the potential of chemically modified miRNA-loaded nucleic acid nanostructures in enhancing DPSC-mediated angiogenesis and supporting dental pulp regeneration. These results highlighted the promising role of chemically modified nucleic acid-based delivery systems as therapeutic agents in regenerative dentistry and tissue engineering.
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Affiliation(s)
- Xiaoling Wei
- Shanghai Stomatological Hospital and School of Stomatology, Fudan University, Shanghai, 200001, China
- Shanghai Key Laboratory of Craniomaxillofacial Development and Diseases, Fudan University, Shanghai, 200001, China
| | - Huaxing Xu
- Shanghai Stomatological Hospital and School of Stomatology, Fudan University, Shanghai, 200001, China
- Shanghai Key Laboratory of Craniomaxillofacial Development and Diseases, Fudan University, Shanghai, 200001, China
| | - Mengqi Zhou
- Shanghai Stomatological Hospital and School of Stomatology, Fudan University, Shanghai, 200001, China
- Shanghai Key Laboratory of Craniomaxillofacial Development and Diseases, Fudan University, Shanghai, 200001, China
| | - Qiangqiang Zhou
- Shanghai Stomatological Hospital and School of Stomatology, Fudan University, Shanghai, 200001, China
- Shanghai Key Laboratory of Craniomaxillofacial Development and Diseases, Fudan University, Shanghai, 200001, China
| | - Mingqiang Li
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Yuehua Liu
- Shanghai Stomatological Hospital and School of Stomatology, Fudan University, Shanghai, 200001, China.
- Shanghai Key Laboratory of Craniomaxillofacial Development and Diseases, Fudan University, Shanghai, 200001, China.
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Tian M, Wang Z, Su Z, Shibata E, Shibata Y, Dutta A, Zang C. Integrative analysis of DNA replication origins and ORC-/MCM-binding sites in human cells reveals a lack of overlap. eLife 2024; 12:RP89548. [PMID: 38567819 PMCID: PMC10990492 DOI: 10.7554/elife.89548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024] Open
Abstract
Based on experimentally determined average inter-origin distances of ~100 kb, DNA replication initiates from ~50,000 origins on human chromosomes in each cell cycle. The origins are believed to be specified by binding of factors like the origin recognition complex (ORC) or CTCF or other features like G-quadruplexes. We have performed an integrative analysis of 113 genome-wide human origin profiles (from five different techniques) and five ORC-binding profiles to critically evaluate whether the most reproducible origins are specified by these features. Out of ~7.5 million union origins identified by all datasets, only 0.27% (20,250 shared origins) were reproducibly obtained in at least 20 independent SNS-seq datasets and contained in initiation zones identified by each of three other techniques, suggesting extensive variability in origin usage and identification. Also, 21% of the shared origins overlap with transcriptional promoters, posing a conundrum. Although the shared origins overlap more than union origins with constitutive CTCF-binding sites, G-quadruplex sites, and activating histone marks, these overlaps are comparable or less than that of known transcription start sites, so that these features could be enriched in origins because of the overlap of origins with epigenetically open, promoter-like sequences. Only 6.4% of the 20,250 shared origins were within 1 kb from any of the ~13,000 reproducible ORC-binding sites in human cancer cells, and only 4.5% were within 1 kb of the ~11,000 union MCM2-7-binding sites in contrast to the nearly 100% overlap in the two comparisons in the yeast, Saccharomyces cerevisiae. Thus, in human cancer cell lines, replication origins appear to be specified by highly variable stochastic events dependent on the high epigenetic accessibility around promoters, without extensive overlap between the most reproducible origins and currently known ORC- or MCM-binding sites.
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Affiliation(s)
- Mengxue Tian
- Center for Public Health Genomics, University of Virginia School of MedicineCharlottesvilleUnited States
- Department of Biochemistry and Molecular Genetics, University of Virginia School of MedicineCharlottesvilleUnited States
| | - Zhenjia Wang
- Center for Public Health Genomics, University of Virginia School of MedicineCharlottesvilleUnited States
| | - Zhangli Su
- Department of Biochemistry and Molecular Genetics, University of Virginia School of MedicineCharlottesvilleUnited States
- Department of Genetics, University of Alabama at BirminghamBirminghamUnited States
| | - Etsuko Shibata
- Department of Biochemistry and Molecular Genetics, University of Virginia School of MedicineCharlottesvilleUnited States
- Department of Genetics, University of Alabama at BirminghamBirminghamUnited States
| | - Yoshiyuki Shibata
- Department of Biochemistry and Molecular Genetics, University of Virginia School of MedicineCharlottesvilleUnited States
- Department of Genetics, University of Alabama at BirminghamBirminghamUnited States
| | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, University of Virginia School of MedicineCharlottesvilleUnited States
- Department of Genetics, University of Alabama at BirminghamBirminghamUnited States
| | - Chongzhi Zang
- Center for Public Health Genomics, University of Virginia School of MedicineCharlottesvilleUnited States
- Department of Biochemistry and Molecular Genetics, University of Virginia School of MedicineCharlottesvilleUnited States
- Department of Public Health Sciences, University of VirginiaCharlottesvilleUnited States
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Thomas JD, Yurkovetskiy AV, Yin M, Bodyak ND, Tang S, Protopopova M, Kelleher E, Jones B, Yang L, Custar D, Catcott KC, Demady DR, Collins SD, Xu L, Bu C, Qin L, Ter-Ovanesyan E, Damelin M, Toader D, Lowinger TB. Development of a Novel DNA Mono-alkylator Platform for Antibody-Drug Conjugates. Mol Cancer Ther 2024; 23:541-551. [PMID: 38354416 DOI: 10.1158/1535-7163.mct-23-0622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 01/02/2024] [Accepted: 02/08/2024] [Indexed: 02/16/2024]
Abstract
Although microtubule inhibitors (MTI) remain a therapeutically valuable payload option for antibody-drug conjugates (ADC), some cancers do not respond to MTI-based ADCs. Efforts to fill this therapeutic gap have led to a recent expansion of the ADC payload "toolbox" to include payloads with novel mechanisms of action such as topoisomerase inhibition and DNA cross-linking. We present here the development of a novel DNA mono-alkylator ADC platform that exhibits sustained tumor growth suppression at single doses in MTI-resistant tumors and is well tolerated in the rat upon repeat dosing. A phosphoramidate prodrug of the payload enables low ADC aggregation even at drug-to-antibody ratios of 5:1 while still delivering a bystander-capable payload that is effective in multidrug resistant (MDR)-overexpressing cell lines. The platform was comparable in xenograft studies to the clinical benchmark DNA mono-alkylator ADC platform DGN459 but with a significantly better tolerability profile in rats. Thus, the activity and tolerability profile of this new platform make it a viable option for the development of ADCs.
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Affiliation(s)
| | | | - Mao Yin
- Formerly Mersana Therapeutics, Inc., Cambridge, Massachusetts
| | | | - Shuyi Tang
- Formerly Mersana Therapeutics, Inc., Cambridge, Massachusetts
| | | | | | - Brian Jones
- Formerly Mersana Therapeutics, Inc., Cambridge, Massachusetts
| | - Liping Yang
- Formerly Mersana Therapeutics, Inc., Cambridge, Massachusetts
| | - Daniel Custar
- Mersana Therapeutics, Inc., Cambridge, Massachusetts
| | | | - Damon R Demady
- Formerly Mersana Therapeutics, Inc., Cambridge, Massachusetts
| | | | - Ling Xu
- Formerly Mersana Therapeutics, Inc., Cambridge, Massachusetts
| | - Charlie Bu
- Formerly Mersana Therapeutics, Inc., Cambridge, Massachusetts
| | - LiuLiang Qin
- Formerly Mersana Therapeutics, Inc., Cambridge, Massachusetts
| | | | - Marc Damelin
- Mersana Therapeutics, Inc., Cambridge, Massachusetts
| | - Dorin Toader
- Mersana Therapeutics, Inc., Cambridge, Massachusetts
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Ramakrishnan S, Cortes-Gomez E, Athans SR, Attwood KM, Rosario SR, Kim SJ, Mager DE, Isenhart EG, Hu Q, Wang J, Woloszynska A. Race-specific coregulatory and transcriptomic profiles associated with DNA methylation and androgen receptor in prostate cancer. Genome Med 2024; 16:52. [PMID: 38566104 PMCID: PMC10988846 DOI: 10.1186/s13073-024-01323-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 03/22/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Prostate cancer is a significant health concern, particularly among African American (AA) men who exhibit higher incidence and mortality compared to European American (EA) men. Understanding the molecular mechanisms underlying these disparities is imperative for enhancing clinical management and achieving better outcomes. METHODS Employing a multi-omics approach, we analyzed prostate cancer in both AA and EA men. Using Illumina methylation arrays and RNA sequencing, we investigated DNA methylation and gene expression in tumor and non-tumor prostate tissues. Additionally, Boolean analysis was utilized to unravel complex networks contributing to racial disparities in prostate cancer. RESULTS When comparing tumor and adjacent non-tumor prostate tissues, we found that DNA hypermethylated regions are enriched for PRC2/H3K27me3 pathways and EZH2/SUZ12 cofactors. Olfactory/ribosomal pathways and distinct cofactors, including CTCF and KMT2A, were enriched in DNA hypomethylated regions in prostate tumors from AA men. We identified race-specific inverse associations of DNA methylation with expression of several androgen receptor (AR) associated genes, including the GATA family of transcription factors and TRIM63. This suggests that race-specific dysregulation of the AR signaling pathway exists in prostate cancer. To investigate the effect of AR inhibition on race-specific gene expression changes, we generated in-silico patient-specific prostate cancer Boolean networks. Our simulations revealed prolonged AR inhibition causes significant dysregulation of TGF-β, IDH1, and cell cycle pathways specifically in AA prostate cancer. We further quantified global gene expression changes, which revealed differential expression of genes related to microtubules, immune function, and TMPRSS2-fusion pathways, specifically in prostate tumors of AA men. Enrichment of these pathways significantly correlated with an altered risk of disease progression in a race-specific manner. CONCLUSIONS Our study reveals unique signaling networks underlying prostate cancer biology in AA and EA men, offering potential insights for clinical management strategies tailored to specific racial groups. Targeting AR and associated pathways could be particularly beneficial in addressing the disparities observed in prostate cancer outcomes in the context of AA and EA men. Further investigation into these identified pathways may lead to the development of personalized therapeutic approaches to improve outcomes for prostate cancer patients across different racial backgrounds.
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Affiliation(s)
- Swathi Ramakrishnan
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Eduardo Cortes-Gomez
- Department of Bioinformatics and Biostatistics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
- Department of Biostatistics, SUNY University at Buffalo, Kimball Tower, Buffalo, NY, 14214, USA
| | - Sarah R Athans
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Kristopher M Attwood
- Department of Bioinformatics and Biostatistics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Spencer R Rosario
- Department of Bioinformatics and Biostatistics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Se Jin Kim
- Department of Pharmaceutical Sciences, SUNY University at Buffalo, Buffalo, NY, 14214, USA
| | - Donald E Mager
- Department of Pharmaceutical Sciences, SUNY University at Buffalo, Buffalo, NY, 14214, USA
- Enhanced Pharmacodynamics, LLC, Buffalo, NY, 14203, USA
| | - Emily G Isenhart
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Qiang Hu
- Department of Bioinformatics and Biostatistics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Jianmin Wang
- Department of Bioinformatics and Biostatistics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Anna Woloszynska
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA.
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Muoio D, Laspata N, Dannenberg RL, Curry C, Darkoa-Larbi S, Hedglin M, Uttam S, Fouquerel E. PARP2 promotes Break Induced Replication-mediated telomere fragility in response to replication stress. Nat Commun 2024; 15:2857. [PMID: 38565848 PMCID: PMC10987537 DOI: 10.1038/s41467-024-47222-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 03/22/2024] [Indexed: 04/04/2024] Open
Abstract
PARP2 is a DNA-dependent ADP-ribosyl transferase (ARTs) enzyme with Poly(ADP-ribosyl)ation activity that is triggered by DNA breaks. It plays a role in the Base Excision Repair pathway, where it has overlapping functions with PARP1. However, additional roles for PARP2 have emerged in the response of cells to replication stress. In this study, we demonstrate that PARP2 promotes replication stress-induced telomere fragility and prevents telomere loss following chronic induction of oxidative DNA lesions and BLM helicase depletion. Telomere fragility results from the activity of the break-induced replication pathway (BIR). During this process, PARP2 promotes DNA end resection, strand invasion and BIR-dependent mitotic DNA synthesis by orchestrating POLD3 recruitment and activity. Our study has identified a role for PARP2 in the response to replication stress. This finding may lead to the development of therapeutic approaches that target DNA-dependent ART enzymes, particularly in cancer cells with high levels of replication stress.
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Affiliation(s)
- Daniela Muoio
- UPMC Hillman Cancer Center, University of Pittsburgh Cancer Institute, Department of Pharmacology and Chemical Biology, Pittsburgh, PA, 15213, USA
| | - Natalie Laspata
- UPMC Hillman Cancer Center, University of Pittsburgh Cancer Institute, Department of Pharmacology and Chemical Biology, Pittsburgh, PA, 15213, USA
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233S. 10th street, Philadelphia, PA, 19107, USA
| | - Rachel L Dannenberg
- Department of Chemistry, The Pennsylvania State University, University park, State College, PA, 16802, USA
| | - Caroline Curry
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233S. 10th street, Philadelphia, PA, 19107, USA
| | - Simone Darkoa-Larbi
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233S. 10th street, Philadelphia, PA, 19107, USA
| | - Mark Hedglin
- Department of Chemistry, The Pennsylvania State University, University park, State College, PA, 16802, USA
| | - Shikhar Uttam
- Department of Computational and Systems Biology, UPMC Hillman Cancer Center, University of Pittsburgh, 5117 Centre Avenue, Pittsburgh, PA, 15213, USA
| | - Elise Fouquerel
- UPMC Hillman Cancer Center, University of Pittsburgh Cancer Institute, Department of Pharmacology and Chemical Biology, Pittsburgh, PA, 15213, USA.
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Padayachy L, Ntallis SG, Halazonetis TD. RECQL4 is not critical for firing of human DNA replication origins. Sci Rep 2024; 14:7708. [PMID: 38565932 PMCID: PMC10987555 DOI: 10.1038/s41598-024-58404-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 03/28/2024] [Indexed: 04/04/2024] Open
Abstract
Human RECQL4, a member of the RecQ helicase family, plays a role in maintaining genomic stability, but its precise function remains unclear. The N-terminus of RECQL4 has similarity to Sld2, a protein required for the firing of DNA replication origins in budding yeast. Consistent with this sequence similarity, the Xenopus laevis homolog of RECQL4 has been implicated in initiating DNA replication in egg extracts. To determine whether human RECQL4 is required for firing of DNA replication origins, we generated cells in which both RECQL4 alleles were targeted, resulting in either lack of protein expression (knock-out; KO) or expression of a full-length, mutant protein lacking helicase activity (helicase-dead; HD). Interestingly, both the RECQL4 KO and HD cells were viable and exhibited essentially identical origin firing profiles as the parental cells. Analysis of the rate of fork progression revealed increased rates in the RECQL4 KO cells, which might be indicative of decreased origin firing efficiency. Our results are consistent with human RECQL4 having a less critical role in firing of DNA replication origins, than its budding yeast homolog Sld2.
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Affiliation(s)
- Laura Padayachy
- Department of Molecular and Cellular Biology, University of Geneva, 1205, Geneva, Switzerland
| | - Sotirios G Ntallis
- Department of Molecular and Cellular Biology, University of Geneva, 1205, Geneva, Switzerland
| | - Thanos D Halazonetis
- Department of Molecular and Cellular Biology, University of Geneva, 1205, Geneva, Switzerland.
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Frommer J, Oppenheimer R, Allott BM, Núñez-Pertíñez S, Wilks TR, Cox LR, Bath J, O'Reilly RK, Turberfield AJ. A New Architecture for DNA-Templated Synthesis in Which Abasic Sites Protect Reactants from Degradation. Angew Chem Int Ed Engl 2024; 63:e202317482. [PMID: 38346169 DOI: 10.1002/anie.202317482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Indexed: 03/01/2024]
Abstract
The synthesis of artificial sequence-defined polymers that match and extend the functionality of proteins is an important goal in materials science. One way of achieving this is to program a sequence of chemical reactions between precursor building blocks by means of attached oligonucleotide adapters. However, hydrolysis of the reactive building blocks has so far limited the length and yield of product that can be obtained using DNA-templated reactions. Here, we report an architecture for DNA-templated synthesis in which reactants are tethered at internal abasic sites on opposite strands of a DNA duplex. We show that an abasic site within a DNA duplex can protect a nearby thioester from degradation, significantly increasing the yield of a DNA-templated reaction. This protective effect has the potential to overcome the challenges associated with programmable, sequence-controlled synthesis of long non-natural polymers by extending the lifetime of the reactive building blocks.
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Affiliation(s)
- Jennifer Frommer
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Robert Oppenheimer
- Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford, OX1 3PU, UK
| | - Benjamin M Allott
- Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford, OX1 3PU, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot, Hodgkin Building, South Parks Road, Oxford, OX1 3QU, UK
| | - Samuel Núñez-Pertíñez
- Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford, OX1 3PU, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot, Hodgkin Building, South Parks Road, Oxford, OX1 3QU, UK
| | - Thomas R Wilks
- Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford, OX1 3PU, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot, Hodgkin Building, South Parks Road, Oxford, OX1 3QU, UK
| | - Liam R Cox
- Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford, OX1 3PU, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot, Hodgkin Building, South Parks Road, Oxford, OX1 3QU, UK
| | - Jonathan Bath
- Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford, OX1 3PU, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot, Hodgkin Building, South Parks Road, Oxford, OX1 3QU, UK
| | - Rachel K O'Reilly
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Andrew J Turberfield
- Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford, OX1 3PU, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot, Hodgkin Building, South Parks Road, Oxford, OX1 3QU, UK
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Hussain S, Tai B, Ali M, Jahan I, Sakina S, Wang G, Zhang X, Yin Y, Xing F. Antifungal potential of lipopeptides produced by the Bacillus siamensis Sh420 strain against Fusarium graminearum. Microbiol Spectr 2024; 12:e0400823. [PMID: 38451229 DOI: 10.1128/spectrum.04008-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/20/2024] [Indexed: 03/08/2024] Open
Abstract
Biological control is a more sustainable and environmentally friendly alternative to chemical fungicides for controlling Fusarium spp. infestations. In this work, Bacillus siamensis Sh420 isolated from wheat rhizosphere showed a high antifungal activity against Fusarium graminearum as a secure substitute for fungicides. Sh420 was identified as B. siamensis using phenotypic evaluation and 16S rDNA gene sequence analysis. An in vitro antagonistic study showed that Sh420's lipopeptide (LP) extract exhibited strong antifungal properties and effectively combated F. graminearum. Meanwhile, lipopeptides have the ability to decrease ergosterol content, which has an impact on the overall structure and stability of the plasma membrane. The PCR-based screening revealed the presence of antifungal LP biosynthetic genes in this strain's genomic DNA. In the crude LP extract of Sh420, we were able to discover several LPs such as bacillomycin, iturins, fengycin, and surfactins using ultra-high-performance liquid chromatography-quadrupole time-of-flight mass spectrometry. Microscopic investigations (fluorescent/transmission electron microscopy) revealed deformities and alterations in the morphology of the phytopathogen upon interaction with LPs. Sh420 LPs have been shown in grape tests to be effective against F. graminearum infection and to stimulate antioxidant activity in fruits by avoiding rust and gray lesions. The overall findings of this study highlight the potential of Sh420 lipopeptides as an effective biological control agent against F. graminearum infestations.IMPORTANCEThis study addresses the potential of lipopeptide (LP) extracts obtained from the strain identified as Bacillus siamensis Sh420. This Sh420 isolate acts as a crucial player in providing a sustainable and environmentally friendly alternative to chemical fungicides for suppressing Fusarium graminearum phytopathogen. Moreover, these LPs can reduce ergosterol content in the phytopathogen influencing the overall structure and stability of its plasma membrane. PCR screening provided confirmation regarding the existence of genes responsible for biosynthesizing antifungal LPs in the genomic DNA of Sh420. Several antibiotic lipopeptide compounds were identified from this bacterial crude extract using ultra-high-performance liquid chromatography-quadrupole time-of-flight mass spectrometry. Microscopic investigations revealed deformities and alterations in the morphology of F. graminearum upon interaction with LPs. Furthermore, studies on fruit demonstrated the efficacy of Sh420 LPs in mitigating F. graminearum infection and stimulating antioxidant activity in fruits, preventing rust and gray lesions.
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Affiliation(s)
- Sarfaraz Hussain
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, Shandong, China
| | - Bowen Tai
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Maratab Ali
- College of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, Shandong, China
| | - Israt Jahan
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Suha Sakina
- Department of Agriculture and Food Technology, Karakoram International University, Gilgit-Baltistan, Pakistan
| | - Gang Wang
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinlong Zhang
- Shandong Xinfurui Agriculture Science Co., Ltd, Liaocheng, Shandong, China
| | - Yixuan Yin
- Shandong Xinfurui Agriculture Science Co., Ltd, Liaocheng, Shandong, China
| | - Fuguo Xing
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
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Alanazi AFR, Parkinson GN, Haider S. Structural Motifs at the Telomeres and Their Role in Regulatory Pathways. Biochemistry 2024; 63:827-842. [PMID: 38481135 PMCID: PMC10993422 DOI: 10.1021/acs.biochem.4c00023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Telomeres are specialized structures, found at the ends of linear chromosomes in eukaryotic cells, that play a crucial role in maintaining the stability and integrity of genomes. They are composed of repetitive DNA sequences, ssDNA overhangs, and several associated proteins. The length of telomeres is linked to cellular aging in humans, and deficiencies in their maintenance are associated with various diseases. Key structural motifs at the telomeres serve to protect vulnerable chromosomal ends. Telomeric DNA also has the ability to form diverse complex DNA higher-order structures, including T-loops, D-loops, R-loops, G-loops, G-quadruplexes, and i-motifs, in the complementary C-rich strand. While many essential proteins at telomeres have been identified, the intricacies of their interactions and structural details are still not fully understood. This Perspective highlights recent advancements in comprehending the structures associated with human telomeres. It emphasizes the significance of telomeres, explores various telomeric structural motifs, and delves into the structural biology surrounding telomeres and telomerase. Furthermore, telomeric loops, their topologies, and the associated proteins that contribute to the safeguarding of telomeres are discussed.
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Affiliation(s)
- Abeer F R Alanazi
- UCL School of Pharmacy, University College London, London WC1N 1AX, United Kingdom
| | - Gary N Parkinson
- UCL School of Pharmacy, University College London, London WC1N 1AX, United Kingdom
| | - Shozeb Haider
- UCL School of Pharmacy, University College London, London WC1N 1AX, United Kingdom
- UCL Centre for Advanced Research Computing, University College London, London WC1H 9RN, United Kingdom
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46
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Shaliutina-Loginova A, Loginov DS. Transferrin maintains the motility rate, ATP content, and DNA integrity of common carp spermatozoa during short-term storage. Anim Reprod Sci 2024; 263:107437. [PMID: 38395011 DOI: 10.1016/j.anireprosci.2024.107437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/09/2024] [Accepted: 02/12/2024] [Indexed: 02/25/2024]
Abstract
Short-term sperm storage is a straightforward and cost-effective method of managing logistics in large scale fish hatchery operations but may result in decline in sperm quality. For effective artificial reproduction of fish, use of an appropriate additive to optimize sperm storage conditions is essential. In this study, it was investigated the effect of purified seminal plasma transferrin (Tf) at 10 μg/ml on relevant parameters in common carp Cyprinus carpio sperm during short-term storage. We compared sperm motility and curvilinear velocity, adenosine triphosphate (ATP) content and DNA fragmentation of fresh spermatozoa to that stored for 24, 48, 72, and 144 h with or without Tf. The percentage of motile cells and the curvilinear velocity of spermatozoa in stored samples for 72 h with transferrin supplementation were greater compared to samples with no added protein. The ATP content in samples without added transferrin was reduced (P < 0.05) after 72 h of storage, in contrast to the levels observed in transferrin-supplemented sperm. A time-dependent increase in DNA fragmentation was observed. Significantly lower DNA damage, expressed as percent tail DNA (10.99 ± 1.28) and olive tail moment (0.54 ± 0.12), was recorded in Tf-supplemented samples stored for 48 h compared to that with no Tf. Hence, it is concluded that the beneficial effects of transferrin on common carp sperm could serve as an additional tool for developing and enhancing short-term sperm preservation procedures commonly used in aquaculture.
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Affiliation(s)
- Anna Shaliutina-Loginova
- University of South Bohemia in České Budějovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, Zátiší 728/II, Vodňany 389 25, Czech Republic; Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, Vestec 252 50, Czech Republic.
| | - Dmitry S Loginov
- BioCeV - Institute of Microbiology of the CAS, Průmyslová 595, Vestec 252 50, Czech Republic
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47
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Liu R, Zhang J, Rodrigues Lima F, Zeng J, Nian Q. Targeting neutrophil extracellular traps: A novel strategy in hematologic malignancies. Biomed Pharmacother 2024; 173:116334. [PMID: 38422658 DOI: 10.1016/j.biopha.2024.116334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/18/2024] [Accepted: 02/22/2024] [Indexed: 03/02/2024] Open
Abstract
Neutrophil extracellular traps (NETs) have emerged as a critical factor in malignant hematologic disease pathogenesis. These structures, comprising DNA, histones, and cytoplasmic proteins, were initially recognized for their role in immune defense against microbial threats. Growing evidence suggests that NETs contribute to malignant cell progression and dissemination, representing a double-edged sword. However, there is a paucity of reports on its involvement in hematological disorders. A comprehensive understanding of the intricate relationship between malignant cells and NETs is necessary to explore effective therapeutic strategies. This review highlights NET formation and mechanisms underlying disease pathogenesis. Moreover, we discuss recent advancements in targeted inhibitor development for selective NET disruption, empowering precise design and efficacious therapeutic interventions for malignant hematologic diseases.
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Affiliation(s)
- Rongxing Liu
- Department of Pharmacy, The Second Affiliated Hospital, Army Medical University, 183 Xinqiao Road, Chongqing 400000, China
| | - Jin Zhang
- Department of Transfusion, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, 32# W. Sec 2, 1stRing Rd, Qingyang District, Chengdu, Sichuan 610072, China
| | - Fernando Rodrigues Lima
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, 2-16 Rue Theroigne deMericourt, Paris 75013, France
| | - Jinhao Zeng
- Department of Gastroenterology, Hospital of Chengdu University of Traditional Chinese Medicine, No.37 Shierqiaolu, Chengdu, Sichuan 610000, China.
| | - Qing Nian
- Department of Transfusion, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, 32# W. Sec 2, 1stRing Rd, Qingyang District, Chengdu, Sichuan 610072, China.
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48
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Vanderperre S, Merabet S. Visualization of the Association of Dimeric Protein Complexes on Specific Enhancers in the Salivary Gland Nuclei of Drosophila Larva. Cells 2024; 13:613. [PMID: 38607052 PMCID: PMC11012150 DOI: 10.3390/cells13070613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/26/2024] [Accepted: 03/28/2024] [Indexed: 04/13/2024] Open
Abstract
Transcription factors (TFs) regulate gene expression by recognizing specific target enhancers in the genome. The DNA-binding and regulatory activity of TFs depend on the presence of additional protein partners, leading to the formation of versatile and dynamic multimeric protein complexes. Visualizing these protein-protein interactions (PPIs) in the nucleus is key for decrypting the molecular cues underlying TF specificity in vivo. Over the last few years, Bimolecular Fluorescence Complementation (BiFC) has been developed in several model systems and applied in the analysis of different types of PPIs. In particular, BiFC has been applied when analyzing PPIs with hundreds of TFs in the nucleus of live Drosophila embryos. However, the visualization of PPIs at the level of specific target enhancers or genomic regions of interest awaits the advent of DNA-labelling methods that can be coupled with BiFC. Here, we present a novel experimental strategy that we have called BiFOR and that is based on the coupling of BiFC with the bacterial ANCHOR DNA-labelling system. We demonstrate that BiFOR enables the precise quantification of the enrichment of specific dimeric protein complexes on target enhancers in Drosophila salivary gland nuclei. Given its versatility and sensitivity, BiFOR could be applied more widely to other tissues during Drosophila development. Our work sets up the experimental basis for future applications of this strategy.
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Affiliation(s)
| | - Samir Merabet
- Institut de Génomique Fonctionnelle de Lyon (IGFL), UMR5242, Ecole Normale Supérieure de Lyon (ENSL), CNRS, Université de Lyon, 69007 Lyon, France;
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Jacob DR, Guiblet WM, Mamayusupova H, Shtumpf M, Ciuta I, Ruje L, Gretton S, Bikova M, Correa C, Dellow E, Agrawal SP, Shafiei N, Drobysevskaja A, Armstrong CM, Lam JDG, Vainshtein Y, Clarkson CT, Thorn GJ, Sohn K, Pradeepa MM, Chandrasekharan S, Brooke GN, Klenova E, Zhurkin VB, Teif VB. Nucleosome reorganisation in breast cancer tissues. Clin Epigenetics 2024; 16:50. [PMID: 38561804 PMCID: PMC10986098 DOI: 10.1186/s13148-024-01656-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Nucleosome repositioning in cancer is believed to cause many changes in genome organisation and gene expression. Understanding these changes is important to elucidate fundamental aspects of cancer. It is also important for medical diagnostics based on cell-free DNA (cfDNA), which originates from genomic DNA regions protected from digestion by nucleosomes. RESULTS We have generated high-resolution nucleosome maps in paired tumour and normal tissues from the same breast cancer patients using MNase-assisted histone H3 ChIP-seq and compared them with the corresponding cfDNA from blood plasma. This analysis has detected single-nucleosome repositioning at key regulatory regions in a patient-specific manner and common cancer-specific patterns across patients. The nucleosomes gained in tumour versus normal tissue were particularly informative of cancer pathways, with ~ 20-fold enrichment at CpG islands, a large fraction of which marked promoters of genes encoding DNA-binding proteins. The tumour tissues were characterised by a 5-10 bp decrease in the average distance between nucleosomes (nucleosome repeat length, NRL), which is qualitatively similar to the differences between pluripotent and differentiated cells. This effect was correlated with gene activity, differential DNA methylation and changes in local occupancy of linker histone variants H1.4 and H1X. CONCLUSIONS Our study offers a novel resource of high-resolution nucleosome maps in breast cancer patients and reports for the first time the effect of systematic decrease of NRL in paired tumour versus normal breast tissues from the same patient. Our findings provide a new mechanistic understanding of nucleosome repositioning in tumour tissues that can be valuable for patient diagnostics, stratification and monitoring.
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Affiliation(s)
- Divya R Jacob
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Wilfried M Guiblet
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Hulkar Mamayusupova
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Mariya Shtumpf
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Isabella Ciuta
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Luminita Ruje
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Svetlana Gretton
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
- School of Engineering, Arts, Science and Technology, University of Suffolk, James Hehir Building, University Avenue, Ipswich, Suffolk, IP3 0FS, UK
| | - Milena Bikova
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Clark Correa
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Emily Dellow
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Shivam P Agrawal
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Navid Shafiei
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | | | - Chris M Armstrong
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Jonathan D G Lam
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Yevhen Vainshtein
- Fraunhofer-Institut für Grenzflächen- und Bioverfahrenstechnik IGB, Nobelstraße 12, 70569, Stuttgart, Germany
| | - Christopher T Clarkson
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
- University College London, Gower St, Bloomsbury, London, WC1E 6BT, UK
| | - Graeme J Thorn
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Kai Sohn
- Fraunhofer-Institut für Grenzflächen- und Bioverfahrenstechnik IGB, Nobelstraße 12, 70569, Stuttgart, Germany
| | - Madapura M Pradeepa
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK
| | - Sankaran Chandrasekharan
- Colchester General Hospital, East Suffolk and North Essex NHS Foundation Trust, Turner Road, Colchester, CO4 5JL, UK
| | - Greg N Brooke
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Elena Klenova
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Victor B Zhurkin
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Vladimir B Teif
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK.
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Krohn C, Jansriphibul K, Dias DA, Rees CA, Akker BVD, Boer JC, Plebanski M, Surapaneni A, O'Carroll D, Richard S, Batstone DJ, Ball AS. Dead in the water - Role of relic DNA and primer choice for targeted sequencing surveys of anaerobic sewage sludge intended for biological monitoring. Water Res 2024; 253:121354. [PMID: 38428359 DOI: 10.1016/j.watres.2024.121354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 03/03/2024]
Abstract
DNA-based monitoring of microbial communities that are responsible for the performance of anaerobic digestion of sewage wastes has the potential to improve resource recoveries for wastewater treatment facilities. By treating sludge with propidium monoazide (PMA) prior to amplicon sequencing, this study explored how the presence of DNA from dead microbial biomass carried over with feed sludge may mislead process-relevant biomarkers, and whether primer choice impacts such assessments. Four common primers were selected for amplicon preparation, also to determine if universal primers have sufficient taxonomic or functional coverage for monitoring ecological performance; or whether two domain-specific primers for Bacteria and Archaea are necessary. Anaerobic sludges of three municipal continuously stirred-tank reactors in Victoria, Australia, were sampled at one time-point. A total of 240 amplicon libraries were sequenced on a Miseq using two universal and two domain-specific primer pairs. Untargeted metabolomics was chosen to complement biological interpretation of amplicon gene-based functional predictions. Diversity, taxonomy, phylogeny and functional potentials were systematically assessed using PICRUSt2, which can predict community wide pathway abundance. The two chosen universal primers provided similar diversity profiles of abundant Bacteria and Archaea, compared to the domain-specific primers. About 16 % of all detected prokaryotic genera covering 30 % of total abundances and 6 % of PICRUSt2-estimated pathway abundances were affected by PMA. This showed that dead biomass in the anaerobic digesters impacted DNA-based assessments, with implications for predicting active processes, such as methanogenesis, denitrification or the identification of organisms associated with biological foams. Hence, instead of running two sequencing runs with two different domain-specific primers, we propose conducting PMA-seq with universal primer pairs for routine performance monitoring. However, dead sludge biomass may have some predictive value. In principal component analysis the compositional variation of 239 sludge metabolites resembled that of 'dead-plus-alive' biomass, suggesting that dead organisms contributed to the potentially process-relevant sludge metabolome.
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Affiliation(s)
- Christian Krohn
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, RMIT University, Building 215, Level 3, Room 003-06, RMIT Bundoora West Campus, 225-245 Plenty Road, Bundoora, Victoria 3083, Australia.
| | - Kraiwut Jansriphibul
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, RMIT University, Building 215, Level 3, Room 003-06, RMIT Bundoora West Campus, 225-245 Plenty Road, Bundoora, Victoria 3083, Australia
| | - Daniel A Dias
- Centre for Advanced Sensory Science (CASS) Food Research Centre, School of Exercise and Nutrition Sciences, Deakin University, Melbourne Burwood Campus, 221 Burwood Highway, Burwood, Victoria 3125, Australia
| | - Catherine A Rees
- Melbourne Water Corporation, 990 La Trobe Street, Docklands, Victoria 3008, Australia
| | - Ben van den Akker
- South Australian Water Corporation, Adelaide, South Australia 5000, Australia
| | - Jennifer C Boer
- Cancer Aging and Vaccine Laboratory, School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria 3083, Australia
| | - Magdalena Plebanski
- Cancer Aging and Vaccine Laboratory, School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria 3083, Australia
| | - Aravind Surapaneni
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, RMIT University, Building 215, Level 3, Room 003-06, RMIT Bundoora West Campus, 225-245 Plenty Road, Bundoora, Victoria 3083, Australia; South East Water, 101 Wells Street, Frankston, Victoria 3199, Australia
| | - Denis O'Carroll
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Stuetz Richard
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Damien J Batstone
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, RMIT University, Building 215, Level 3, Room 003-06, RMIT Bundoora West Campus, 225-245 Plenty Road, Bundoora, Victoria 3083, Australia; Australian Centre for Water and Environmental Biotechnology (ACWEB), Gehrmann Building, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Andrew S Ball
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, RMIT University, Building 215, Level 3, Room 003-06, RMIT Bundoora West Campus, 225-245 Plenty Road, Bundoora, Victoria 3083, Australia
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