Article
Environmental Sciences
Wenya Feng, Zijuan Qi, Zheng Dong, Wei Liu, Ming Xu, Ming Gao, Sijin Liu
Summary: The study reveals that MT1DP is involved in Cd-induced DNA damage and replication stress, playing a significant role in Cd-induced carcinogenesis. Cd exposure triggers DNA damage response, increases replication stress, and leads to genomic instability.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Cell Biology
Charlotte Hodson, Sylvie van Twest, Malgorzata Dylewska, Julienne J. O'Rourke, Winnie Tan, Vincent J. Murphy, Mannu Walia, Lara Abbouche, Jadwiga Nieminuszczy, Elyse Dunn, Rohan Bythell-Douglas, Jorg Heierhorst, Wojciech Niedzwiedz, Andrew J. Deans
Summary: R loops, stable DNA:RNA hybrids that arise from stalled RNA polymerase, can cause genome instability. Branchpoint translocases like FANCM can displace R loops in cells, particularly in regions prone to R-loops. These enzymes are more effective than helicases in resolving R loops, and their depletion can have additive effects on R-loop accumulation and DNA damage in human cells.
Review
Biochemistry & Molecular Biology
Piero R. Bianco
Summary: The rescue of stalled DNA replication forks is crucial for cell viability. Both the bacterial helicase RecG and the eukaryotic enzyme SMARCAL1 can regress forks, but there are key differences between them, including their directionality and processivity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Yaqun Liu, Xia Wu, Yves d'Aubenton-Carafa, Claude Thermes, Chun-Long Chen
Summary: During cell division, the activation of thousands of DNA replication origins ensures the complete duplication of the human genome. However, replication fork progression can be hindered by transcription-replication conflicts, with head-on conflicts being more detrimental. In this study, a bioinformatics toolkit called OKseqHMM was developed to analyze Okazaki fragment sequencing data and accurately predict replication initiation and termination, as well as replication fork directionality, in various organisms. This toolkit can greatly contribute to studying genome instability and its impact on human health.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Oncology
Safa Majeed, Mansi K. Aparnathi, Kevin C. J. Nixon, Vidhyasagar Venkatasubramanian, Fariha Rahman, Lifang Song, Jessica Weiss, Ranya Barayan, Vijithan Sugumar, Samir H. Barghout, Joel D. Pearson, Rod Bremner, Aaron D. Schimmer, Ming S. Tsao, Geoffrey Liu, Benjamin H. Lok
Summary: TAK-243 exhibits efficacy in preclinical models of small cell lung cancer (SCLC), with associations to various gene sets. TAK-243 synergizes with cisplatin/etoposide chemotherapy (C/E) and PARP inhibitor olaparib. TAK-243 is a potential therapeutic strategy to improve SCLC patient outcomes.
CLINICAL CANCER RESEARCH
(2022)
Review
Plant Sciences
Supriyo Chowdhury, Arpita Basu Chowdhury, Manish Kumar, Supriya Chakraborty
Summary: This review provides insights into the roles of heterotrimeric RPA protein complexes in DNA metabolism in plants, emphasizing the need for further functional studies and highlighting gaps in current research. The review also suggests the development of specific methods for analyzing the biological roles of plant RPA complexes and proposes a hypothetical model for the regulatory role of posttranslational modifications in DNA metabolism in plants based on information from animal systems. Overall, the review aims to stimulate RPA research in plants and shift the focus towards functional studies to better understand dynamic DNA metabolism in plants.
Article
Multidisciplinary Sciences
Mehmet Gul, Esra Ayan, Ebru Destan, J. Austin Johnson, Alaleh Shafiei, Abdullah Kepceoglu, Merve Yilmaz, Fatma Betuel Ertem, Ilkin Yapici, Bilge Tosun, Niluefer Baldir, Nurettin Tokay, Zelis Nergiz, Gozde Karakadioglu, Seyide Seda Paydos, Cahine Kulakman, Cengiz Kaan Ferah, Omur Guven, Necati Atalay, Enver Kamil Akcan, Haluk Cetinok, Nazli Eylul Arslan, Kardelen Sabanoglu, Bengisu Asci, Serra Tavli, Helin Gumusboga, Sevde Altuntas, Masami Otsuka, Mikako Fujita, Saban Tekin, Halilibrahim Ciftci, Serdar Durdagi, Ezgi Karaca, Burcu Kaplan Turkoz, Burak Veli Kabasakal, Ahmet Kati, Hasan DeMirci
Summary: High-resolution biomacromolecular structure determination is crucial for understanding protein function and dynamics. Serial crystallography has limitations in terms of sample volume requirements and access to X-ray beamtime. To overcome these limitations, a plate-reader module adapted for a 72-well Terasaki plate is introduced for biomacromolecule structure determination using a home X-ray source. The first ambient temperature lysozyme structure determined at the Turkish light source (Turkish DeLight) provides valuable information about the structural dynamics of the lysozyme. Turkish DeLight offers robust and rapid ambient temperature biomacromolecular structure determination with minimal radiation damage.
SCIENTIFIC REPORTS
(2023)
Article
Oncology
Pamela S. VanderVere-Carozza, Navnath S. Gavande, Shadia I. Jalal, Karen E. Pollok, Elmira Ekinci, Joshua Heyza, Steve M. Patrick, Andi Masters, John J. Turchi, Katherine S. Pawelczak
Summary: RPA plays important roles in lung cancer as a negative prognostic biomarker and as a predictive marker for chemotherapy response. Second-generation RPA inhibitors show increased cellular permeability and exhibit anticancer activity. Chemical RPA inhibition enhances the activity of various cancer therapeutics.
FRONTIERS IN ONCOLOGY
(2022)
Article
Multidisciplinary Sciences
Luke A. Yates, Elias A. Tannous, R. Marc Morgan, Peter M. Burgers, Xiaodong Zhang
Summary: This study reveals the phosphorylation circuit that regulates checkpoint recruitment and function in response to DNA damage. The interaction between Ddc2 and RPA modulates the association between RPA and ssDNA, and phosphorylated Ddc2 enhances its recruitment to RPA-ssDNA, promoting DNA damage checkpoint signaling.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Cell Biology
Deepa Bisht, Ketki Patne, Radhakrishnan Rakesh, Rohini Muthuswami
Summary: SMARCAL1 and BRG1, two ATP-dependent chromatin remodeling proteins, interact with each other and their interaction is dependent on their ATPase activity. Mutations associated with SIOD and CSS4 prevent their interaction.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Lilas Courtot, Elodie Bournique, Chrystelle Maric, Laure Guitton-Sert, Miguel Madrid-Mencia, Vera Pancaldi, Jean-Charles Cadoret, Jean-Sebastien Hoffmann, Valerie Bergoglio
Summary: This study reveals that low replication stress can lead to advanced DNA replication timing, which is cell-type specific and involves large heterochromatin domains. These advanced events can be inherited by the next generation of cells, leading to changes in chromatin accessibility, replication origin landscape, and gene expression.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Editorial Material
Cell Biology
Jean-Sebastien Hoffmann
Summary: The major challenge in DNA replication is to ensure the transmission of intact genetic material to daughter cells. Despite extensive research on the cellular responses to replication problems and their source, the transmission of genome modifications and their heritability in mitosis has been less documented. Recent studies have shown that low replication stress can impact the next generation of cells, transmitting DNA damage and altering the replication timing program of chromosomal domains in daughter cells. This progression of replication issues into mitosis and daughter cells may provide advantages by alerting cells to risky loci and offering an adaptive mechanism to anticipate future problems, especially in the context of cancer cell resistance to therapy.
Article
Virology
Tareq Abualfaraj, Nafiseh Chalabi Hagkarim, Robert Hollingworth, Laura Grange, Satpal Jhujh, Grant S. Stewart, Roger J. Grand
Summary: The Ad12E1B55K protein affects cellular DNA damage response pathways and DNA replication by interacting with multiple proteins, leading to genomic instability.
Article
Biochemistry & Molecular Biology
Sabrina X. Van Ravenstein, Kavi P. Mehta, Tamar Kavlashvili, Jo Ann W. Byl, Runxiang Zhao, Neil Osheroff, David Cortez, James M. Dewar
Summary: Using Xenopus egg extracts, this study demonstrates that the TOP2 poisons etoposide and doxorubicin inhibit DNA replication through different mechanisms. Etoposide induces TOP2-dependent DNA breaks and TOP2-dependent fork stalling, while doxorubicin stalls replication forks independently of TOP2 by intercalating into parental DNA.
Article
Multidisciplinary Sciences
Yo-Chuen Lin, Dazhen Liu, Arindam Chakraborty, Lyudmila Y. Kadyrova, You Jin Song, Qinyu Hao, Jaba Mitra, Rosaline Y. C. Hsu, Mariam K. Arif, Sneha Adusumilli, Ting-Wei Liao, Taekjip Ha, Farid A. Kadyrov, Kannanganattu V. Prasanth, Supriya G. Prasanth
Summary: This article investigates the role of Orc6, a component of the origin recognition complex (ORC), in DNA replication. The study discovers that Orc6 localizes at the replication fork and acts as an accessory factor of the mismatch repair (MMR) complex. In response to oxidative damage during the S phase, Orc6 promotes MMR complex assembly and activity, enabling efficient MMR. This suggests that hOrc6 plays a fundamental role in genome surveillance during DNA replication.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Biochemistry & Molecular Biology
Li Duan, Xiao Xu, Limei Xu, Hongfei Chen, Xingfu Li, Murad Alahdal, Yin Xiao, Yujie Liang, Jiang Xia
Summary: Osteoarthritis is a degenerative disease that affects the quality of life in the elderly population, with no ideal treatment strategies currently available. Studies have suggested that exosomes may play an important role in the treatment of osteoarthritis.
CURRENT MEDICINAL CHEMISTRY
(2021)
Review
Pharmacology & Pharmacy
Yujie Liang, Xiao Xu, Limei Xu, Indira Prasadam, Li Duan, Yin Xiao, Jiang Xia
Summary: Intra-articular drug delivery is a conservative treatment method that improves the bioavailability of therapeutic composites in OA joint cavity. New targeted nano-based drug delivery systems and gene delivery for OA therapy show promising prospects.
JOURNAL OF DRUG TARGETING
(2021)
Article
Multidisciplinary Sciences
Yongming Du, Yinxia Yan, Si Xie, Hao Huang, Xin Wang, Ray Kit Ng, Ming-Ming Zhou, Chengmin Qian
Summary: This study uncovers the mechanism by which Spindlin1 acts together with C11orf84 to recognize the non-canonical bivalent mark H3K4me3K9me3, essential for the activation of rRNA transcription.
NATURE COMMUNICATIONS
(2021)
Review
Pharmacology & Pharmacy
Cheng Wang, Tingting Hong, Pengfei Cui, Jianhao Wang, Jiang Xia
Summary: This article reviews recent studies on the delivery and formulation of antimicrobial peptides, categorizing strategies driven by physical interactions or chemical conjugation reactions, and covering carriers from inorganic solid nanoparticles to organic micelles, liposomes, and hydrogels. Targeted delivery, responsive release, and strategies to increase oral bioavailability of antimicrobial peptides are discussed, highlighting the recent progress towards clinical application.
ADVANCED DRUG DELIVERY REVIEWS
(2021)
Article
Biochemical Research Methods
Ruidi Wang, Miao Liu, Han Wang, Jiang Xia, Hongbin Li
Summary: Developing peptide tags that can bind target proteins covalently under mild conditions is crucial for various applications. The GB tags developed in this study show high specificity and yield in covalently labeling target proteins under oxidizing conditions, with improved thermodynamic stability and binding affinity. These new GB tags have potential applications in biochemical labeling and biomaterials such as protein hydrogels.
BIOCONJUGATE CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Yongming Du, Chengmin Qian
Summary: Bivalent chromatin with active H3K4me3 and repressive H3K27me3 can regulate gene expression, but the molecular connection between bivalent chromatin and transcriptional regulation is still unclear.
Article
Chemistry, Multidisciplinary
Yue Wang, Min Liu, Qixin Wei, Wanjie Wu, Yanping He, Jiayang Gao, Renjie Zhou, Liwen Jiang, Jianan Qu, Jiang Xia
Summary: This study demonstrates the construction of synthetic multienzyme condensates through LLPS, which significantly enhances the biosynthesis of α-farnesene.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Physical
Qixin Wei, Yue Wang, Zhenjun Liu, Min Liu, Sheng Cao, Hao Jiang, Jiang Xia
Summary: Assembling enzymes into complexes increases production efficiency and yield of desired products during biosynthesis. This study demonstrates the construction of membrane-bound multienzyme complexes, which can independently produce specific products both in vitro and in vivo.
Article
Chemistry, Multidisciplinary
Dingdong Yuan, Yu Zhang, King Hoo Lim, Stephen King Pong Leung, Xizi Yang, Yujie Liang, Wilson Chun Yu Lau, Kwan T. Chow, Jiang Xia
Summary: This study reports a peptide-guided, proximity-driven group transfer reaction for site-selective acetylation of a single lysine residue in IgG. The reaction proceeded efficiently under physiological conditions without the need for deglycosylation or catalysts, allowing further derivatization of IgG. The method was also used to synthesize antibody-lipid conjugates and antibody-conjugated liposomes for targeted cancer cell therapy. Additionally, a bispecific antibody complex showed potent in vitro cytotoxicity at nanomolar concentrations.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Review
Biotechnology & Applied Microbiology
Yujie Liang, Zoya Iqbal, Jianping Lu, Jianhong Wang, Hao Zhang, Xi Chen, Li Duan, Jiang Xia
Summary: Developing strategies for safe and effective drug delivery into the CNS is crucial. Cell-derived nanovesicles (CDNs), particularly extracellular vesicles and exosomes, show promise as CNS-targeted drug carriers due to their stability, biocompatibility, homing ability, and ability to penetrate biological barriers. In this review, we focus on the application of CDNs in brain-targeted drug delivery, including recent methods of exosome derivation and engineering. We discuss the limitations and future development of CDN-based brain-targeted delivery systems, highlighting their potential in treating neurological diseases.
Review
Biochemistry & Molecular Biology
Min Liu, Yue Wang, Hao Jiang, Yongxu Han, Jiang Xia
Summary: In nature, enzymes that catalyze sequential reactions are often formed as clusters or complexes. Synthetic versions of these multienzyme complexes have been developed to enhance catalytic rates and improve microbial production of valuable chemicals. These complexes optimize metabolic fluxes, increase product yield, and have the potential for large-scale industrial applications. However, there is still a need for strategies to balance dynamicity and confinement, and achieve better control of local compartmentalization, similar to natural multienzyme complexes.
Article
Nanoscience & Nanotechnology
Biao Wang, Donghui Zhao, Yuting Li, Xinpei Zhou, Zexuan Hui, Xiaoling Lei, Lin Qiu, Yang Bai, Cheng Wang, Jiang Xia, Yang Xuan, Pengju Jiang, Jianhao Wang
Summary: In order to prevent the development of drug resistance during antibiotic treatment of wound infections, the use of antimicrobial peptides (AMPs) has been explored. However, challenges such as low bioavailability, rapid degradation of AMPs, and the difficulty of eliminating bacteria in deep tissue hinder its application. To address these issues, microneedle patches containing AMPs and recombinant type III humanized collagen (Col III) were designed for slow and controlled release to effectively eradicate bacteria in deep wound tissue and promote wound healing. This strategy demonstrates the potential of a microneedle-based antimicrobial drug delivery system.
ACS APPLIED NANO MATERIALS
(2023)
Article
Chemistry, Multidisciplinary
Yishu Bao, Hongfei Chen, Zhiyi Xu, Jiayang Gao, Liwen Jiang, Jiang Xia
Summary: The article describes a new fluorescent molecule that can deliver proteins into mammalian cells and release the payload into the cytosol through photoinduced disintegration.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Review
Materials Science, Biomaterials
Zoya Iqbal, Khurrum Rehman, Jiang Xia, Maryam Shabbir, Muhammad Zaman, Yujie Liang, Li Duan
Summary: RISPR-Cas9 has great potential in gene therapy, but its application is hindered by limited delivery methods. Biomaterial-based drug delivery systems can overcome these challenges and provide precise gene editing with reduced side effects. This review discusses the current status and progress of CRISPR/Cas9 delivery approaches, including polymeric nanoparticles, liposomes, extracellular vesicles, inorganic nanoparticles, and hydrogels. Targeted delivery vehicles for CRISPR systems are also highlighted.
BIOMATERIALS SCIENCE
(2023)
Review
Materials Science, Biomaterials
Yujie Liang, Zoya Iqbal, Jianhong Wang, Limei Xu, Xiao Xu, Kan Ouyang, Hao Zhang, Jianping Lu, Li Duan, Jiang Xia
Summary: Genome editing technology has the potential to treat incurable diseases, but the development of delivery systems is lagging behind. Extracellular vesicles (EVs), as natural nanocarriers, have advantages of biocompatibility and stability, making them a promising drug delivery vehicle.
BIOMATERIALS SCIENCE
(2022)