1
|
Río P, Zubicaray J, Navarro S, Gálvez E, Sánchez-Domínguez R, Nicoletti E, Sebastián E, Rothe M, Pujol R, Bogliolo M, John-Neek P, Bastone AL, Schambach A, Wang W, Schmidt M, Larcher L, Segovia JC, Yáñez RM, Alberquilla O, Díez B, Fernández-García M, García-García L, Ramírez M, Galy A, Lefrere F, Cavazzana M, Leblanc T, García de Andoin N, López-Almaraz R, Catalá A, Barquinero J, Rodríguez-Perales S, Rao G, Surrallés J, Soulier J, Díaz-de-Heredia C, Schwartz JD, Sevilla J, Bueren JA. Haematopoietic gene therapy of non-conditioned patients with Fanconi anaemia-A: results from open-label phase 1/2 (FANCOLEN-1) and long-term clinical trials. Lancet 2025; 404:2584-2592. [PMID: 39642902 DOI: 10.1016/s0140-6736(24)01880-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 09/01/2024] [Accepted: 09/04/2024] [Indexed: 12/09/2024]
Abstract
BACKGROUND Allogeneic haematopoietic stem-cell transplantation is the standard treatment for bone marrow failure (BMF) in patients with Fanconi anaemia, but transplantation-associated complications such as an increased incidence of subsequent cancer are frequent. The aim of this study was to evaluate the safety and efficacy of the infusion of autologous gene-corrected haematopoietic stem cells as an alternative therapy for these patients. METHODS This was an open-label, investigator-initiated phase 1/2 clinical trial (FANCOLEN-1) and long-term follow-up trial (up to 7 years post-treatment) in Spain. Mobilised peripheral blood (PB) CD34+ cells from nine patients with Fanconi anaemia-A in the early stages of BMF were transduced with a therapeutic FANCA-encoding lentiviral vector and re-infused without any cytotoxic conditioning treatment. The primary efficacy endpoint of FANCOLEN-1 was the engraftment of transduced cells, as defined by the detection of at least 0·1 therapeutic vector copies per nucleated cell of patient bone marrow (BM) or PB at the second year post-infusion, without this percentage having declined substantially over the previous year. The safety coprimary endpoint was adverse events during the 3 years after infusion. The completed open-label phase 1/2 and the ongoing long-term clinical trials are registered with ClinicalTrials.gov, NCT03157804; EudraCT, 2011-006100-12; and NCT04437771, respectively. FINDINGS There were eight evaluable treated patients with Fanconi anaemia-A. Patients were recruited between Jan 7, 2016 and April 3, 2019. The primary endpoint was met in five of the eight evaluable patients (62·50%). The median number of therapeutic vector copies per nucleated cell of patient BM and PB at the second year post-infusion was 0·18 (IQR 0·01-0·20) and 0·06 (0·01-0·19), respectively. No genotoxic events related to the gene therapy were observed. Most treatment-emergent adverse events (TEAEs) were non-serious and assessed as not related to therapeutic FANCA-encoding lentiviral vector. Nine serious adverse events (grade 3-4) were reported in six patients, one was considered related to medicinal product infusion, and all resolved without sequelae. Cytopenias and viral infections (common childhood illnesses) were the most frequently reported TEAEs. INTERPRETATION These results show for the first time that haematopoietic gene therapy without genotoxic conditioning enables sustained engraftment and reversal of BMF progression in patients with Fanconi anaemia. FUNDING European Commission, Instituto de Salud Carlos III, and Rocket Pharmaceuticals.
Collapse
Affiliation(s)
- Paula Río
- Biomedical Innovation Unit, Center for Research on Energy, Environment and Technology (CIEMAT), Madrid, Spain; Biomedical Network Research Center for Rare Diseases (CIBERER), Madrid, Spain; Sanitary Research Institute Fundación Jiménez Díaz (U.A.M), Madrid, Spain
| | - Josune Zubicaray
- Biomedical Network Research Center for Rare Diseases (CIBERER), Madrid, Spain; Pediatric Hematology and Oncology Department, Hospital Infantil Universitario Niño Jesús, Madrid, Spain; Foundation for the Biomedical Research, Hospital Infantil Universitario Niño Jesús, Madrid, Spain
| | - Susana Navarro
- Biomedical Innovation Unit, Center for Research on Energy, Environment and Technology (CIEMAT), Madrid, Spain; Biomedical Network Research Center for Rare Diseases (CIBERER), Madrid, Spain; Sanitary Research Institute Fundación Jiménez Díaz (U.A.M), Madrid, Spain
| | - Eva Gálvez
- Biomedical Network Research Center for Rare Diseases (CIBERER), Madrid, Spain; Pediatric Hematology and Oncology Department, Hospital Infantil Universitario Niño Jesús, Madrid, Spain; Foundation for the Biomedical Research, Hospital Infantil Universitario Niño Jesús, Madrid, Spain
| | - Rebeca Sánchez-Domínguez
- Biomedical Innovation Unit, Center for Research on Energy, Environment and Technology (CIEMAT), Madrid, Spain; Biomedical Network Research Center for Rare Diseases (CIBERER), Madrid, Spain; Sanitary Research Institute Fundación Jiménez Díaz (U.A.M), Madrid, Spain
| | | | - Elena Sebastián
- Biomedical Network Research Center for Rare Diseases (CIBERER), Madrid, Spain; Pediatric Hematology and Oncology Department, Hospital Infantil Universitario Niño Jesús, Madrid, Spain; Foundation for the Biomedical Research, Hospital Infantil Universitario Niño Jesús, Madrid, Spain
| | - Michael Rothe
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | - Roser Pujol
- Biomedical Network Research Center for Rare Diseases (CIBERER), Madrid, Spain; Institut de Recerca Sant Pau, Universitat Autónoma de Barcelona, Barcelona, Spain; Unit of Genomic Medicine, Institut de Recerca de l'Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Massimo Bogliolo
- Biomedical Network Research Center for Rare Diseases (CIBERER), Madrid, Spain; Institut de Recerca Sant Pau, Universitat Autónoma de Barcelona, Barcelona, Spain; Serra Hunter Fellow, Department of Genetics and Microbiology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Barcelona, Spain; Unit of Genomic Medicine, Institut de Recerca de l'Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Philipp John-Neek
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | | | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Lise Larcher
- Université Paris Cité, Inserm, CNRS, Hôpital Saint-Louis, APHP, Paris, France
| | - José C Segovia
- Biomedical Innovation Unit, Center for Research on Energy, Environment and Technology (CIEMAT), Madrid, Spain; Biomedical Network Research Center for Rare Diseases (CIBERER), Madrid, Spain; Sanitary Research Institute Fundación Jiménez Díaz (U.A.M), Madrid, Spain
| | - Rosa M Yáñez
- Biomedical Innovation Unit, Center for Research on Energy, Environment and Technology (CIEMAT), Madrid, Spain; Biomedical Network Research Center for Rare Diseases (CIBERER), Madrid, Spain; Sanitary Research Institute Fundación Jiménez Díaz (U.A.M), Madrid, Spain
| | - Omaira Alberquilla
- Biomedical Innovation Unit, Center for Research on Energy, Environment and Technology (CIEMAT), Madrid, Spain; Biomedical Network Research Center for Rare Diseases (CIBERER), Madrid, Spain; Sanitary Research Institute Fundación Jiménez Díaz (U.A.M), Madrid, Spain
| | - Begoña Díez
- Biomedical Innovation Unit, Center for Research on Energy, Environment and Technology (CIEMAT), Madrid, Spain; Biomedical Network Research Center for Rare Diseases (CIBERER), Madrid, Spain; Sanitary Research Institute Fundación Jiménez Díaz (U.A.M), Madrid, Spain
| | - María Fernández-García
- Biomedical Innovation Unit, Center for Research on Energy, Environment and Technology (CIEMAT), Madrid, Spain; Biomedical Network Research Center for Rare Diseases (CIBERER), Madrid, Spain; Sanitary Research Institute Fundación Jiménez Díaz (U.A.M), Madrid, Spain
| | - Laura García-García
- Biomedical Innovation Unit, Center for Research on Energy, Environment and Technology (CIEMAT), Madrid, Spain; Biomedical Network Research Center for Rare Diseases (CIBERER), Madrid, Spain; Sanitary Research Institute Fundación Jiménez Díaz (U.A.M), Madrid, Spain
| | - Manuel Ramírez
- Pediatric Hematology and Oncology Department, Hospital Infantil Universitario Niño Jesús, Madrid, Spain; Sanitary Research Institute Fundación La Princesa, Madrid, Spain
| | - Anne Galy
- Genethon, UMR_S951, Université Paris-Saclay, Univ Evry, Inserm, Evry-Courcouronnes, France
| | - Francois Lefrere
- Hôpital Universitaire Necker Enfants-Malades, Assistance Publique Hôpitaux de Paris GHU Paris Centre, Université Paris Cité, Paris, France; Centre D'Investigation Clinique en Biotherapie INSERM, Institut Imagine, Paris, France
| | - Marina Cavazzana
- Hôpital Universitaire Necker Enfants-Malades, Assistance Publique Hôpitaux de Paris GHU Paris Centre, Université Paris Cité, Paris, France; Centre D'Investigation Clinique en Biotherapie INSERM, Institut Imagine, Paris, France
| | - Thierry Leblanc
- Robert-Debré University Hospital (APHP and Université Paris Cité), Paris, France
| | - Nagore García de Andoin
- Donostia Universitary Hospital, San Sebastián, Spain; Biogipuzkoa Health Research Institute, San Sebastián, Spain
| | - Ricardo López-Almaraz
- Cruces Universitary Hospital, Barakaldo, Spain; Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Albert Catalá
- Hospital Sant Joan de Déu, Barcelona, Spain; Research Institute Sant Joan de Déu, Barcelona, Spain
| | | | | | | | - Jordi Surrallés
- Biomedical Network Research Center for Rare Diseases (CIBERER), Madrid, Spain; Institut de Recerca Sant Pau, Universitat Autónoma de Barcelona, Barcelona, Spain; Unit of Genomic Medicine, Institut de Recerca de l'Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Jean Soulier
- Université Paris Cité, Inserm, CNRS, Hôpital Saint-Louis, APHP, Paris, France
| | - Cristina Díaz-de-Heredia
- Biomedical Network Research Center for Rare Diseases (CIBERER), Madrid, Spain; Vall d'Hebron Institut de Recerca, Barcelona, Spain; Pediatric Haematology and Oncology Department, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | | | - Julián Sevilla
- Biomedical Network Research Center for Rare Diseases (CIBERER), Madrid, Spain; Pediatric Hematology and Oncology Department, Hospital Infantil Universitario Niño Jesús, Madrid, Spain; Foundation for the Biomedical Research, Hospital Infantil Universitario Niño Jesús, Madrid, Spain
| | - Juan A Bueren
- Biomedical Innovation Unit, Center for Research on Energy, Environment and Technology (CIEMAT), Madrid, Spain; Biomedical Network Research Center for Rare Diseases (CIBERER), Madrid, Spain; Sanitary Research Institute Fundación Jiménez Díaz (U.A.M), Madrid, Spain.
| |
Collapse
|
2
|
Wang X, Li J, Zhou Y, Zhang J, Wang L, Liu Y, Yang X, Han H, Wang Q, Wang Y. Functional analysis of type II chalcone isomerase ( CHI) genes in regulating soybean ( Glycine max L.) nodule formation. GM CROPS & FOOD 2025; 16:305-317. [PMID: 40165359 PMCID: PMC11970754 DOI: 10.1080/21645698.2025.2486280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2025] [Revised: 03/26/2025] [Accepted: 03/26/2025] [Indexed: 04/02/2025]
Abstract
Biological nitrogen fixation (BNF) is the most cost-effective and environmentally benign method for nitrogen fertilization. Isoflavones are important signaling factors for BNF in leguminous plants. Whether chalcone isomerase (CHI), the key enzyme gene in the flavonoid synthesis pathway, contributes to soybean (Glycine max) nodulation has not yet been fully clarified. In the present study, we identified the functions of three types of GmCHI for BNF using a hairy root system. The results showed that GmCHI1A and GmCHI1B1 positively increased nodulation while GmCHI1B2 did not, with the GmCHI1A gene having a greater effect than GmCHI1B1. Meanwhile, the daidzein and genistein contents were significantly increased in composite plants overexpressing GmCHI1A and reduced in composite plants, thus interfering with GmCHI1A. However, overexpression of GmCHI1B1 significantly increased the content of glycitein but not daidzein, genistein content implied that homologous genes exhibit functional differentiation. These results provide a reference for subsequent studies on improving nitrogen fixation in soybeans and providing functional genes for the improvement of new varieties.
Collapse
Affiliation(s)
| | | | - Yuxue Zhou
- College of Plant Science, Jilin University, Changchun, China
| | - Jinhao Zhang
- College of Plant Science, Jilin University, Changchun, China
| | - Le Wang
- College of Plant Science, Jilin University, Changchun, China
| | - Yajing Liu
- College of Plant Science, Jilin University, Changchun, China
| | - Xuguang Yang
- College of Plant Science, Jilin University, Changchun, China
| | - Hongshuang Han
- College of Plant Science, Jilin University, Changchun, China
| | - Qingyu Wang
- College of Plant Science, Jilin University, Changchun, China
| | - Ying Wang
- College of Plant Science, Jilin University, Changchun, China
| |
Collapse
|
3
|
Deshpande G, Das S, Roy AE, Ratnaparkhi GS. A face-off between Smaug and Caspar modulates primordial germ cell count and identity in Drosophila embryos. Fly (Austin) 2025; 19:2438473. [PMID: 39718186 DOI: 10.1080/19336934.2024.2438473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2024] [Revised: 11/26/2024] [Accepted: 12/01/2024] [Indexed: 12/25/2024] Open
Abstract
Proper formation and specification of Primordial Germ Cells (PGCs) is of special significance as they gradually transform into Germline Stem Cells (GSCs) that are ultimately responsible for generating the gametes. Intriguingly, not only the PGCs constitute the only immortal cell type but several specific determinants also underlying PGC specification such as Vasa, Nanos and Germ-cell-less are conserved through evolution. In Drosophila melanogaster, PGC formation and specification depends on two independent factors, the maternally deposited specialized cytoplasm (or germ plasm) enriched in germline determinants, and the mechanisms that execute the even partitioning of these determinants between the daughter cells. Prior work has shown that Oskar protein is necessary and sufficient to assemble the functional germ plasm, whereas centrosomes associated with the nuclei that invade the germ plasm are responsible for its equitable distribution. Our recent data suggests that Caspar, the Drosophila orthologue of human Fas-associated factor-1 (FAF1) is a novel regulator that modulates both mechanisms that underlie the determination of PGC fate. Consistently, early blastoderm embryos derived from females compromised for caspar display reduced levels of Oskar and defective centrosomes.
Collapse
Affiliation(s)
- Girish Deshpande
- Department of Biology, Indian Institute of Science Education & Research, Pune, India
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Subhradip Das
- Department of Biology, Indian Institute of Science Education & Research, Pune, India
| | - Adheena Elsa Roy
- Department of Biology, Indian Institute of Science Education & Research, Pune, India
| | - Girish S Ratnaparkhi
- Department of Biology, Indian Institute of Science Education & Research, Pune, India
| |
Collapse
|
4
|
Zhang M, Lu Z. tRNA modifications: greasing the wheels of translation and beyond. RNA Biol 2025; 22:1-25. [PMID: 39723662 DOI: 10.1080/15476286.2024.2442856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 11/29/2024] [Accepted: 12/11/2024] [Indexed: 12/28/2024] Open
Abstract
Transfer RNA (tRNA) is one of the most abundant RNA types in cells, acting as an adaptor to bridge the genetic information in mRNAs with the amino acid sequence in proteins. Both tRNAs and small fragments processed from them play many nonconventional roles in addition to translation. tRNA molecules undergo various types of chemical modifications to ensure the accuracy and efficiency of translation and regulate their diverse functions beyond translation. In this review, we discuss the biogenesis and molecular mechanisms of tRNA modifications, including major tRNA modifications, writer enzymes, and their dynamic regulation. We also summarize the state-of-the-art technologies for measuring tRNA modification, with a particular focus on 2'-O-methylation (Nm), and discuss their limitations and remaining challenges. Finally, we highlight recent discoveries linking dysregulation of tRNA modifications with genetic diseases.
Collapse
Affiliation(s)
- Minjie Zhang
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Medical Epigenetics, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Zhipeng Lu
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
- Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA
| |
Collapse
|
5
|
Wencker FDR, Lyon SE, Breaker RR. Evidence that ribosomal protein bS21 is a component of the OLE ribonucleoprotein complex. RNA Biol 2025; 22:1-14. [PMID: 40322971 PMCID: PMC12054373 DOI: 10.1080/15476286.2025.2491842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/25/2025] [Accepted: 04/03/2025] [Indexed: 05/08/2025] Open
Abstract
OLE RNAs represent a large and highly structured noncoding RNA (ncRNA) class that is mostly found in Gram-positive extremophiles and/or anaerobes of the Bacillota phylum. These ~600-nucleotide RNAs are among the most structurally complex and well-conserved large ncRNAs whose precise biochemical functions remain to be established. In Halalkalibacterium halodurans, OLE RNA is involved in the adaptation to various unfavourable growth conditions, including exposure to cold (≤20°C), ethanol (≥3% [v/v]), excess Mg2+ (≥4 mM), and non-glucose carbon/energy sources. OLE forms a ribonucleoprotein (RNP) complex with the OLE-associated proteins A, B and C, which are known to be essential for OLE RNP complex function in this species. Bacteria lacking OLE RNA (Δole) or a functional OLE RNP complex exhibit growth defects under the stresses listed above. Here, we demonstrate that ribosomal protein bS21 is a natural component of the OLE RNP complex and we map its precise RNA binding site. The presence of bS21 results in a conformational change in OLE RNA resembling a k-turn substructure previously reported to be relevant to the function of the OLE RNP complex. Mutational disruption of the bS21 protein or its OLE RNA binding site results in growth inhibition under cold and ethanol stress to the same extent as the deletion of the gene for OLE RNA. These findings are consistent with the hypothesis that bS21 is a biologically relevant component of the OLE RNP complex under a subset of stresses managed by the OLE RNP complex.
Collapse
Affiliation(s)
- Freya D. R. Wencker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Seth E. Lyon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Ronald R. Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| |
Collapse
|
6
|
Victor Atoki A, Aja PM, Shinkafi TS, Ondari EN, Adeniyi AI, Fasogbon IV, Dangana RS, Shehu UU, Akin-Adewumi A. Exploring the versatility of Drosophila melanogaster as a model organism in biomedical research: a comprehensive review. Fly (Austin) 2025; 19:2420453. [PMID: 39722550 DOI: 10.1080/19336934.2024.2420453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 10/16/2024] [Accepted: 10/16/2024] [Indexed: 12/28/2024] Open
Abstract
Drosophila melanogaster is a highly versatile model organism that has profoundly advanced our understanding of human diseases. With more than 60% of its genes having human homologs, Drosophila provides an invaluable system for modelling a wide range of pathologies, including neurodegenerative disorders, cancer, metabolic diseases, as well as cardiac and muscular conditions. This review highlights key developments in utilizing Drosophila for disease modelling, emphasizing the genetic tools that have transformed research in this field. Technologies such as the GAL4/UAS system, RNA interference (RNAi) and CRISPR-Cas9 have enabled precise genetic manipulation, with CRISPR-Cas9 allowing for the introduction of human disease mutations into orthologous Drosophila genes. These approaches have yielded critical insights into disease mechanisms, identified novel therapeutic targets and facilitated both drug screening and toxicological studies. Articles were selected based on their relevance, impact and contribution to the field, with a particular focus on studies offering innovative perspectives on disease mechanisms or therapeutic strategies. Our findings emphasize the central role of Drosophila in studying complex human diseases, underscoring its genetic similarities to humans and its effectiveness in modelling conditions such as Alzheimer's disease, Parkinson's disease and cancer. This review reaffirms Drosophila's critical role as a model organism, highlighting its potential to drive future research and therapeutic advancements.
Collapse
Affiliation(s)
| | - Patrick Maduabuchi Aja
- Department of Biochemistry, Kampala International University, Ishaka, Uganda
- Department of Biochemistry, Faculty of Science, Ebonyi State University, Abakaliki, Nigeria
| | | | - Erick Nyakundi Ondari
- Department of Biochemistry, Kampala International University, Ishaka, Uganda
- School of Pure and Applied Sciences, Department of Biological Sciences, Kisii University, Kisii, Kenya
| | | | | | | | - Umar Uthman Shehu
- Department of Physiology, Kampala International University, Ishaka, Uganda
| | | |
Collapse
|
7
|
Jin T, Li SY, Zheng HL, Liu XD, Huang Y, Ma G, Zhao YX, Zhao XT, Yang L, Wang QH, Wang HJ, Gu C, Pan Z, Lin F. Gut microbes-spinal connection is required for itch sensation. Gut Microbes 2025; 17:2495859. [PMID: 40289281 PMCID: PMC12036491 DOI: 10.1080/19490976.2025.2495859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2024] [Revised: 03/23/2025] [Accepted: 04/10/2025] [Indexed: 04/30/2025] Open
Abstract
The gut microbiota has been linked to a number of neurological disorders. However, it is unclear whether the gut microbiota is involved in the genesis of chronic itch, a refractory condition that afflicts patients both physically and mentally. Here, we report that depletion of gut microbiota enhances tolerance to itch in mice orally administered with antibiotics (ABX) and mice free of germ. Of note, oral gavage with Bacteroides fragilis (B. fragilis), a prominent species of the genus Bacteroides with most differential change, corrected the ABX-induced itch dysfunction through its driven metabolite acetyl-l-carnitine (ALC). Mechanistically, gut microbiota or B. fragilis depletion caused a decrease in RNA N6-methyladenosine (m6A) demethylase FTO expression in the dorsal horn and a consequent increase in RNA m6A sites in Mas-related G protein-coupled receptor F (MrgprF) mRNA, leading to decreased MRGPRF protein. The downregulation of FTO was triggered by inactivation of ETS proto-oncogene 1 (ETS1), a transcription factor that binds to the Fto promoter. These findings support a gut microbe - spinal connection in modulation of itch sensation in RNA m6A epigenetic-dependent manner and highlight a critical role of ALC in linking the altered B. fragilis and itch dysfunction.
Collapse
Affiliation(s)
- Tong Jin
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou, China
- Department of Pain, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Si-Yuan Li
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou, China
| | - Hong-Li Zheng
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou, China
- Department of Pain, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
- Anesthesiology Department, Suzhou Municipal Hospital, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, China
| | - Xiao-Dan Liu
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou, China
- Department of Anesthesiology, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan, China
| | - Yue Huang
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou, China
| | - Gan Ma
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou, China
| | - Ya-Xuan Zhao
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou, China
| | - Xiao-Tian Zhao
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou, China
| | - Li Yang
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou, China
| | - Qi-Hui Wang
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou, China
| | - Hong-Jun Wang
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou, China
| | - Chengyong Gu
- Anesthesiology Department, Suzhou Municipal Hospital, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, China
| | - Zhiqiang Pan
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou, China
| | - Fuqing Lin
- Department of Pain, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
| |
Collapse
|
8
|
Funikov S, Rezvykh A, Akulenko N, Liang J, Sharakhov IV, Kalmykova A. Analysis of somatic piRNAs in the malaria mosquito Anopheles coluzzii reveals atypical classes of genic small RNAs. RNA Biol 2025; 22:1-16. [PMID: 39916410 PMCID: PMC11834523 DOI: 10.1080/15476286.2025.2463812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 01/28/2025] [Accepted: 02/03/2025] [Indexed: 02/18/2025] Open
Abstract
Piwi-interacting small RNAs (piRNA) play a key role in controlling the activity of transposable elements (TEs) in the animal germline. In diverse arthropod species, including the pathogen vectors mosquitoes, the piRNA pathway is also active in nongonadal somatic tissues, where its targets and functions are less clear. Here, we studied the features of small RNA production in head and thorax tissues of an uninfected laboratory strain of Anopheles coluzzii focusing on the 24-32-nt-long RNAs. Small RNAs derived from repetitive elements constitute a minor fraction while most small RNAs process from long noncoding RNAs (lncRNAs) and protein-coding gene mRNAs. The majority of small RNAs derived from repetitive elements and lncRNAs exhibited typical piRNAs features. By contrast, majority of protein-coding gene-derived 24-32 nt small RNAs lack the hallmarks of piRNAs and have signatures of nontemplated 3' end tailing. Most of the atypical small RNAs exhibit female-biased expression and originate from mitochondrial and nuclear genes involved in energy metabolism. We also identified atypical genic small RNAs in Anopheles gambiae somatic tissues, which further validates the noncanonical mechanism of their production. We discuss a novel mechanism of small RNA production in mosquito somatic tissues and the possible functional significance of genic small RNAs.
Collapse
Affiliation(s)
- Sergei Funikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander Rezvykh
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Natalia Akulenko
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Jiangtao Liang
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Igor V. Sharakhov
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
- The Center for Emerging, Zoonotic, and Arthropod-Borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
- Department of Genetics and Cell Biology, Tomsk State University, Tomsk, Russia
| | - Alla Kalmykova
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
| |
Collapse
|
9
|
Zhao Z, Geisbrecht ER. Stage-specific modulation of Drosophila gene expression with muscle GAL4 promoters. Fly (Austin) 2025; 19:2447617. [PMID: 39772988 PMCID: PMC11730430 DOI: 10.1080/19336934.2024.2447617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2024] [Revised: 12/19/2024] [Accepted: 12/20/2024] [Indexed: 01/11/2025] Open
Abstract
The bipartite GAL4/UAS system is the most widely used method for targeted gene expression in Drosophila melanogaster and facilitates rapid in vivo genetic experimentation. Defining precise gene expression patterns for tissues and/or cell types under GAL4 control will continue to evolve to suit experimental needs. However, the precise spatial and temporal expression patterns for some commonly used muscle tissue promoters are still unclear. This missing information limits the precise timing of experiments during development. Here, we focus on three muscle-enriched GAL4 drivers (Mef2-GAL4, C57-GAL4 and G7-GAL4) to better inform selection of the most appropriate muscle promoter for experimental needs. Specifically, C57-GAL4 and G7-GAL4 turn on in the first or second instar larval stages, respectively, and can be used to bypass myogenesis for studies of muscle function after development.
Collapse
Affiliation(s)
- Ziwei Zhao
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, USA
| | - Erika R Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, USA
| |
Collapse
|
10
|
Moyo B, Brown LBC, Khondaker II, Bao G. Engineering adeno-associated viral vectors for CRISPR/Cas based in vivo therapeutic genome editing. Biomaterials 2025; 321:123314. [PMID: 40203649 DOI: 10.1016/j.biomaterials.2025.123314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2024] [Revised: 03/30/2025] [Accepted: 04/01/2025] [Indexed: 04/11/2025]
Abstract
The recent approval of the first gene editing therapy for sickle cell disease and transfusion-dependent beta-thalassemia by the U.S. Food and Drug Administration (FDA) demonstrates the immense potential of CRISPR (clustered regularly interspaced short palindromic repeats) technologies to treat patients with genetic disorders that were previously considered incurable. While significant advancements have been made with ex vivo gene editing approaches, the development of in vivo CRISPR/Cas gene editing therapies has not progressed as rapidly due to significant challenges in achieving highly efficient and specific in vivo delivery. Adeno-associated viral (AAV) vectors have shown great promise in clinical trials as vehicles for delivering therapeutic transgenes and other cargos but currently face multiple limitations for effective delivery of gene editing machineries. This review elucidates these challenges and highlights the latest engineering strategies aimed at improving the efficiency, specificity, and safety profiles of AAV-packaged CRISPR/Cas systems (AAV-CRISPR) to enhance their clinical utility.
Collapse
Affiliation(s)
- Buhle Moyo
- Department of Bioengineering, Rice University, Houston, TX, 77030, USA
| | - Lucas B C Brown
- Department of Bioengineering, Rice University, Houston, TX, 77030, USA; Graduate Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, 77030, USA
| | - Ishika I Khondaker
- Department of Bioengineering, Rice University, Houston, TX, 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX, 77030, USA.
| |
Collapse
|
11
|
Kothe CI, Renault P. Metagenomic driven isolation of poorly culturable species in food. Food Microbiol 2025; 129:104722. [PMID: 40086981 DOI: 10.1016/j.fm.2025.104722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2024] [Revised: 01/02/2025] [Accepted: 01/02/2025] [Indexed: 03/16/2025]
Abstract
Although isolating microorganisms from food microbiota may appear less challenging than from the gut or environmental sources, recovering all representative species from food remains a difficult task. Here, we showed by metagenomic analysis that several abundant species had escaped isolation in a previous study of ten cheeses, including several previously uncharacterized species. This highlights the ongoing challenge of achieving a comprehensive recovery of microbes from food. To address this gap, we designed a novel strategy integrating metagenomics-based probes targeting the species of interest, coupled with an incremental culturing approach using pooled samples. As proof of concept, we applied this strategy to two cheeses containing species that were not isolated in our previous study, with the objective of isolating all species present at levels above 2% and, in particular, potential novel food species. Through this approach, we successfully performed the targeted isolation of two Psychrobacter and two Vibrio species from the first cheese, and four Halomonas and two Pseudoalteromonas species from the second one. Notably, P. undina and V. litoralis represented, as far as we know, the first cheese isolates characterized for these species. However, we were unable to isolate a novel species of Pseudoalteromonas, with no characterized representative to date, and Marinomonas foliarum, previously isolated from marine environment. Using metagenome-assembled genomes (MAGs) and metagenomic analysis, we discussed the possible reasons for their non-recovery. Finally, this strategy offers a promising approach for isolating a set of strains representative of the microbial diversity present in food ecosystems. These isolates can serve as a basis for investigating their roles in the communities, their impact on product development, safety implications and their potential in the development of starter cultures.
Collapse
Affiliation(s)
- Caroline Isabel Kothe
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Pierre Renault
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France.
| |
Collapse
|
12
|
Koyama T, Saeed U, Rewitz K, Halberg KV. The Integrative Physiology of Hormone Signaling: Insights from Insect Models. Physiology (Bethesda) 2025; 40:0. [PMID: 39887191 DOI: 10.1152/physiol.00030.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 11/18/2024] [Accepted: 01/24/2025] [Indexed: 02/01/2025] Open
Abstract
Hormones orchestrate virtually all physiological processes in animals and enable them to adjust internal responses to meet diverse physiological demands. Studies in both vertebrates and insects have uncovered many novel hormones and dissected the physiological mechanisms they regulate, demonstrating a remarkable conservation in endocrine signaling across the tree of life. In this review, we focus on recent advances in insect research, which have provided a more integrative view of the conserved interorgan communication networks that control physiology. These new insights have been driven by experimental advantages inherent to insects, which over the past decades have aligned with new technologies and sophisticated genetic tools, to transform insect genetic models into a powerful testbed for posing new questions and exploring longstanding issues in endocrine research. Here, we illustrate how insect studies have addressed classic questions in three main areas, hormonal control of growth and development, neuroendocrine regulation of ion and water balance, and hormonal regulation of behavior and metabolism, and how these discoveries have illuminated our fundamental understanding of endocrine signaling in animals. The application of integrative physiology in insect systems to questions in endocrinology and physiology is expanding and is poised to be a crucible of discovery, revealing fundamental mechanisms of hormonal regulation that underlie animal adaptations to their environments.
Collapse
Affiliation(s)
- Takashi Koyama
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Usama Saeed
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kim Rewitz
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kenneth V Halberg
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
13
|
Syed AM, Karius AK, Ma J, Wang PY, Hwang PM. Mitochondrial Dysfunction in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome. Physiology (Bethesda) 2025; 40:0. [PMID: 39960432 DOI: 10.1152/physiol.00056.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2024] [Revised: 12/27/2024] [Accepted: 02/11/2025] [Indexed: 04/26/2025] Open
Abstract
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a debilitating multisystem disorder of unclear etiology that affects many individuals worldwide. One of its hallmark symptoms is prolonged fatigue following exertion, a feature also observed in long COVID, suggesting an underlying dysfunction in energy production in both conditions. Here, mitochondrial dysfunction and its potential pathogenetic role in these disorders are reviewed.
Collapse
Affiliation(s)
- Abu Mohammad Syed
- Cardiovascular Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, United States
| | - Alexander K Karius
- Cardiovascular Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, United States
| | - Jin Ma
- Cardiovascular Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, United States
| | - Ping-Yuan Wang
- Cardiovascular Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, United States
| | - Paul M Hwang
- Cardiovascular Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, United States
| |
Collapse
|
14
|
Chen Y, Xu R, Meng F. Biodegradable polylactic acid plastic can aid to achieve partial nitrification/denitrification for low carbon to nitrogen ratio wastewater treatment: Performance and microbial mechanism. BIORESOURCE TECHNOLOGY 2025; 427:132411. [PMID: 40118223 DOI: 10.1016/j.biortech.2025.132411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2025] [Revised: 03/17/2025] [Accepted: 03/17/2025] [Indexed: 03/23/2025]
Abstract
The partial nitrification/denitrification (PND) process is a green biotechnology for nitrogen removal in low carbon to nitrogen ratio wastewater, however, inhibiting nitrite-oxidizing bacteria (NOB) remains a challenge. This study uncovered that polylactic acid (PLA) can eliminate NOB and regulate the structure and function of nitrogen-transforming bacteria (NTB). An anoxic/aerobic membrane bioreactor with PLA achieved a total nitrogen removal efficiency of 64.8%, much higher than the 32.4% without PLA. Nitrite accumulation during nitrification stage reached 66.7% with PLA addition. Ammonia-oxidizing bacteria were transiently inhibited by PLA but recovered quickly. NOB were maintained at low levels due to the absence of genes for protein and DNA repair, while denitrifiers lacking NarGHI/NapAB genes were enriched. OLB8, with a relative abundance of 13.7%, played a central role in regulating NTB interaction and facilitating PND. In summary, this study provided a new strategy for improving nitrogen removal from wastewater through the reuse of PLA plastics.
Collapse
Affiliation(s)
- Yanxi Chen
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou 510275, PR China
| | - Ronghua Xu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou 510275, PR China
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou 510275, PR China.
| |
Collapse
|
15
|
Parimita S, Das A, Samanta S. Vestigial-like family member 1 (VGLL1): An emerging candidate in tumor progression. Biochem Biophys Res Commun 2025; 766:151889. [PMID: 40300335 DOI: 10.1016/j.bbrc.2025.151889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2025] [Revised: 04/19/2025] [Accepted: 04/23/2025] [Indexed: 05/01/2025]
Abstract
Vestigial-like family member 1 (VGLL1), a product of an X-linked gene (VGLL1), belongs to a family of transcriptional co-activators including VGLL2, VGLL3 and VGLL4. These proteins are called vestigial-like because of the structural and functional similarities with the Drosophila ortholog vestigial (vg). VGLL1 is usually expressed in human placenta, and has also been detected in many aggressive cancers. For this reason, it is called an onco-placental protein. It can bind and activate the TEA-domain containing transcription factors TEAD1-4, and the interaction is mediated through a conserved 'valine-x-x-histidine-phenylalanine' domain (VxxHF, x denotes any amino acid) present in VGLL1 protein. Prior studies indicate a pro-tumorigenic role for this protein in several cancers including carcinoma of the breast. This review aims at summarizing our present knowledge about the functions of VGLL1, and the mechanisms that regulate its expression in cancer.
Collapse
Affiliation(s)
- Shubhashree Parimita
- Department of Applied Biology, Council of Scientific & Industrial Research-Indian Institute of Chemical Technology (CSIR-IICT), Uppal Road, Tarnaka, Hyderabad, TS, 500007, India; Academy of Scientific and Innovative Research, Ghaziabad, 201002, India
| | - Amitava Das
- Department of Applied Biology, Council of Scientific & Industrial Research-Indian Institute of Chemical Technology (CSIR-IICT), Uppal Road, Tarnaka, Hyderabad, TS, 500007, India; Academy of Scientific and Innovative Research, Ghaziabad, 201002, India
| | - Sanjoy Samanta
- Department of Applied Biology, Council of Scientific & Industrial Research-Indian Institute of Chemical Technology (CSIR-IICT), Uppal Road, Tarnaka, Hyderabad, TS, 500007, India; Academy of Scientific and Innovative Research, Ghaziabad, 201002, India.
| |
Collapse
|
16
|
Shrestha A, Pillis DM, Felker S, Chi M, Wagner K, Gbotosho OT, Sieling J, Shadid M, Malik P. Preclinical efficacy of a modified gamma-globin lentivirus gene therapy in Berkeley sickle cell anemia mice and human xenograft models. Mol Ther Methods Clin Dev 2025; 33:101439. [PMID: 40176947 PMCID: PMC11964741 DOI: 10.1016/j.omtm.2025.101439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Accepted: 02/18/2025] [Indexed: 04/05/2025]
Abstract
We previously showed correction of sickle cell anemia (SCA) in mice utilizing a lentiviral vector (LV) expressing human γ-globin. Herein, we made a G16D mutation in the γ-globin gene to generate the G16D mutation (GbGM) LV to increase fetal hemoglobin formation. We also generated an insulated version of this LV, GbGMI, inserting a 36-bp insulator from the Foamy virus in the long terminal repeats of the LV. Preclinical batches of GbGM and GbGMI LV showed both were highly efficacious in correcting SCA in mice, with sustained gene transfer in primary transplanted SCA mice and high hematopoietic stem cell (HSC) transduction in colony-forming unit-spleen in secondary transplanted mice. CRISPR-mediated targeting of the proviruses into the LMO2 proto-oncogene showed remarkably reduced LMO2 activation by both insulated and uninsulated LV, compared to the SFFV γ-RV vector targeted to the same locus. We therefore used the GbGM LV to perform preclinical human CD34+ gene transfer. We assessed gene transfer and engraftment of human HSCs in two immunocompromised mouse models: persistent stable GbGM-transduced cell engraftment was comparable to that of untransduced cells with no detrimental effects on hematopoiesis up to 20 weeks post transplant. These robust preclinical studies in mouse and human HSCs allowed its translation into a clinical trial.
Collapse
Affiliation(s)
- Archana Shrestha
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center (CCHMC), Cincinnati, OH 45229, USA
- Aruvant Sciences, New York, NY 10036, USA
| | - Devin M. Pillis
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center (CCHMC), Cincinnati, OH 45229, USA
| | - Sydney Felker
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center (CCHMC), Cincinnati, OH 45229, USA
| | - Mengna Chi
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center (CCHMC), Cincinnati, OH 45229, USA
| | - Kimberly Wagner
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center (CCHMC), Cincinnati, OH 45229, USA
| | - Oluwabukola T. Gbotosho
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center (CCHMC), Cincinnati, OH 45229, USA
| | | | | | - Punam Malik
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center (CCHMC), Cincinnati, OH 45229, USA
- Division of Hematology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45229, USA
| |
Collapse
|
17
|
Tahir D, Geolier V, Bruant H, Le Flèche-Matéos A, Mallet A, Varloud M, Civat C, Girerd-Chambaz Y, Montano S, Pion C, Ferquel E, Pavot V, Choumet V. A Lyme disease mRNA vaccine targeting Borrelia burgdorferi OspA induces strong immune responses and prevents transmission in mice. MOLECULAR THERAPY. NUCLEIC ACIDS 2025; 36:102514. [PMID: 40226328 PMCID: PMC11986965 DOI: 10.1016/j.omtn.2025.102514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2024] [Accepted: 03/07/2025] [Indexed: 04/15/2025]
Abstract
Lyme borreliosis (LB), caused by Borrelia burgdorferi sensu lato, is one of the most common tick-borne diseases in the northern hemisphere. Given its increasing global incidence, LB remains a major public health concern and the development of an effective vaccine is recognized as a key component of the overall disease prevention strategy. Here, we present results obtained with newly developed lipid nanoparticle-encapsulated mRNA vaccine candidates encoding the outer surface protein A (OspA) of B. burgdorferi sensu stricto (Bbss) serotype 1 (mRNA-OspA) with or without a secretion signal (SS) or a transmembrane domain. We evaluated the immunogenicity and protective efficacy of the mRNA-OspA vaccine candidates in a tick-fed mouse challenge model compared with an adjuvanted OspA protein subunit vaccine and the licensed canine vaccine Recombitek Lyme. At the doses tested, the mRNA-OspA vaccines induced significantly higher OspA-specific immunoglobulin G titers than the protein-based vaccines, as well as functional antibodies measured by serum bactericidal assay against Bbss strain B31. Complete protection against transmission was observed in the group immunized with the mRNA-OspA without SS. Overall, these data demonstrate that an mRNA-OspA vaccine can be effective against LB infection and could be used in the future for the prevention of Lyme disease.
Collapse
Affiliation(s)
- Djamel Tahir
- Institut Pasteur, Environnement et Risques Infectieux, Université Paris Cité, 75015 Paris, France
- Institut Pasteur, Ultrastructural Bio-Imaging Core Facility, 75015 Paris, France
| | - Virginie Geolier
- Institut Pasteur, Environnement et Risques Infectieux, Université Paris Cité, 75015 Paris, France
| | - Hugo Bruant
- Institut Pasteur, Environnement et Risques Infectieux, Université Paris Cité, 75015 Paris, France
| | - Anne Le Flèche-Matéos
- Institut Pasteur, Environnement et Risques Infectieux, Université Paris Cité, 75015 Paris, France
| | - Adeline Mallet
- Institut Pasteur, Ultrastructural Bio-Imaging Core Facility, 75015 Paris, France
| | - Marie Varloud
- Ceva Santé Animale, 10 Avenue de la Ballastière, 33500 Libourne, France
| | - Céline Civat
- Sanofi Vaccines R&D, Campus Mérieux, 69280 Marcy l’Etoile, France
| | | | - Sandrine Montano
- Sanofi Vaccines R&D, Campus Mérieux, 69280 Marcy l’Etoile, France
| | - Corinne Pion
- Sanofi Vaccines R&D, Campus Mérieux, 69280 Marcy l’Etoile, France
| | - Elisabeth Ferquel
- Institut Pasteur, Environnement et Risques Infectieux, Université Paris Cité, 75015 Paris, France
| | - Vincent Pavot
- Sanofi Vaccines R&D, Campus Mérieux, 69280 Marcy l’Etoile, France
| | - Valérie Choumet
- Institut Pasteur, Environnement et Risques Infectieux, Université Paris Cité, 75015 Paris, France
| |
Collapse
|
18
|
Peng K, Zhao G, Zhao H, Noda NN, Zhang H. The autophagy protein ATG-9 regulates lysosome function and integrity. J Cell Biol 2025; 224:e202411092. [PMID: 40202485 PMCID: PMC11980680 DOI: 10.1083/jcb.202411092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2024] [Revised: 03/05/2025] [Accepted: 03/11/2025] [Indexed: 04/10/2025] Open
Abstract
The transmembrane autophagy protein ATG9 has multiple functions essential for autophagosome formation. Here, we uncovered a novel function of ATG-9 in regulating lysosome biogenesis and integrity in Caenorhabditis elegans. Through a genetic screen, we identified that mutations attenuating the lipid scrambling activity of ATG-9 suppress the autophagy defect in epg-5 mutants, in which non-degradative autolysosomes accumulate. The scramblase-attenuated ATG-9 mutants promote lysosome biogenesis and delivery of lysosome-localized hydrolases and also facilitate the maintenance of lysosome integrity. Through manipulation of phospholipid levels, we found that a reduction in phosphatidylethanolamine (PE) also suppresses the autophagy defects and lysosome damage associated with impaired lysosomal degradation. Our results reveal that modulation of phospholipid composition and distribution, e.g., by attenuating the scramblase activity of ATG-9 or reducing the PE level, regulates lysosome function and integrity.
Collapse
Affiliation(s)
- Kangfu Peng
- National Laboratory of Biomacromolecules, New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Guoxiu Zhao
- National Laboratory of Biomacromolecules, New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Hongyu Zhao
- National Laboratory of Biomacromolecules, New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China
| | - Nobuo N. Noda
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
- Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan
| | - Hong Zhang
- National Laboratory of Biomacromolecules, New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, P.R. China
| |
Collapse
|
19
|
Kutyrieva-Nowak N, Pantelić A, Isaković S, Kanellis AK, Vidović M, Leszczuk A. Effect of the overexpression of the GGP1 gene on cell wall remodelling and redox state in the tomato fruit. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2025; 355:112470. [PMID: 40074203 DOI: 10.1016/j.plantsci.2025.112470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2025] [Revised: 02/22/2025] [Accepted: 03/06/2025] [Indexed: 03/14/2025]
Abstract
Tomato fruit ripening is a complex physiological process that involves morphological, anatomical, biochemical, and molecular alterations. One of these changes occurring during ripening is the softening of the fruit, which is attributed to modifications in the biosynthesis and degradation of individual cell wall components, i.e. polysaccharides and proteoglycans. In addition, ripening is affected by redox processes, and interplay of the reactive oxygen species (ROS) and specific antioxidants, enzymes, ascorbate, and phenolic compounds. The present study aims to determine the impact of the overexpression of the GDP-l-galactose phosphorylase (GGP1) gene under the control of two fruit-specific promoters, namely PPC - phosphoenolpyruvate carboxylase and PG - polygalacturonase on cell wall properties, activities of H2O2-regulating enzymes and the abundance of phenolic compounds. PPC-GGP1 and PG-GGP1 transgenic lines revealed significant structural changes in fruit parenchyma, compared to wild type fruit, followed by a disturbance in the spatial distribution and molecular & chemical composition of homogalacturonans. In addition, cell wall-bound monolignol, p-coumaryl alcohol was higher in transgenic fruit compared with wild type ones. Lastly, the catalase and ascorbate peroxidase activities were lower in PPC-GGP1 fruits, indicating changes in the regulation of antioxidative defense during the ripening process of this line. These results suggest that overexpression of the GGP1 gene affects the cell wall remodelling and redox state in the red ripe tomato fruits.
Collapse
Affiliation(s)
| | - Ana Pantelić
- Group for Plant Molecular Biology, Department of Microbiology and Plant Biology, Institute of Molecular Genetics and Genetic Engineering (IMGGE), University of Belgrade, Vojvode Stepe 444a, Belgrade 11-042, Serbia.
| | - Stefan Isaković
- Group for Plant Molecular Biology, Department of Microbiology and Plant Biology, Institute of Molecular Genetics and Genetic Engineering (IMGGE), University of Belgrade, Vojvode Stepe 444a, Belgrade 11-042, Serbia.
| | - Angelos K Kanellis
- Group of Biotechnology of Pharmaceutical Plants, Lab of Pharmacognosy, Department of Pharmaceutical Sciences, Aristotle University of Thessaloniki, Thessaloniki 54-124, Greece.
| | - Marija Vidović
- Group for Plant Molecular Biology, Department of Microbiology and Plant Biology, Institute of Molecular Genetics and Genetic Engineering (IMGGE), University of Belgrade, Vojvode Stepe 444a, Belgrade 11-042, Serbia.
| | - Agata Leszczuk
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, Lublin 20-290, Poland.
| |
Collapse
|
20
|
Kordi R, Andrews TJ, Hicar MD. Infections, genetics, and Alzheimer's disease: Exploring the pathogenic factors for innovative therapies. Virology 2025; 607:110523. [PMID: 40174330 DOI: 10.1016/j.virol.2025.110523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2025] [Revised: 03/20/2025] [Accepted: 03/26/2025] [Indexed: 04/04/2025]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative condition that creates a significant global health challenge and profoundly affects patients and their families. Recent research has highlighted the critical role of microorganisms, particularly viral infections, in the pathogenesis of AD. The involvement of viral infections in AD pathogenesis is predominantly attributed to their ability to induce neuroinflammation and amyloid beta (Aβ) deposition in the brain. The extant research exploring the relationship between viruses and AD has focused largely on Herpesviridae family. Traces of Herpesviruses, such as Herpes Simplex Virus-1 and Epstein Barr Virus, have been found in the brains of patients with AD. These viruses are thought to contribute to the disease progression by triggering chronic inflammatory responses in the brain. They can remain dormant in the brain, and become reactivated due to stress, a secondary viral infection, or immune-senescence in older adults. This review focuses on the association between Herpesviridae and bacterial infections with AD. We explore the genetic factors that might regulate viral illness and discuss clinical trials investigating antiviral and anti-inflammatory agents as possible therapeutic strategies to mitigate cognitive decline in patients with AD. In summary, understanding the interplay between infections, genetic factors, and AD pathogenesis may pave the way for novel therapeutic approaches, facilitating better management and possibly even prevent this debilitating disease.
Collapse
Affiliation(s)
- Ramesh Kordi
- Department of Pediatrics, Division of Infectious Diseases, State University of New York at Buffalo, Buffalo, NY, 14203, USA
| | - Ted J Andrews
- Department of Pediatrics, Division of Developmental Pediatrics and Rehabilitation, State University of New York at Buffalo, Buffalo, NY, 14203, USA
| | - Mark D Hicar
- Department of Pediatrics, Division of Infectious Diseases, State University of New York at Buffalo, Buffalo, NY, 14203, USA.
| |
Collapse
|
21
|
Amini SR, Adams M, Hammer MP, Briggs G, Donaldson JA, Ebner BC, Unmack PJ. Cryptic species, biogeography, and patterns of introgression in the fish genus Mogurnda (Eleotridae) from the Australian wet tropics: A purple patch for purple-spots. Mol Phylogenet Evol 2025; 207:108344. [PMID: 40188977 DOI: 10.1016/j.ympev.2025.108344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 03/04/2025] [Accepted: 03/30/2025] [Indexed: 04/11/2025]
Abstract
Accurately delimiting species is an essential first step towards understanding the true biodiversity of an ecosystem and any subsequent efforts to identify and protect taxa at risk of extinction. Current molecular evidence suggests that purple-spotted gudgeons (genus Mogurnda) harbour high levels of cryptic biodiversity across their broad distributional range. The present study uses a large single nucleotide polymorphism (SNP) dataset plus a companion allozyme dataset to clarify taxonomic uncertainty, patterns of introgression, and biogeographic relationships among Mogurnda populations within the Queensland Wet Tropics (QWT), a known biodiversity hotspot. Both datasets were strongly concordant in identifying a total of seven taxa split among distinct southern, northern, and lowlands groups. No two taxa were found in strict sympatry, but many appear to be parapatric and occur within the same drainage basin. Although clear evidence of introgression was only evident at six sites (∼4%), the genomic signature of modest historic admixture between proximally-distributed taxa was detected at multiple other sites. Nevertheless, all primary genetic and phylogenetic analyses strongly supported the integrity and diagnosability of these seven taxa. We therefore nominate these as novel candidate species for what appears to be yet another hyper-cryptic complex within the Australian freshwater ichthyological fauna. These results offer up intriguing ecological scenarios and conservation implications for multiple candidate species with narrow ranges in specialised habitat. We conclude by exploring the major biogeographic patterns displayed by QWT Mogurnda.
Collapse
Affiliation(s)
- Samuel R Amini
- Centre for Applied Water Science, Institute for Applied Ecology, University of Canberra ACT 2617, Australia
| | - Mark Adams
- Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, SA 5000, Australia; School of Biological Sciences, University of Adelaide, SA 5005 Australia
| | - Michael P Hammer
- Natural Sciences, Museum and Art Gallery of the Northern Territory, Darwin, NT 0801, Australia
| | - Glenn Briggs
- 19-21 Raleigh St, Seville Victoria 3139, Australia
| | | | - Brendan C Ebner
- TropWATER, James Cook University, Townsville, Qld, Australia; CSIRO Land and Water, Tropical Forest Research Centre, Atherton, Qld, Australia; Grafton Fisheries Centre, Grafton, NSW, Australia
| | - Peter J Unmack
- Centre for Applied Water Science, Institute for Applied Ecology, University of Canberra ACT 2617, Australia; School of Biological Sciences, Monash University Vic 3800, Australia.
| |
Collapse
|
22
|
Wani SM, Chesti A, Rehman S, Chandra Nautiyal V, Bhat IA, Ahmad I. Repurposing and reusing aquaculture wastes through a biosecure microfloc technology. ENVIRONMENTAL RESEARCH 2025; 274:121214. [PMID: 40015429 DOI: 10.1016/j.envres.2025.121214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2024] [Revised: 01/29/2025] [Accepted: 02/22/2025] [Indexed: 03/01/2025]
Abstract
Intensive aquaculture waste management is a significant challenge in the aquaculture industry, often contributing to environmental issues. Intensive aquaculture techniques demand new strategies and alternatives aimed at achieving sustainability. Repurposing and reusing wastes through innovative technologies can mitigate their negative impact. Biofloc technology (BFT) or bio-colloidal technology is based on the concept of aquaculture waste utilization by heterotrophic microbial biomass and presents a biosecure and sustainable solution. The dynamics of BFT are shaped by ecological interactions like commensalism, competition, and predation, forming a trophic micro-network consisting of rotifers, ciliates, heterotrophic bacteria, and microalgae. Metagenomic studies showed dominance of microbial communities within the biofloc, such as Cyanobacteria, Nitrosomonas, Proteobacteria, Bacteroidetes, Pseudomonadota, Rhodobacteraceae and Bacillus species that play a crucial role in the mineralization and bioremediation of waste. These microbes also help to break down hazardous toxic compounds into non-toxic, beneficial nutrients, which are subsequently utilized as food by fish and shellfish. Also, recycling waste reduces pollution, improves water quality, and enhances the efficiency of aquaculture system. With increasing incidences of microbial diseases and growing expenses for energy, biosecurity with BFT seems, by all means a sustainable production method for aquaculture. The incorporation of biosecure biofloc technology into aquaculture practices enhances environmental sustainability while optimizing resource use, creating more eco-friendly and cost-effective systems. This review highlights key aspects such as the microbial dynamics, role of metagenomics in identifying the bacterial communities, bioremediation of aquaculture waste, biosecurity concerns, and the biocontrol of pathogenic microbes across various biofloc systems.
Collapse
Affiliation(s)
- Sayima Majeed Wani
- Faculty of Fisheries, Sher-e-Kashmir University of Agricultural Sciences and Technology-Kashmir, Rangil, Ganderbal, 190006, India
| | - Anayitullah Chesti
- Faculty of Fisheries, Sher-e-Kashmir University of Agricultural Sciences and Technology-Kashmir, Rangil, Ganderbal, 190006, India
| | - Saima Rehman
- ICAR - Central Marine Fisheries Research Institute, Kochi, 682018, India
| | | | - Irfan Ahmad Bhat
- Faculty of Fisheries, Sher-e-Kashmir University of Agricultural Sciences and Technology-Kashmir, Rangil, Ganderbal, 190006, India
| | - Irshad Ahmad
- Faculty of Fisheries, Sher-e-Kashmir University of Agricultural Sciences and Technology-Kashmir, Rangil, Ganderbal, 190006, India.
| |
Collapse
|
23
|
Tang K, Ye T, He Y, Ba X, Xia D, Peng E, Chen Z, Ye Z, Yang X. Ferroptosis, necroptosis, and pyroptosis in calcium oxalate crystal-induced kidney injury. Biochim Biophys Acta Mol Basis Dis 2025; 1871:167791. [PMID: 40086520 DOI: 10.1016/j.bbadis.2025.167791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2024] [Revised: 01/24/2025] [Accepted: 03/04/2025] [Indexed: 03/16/2025]
Abstract
Kidney stones represent a highly prevalent urological disorder worldwide, with high incidence and recurrence rates. Calcium oxalate (CaOx) crystal-induced kidney injury serves as the foundational mechanism for the formation and progression of CaOx stones. Regulated cell death (RCD) such as ferroptosis, necroptosis, and pyroptosis are essential in the pathophysiological process of kidney injury. Ferroptosis, a newly discovered RCD, is characterized by its reliance on iron-mediated lipid peroxidation. Necroptosis, a widely studied programmed necrosis, initiates with a necrotic phenotype that resembles apoptosis in appearance. Pyroptosis, a type of RCD that involves the gasdermin protein, is accompanied by inflammation and immune response. In recent years, increasing amounts of evidence has demonstrated that ferroptosis, necroptosis, and pyroptosis are significant pathophysiological processes involved in CaOx crystal-induced kidney injury. Herein, we summed up the roles of ferroptosis, necroptosis, and pyroptosis in CaOx crystal-induced kidney injury. Furthermore, we delved into the curative potential of ferroptosis, necroptosis, and pyroptosis in CaOx crystal-induced kidney injury.
Collapse
Affiliation(s)
- Kun Tang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tao Ye
- Department of Geriatric Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu He
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaozhuo Ba
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ding Xia
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ejun Peng
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhiqiang Chen
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhangqun Ye
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoqi Yang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| |
Collapse
|
24
|
Khalife M, Jia T, Caron P, Shreim A, Genoux A, Cristini A, Pucciarelli A, Leverve M, Lepeltier N, García-Rodríguez N, Dalonneau F, Ramachandran S, Fernandez Martinez L, Marcion G, Lemaitre N, Brambilla E, Garrido C, Hammond E, Huertas P, Gazzeri S, Sordet O, Eymin B. SRSF2 overexpression induces transcription-/replication-dependent DNA double-strand breaks and interferes with DNA repair pathways to promote lung tumor progression. NAR Cancer 2025; 7:zcaf011. [PMID: 40181846 PMCID: PMC11963763 DOI: 10.1093/narcan/zcaf011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 02/04/2025] [Accepted: 03/13/2025] [Indexed: 04/05/2025] Open
Abstract
SRSF2 (serine/arginine-rich splicing factor 2) is a critical regulator of pre-messenger RNA splicing, which also plays noncanonical functions in transcription initiation and elongation. Although elevated levels of SRSF2 are associated with advanced stages of lung adenocarcinoma (LUAD), the mechanisms connecting SRSF2 to lung tumor progression remain unknown. We show that SRSF2 overexpression increases global transcription and replicative stress in LUAD cells, which correlates with the production of DNA damage, notably double-strand breaks (DSBs), likely resulting from conflicts between transcription and replication. Moreover, SRSF2 regulates DNA repair pathways by promoting homologous recombination and inhibiting nonhomologous end joining. Mechanistically, SRSF2 interacts with and enhances MRE11 (meiotic recombination 11) recruitment to chromatin, while downregulating 53BP1 messenger RNA and protein levels. Both events are likely contributing to SRSF2-mediated DNA repair process rerouting. Lastly, we show that SRSF2 and MRE11 expression is commonly elevated in LUAD and predicts poor outcome of patients. Altogether, our results identify a mechanism by which SRSF2 overexpression promotes lung cancer progression through a fine control of both DSB production and repair. Finally, we show that SRSF2 knockdown impairs late repair of ionizing radiation-induced DSBs, suggesting a more global function of SRSF2 in DSB repair by homologous recombination.
Collapse
Affiliation(s)
- Manal Khalife
- University Grenoble Alpes, INSERM U1209, CNRS UMR5309, Team RNA Splicing, Cell Signaling and Response to Therapies, Institute for Advanced Biosciences, Grenoble F38000, France
| | - Tao Jia
- University Grenoble Alpes, INSERM U1209, CNRS UMR5309, Team RNA Splicing, Cell Signaling and Response to Therapies, Institute for Advanced Biosciences, Grenoble F38000, France
| | - Pierre Caron
- University Grenoble Alpes, INSERM U1209, CNRS UMR5309, Team RNA Splicing, Cell Signaling and Response to Therapies, Institute for Advanced Biosciences, Grenoble F38000, France
| | - Amani Shreim
- University Grenoble Alpes, INSERM U1209, CNRS UMR5309, Team RNA Splicing, Cell Signaling and Response to Therapies, Institute for Advanced Biosciences, Grenoble F38000, France
| | - Aurelie Genoux
- University Grenoble Alpes, INSERM U1209, CNRS UMR5309, Team RNA Splicing, Cell Signaling and Response to Therapies, Institute for Advanced Biosciences, Grenoble F38000, France
| | - Agnese Cristini
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, CNRS, Toulouse 31037, France
| | - Amelie Pucciarelli
- University Grenoble Alpes, INSERM U1209, CNRS UMR5309, Team RNA Splicing, Cell Signaling and Response to Therapies, Institute for Advanced Biosciences, Grenoble F38000, France
| | - Marie Leverve
- University Grenoble Alpes, INSERM U1209, CNRS UMR5309, Team RNA Splicing, Cell Signaling and Response to Therapies, Institute for Advanced Biosciences, Grenoble F38000, France
| | - Nina Lepeltier
- University Grenoble Alpes, INSERM U1209, CNRS UMR5309, Team RNA Splicing, Cell Signaling and Response to Therapies, Institute for Advanced Biosciences, Grenoble F38000, France
| | - Néstor García-Rodríguez
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla 41080, Spain; Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla/CSIC, Sevilla 41092, Spain
| | - Fabien Dalonneau
- University Grenoble Alpes, INSERM U1209, CNRS UMR5309, Team RNA Splicing, Cell Signaling and Response to Therapies, Institute for Advanced Biosciences, Grenoble F38000, France
| | - Shaliny Ramachandran
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Lara Fernandez Martinez
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, CNRS, Toulouse 31037, France
| | - Guillaume Marcion
- INSERM, UMR1231, Faculty of Medicine and Pharmacy, Université de Bourgogne Franche-Comté, Dijon F21000, France
| | - Nicolas Lemaitre
- University Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Team Tumor Molecular Pathology and Biomarkers, Institute for Advanced Biosciences, Grenoble F38000, France
| | - Elisabeth Brambilla
- University Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Team Tumor Molecular Pathology and Biomarkers, Institute for Advanced Biosciences, Grenoble F38000, France
| | - Carmen Garrido
- INSERM, UMR1231, Faculty of Medicine and Pharmacy, Université de Bourgogne Franche-Comté, Dijon F21000, France
| | - Ester M Hammond
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Pablo Huertas
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla 41080, Spain; Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla/CSIC, Sevilla 41092, Spain
| | - Sylvie Gazzeri
- University Grenoble Alpes, INSERM U1209, CNRS UMR5309, Team RNA Splicing, Cell Signaling and Response to Therapies, Institute for Advanced Biosciences, Grenoble F38000, France
| | - Olivier Sordet
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, CNRS, Toulouse 31037, France
| | - Beatrice Eymin
- University Grenoble Alpes, INSERM U1209, CNRS UMR5309, Team RNA Splicing, Cell Signaling and Response to Therapies, Institute for Advanced Biosciences, Grenoble F38000, France
| |
Collapse
|
25
|
Zhang Z, Mao C, Wu Y, Wang Y, Cong H. Application of non‑coding RNAs in tumors (Review). Mol Med Rep 2025; 31:164. [PMID: 40211701 PMCID: PMC12015154 DOI: 10.3892/mmr.2025.13529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2024] [Accepted: 01/31/2025] [Indexed: 04/25/2025] Open
Abstract
Tumors are associated with the highest mortality rates worldwide. For more than a decade, research has focused on the genetic involvement of proteins in cancer; however, a complete class of molecular non‑coding (nc)RNAs have been discovered in recent years, and these are considered to be associated with cancer. Notably, ncRNAs are highly conserved and multifunctional. These interact with multiple signaling pathways, influencing cell cycle progression and various physiological processes. Therefore, the present review aimed to investigate ncRNA, microRNA, transfer RNA‑derived small RNA, PIWI‑interacting RNA and long non‑coding RNA to further understand the associated generation processes, functional mechanisms and therapeutic roles in tumors. The present review demonstrated the critical role of ncRNAs in tumors, and may provide a novel theoretical basis for the role of ncRNAs as biomarkers or therapeutic tools in the treatment of cancer.
Collapse
Affiliation(s)
- Zhihan Zhang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
- Department of Clinical Medicine, Medical School of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Chunyan Mao
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
- Department of Clinical Medicine, Medical School of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Yi Wu
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
- Department of Clinical Medicine, Medical School of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Yin Wang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
- Department of Clinical Medicine, Medical School of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Hui Cong
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
- Department of Blood Transfusion, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| |
Collapse
|
26
|
Safaei S, Derakhshan-sefidi M, Karimi A. Wolbachia: A bacterial weapon against dengue fever- a narrative review of risk factors for dengue fever outbreaks. New Microbes New Infect 2025; 65:101578. [PMID: 40176883 PMCID: PMC11964561 DOI: 10.1016/j.nmni.2025.101578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2024] [Revised: 01/10/2025] [Accepted: 03/06/2025] [Indexed: 04/05/2025] Open
Abstract
Arboviruses constitute the largest known group of viruses and are responsible for various infections that impose significant socioeconomic burdens worldwide, particularly due to their link with insect-borne diseases. The increasing incidence of dengue fever in non-endemic regions underscores the urgent need for innovative strategies to combat this public health threat. Wolbachia, a bacterium, presents a promising biological control method against mosquito vectors, offering a novel approach to managing dengue fever. We systematically investigated biomedical databases (PubMed, Web of Science, Google Scholar, Science Direct, and Embase) using "AND" as a Boolean operator with keywords such as "dengue fever," "dengue virus," "risk factors," "Wolbachia," and "outbreak." We prioritized articles that offered significant insights into the risk factors contributing to the outbreak of dengue fever and provided an overview of Wolbachia's characteristics and functions in disease management, considering studies published until December 25, 2024. Field experiments have shown that introducing Wolbachia-infected mosquitoes can effectively reduce mosquito populations and lower dengue transmission rates, signifying its potential as a practical approach for controlling this disease.
Collapse
Affiliation(s)
- Sahel Safaei
- Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | | | | |
Collapse
|
27
|
Sénépart O, Legay C, Hamraoui A. Managing surface energy dynamics for enhanced axonal growth: An overview of present and future challenges. BIOPHYSICS REVIEWS 2025; 6:021301. [PMID: 40321901 PMCID: PMC12045649 DOI: 10.1063/5.0237085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2024] [Accepted: 04/10/2025] [Indexed: 05/08/2025]
Abstract
To create functional neuronal circuit units during nervous system development and/or regeneration, axons are subjected to guidance signals. Expression of these signals occurs in spatiotemporal variations and is translated by the growth cone into a pathway to reach the connecting target which can be a neuron or a non-neuronal cell such as a muscle cell. This path is generated by interactions with the surrounding environment such as cells or the extracellular matrix, a complex molecular substrate. Understanding the interactions with this last component is essential to stimulate nerve regeneration in the context of motor peripheral nerve trauma, the most common source of disabilities, increasing with aging. The goal is to mimic its composition and specific characteristics using innovative biomaterials and/or implants. This review highlights some aspects of the recent findings in nerve repair. After an introduction to the peripheral nervous system, we present an overview of nerve degeneration and regeneration mechanisms before detailing the strategies used nowadays to optimize nerve (re)growth with a specific focus on the use of electric field. We discuss the advantages and limits of each option in terms of therapeutic applications.
Collapse
Affiliation(s)
| | - Claire Legay
- Université Paris Cité, CNRS, Saints-Pères Paris Institute for the Neurosciences, F-75006 Paris, France
| | | |
Collapse
|
28
|
Han Z, Jiang S, Xie J, Lucreche Poupina IS, Mo X, Sui L, Qian P, Tang X. Characterization and functional analysis of the small heat shock protein HSP19.5 in Bombyx mori in response to Nosema bombycis infection. J Invertebr Pathol 2025; 210:108289. [PMID: 39988027 DOI: 10.1016/j.jip.2025.108289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2024] [Revised: 01/13/2025] [Accepted: 02/17/2025] [Indexed: 02/25/2025]
Abstract
Small heat shock proteins (sHSPs) are molecular chaperones known for their role in maintaining cellular homeostasis and protecting cells from various environmental stresses. This study focuses on the silkworm small heat shock protein HSP19.5 and its potential functions in the context of Nosema bombycis infection, a microsporidian pathogen causing severe disease in the sericulture industry. We cloned and characterized HSP19.5 and revealed its expression patterns in different silkworm tissues and developmental stages. Our results indicate that HSP19.5 expression is significantly up-regulated in response to N. bombycis infection, suggesting a role in the host stress response. Through a series of experiments, including RNA interference and overexpression analyses, we demonstrated that HSP19.5 promotes N. bombycis proliferation, possibly by inhibiting host cell apoptosis and regulating intracellular ROS levels. The cytoplasmic localization of HSP19.5 in silkworm cells is consistent with its function as a molecular chaperone. The results enhance our understanding of the complex host-pathogen interactions between silkworms and N. bombycis, and provides insights that may inform the development of novel strategies to control the pebrine disease.
Collapse
Affiliation(s)
- Zhenghao Han
- Jiangsu Key Laboratory of Sericultural and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Shidong Jiang
- Guangxi Key Laboratory of Sericultural Genetic Improvement and Efficient Breeding, NanNing 530007, China; Guangxi Zhuang Autonomous Region Sericulture Technology Promotion Terminal, NanNing 530007, China
| | - Jingxian Xie
- Jiangsu Key Laboratory of Sericultural and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Ibouanga Sama Lucreche Poupina
- Jiangsu Key Laboratory of Sericultural and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Xiaoli Mo
- Jiangsu Key Laboratory of Sericultural and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Li Sui
- Jiangsu Key Laboratory of Sericultural and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Ping Qian
- Jiangsu Key Laboratory of Sericultural and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, China
| | - Xudong Tang
- Jiangsu Key Laboratory of Sericultural and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, China; Zhenjiang ZhongNong Biotechnology Co., LTD, Zhenjiang 212101, China.
| |
Collapse
|
29
|
MacDonald MR, Gulick AM. An efficient lysate-based approach for biosynthesis of the pyrrolobenzodiazepine natural product tilimycin. J Biotechnol 2025; 402:87-95. [PMID: 40120764 PMCID: PMC12001866 DOI: 10.1016/j.jbiotec.2025.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2025] [Revised: 03/14/2025] [Accepted: 03/17/2025] [Indexed: 03/25/2025]
Abstract
Many bacteria use nonribosomal peptide synthetases (NRPSs), a family of multidomain enzymes that produce peptide natural products using an assembly line strategy. One class of such compounds are pyrrolobenzodiazepines, which have DNA alkylating activity. One example is tilimycin, a compound produced by the human gut microbiota that plays a role in epithelial damage during antibiotic-associated dysbiosis. The production of analogs of these natural products may facilitate the discovery of novel bioactive molecules. However, the synthesis of these natural products typically requires significant resources and time to produce in sufficient amounts for microbial and biochemical testing. Biocatalysis offers an environmentally friendly approach, but enzyme yield and stability, particularly with large multidomain enzymes that are often used in natural product pathways, can limit biochemical reactions with purified protein. Here, we demonstrate a cell lysate-based method to synthesize the nonribosomal peptide natural product tilimycin directly from the substrates 3-hydroxyanthranilic acid and L-proline with lysates from E. coli cell lines that express the tilimycin biosynthetic proteins. We present our protocol optimization and scale-up to produce tilimycin in a fast, efficient manner.
Collapse
Affiliation(s)
- Monica R MacDonald
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, SUNY, 955 Main Street, Buffalo, NY 14203, United States.
| | - Andrew M Gulick
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, SUNY, 955 Main Street, Buffalo, NY 14203, United States.
| |
Collapse
|
30
|
Li Y, Wu Y, Shao J, Shi J, Sun L, Hong Y, Wang X. Stresses in the food chain and their impact on antibiotic resistance of foodborne pathogens: A review. Food Microbiol 2025; 128:104741. [PMID: 39952755 DOI: 10.1016/j.fm.2025.104741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2024] [Revised: 01/07/2025] [Accepted: 01/31/2025] [Indexed: 02/17/2025]
Abstract
Antibiotic resistance in foodborne pathogens represents a major public health concern. The farm-to-fork continuum is recognized as a critical pathway for the development and spread of this resistance. Throughout the food chain, foodborne pathogens are exposed to diverse environmental stresses, including temperature extremes, osmotic pressure, food additives, and disinfectants, and others. These stress factors can influence antibiotic resistance, with effects varying based on the type and intensity of stress, the pathogen species and strain, and the specific antibiotic involved. Stress conditions can trigger bacterial adaptive responses, such as general stress response systems, the SOS response, and genetic mutations, which can confer cross-protection and enhance antibiotic resistance. Conversely, stress-induced injury or metabolic suppression may increase bacterial susceptibility to certain antibiotics. Understanding these complex interactions is crucial, as suboptimal food processing can inadvertently select for resistant strains. Investigating the molecular mechanisms underlying stress adaptation is essential for developing effective strategies to mitigate antibiotic resistance. Optimizing food processing protocols and implementing robust monitoring systems throughout the food chain are essential steps to reduce these risks. A comprehensive understanding of stress-induced antibiotic resistance will provide a scientific basis for improving food safety and safeguarding global public health.
Collapse
Affiliation(s)
- Yun Li
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Yufan Wu
- Centre of Analysis and Test, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Jingdong Shao
- Technology Center of Zhangjiagang Customs, Suzhou, China
| | - Juping Shi
- Zhangjiagang Centre for Disease Control and Prevention, Suzhou, China
| | - Lu Sun
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Yi Hong
- Food Microbiology and Food Preservation Research Unit, Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, Belgium
| | - Xiang Wang
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China.
| |
Collapse
|
31
|
Vera-Duarte GR, Eskenazi-Betech R, De la Fuente-Batta I, Carreño-Bolaños D, Chacón-Camacho OF, Zenteno JC, Graue-Hernandez EO. Unveiling the complexity of Schimmelpenning-Feuerstein-Mims syndrome: A comprehensive case study. Am J Ophthalmol Case Rep 2025; 38:102321. [PMID: 40290853 PMCID: PMC12023775 DOI: 10.1016/j.ajoc.2025.102321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2024] [Revised: 01/23/2025] [Accepted: 03/23/2025] [Indexed: 04/30/2025] Open
Abstract
Purpose The purpose of this study was to report the comprehensively examined patient exhibiting oculocutaneous clinical features of Schimmelpenning-Feuerstein-Mims syndrome (SFMS). Background Schimmelpenning-Feuerstein-Mims syndrome (SFMS) is a rare phakomatosis characterized by the presence of sebaceous hamartomas on the skin along with extracutaneous abnormalities involving various neuroectodermal systems. The syndrome is typically sporadic and can originate from postzygotic mutations in genes implicated in the RAS signaling pathway (RAS proteins and their downstream pathways play pivotal roles in cell proliferation, differentiation, survival, and cell death): HRAS (11p15), NRAS (1p13), and KRAS (12p12). This case report involves a comprehensively examined patient exhibiting oculocutaneous clinical features of SFM, without neurological or involvement in other areas. Clinical and molecular diagnoses enable tailored monitoring of potentially affected organs and systems, involving a multidisciplinary approach by various medical specialists. Conclusion and importance The SFM is attributed to a pathogenic variant in KRAS gene. The molecular analysis in individuals suspected of SFMS involves identifying the somatic mutation in affected tissues and comparing it with non-affected tissues, such as mucosa or blood. Early detection and appropriate treatment of ophthalmological abnormalities associated with SFM are crucial to improving the quality of life and visual prognosis of affected individuals.
Collapse
Affiliation(s)
- Guillermo Raul Vera-Duarte
- Department of Cornea, External Disease and Refractive Surgery, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico
| | - Ruth Eskenazi-Betech
- Department of Cornea, External Disease and Refractive Surgery, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico
| | - Isabel De la Fuente-Batta
- Department of Cornea, External Disease and Refractive Surgery, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico
| | - David Carreño-Bolaños
- Department of Genetics, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico
| | - Oscar F. Chacón-Camacho
- Department of Genetics, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico
- Laboratorio 5 Edificio A-4, Carrera de Médico Cirujano, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Mexico
| | - Juan C. Zenteno
- Department of Genetics, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico
- Biochemistry Department, Faculty Medicine, National Autonomous University of Mexico, Mexico City, Mexico
- Rare Diseases Diagnostic Unit, Faculty of Medicine, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | - Enrique O. Graue-Hernandez
- Department of Cornea, External Disease and Refractive Surgery, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico
| |
Collapse
|
32
|
Siddiqui JA, Fan R, Liu Y, Syed AH, Benlin Y, Chu Q, Ding Z, Ghani MI, Liu X, Wakil W, Liu DD, Chen X, Cernava T, Smagghe G. The larval gut of Spodoptera frugiperda harbours culturable bacteria with metabolic versatility after insecticide exposure. INSECT MOLECULAR BIOLOGY 2025; 34:452-469. [PMID: 39952648 DOI: 10.1111/imb.12983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2024] [Accepted: 01/02/2025] [Indexed: 02/17/2025]
Abstract
Spodoptera frugiperda (fall armyworm) poses a substantial risk to crops worldwide, resulting in considerable economic damage. The gut microbiota of insects plays crucial roles in digestion, nutrition, immunity, growth and, sometimes, the degradation of insecticides. The current study examines the effect of synthetic insecticides on the gut microbiome of third instar S. frugiperda larvae using both culture-dependent techniques and 16S rRNA gene sequencing for bacterial community profiling and diversity analysis. In untreated larvae, the sequencing approach revealed a diverse microbiome dominated by the phyla Firmicutes, Proteobacteria and Bacteroidota, with key genera including Bacteroides, Faecalibacterium and Pelomonas. In parallel, 323 bacterial strains were isolated and assigned to the orders Bacillales, Burkholderiales, Enterobacterales, Flavobacteriales, Lactobacillales, Micrococcales, Neisseriaies, Pseudomonadales, Sphingobacteriales and Xanthomonadales. The prevailing culturable species included Serratia marcescens, Klebsiella variicola and Enterobacter quasiroggenkampii. Treatment with sublethal concentrations of three insecticides (broflanilide, spinosad and indoxacarb) caused significant changes in gut microbiome diversity and composition. Treated larvae showed a shift towards increased Proteobacteria abundance and decreased Firmicutes. Specifically, Acinetobacter and Rhodococcus were dominant in treated samples. Functional predictions highlighted significant metabolic versatility involving nutrient processing, immune response, detoxification, xenobiotic metabolism, and stress response, suggesting microbial adaptation to insecticide exposure. Network correlation analysis highlighted disrupted microbial interactions and altered community structures under insecticide treatment. These findings enhance our understanding of how insecticides impact the gut microbiota in S. frugiperda and may inform future strategies for managing pest resistance through microbiome-based approaches.
Collapse
Affiliation(s)
- Junaid Ali Siddiqui
- College of Agriculture/College of Life Sciences, Guizhou University, Guiyang, China
- Guizhou Provincial Science and Technology Department, Guizhou-Europe Environmental Biotechnology and Agricultural Informatics Oversea Innovation Center in Guizhou University, Guiyang, China
| | - Ruidong Fan
- College of Agriculture/College of Life Sciences, Guizhou University, Guiyang, China
- Guizhou Provincial Science and Technology Department, Guizhou-Europe Environmental Biotechnology and Agricultural Informatics Oversea Innovation Center in Guizhou University, Guiyang, China
- Institute of Entomology, Guizhou University, Guiyang, China
| | - Yanjiang Liu
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa, China
| | - Ali Hassan Syed
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Yi Benlin
- College of Agriculture/College of Life Sciences, Guizhou University, Guiyang, China
- Guizhou Provincial Science and Technology Department, Guizhou-Europe Environmental Biotechnology and Agricultural Informatics Oversea Innovation Center in Guizhou University, Guiyang, China
| | - Qingshuai Chu
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa, China
| | - Zeyang Ding
- College of Agriculture/College of Life Sciences, Guizhou University, Guiyang, China
- Guizhou Provincial Science and Technology Department, Guizhou-Europe Environmental Biotechnology and Agricultural Informatics Oversea Innovation Center in Guizhou University, Guiyang, China
- Institute of Entomology, Guizhou University, Guiyang, China
| | - Muhammad Imran Ghani
- College of Agriculture/College of Life Sciences, Guizhou University, Guiyang, China
- Guizhou Provincial Science and Technology Department, Guizhou-Europe Environmental Biotechnology and Agricultural Informatics Oversea Innovation Center in Guizhou University, Guiyang, China
| | - Xuemi Liu
- College of Agriculture/College of Life Sciences, Guizhou University, Guiyang, China
- Guizhou Provincial Science and Technology Department, Guizhou-Europe Environmental Biotechnology and Agricultural Informatics Oversea Innovation Center in Guizhou University, Guiyang, China
| | - Waqas Wakil
- Department of Entomology, University of Agriculture, Faisalabad, Pakistan
| | - Dong-Dong Liu
- College of Agriculture/College of Life Sciences, Guizhou University, Guiyang, China
- Institute of Entomology, Guizhou University, Guiyang, China
| | - Xiaoyulong Chen
- College of Agriculture/College of Life Sciences, Guizhou University, Guiyang, China
- Guizhou Provincial Science and Technology Department, Guizhou-Europe Environmental Biotechnology and Agricultural Informatics Oversea Innovation Center in Guizhou University, Guiyang, China
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa, China
| | - Tomislav Cernava
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK
| | - Guy Smagghe
- College of Agriculture/College of Life Sciences, Guizhou University, Guiyang, China
- Institute of Entomology, Guizhou University, Guiyang, China
- Department of Plants and Crops, Ghent University, Ghent, Belgium
- Department of Biology, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| |
Collapse
|
33
|
Beyea J. False and Misleading Claims of Scientific Misconduct in Early Research into Radiation Dose-response: Part 1. Overlooking Key Historical Text. HEALTH PHYSICS 2025; 128:507-523. [PMID: 39656129 PMCID: PMC12036784 DOI: 10.1097/hp.0000000000001932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/24/2025]
Abstract
ABSTRACT In reviewing a video series that they created for the website of the Health Physics Society (HPS), past leaders of the Health Physics Society have treated as authoritative and trustworthy the scientific misconduct theories of University of Massachusetts Professor Edward Calabrese. No mention is made of detailed critiques of Calabrese's work. I show that Calabrese's historical work as presented by HPS's authors is unreliable because it overlooks key historical text and key statistical concepts about the limits of an early atomic bomb genetics study. When these errors are corrected, claims of scientific misconduct on the part of historical figures evaporate. Claims of threshold behavior in early radiation genetic experiments are wrong for atomic bomb data. Calabrese's unique claims about thresholds in early animal genetic data are not credible for human cancer, given the doses at which they were carried out (>30 R). Recent epidemiological studies of both acute and protracted exposure in humans fail to show dose-rate effects or a dose threshold above 30 R. Such results from human data should be more relevant for most regulators and review committees than Calabrese's claims about old data on animals. Disclaimers, errata, and links to critiques should be added to the HPS webpage hosting the 22-part video series. Failure to do so can cause damage to reputations and historical accuracy because it erroneously validates Calabrese's inflammatory claims of scientific misconduct against past scientists, including three Nobel Prize winners, members of the NAS, and presidents of the AAAS.
Collapse
Affiliation(s)
- Jan Beyea
- Senior Scientist Emeritus, Consulting in the Public Interest
| |
Collapse
|
34
|
Gross CA. Peering into the Bacterial Cell: From Transcription to Functional Genomics. J Mol Biol 2025; 437:169087. [PMID: 40081792 DOI: 10.1016/j.jmb.2025.169087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2025] [Revised: 03/07/2025] [Accepted: 03/07/2025] [Indexed: 03/16/2025]
Abstract
I started my faculty career in 1981 at the UW-Madison in the Department of Bacteriology and moved to the University of California, San Francisco in 1993, where I am a Professor in the Departments of Microbiology and Immunology and Cell and Tissue Biology. In this article, I first review my contributions to understanding the molecular biology of the bacterial transcriptional apparatus and the global role of alternative sigmas (σs), a major pillar of bacterial transcriptional control. I then discuss my role in spearheading the development of bacterial systems biology, specifically to the genome-wide phenotyping approaches necessary for rapid understanding of gene function and the molecular basis of pathway connections across the bacterial universe.
Collapse
Affiliation(s)
- Carol A Gross
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA; Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, USA; California Institute of Quantitative Biology, University of California, San Francisco, San Francisco, CA, USA.
| |
Collapse
|
35
|
Nguyen TV, Alfarsi A, Nguyen HT, Davidson G, Lloyd NDR, Kumar A. Metabolic disruptions induced by low concentrations of DMSO in RTgill-W1 fish cells: The importance of solvent controls in in vitro studies. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2025; 283:107354. [PMID: 40209297 DOI: 10.1016/j.aquatox.2025.107354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2025] [Revised: 04/04/2025] [Accepted: 04/04/2025] [Indexed: 04/12/2025]
Abstract
Dimethyl sulfoxide (DMSO) is a widely used solvent in biological research due to its ability to enhance membrane permeability, facilitating drug delivery and molecular transport across cellular membranes. However, its effects on cellular metabolism, especially at low concentrations, remain insufficiently understood. This study investigated the metabolic disruptions induced by 0.1-10 % DMSO in the RTgill-W1 fish cell line, focusing on changes in cell viability, oxidative stress, and key metabolic pathways. Results revealed that DMSO exposure caused dose-dependent declines in cell viability at 0.5 % DMSO and increases in reactive oxygen species (ROS) at 4 % and higher, indicating elevated oxidative stress. Metabolomic profiling revealed altered levels of numerous metabolites and significant impacts on 41 metabolic pathways belonging to five major functional groups: amino acid metabolism, carbohydrate metabolism, lipid metabolism, vitamin and co-factor metabolism, and nucleotide metabolism. The effects were observed across all exposure concentrations (0.1, 0.5, 1, 4, and 8 %), with more pronounced impacts at higher concentrations. These findings highlight that DMSO, even at low concentrations (≤ 0.5 %), can have widespread effects on cellular metabolism, impacting experimental outcomes in in vitro studies. This study provides valuable insights into the biochemical impacts of DMSO on fish cell lines and emphasizes a caution in using DMSO in biological research to minimize unintended cellular effects. Additionally, it highlights the critical need to include solvent controls at matching concentrations to accurately distinguish solvent-induced effects from those caused by experimental treatments.
Collapse
Affiliation(s)
- Thao V Nguyen
- CSIRO Environment, Waite Campus, Urrbrae, South Australia 5064, Australia.
| | - Ali Alfarsi
- CSIRO Environment, Waite Campus, Urrbrae, South Australia 5064, Australia
| | - Huong Thanh Nguyen
- CSIRO Environment, Waite Campus, Urrbrae, South Australia 5064, Australia
| | - Georgia Davidson
- The Australian Wine Research Institute, PO Box 46, Glenside, SA 5065, Australia; Metabolomics Australia, PO Box 46, Glenside, SA 5065, Australia
| | - Natoiya D R Lloyd
- The Australian Wine Research Institute, PO Box 46, Glenside, SA 5065, Australia; Metabolomics Australia, PO Box 46, Glenside, SA 5065, Australia
| | - Anu Kumar
- CSIRO Environment, Waite Campus, Urrbrae, South Australia 5064, Australia.
| |
Collapse
|
36
|
Gottesman S. Bacterial Regulatory Circuits are Linked and Extended by Small RNAs. J Mol Biol 2025; 437:169059. [PMID: 40043836 PMCID: PMC12021557 DOI: 10.1016/j.jmb.2025.169059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2024] [Revised: 02/25/2025] [Accepted: 02/26/2025] [Indexed: 03/16/2025]
Abstract
I was lucky to start my research career as the molecular biology revolution was taking hold, providing a constantly increasing set of tools and questions to investigate. Starting from a fascination with bacteria and their ability to adapt to different conditions, I've investigated post-translational mechanisms and their role in the ability of E. coli to respond to stress. My research career has been primarily at the National Institutes of Health, where I run a group within the Laboratory of Molecular Biology, NCI and hold the title of NIH Distinguished Investigator. Our lab has been interested in both energy-dependent proteolysis, discussed very briefly here, and small regulatory RNAs (sRNAs). The major group of such sRNAs act by pairing with target mRNAs with the aid of the RNA chaperone Hfq, mediating both positive and negative regulation of translation and mRNA stability. Both in our own lab and in a continuing and highly productive collaboration with the laboratory of Gisela (Gigi) Storz, we have used global approaches to identify novel sRNAs, identified how many of them are regulated, both at the level of transcription and stability, and worked on understanding the role of these sRNAs in regulatory networks. Our continued work explores regulators of sRNA and Hfq function. Here, Gigi and I have split summaries of our findings, and hope that our two chapters will be read together.
Collapse
|
37
|
Zhou Z, Duan Y, Li Y, Zhang P, Li Q, Yu L, Han C, Huo J, Chen W, Xiao Y. CYP98A monooxygenases: a key enzyme family in plant phenolic compound biosynthesis. HORTICULTURE RESEARCH 2025; 12:uhaf074. [PMID: 40303436 PMCID: PMC12038246 DOI: 10.1093/hr/uhaf074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2024] [Accepted: 02/25/2025] [Indexed: 05/02/2025]
Abstract
Phenolic compounds are derived from the phenylpropanoid metabolic pathways of plants and include phenylpropionic acids, lignins, coumarins, and flavonoids. These compounds are among the most abundant and diverse classes of secondary metabolites found throughout the plant kingdom. Phenolic compounds play critical roles in the growth, development, and stress resistance of horticultural plants. Moreover, some phenolic compounds exhibit substantial biological activities, and they are widely utilized across various sectors, such as the pharmaceutical and food industries. The cytochrome P450 monooxygenase 98A subfamily (CYP98A) is involved mainly in the biosynthesis of phenolic compounds, mediating the meta-hydroxylation of aromatic rings in the common phenylpropane biosynthesis pathways of phenolic compounds. However, research on this family of oxidases is currently fragmented, and a systematic and comprehensive review has not yet been conducted. This review offers an exhaustive summary of the molecular features of the CYP98A family and the functions of CYP98A monooxygenases in the biosynthesis of different types of phenolic compounds. In addition, this study provides a reference for the exploration and functional study of plant CYP98A family enzymes. An enhanced understanding of CYP98A monooxygenases can help in the cultivation of high-quality horticultural plants with increased resistance to biotic and abiotic stresses and enhanced accumulation of natural bioactive compounds via metabolic engineering strategies. Moreover, the structural optimization and modification of CYP98A monooxygenases can provide additional potential targets for synthetic biology, enabling the efficient in vitro production of important phenolic compounds to address production supply conflicts.
Collapse
Affiliation(s)
- Zheng Zhou
- State Key Laboratory of Discovery and Utilization of Functional Components in Traditional Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Pudong New Area, Shanghai 201203, China
- Navy Special Medical Centre, Second Military Medical University, 800 Xiangyin Road, Yangpu District, Shanghai 200433, China
| | - Yonghao Duan
- State Key Laboratory of Discovery and Utilization of Functional Components in Traditional Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Pudong New Area, Shanghai 201203, China
| | - Yajing Li
- State Key Laboratory of Discovery and Utilization of Functional Components in Traditional Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Pudong New Area, Shanghai 201203, China
| | - Pan Zhang
- State Key Laboratory of Discovery and Utilization of Functional Components in Traditional Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Pudong New Area, Shanghai 201203, China
| | - Qing Li
- Department of Pharmacy, Changzheng Hospital, Second Military Medical University, 415 Fengyang Road, Huangpu District, Shanghai 200003, China
| | - Luyao Yu
- Navy Special Medical Centre, Second Military Medical University, 800 Xiangyin Road, Yangpu District, Shanghai 200433, China
| | - Cuicui Han
- Navy Special Medical Centre, Second Military Medical University, 800 Xiangyin Road, Yangpu District, Shanghai 200433, China
| | - Juncheng Huo
- Department of Pharmacy, Changzheng Hospital, Second Military Medical University, 415 Fengyang Road, Huangpu District, Shanghai 200003, China
| | - Wansheng Chen
- State Key Laboratory of Discovery and Utilization of Functional Components in Traditional Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Pudong New Area, Shanghai 201203, China
- Department of Pharmacy, Changzheng Hospital, Second Military Medical University, 415 Fengyang Road, Huangpu District, Shanghai 200003, China
| | - Ying Xiao
- State Key Laboratory of Discovery and Utilization of Functional Components in Traditional Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Pudong New Area, Shanghai 201203, China
| |
Collapse
|
38
|
Zhao Q, Wang T, Pei FJ, Chen Y, Chang XY, Mi JM, Zhang YM. Phenotypic Plasticity of Grain Size-Related Traits in Main-Crop and Ratoon Rice. PLANT, CELL & ENVIRONMENT 2025; 48:3890-3901. [PMID: 39834074 DOI: 10.1111/pce.15397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2024] [Revised: 11/27/2024] [Accepted: 01/08/2025] [Indexed: 01/22/2025]
Abstract
Grain size and weight of main-crop are larger than those of ratoon rice, indicating that increasing grain size and weight of ratoon rice is an effective way to increase rice yield. Thus, grain length (GL), grain width (GW), and thousand-grain weight (TGW) of main-crop and ratoon rice in 159 indica rice accessions were used to associate with 2 017 495 SNP markers to detect quantitative trait nucleotides (QTNs) and their interactions with meteorological factors (QMIs), such as temperature and sunlight hours. Around 59 QMIs identified for temperature and 80 QMIs identified for sunlight hours, first, candidate gene LOC_Os02g40840 for GW and LOC_Os04g45480 for TGW were found to interact with temperature, while LOC_Os01g19970 for GL, LOC_Os02g39360 and LOC_Os07g05720 for GW, and LOC_Os07g49460 for TGW were found to interact with sunlight hours. Based on the results of previous studies, LOC_Os04g45480 exhibits high expression levels in the main-crop under higher temperature, thereby enhancing the accumulation of the auxin receptor TIR1. TIR1, in turn, promotes starch accumulation in the endosperm, explaining why TGW is heavier in main-crop than in ratoon rice. Finally, the analysis of best linear unbiased prediction values revealed 1 (LOC_Os08g10350) and 3 (LOC_Os02g50860, LOC_Os08g28680, and LOC_Os08g29160) candidate genes responsible for GW and TGW, respectively. In addition, we discussed the four available and six unavailable candidate genes in ratoon rice breeding. This study provides new method and genes for studying differences in grain size-related traits between main-crop and ratoon rice.
Collapse
Affiliation(s)
- Qiong Zhao
- Department of Crop Genetics and Breeding, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Tian Wang
- Department of Crop Genetics and Breeding, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Fa-Jing Pei
- Department of Crop Genetics and Breeding, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Ying Chen
- Department of Crop Genetics and Breeding, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiao-Yu Chang
- Department of Crop Genetics and Breeding, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jia-Ming Mi
- Department of Crop Genetics and Breeding, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Yuan-Ming Zhang
- Department of Crop Genetics and Breeding, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
39
|
Tan YH, Poong SW, Beardall J, Phang SM, Lim PE. Metabolomic and physiological analyses of two picochlorophytes from distinct oceanic latitudes under future ocean acidification and warming. MARINE ENVIRONMENTAL RESEARCH 2025; 208:107095. [PMID: 40163968 DOI: 10.1016/j.marenvres.2025.107095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2024] [Revised: 02/27/2025] [Accepted: 03/20/2025] [Indexed: 04/02/2025]
Abstract
Phytoplankton are cosmopolitan marine photosynthetic organisms that are vital to biogeochemical cycles and marine ecosystems. The current rise in atmospheric CO2 and surface ocean temperatures are poised to disrupt the ecological niches of phytoplankton. Picochlorophytes, a broad taxon of small green eukaryotic phytoplankton, have been shown to perform well under future rising oceanic CO2 and temperature scenarios. This study investigates the acclimation responses of cosmopolitan picochlorophytes from the Chlorella-lineage under high CO2 (1000 p.p.m.) and a rise of 4 °C (8 °C - polar picochlorophyte; 32 °C, tropical picochlorophyte). In order to determine how the future ocean warming and acidification might affect picochlorophytes, a polar strain of Chlorella and a tropical Parachlorella were selected, and their physiology and GCMS-based metabolomics were investigated. Growth rate and cellular dimensions (diameter, volume, and surface area) of Chlorella significantly increased in all environmental future scenarios compared to Parachlorella. Photosynthetic parameters of the picochlorophytes studied showed acclimation, with high temperature and high CO2 triggering the adaptation of Fv/Fm, NPQmax, and Ek of Chlorella and Parachlorella, respectively. High CO2 induced the most changes in the Chlorella metabolome, altering the levels of metabolites related to amino acids and their derivatives, glutathione production, carbohydrates, and photochemical quenching. Combined high CO2/temperature altered Parachlorella's metabolome, though with a small number of biomarkers detected. This study provided evidence to support the hypothesis that picochlorophytes could thrive in a more acidified and warmer ocean.
Collapse
Affiliation(s)
- Yong-Hao Tan
- Institute of Ocean & Earth Sciences, University of Malaya, Kuala Lumpur, Malaysia; Office of Postgraduate Studies, UCSI University, Kuala Lumpur, Malaysia
| | - Sze-Wan Poong
- Institute of Ocean & Earth Sciences, University of Malaya, Kuala Lumpur, Malaysia.
| | - John Beardall
- School of Biological Sciences, Monash University, Clayton, Australia
| | - Siew-Moi Phang
- Institute of Ocean & Earth Sciences, University of Malaya, Kuala Lumpur, Malaysia; Office of Postgraduate Studies, UCSI University, Kuala Lumpur, Malaysia; Faculty of Applied Sciences, UCSI University, Kuala Lumpur, Malaysia
| | - Phaik-Eem Lim
- Institute of Ocean & Earth Sciences, University of Malaya, Kuala Lumpur, Malaysia.
| |
Collapse
|
40
|
Denkiewicz-Kruk M, Chaudhry D, Krasilia A, Jedrychowska M, Fijalkowska IJ, Dmowski M. Effects of CDC45 mutations on DNA replication and genome stability. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2025; 1872:119936. [PMID: 40139510 DOI: 10.1016/j.bbamcr.2025.119936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2024] [Revised: 02/28/2025] [Accepted: 03/18/2025] [Indexed: 03/29/2025]
Abstract
Cdc45 is a non-catalytic subunit of the CMG helicase complex that is recruited to the autonomously replicating sequence at the onset of DNA replication. The Cdc45 protein is required for the initiation of DNA replication as well as for nascent DNA strand synthesis. It interacts with Mcm2 and Psf1 elements of CMG helicase, as well as with Sld3, an initiation factor, and Pol2, the catalytic subunit of DNA polymerase epsilon (Pol ε). In this study, we analyzed the effects of amino acid substitutions in the Cdc45 region involved in the interaction of this protein with Mcm2-7 (Cdc45-1), Psf1 (Cdc45-26), and Sld3 (Cdc45-25, Cdc45-35). We found that mutations in CDC45 resulted in defective DNA replication. Under permissive conditions, delayed DNA synthesis was observed. At restrictive temperatures, the mutant cells were unable to efficiently replicate DNA. However, after the initiation of DNA replication under permissive conditions, the four analyzed CDC45 mutants exhibited DNA synthesis under the restrictive conditions. Moreover, we observed increased mutation rates, mainly dependent on DNA polymerase zeta (Pol ζ), as well as increased incidence of replication errors. These findings confirm the essential function of Cdc45 in DNA replication initiation and demonstrate that impaired Cdc45 subunit has an impact on the fidelity of the nascent DNA strand synthesis. The changes in cell function observed in this study, related to defects in Cdc45 function, may help understand some diseases associated with CDC45.
Collapse
Affiliation(s)
- Milena Denkiewicz-Kruk
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Deepali Chaudhry
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Alina Krasilia
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Malgorzata Jedrychowska
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Iwona J Fijalkowska
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
| | - Michal Dmowski
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
| |
Collapse
|
41
|
Sanchez-Aranguren L, Al Tahan MA, Uppal M, Juvale P, Marwah MK. Mitochondrial-targeted liposome-based drug delivery - therapeutic potential and challenges. J Drug Target 2025; 33:575-586. [PMID: 39620468 DOI: 10.1080/1061186x.2024.2437440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2024] [Revised: 11/22/2024] [Accepted: 11/26/2024] [Indexed: 12/10/2024]
Abstract
Liposomes, as nanocarriers for therapeutics, are a prominent focus in translational medicine. Given their biocompatibility, liposomes are suitable drug delivery systems rendering highly efficient therapeutic outcomes with minimal off-site toxicity. In different scenarios of human disease, it is essential not only to maintain therapeutic drug levels but also to target them to the appropriate intracellular compartment. Mitochondria regulate cellular signalling, calcium balance, and energy production, playing a crucial role in various human diseases. The notion of focusing on mitochondria for targeted drug delivery was proposed several decades ago, yet the practical application of this idea and its translation to clinical use is still in development. Mitochondrial-targeted liposomes offer an alternative to standard drug delivery systems, potentially reducing off-target interactions, side effects, and drug dosage or frequency. To advance this field, it is imperative to integrate various disciplines such as efficient chemical design, pharmacology, pharmaceutics, and cell biology. This review summarises scientific advances in the design, development and characterisation of novel liposome-based drug delivery systems targeting the mitochondria while revisiting their translational potential.
Collapse
Affiliation(s)
- Lissette Sanchez-Aranguren
- College of Health and Life Sciences, Aston Medical School, Aston University, Birmingham, UK
- Translational Medicine Research Group, Aston Medical School, Aston University, Birmingham, UK
| | - Mohamad Anas Al Tahan
- College of Health and Life Sciences, Aston Medical School, Aston University, Birmingham, UK
- Translational Medicine Research Group, Aston Medical School, Aston University, Birmingham, UK
| | - Muhammad Uppal
- College of Health and Life Sciences, Aston Medical School, Aston University, Birmingham, UK
| | - Parag Juvale
- College of Health and Life Sciences, Aston Medical School, Aston University, Birmingham, UK
| | - Mandeep Kaur Marwah
- College of Health and Life Sciences, Aston Medical School, Aston University, Birmingham, UK
- Translational Medicine Research Group, Aston Medical School, Aston University, Birmingham, UK
| |
Collapse
|
42
|
Iqbal A, Bao H, Wang J, Liu H, Liu J, Huang L, Li D. Role of jasmonates in plant response to temperature stress. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2025; 355:112477. [PMID: 40097048 DOI: 10.1016/j.plantsci.2025.112477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2024] [Revised: 03/06/2025] [Accepted: 03/12/2025] [Indexed: 03/19/2025]
Abstract
The ambient temperature exerts a significant influence on the growth and development of plants, which are sessile organisms. Exposure to extreme temperatures, both low and high, has a detrimental impact on plant growth and development, crop yields, and even geographical distribution. Jasmonates constitute a class of lipid hormones that regulate plant tolerance to biotic and abiotic stresses. Recent studies have revealed that jasmonate biosynthesis and signaling pathways are integral to plant responses to both high and low temperatures. Exogenous application of jasmonate improves cold and heat tolerance in plants and reduces cold injury in fruits and vegetables during cold storage. Jasmonate interacts with low and high temperature key response factors and engages in crosstalk with primary and secondary metabolic pathways, including hormones, under conditions of temperature stress. This review presents a comprehensive summary of the jasmonate synthesis and signal transduction pathway, as well as an overview of the functions and mechanisms of jasmonate in response to temperature stress.
Collapse
Affiliation(s)
- Aafia Iqbal
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Henan Bao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Jian Wang
- College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin 150080, China
| | - Huijie Liu
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Jiangtao Liu
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Liqun Huang
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha 410081, China.
| | - Dongping Li
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha 410081, China.
| |
Collapse
|
43
|
Pan Y, Zhang Q, Xu C, Sun Y, Zheng Q, Yang S, Lv S. Exploring Rad51 inhibition mechanisms of B02 and IBR2 and identifying prospective drug candidates for Rad51: A computational investigation. Comput Biol Med 2025; 191:110105. [PMID: 40233679 DOI: 10.1016/j.compbiomed.2025.110105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Revised: 03/22/2025] [Accepted: 03/26/2025] [Indexed: 04/17/2025]
Abstract
Rad51 recombinase is a crucial mediator in homologous recombination, upregulation of Rad51 expression is associated with adverse prognostic outcomes in various types of cancers, rendering it an attractive therapeutic target. Several inhibitors targeting Rad51 have been developed, but their precise interactions with Rad51 at the molecular level and the specific mechanisms by which they inhibit Rad51 function remain largely unexplored. Herein, we employ atomistic molecular simulations, advanced sampling techniques and computational methodologies to elucidate the mechanisms underlying the inhibitory effects of Rad51 inhibitors B02 and IBR2 on Rad51 protein dynamics. Moreover, we leverage multilevel virtual screening strategies to identify potential Rad51 inhibitors from the ChemBL database, emphasizing the pivotal role of key residues within the inhibitor binding pocket for effective inhibitor-protein interaction. Our findings provide insights into the effects of B02 and IBR2 on the molecular dynamics of Rad51 and the alteration of the residue communication network. At the same time, we identified that Cmp-4 and Cmp-9 exhibit dynamics properties similar to Rad51 inhibitors B02 and IBR2, suggesting their potential as candidate therapeutic agents. Our study provides valuable insights into the inhibitory mechanisms of Rad51 inhibitors, offering important theoretical insights for the future development of drugs targeting the Rad51.
Collapse
Affiliation(s)
- Yue Pan
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
| | - Qianhe Zhang
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
| | - Chaojian Xu
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
| | - Yang Sun
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
| | - Qingchuan Zheng
- School of Pharmaceutical Sciences, Jilin University, 2699 Qianjin Street, Changchun, 130012, China; Institute of Theoretical Chemistry, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
| | - Shuo Yang
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
| | - Shaowu Lv
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun, 130012, China; Bioarchaeology Laboratory, Jilin University, 2699 Qianjin Street, Changchun, 130012, China.
| |
Collapse
|
44
|
Chen Q, Chen Y, Zheng Q. The RNA-binding protein LSM family regulating reproductive development via different RNA metabolism. Biochim Biophys Acta Mol Basis Dis 2025; 1871:167808. [PMID: 40139411 DOI: 10.1016/j.bbadis.2025.167808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2024] [Revised: 03/18/2025] [Accepted: 03/18/2025] [Indexed: 03/29/2025]
Abstract
The LSM (Like-Sm) protein family, characterized by highly conserved LSM domains, is integral to ribonucleic acid (RNA) metabolism. Ubiquitously present in both eukaryotes and select prokaryotes, these proteins bind to RNA molecules with high specificity through their LSM domains. They can also form ring-shaped complexes with other proteins, thereby facilitating various fundamental cellular processes such as mRNA degradation, splicing, and ribosome biogenesis. LSM proteins play crucial roles in gametogenesis, early embryonic development, sex determination, gonadal maturation, and reproductive system formation. In pathological conditions, the absence of LSM14B leads to arrest of oocytes at mid-meiosis, downregulation of LSM4 expression is associated with abnormal spermatogenesis, and aberrant expression of LSM1 protein is linked to the occurrence and progression of breast cancer. This review focuses on the recent advances in the functional research of LSM proteins in reproduction.
Collapse
Affiliation(s)
- Qin Chen
- Prenatal Diagnosis Center, The Eighth Affiliated Hospital, Sun Yat-sen University, 3025# Shennan Road, Shenzhen 518033, PR China
| | - Ying Chen
- Prenatal Diagnosis Center, The Eighth Affiliated Hospital, Sun Yat-sen University, 3025# Shennan Road, Shenzhen 518033, PR China
| | - Qingliang Zheng
- Prenatal Diagnosis Center, The Eighth Affiliated Hospital, Sun Yat-sen University, 3025# Shennan Road, Shenzhen 518033, PR China.
| |
Collapse
|
45
|
Ferrari L, Buoli M, Borroni E, Nosari G, Ceresa A, Antonangeli LM, Monti P, Matsagani R, Bollati V, Pesatori AC, Carugno M. DNA methylation of core clock genes in patients with major depressive disorder: Association with air pollution exposure and disease severity. Psychiatry Res 2025; 348:116466. [PMID: 40184933 DOI: 10.1016/j.psychres.2025.116466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2025] [Revised: 03/13/2025] [Accepted: 03/24/2025] [Indexed: 04/07/2025]
Abstract
BACKGROUND Major Depressive Disorder (MDD) is a multifactorial disease which could be influenced by exposure to air pollution through disruption of sleep-wake cycles and other circadian-related behaviors. Our study aimed to investigate the interplay between air pollution exposure, DNA methylation of core clock genes involved in circadian rhythms, and MDD severity. METHODS Four hundred sixteen MDD patients (64 % females) agreed to participate and donated a blood sample to measure DNA methylation of the core clock genes CRY1, PER1, PER2, CLOCK, BMAL1. MDD severity and functioning was assessed using five rating scales. Daily mean estimates of particulate matter with diameter ≤ 2.5 μm (PM2.5) and nitrogen dioxide (NO2) were assigned to study participants based on their residential address, and averaged to estimate different cumulative exposure windows. Multivariate regression models were applied to assess associations between air pollutants and core clock genes methylation and between DNA methylation of those same genes and MDD severity. RESULTS PM2.5 exposure in the six months preceding recruitment was associated with CLOCK hypomethylation (β=-0.11, 95 % confidence interval [CI]:0.20; -0.02) and CRY1 hypermethylation (β=0.32, 95 %CI: 0.06; 0.58). All NO2 exposure windows were associated with CRY1 hypermethylation. Increasing methylation of CLOCK was associated with lower MDD severity considering several scales (e.g., Hamilton Depression Rating Scale: β=-7.21, 95 %CI:3.97; -0.44). CONCLUSIONS Taken together our findings shed some light on the complex mechanism underlying the pathogenesis of MDD, with a potentially relevant role of the environment and of its impact on epigenetic mechanisms altering the expression of core clock genes.
Collapse
Affiliation(s)
- Luca Ferrari
- EPIGET Lab, Department of Clinical Sciences and Community Health, Dipartimento di Eccellenza 2023-2027, University of Milan, Milan, Italy
| | - Massimiliano Buoli
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy; Department of Neurosciences and Mental Health, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Elisa Borroni
- EPIGET Lab, Department of Clinical Sciences and Community Health, Dipartimento di Eccellenza 2023-2027, University of Milan, Milan, Italy
| | - Guido Nosari
- Department of Neurosciences and Mental Health, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Alessandro Ceresa
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Laura Maria Antonangeli
- EPIGET Lab, Department of Clinical Sciences and Community Health, Dipartimento di Eccellenza 2023-2027, University of Milan, Milan, Italy
| | - Paola Monti
- EPIGET Lab, Department of Clinical Sciences and Community Health, Dipartimento di Eccellenza 2023-2027, University of Milan, Milan, Italy
| | - Rachele Matsagani
- EPIGET Lab, Department of Clinical Sciences and Community Health, Dipartimento di Eccellenza 2023-2027, University of Milan, Milan, Italy
| | - Valentina Bollati
- EPIGET Lab, Department of Clinical Sciences and Community Health, Dipartimento di Eccellenza 2023-2027, University of Milan, Milan, Italy; Occupational Health Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Angela Cecilia Pesatori
- EPIGET Lab, Department of Clinical Sciences and Community Health, Dipartimento di Eccellenza 2023-2027, University of Milan, Milan, Italy; Occupational Health Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Michele Carugno
- EPIGET Lab, Department of Clinical Sciences and Community Health, Dipartimento di Eccellenza 2023-2027, University of Milan, Milan, Italy; Occupational Health Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.
| |
Collapse
|
46
|
Nair SR, Nihad M, Shenoy P S, Gupta S, Bose B. Unveiling the effects of micro and nano plastics in embryonic development. Toxicol Rep 2025; 14:101954. [PMID: 40104046 PMCID: PMC11914762 DOI: 10.1016/j.toxrep.2025.101954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2024] [Revised: 02/04/2025] [Accepted: 02/05/2025] [Indexed: 03/20/2025] Open
Abstract
The improper disposal and degradation of plastics causes the formation and spread of micro and nano-sized plastic particles in the ecosystem. The widespread presence of these micro and nanoplastics leads to their accumulation in the biotic and abiotic components of the environment, thereby affecting the cellular and metabolic functions of organisms. Despite being classified as xenobiotic agents, information about their sources and exposure related to reproductive health is limited. Micro and nano plastic exposure during early developmental stages can cause abnormal embryonic development. It can trigger neurotoxicity and inflammatory responses as well in the developing embryo. In embryonic development, a comprehensive study of their role in pluripotency, gastrulation, and multi-differentiation potential is scarce. Due to ethical concerns associated with the direct use of human embryos, pluripotent cells and its 3D in vitro models (with cell lines) are an alternative source for effective research. Thus, the 3D Embryoid body (EB) model provides a platform for conducting embryotoxicity and multi-differentiation potential research. Pluripotent stem cells such as embryonic and induced pluripotent stem cells derived embryoid bodies (EBs) serve as a robust 3D in vitro model that mimics characteristics similar to that of human embryos. Thus, the 3D EB model provides a platform for conducting embryotoxicity and multi-differentiation potential research. Accordingly, this review discusses the significance of 3D in vitro models in conducting effective embryotoxicity research. Further, we also evaluated the possible sources/routes of microplastic generation and analyzed their surface chemistry and cytotoxic effects reported till date.
Collapse
Affiliation(s)
- Sanjay R Nair
- Stem Cells and Regenerative Medicine Centre, Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, Karnataka 575018, India
| | - Muhammad Nihad
- Stem Cells and Regenerative Medicine Centre, Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, Karnataka 575018, India
| | - Sudheer Shenoy P
- Stem Cells and Regenerative Medicine Centre, Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, Karnataka 575018, India
| | - Sebanti Gupta
- Division of Data Analytics, Bioinformatics and Structural Biology, Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, Karnataka 575018, India
| | - Bipasha Bose
- Stem Cells and Regenerative Medicine Centre, Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, Karnataka 575018, India
| |
Collapse
|
47
|
Nguyen SA, Sakata T, Shirahige K, Sutani T. Regulation of pericentromeric DNA loop size via Scc2-cohesin interaction. iScience 2025; 28:112322. [PMID: 40271018 PMCID: PMC12017868 DOI: 10.1016/j.isci.2025.112322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 12/16/2024] [Accepted: 03/26/2025] [Indexed: 04/25/2025] Open
Abstract
Cohesin exhibits DNA loop extrusion when bound to the ATPase activator Scc2 (NIPBL in humans), which has been proposed to organize higher-order chromosome folding. In budding yeast, most chromosome-bound cohesins lack Scc2. How the Scc2-cohesin interaction is regulated on the chromosome and its physiological consequences remain unclear. Here, we show that the deletion of both ECO1 and WPL1, two known cohesin regulators, but not either alone, caused Scc2-cohesin co-localization in metaphase, particularly around centromeres, using calibrated chromatin immunoprecipitation sequencing (ChIP-seq). Eco1's mitotic activity was required to prevent this co-localization in Δwpl1. We also demonstrate that Scc2-cohesin co-localization enlarged pericentromeric DNA loops, linking centromeres to genome sites hundreds of kilobases away, and delayed mitotic chromosome segregation. These findings suggest that Wpl1 and Eco1 cooperatively regulate Scc2-cohesin interaction, restrict pericentromeric DNA loop size, and facilitate chromosome segregation.
Collapse
Affiliation(s)
- Sao Anh Nguyen
- Institute for Quantitative Biosciences, The University of Tokyo 1-1-1 Yayoi, Bunkyo-Ku, Tokyo 113-0032, Japan
| | - Toyonori Sakata
- Institute for Quantitative Biosciences, The University of Tokyo 1-1-1 Yayoi, Bunkyo-Ku, Tokyo 113-0032, Japan
- Department of Cell and Molecular Biology, Karolinska Institutet Tomtebodavägen 16, 171 77 Stockholm, Sweden
| | - Katsuhiko Shirahige
- Institute for Quantitative Biosciences, The University of Tokyo 1-1-1 Yayoi, Bunkyo-Ku, Tokyo 113-0032, Japan
- Department of Cell and Molecular Biology, Karolinska Institutet Tomtebodavägen 16, 171 77 Stockholm, Sweden
| | - Takashi Sutani
- Institute for Quantitative Biosciences, The University of Tokyo 1-1-1 Yayoi, Bunkyo-Ku, Tokyo 113-0032, Japan
| |
Collapse
|
48
|
Pinheiro M, Lopes C, Alves N, Almeida E, Morais H, Ribeiro M, Barros S, Raimundo J, Caetano M, Neuparth T, Santos MM. Microplastics in the deep: Suspended particles affect the model species Mytilus galloprovincialis under hyperbaric conditions. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2025; 373:126195. [PMID: 40185189 DOI: 10.1016/j.envpol.2025.126195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2025] [Revised: 03/28/2025] [Accepted: 04/02/2025] [Indexed: 04/07/2025]
Abstract
Microplastics (MPs) are small plastic particles that result from the degradation of bigger fragments or introduced into the environment as primary particles. Their reduced size makes them available for ingestion by marine organisms, particularly in subtidal and deep-sea environments, which represent the largest sinks for MPs in the ocean. However, there is a lack of data regarding the effects of MPs in subtidal and deep-sea ecosystems. Thus, the present study aimed to assess the effects of MPs under hyperbaric conditions. Juvenile mussels, Mytilus galloprovincialis, were exposed to three concentrations of polyethylene MPs: 0.1, 1 and 10 mg/L, in a mixture of sizes (38-45, 75-90 and 180-212 μm), at different pressures: 1, 4 and 50 Bar, for 96 h. After exposure, the filtration rate, biochemical markers of oxidative stress and transcriptomic profile were analyzed to assess the effects of MPs. Results indicate that MPs affected functional endpoints, with a significant decrease in the filtration rate of mussels exposed to MPs at 1 mg/L and higher. Similarly, all tested oxidative stress biomarkers were affected in a treatment, concentration and pressure-dependent manner. RNA-seq analysis performed in organisms exposed to 1 mg/L of MPs at 4 Bar identified several affected signaling pathways (430 differentially expressed genes) including cellular senescence, the MAPK, RAS PI3K-Akt signaling pathways, apoptosis, among others. Overall, the results here presented corroborate the hypothesis that MPs affect exposed organisms under short-term hyperbaric conditions. These findings highlight the need to study MPs effects in subtidal and deep-sea taxa and address, in future studies, combined effects with other stressors such as contaminants that might be sorbed to the surface of the particles. These findings also indicate that improving hazard assessment of MPs under hyperbaric conditions is paramount to support risk assessment and the implementation of mitigation strategies.
Collapse
Affiliation(s)
- Marlene Pinheiro
- CIIMAR/CIMAR-LA - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos S/N, 4450-208, Matosinhos, Portugal; FCUP - Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre S/N, 4169-007, Porto, Portugal.
| | - Clara Lopes
- CIIMAR/CIMAR-LA - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos S/N, 4450-208, Matosinhos, Portugal; IPMA - Portuguese Institute for Sea and Atmosphere, Rua Alfredo Magalhães Ramalho 6, 1495-165, Algés, Portugal
| | - Nélson Alves
- CIIMAR/CIMAR-LA - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos S/N, 4450-208, Matosinhos, Portugal; FCUP - Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre S/N, 4169-007, Porto, Portugal
| | - Eunice Almeida
- CIIMAR/CIMAR-LA - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos S/N, 4450-208, Matosinhos, Portugal; FCUP - Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre S/N, 4169-007, Porto, Portugal
| | - Hugo Morais
- CIIMAR/CIMAR-LA - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos S/N, 4450-208, Matosinhos, Portugal; FCUP - Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre S/N, 4169-007, Porto, Portugal
| | - Marta Ribeiro
- CIIMAR/CIMAR-LA - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos S/N, 4450-208, Matosinhos, Portugal
| | - Susana Barros
- CIIMAR/CIMAR-LA - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos S/N, 4450-208, Matosinhos, Portugal
| | - Joana Raimundo
- CIIMAR/CIMAR-LA - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos S/N, 4450-208, Matosinhos, Portugal; IPMA - Portuguese Institute for Sea and Atmosphere, Rua Alfredo Magalhães Ramalho 6, 1495-165, Algés, Portugal
| | - Miguel Caetano
- CIIMAR/CIMAR-LA - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos S/N, 4450-208, Matosinhos, Portugal; IPMA - Portuguese Institute for Sea and Atmosphere, Rua Alfredo Magalhães Ramalho 6, 1495-165, Algés, Portugal
| | - Teresa Neuparth
- CIIMAR/CIMAR-LA - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos S/N, 4450-208, Matosinhos, Portugal
| | - Miguel M Santos
- CIIMAR/CIMAR-LA - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos S/N, 4450-208, Matosinhos, Portugal; FCUP - Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre S/N, 4169-007, Porto, Portugal.
| |
Collapse
|
49
|
Scacchi A, Rigoni C, Haataja M, Timonen JVI, Sammalkorpi M. A coarse-grained model for aqueous two-phase systems: Application to ferrofluids. J Colloid Interface Sci 2025; 686:1135-1146. [PMID: 39933351 DOI: 10.1016/j.jcis.2025.01.256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2024] [Revised: 01/29/2025] [Accepted: 01/29/2025] [Indexed: 02/13/2025]
Abstract
Aqueous two-phase systems (ATPSs), phase-separating solutions of water soluble but mutually immiscible molecular species, offer fascinating prospects for selective partitioning, purification, and extraction. Here, we formulate a general Brownian dynamics based coarse-grained simulation model for an ATPS of two water soluble but mutually immiscible polymer species. Including additional solute species into the model is straightforward, which enables capturing the assembly and partitioning response of, e.g., nanoparticles (NPs), additional macromolecular species, or impurities in the ATPS. We demonstrate that the simulation model captures satisfactorily the phase separation, partitioning, and interfacial properties of an actual ATPS using a model ATPS in which a polymer mixture of dextran and polyethylene glycol (PEG) phase separates, and magnetic NPs selectively partition into one of the two polymeric phases. Phase separation and NP partitioning are characterized both via the computational model and experimentally, under different conditions. The simulation model captures the trends observed in the experimental system and quantitatively links the partitioning behavior to the component species interactions. Finally, the simulation model reveals that the ATPS interface fluctuations in systems with magnetic NPs as a partitioned species can be controlled by the magnetic field at length scales much smaller than those probed experimentally to date.
Collapse
Affiliation(s)
- Alberto Scacchi
- Department of Mechanical and Materials Engineering, University of Turku, Vesilinnantie 5, 20500 Turku, Finland; Department of Applied Physics, Aalto University, Konemiehentie 1, 02150 Espoo, Finland; Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland.
| | - Carlo Rigoni
- Department of Applied Physics, Aalto University, Konemiehentie 1, 02150 Espoo, Finland; Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland; Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Mikko Haataja
- Department of Mechanical and Aerospace Engineering, and Princeton Materials Institute (PMI), Princeton University, Princeton, NJ 08544, United States
| | - Jaakko V I Timonen
- Department of Applied Physics, Aalto University, Konemiehentie 1, 02150 Espoo, Finland; Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
| | - Maria Sammalkorpi
- Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland; Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
| |
Collapse
|
50
|
Chen T, Chen J, Guo M, Liu Y, Wang J, Fang Y, Chen Y, Zhang A. IL-33 exerts neuroprotective effects through activation of ST2/AKT signaling axis in microglia after subarachnoid hemorrhage in rats. Neuropharmacology 2025; 269:110336. [PMID: 39947392 DOI: 10.1016/j.neuropharm.2025.110336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Revised: 01/27/2025] [Accepted: 01/27/2025] [Indexed: 02/16/2025]
Abstract
BACKGROUND AND PURPOSE ST2, a member of the interleukin-1 (IL-1) receptor family, along with its ligand IL-33, plays critical roles in immune regulation and inflammatory responses. This study investigates the roles of endogenous IL-33/ST2 signaling in subarachnoid hemorrhage (SAH) and elucidates the underlying mechanisms. METHODS Dynamic changes in endogenous IL-33 levels were examined following SAH induction in vivo. Rats underwent the endovascular perforation model of SAH and were randomly assigned to receive either recombinant IL-33 (rIL-33) or a vehicle, administered intranasally 1 h post-SAH. ST2 siRNA or an AKT selective inhibitor was administered intraperitoneally (i.p.) 48 h prior to SAH induction to explore the potential mechanisms of IL-33-mediated neuroprotection. RESULTS Endogenous IL-33 and ST2 levels were elevated in in vitro models of SAH. Exogenous IL-33 significantly alleviated neuronal apoptosis, reduced brain edema, and enhanced short-term neurofunction in a dose-dependent manner following SAH in rats. CONCLUSION Exogenous rIL-33 alleviates SAH-induced neurological deficits by promoting M2-like polarization of microglia post-SAH. These findings suggest a potential role of the microglial ST2/AKT axis in IL-33-related neuroprotection, which warrants further investigation.
Collapse
Affiliation(s)
- Ting Chen
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China; Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, China
| | - Jiarui Chen
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China; Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, China
| | - Mengchen Guo
- Department of Dermatology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yibo Liu
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China; Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, China
| | - Junjie Wang
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China; Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, China
| | - Yuanjian Fang
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China; Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, China.
| | - Yan Chen
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China; Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, China.
| | - Anke Zhang
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China; Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, China.
| |
Collapse
|