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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.
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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.
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Zhao W, Lin L, Kelly KM, Opsasnick LA, Needham BL, Liu Y, Sen S, Smith JA. Epigenome-wide association study of perceived discrimination in the Multi-Ethnic Study of Atherosclerosis (MESA). Epigenetics 2025; 20:2445447. [PMID: 39825881 DOI: 10.1080/15592294.2024.2445447] [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: 06/24/2024] [Revised: 12/11/2024] [Accepted: 12/16/2024] [Indexed: 01/20/2025] Open
Abstract
Perceived discrimination, recognized as a chronic psychosocial stressor, has adverse consequences on health. DNA methylation (DNAm) may be a potential mechanism by which stressors get embedded into the human body at the molecular level and subsequently affect health outcomes. However, relatively little is known about the effects of perceived discrimination on DNAm. To identify the DNAm sites across the epigenome that are associated with discrimination, we conducted epigenome-wide association analyses (EWAS) of three discrimination measures (everyday discrimination, race-related major discrimination, and non-race-related major discrimination) in 1,151 participants, including 565 non-Hispanic White, 221 African American, and 365 Hispanic individuals, from the Multi-Ethnic Study of Atherosclerosis (MESA). We conducted both race/ethnicity-stratified analyses as well as trans-ancestry meta-analyses. At false discovery rate of 10%, 7 CpGs and 4 differentially methylated regions (DMRs) containing 11 CpGs were associated with perceived discrimination exposures in at least one racial/ethnic group or in meta-analysis. Identified CpGs and/or nearby genes have been implicated in cellular development pathways, transcription factor binding, cancer and multiple autoimmune and/or inflammatory diseases. Of the identified CpGs (7 individual CpGs and 11 within DMRs), two CpGs and one CpG within a DMR were associated with expression of cis genes NDUFS5, AK1RIN1, NCF4 and ADSSL1. Our study demonstrated the potential influence of discrimination on DNAm and subsequent gene expression.
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Affiliation(s)
- Wei Zhao
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Lisha Lin
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Kristen M Kelly
- Institute for Behavioral Genetics, University of Colorado, Boulder, CO, USA
| | - Lauren A Opsasnick
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Belinda L Needham
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Yongmei Liu
- Department of Medicine, Divisions of Cardiology and Neurology, Duke University Medical Center, Durham, NC, USA
| | - Srijan Sen
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
| | - Jennifer A Smith
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
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Nguyen TD, Winek MA, Rao MK, Dhyani SP, Lee MY. Nuclear envelope components in vascular mechanotransduction: emerging roles in vascular health and disease. Nucleus 2025; 16:2453752. [PMID: 39827403 DOI: 10.1080/19491034.2025.2453752] [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: 10/08/2024] [Revised: 01/08/2025] [Accepted: 01/09/2025] [Indexed: 01/22/2025] Open
Abstract
The vascular network, uniquely sensitive to mechanical changes, translates biophysical forces into biochemical signals for vessel function. This process relies on the cell's architectural integrity, enabling uniform responses to physical stimuli. Recently, the nuclear envelope (NE) has emerged as a key regulator of vascular cell function. Studies implicate nucleoskeletal elements (e.g. nuclear lamina) and the linker of nucleoskeleton and cytoskeleton (LINC) complex in force transmission, emphasizing nucleo-cytoskeletal communication in mechanotransduction. The nuclear pore complex (NPC) and its component proteins (i.e. nucleoporins) also play roles in cardiovascular disease (CVD) progression. We herein summarize evidence on the roles of nuclear lamina proteins, LINC complex members, and nucleoporins in endothelial and vascular cell mechanotransduction. Numerous studies attribute NE components in cytoskeletal-related cellular behaviors to insinuate dysregulation of nucleocytoskeletal feedback and nucleocytoplasmic transport as a mechanism of endothelial and vascular dysfunction, and hence implications for aging and vascular pathophysiology.
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Affiliation(s)
- Tung D Nguyen
- Department of Physiology and Biophysics, The University of Illinois at Chicago - College of Medicine, Chicago, IL, USA
- The Center for Cardiovascular Research, The University of Illinois at Chicago - College of Medicine, Chicago, IL, USA
| | - Michael A Winek
- Department of Physiology and Biophysics, The University of Illinois at Chicago - College of Medicine, Chicago, IL, USA
| | - Mihir K Rao
- Department of Physiology and Biophysics, The University of Illinois at Chicago - College of Medicine, Chicago, IL, USA
| | - Shaiva P Dhyani
- Department of Physiology and Biophysics, The University of Illinois at Chicago - College of Medicine, Chicago, IL, USA
| | - Monica Y Lee
- Department of Physiology and Biophysics, The University of Illinois at Chicago - College of Medicine, Chicago, IL, USA
- The Center for Cardiovascular Research, The University of Illinois at Chicago - College of Medicine, Chicago, IL, USA
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Zhang S, Miao L, Tian X, Yang B, Luo B. Opportunities and challenges of immuno-oncology: A bibliometric analysis from 2014 to 2023. Hum Vaccin Immunother 2025; 21:2440203. [PMID: 39885669 PMCID: PMC11792843 DOI: 10.1080/21645515.2024.2440203] [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: 09/11/2024] [Revised: 11/22/2024] [Accepted: 12/06/2024] [Indexed: 02/01/2025] Open
Abstract
The emergence of immuno-oncology (IO) has led to revolutionary changes in the field of cancer treatment. Despite notable advancements in this field, a thorough exploration of its full depth and extent has yet to be performed. This study provides a comprehensive overview of publications pertaining to IO. Publications on IO from 2014 to 2023 were retrieved by searching the Web of Science Core Collection database (WoSCC). VOSviewer software and Citespace software were used for the visualized analysis. A total of 1,874 articles have been published in the IO domain. The number of publications and citations has been increasing annually. This study also examines the primary research directions within the field of IO. In conclusion, this study offers a comprehensive overview of the opportunities and challenges associated with IO, illuminating the current status of research and indicating potential future trajectories in this rapidly progressing field. This study provides a comprehensive survey of the current research status and hot spots within the field of IO. It will assist researchers in comprehending the current research emphasis and development trends in this field and offers guidance for future research directions.
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Affiliation(s)
- Siqi Zhang
- School of Clinical Traditional Chinese Medicine, Hubei University of Chinese Medicine, Wuhan, China
- Department of Oncology, Affiliated Hospital of Hubei University of Chinese Medicine, Wuhan, China
- Department of Oncology, Hubei Province Academy of Traditional Chinese Medicine, Wuhan, China
| | - Lina Miao
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiaoxia Tian
- School of Clinical Traditional Chinese Medicine, Hubei University of Chinese Medicine, Wuhan, China
| | - Bingxu Yang
- School of Clinical Traditional Chinese Medicine, Hubei University of Chinese Medicine, Wuhan, China
| | - Baoping Luo
- School of Clinical Traditional Chinese Medicine, Hubei University of Chinese Medicine, Wuhan, China
- Department of Oncology, Affiliated Hospital of Hubei University of Chinese Medicine, Wuhan, China
- Department of Oncology, Hubei Province Academy of Traditional Chinese Medicine, Wuhan, China
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Huang C, Chu LM, Liang B, Wu HL, Li BS, Ren S, Hou ML, Nie HC, Kong LY, Fan LQ, Du J, Zhu WB. Comparative genetic analysis of blood and semen samples in sperm donors from Hunan, China. Ann Med 2025; 57:2447421. [PMID: 39757988 PMCID: PMC11721621 DOI: 10.1080/07853890.2024.2447421] [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: 10/18/2023] [Revised: 11/17/2024] [Accepted: 11/22/2024] [Indexed: 01/07/2025] Open
Abstract
OBJECTIVES At present, most genetic tests or carrier screening are performed with blood samples, and the known carrier rate of disease-causing variants is also derived from blood. For semen donors, what is really passed on to offspring is the pathogenic variant in their sperm. This study aimed to determine whether pathogenic variants identified in the sperm of young semen donors are also present in their blood, and whether matching results for blood are consistent with results for sperm. METHODS We included 40 paired sperm and blood samples from 40 qualified semen donors at the Hunan Province Human Sperm Bank of China. All samples underwent exome sequencing (ES) analysis, and the pathogenicity was assessed according to the American College of Medical Genetics (ACMG) guidelines. Scoring for sperm donation matching, which was based on gene scoring and variant scoring, was also used to assess the consistency of sperm and blood genetic test results. RESULTS A total of 108 pathogenic (P)/likely pathogenic (LP) variants in 82 genes were identified. The highest carrier had 7 variants, and there was also one donor did not carry any P/LP variant. On average, each donor carried 2.7 P/LP variants. Among all the P/LP variants, missense mutation was the dominant type and most of them were located in exonic regions. Chromosome 1 harboured the largest number of variants and no pathogenic copy number variants (CNV) was identified in semen donors. The P/LP variant of all the 40 semen donors was consistent by comparing sperm and blood. Except for one case that was slightly different, the rest simulated matching results for blood were all consistent with results for sperm. CONCLUSIONS It is reasonable to choose either blood or sperm for genetic screening in semen donors.
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Affiliation(s)
- Chuan Huang
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive & Genetic Hospital of International Trust and Investment Corporation (CITIC)-Xiangya, Changsha, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Li-Ming Chu
- Basecare Medical Device Co., Ltd, Suzhou, China
| | - Bo Liang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hui-Lan Wu
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive & Genetic Hospital of International Trust and Investment Corporation (CITIC)-Xiangya, Changsha, China
| | - Bai-Shun Li
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive & Genetic Hospital of International Trust and Investment Corporation (CITIC)-Xiangya, Changsha, China
| | - Shuai Ren
- Basecare Medical Device Co., Ltd, Suzhou, China
| | | | - Hong-Chuan Nie
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive & Genetic Hospital of International Trust and Investment Corporation (CITIC)-Xiangya, Changsha, China
| | | | - Li-Qing Fan
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive & Genetic Hospital of International Trust and Investment Corporation (CITIC)-Xiangya, Changsha, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Juan Du
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive & Genetic Hospital of International Trust and Investment Corporation (CITIC)-Xiangya, Changsha, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Wen-Bing Zhu
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive & Genetic Hospital of International Trust and Investment Corporation (CITIC)-Xiangya, Changsha, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Sciences, Central South University, Changsha, China
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Sharma NK, Singh P, Saha B, Bhardwaj A, Iquebal MA, Pal Y, Nayan V, Jaiswal S, Giri SK, Legha RA, Bhattacharya TK, Kumar D, Rai A. Genome wide landscaping of copy number variations for horse inter-breed variability. Anim Biotechnol 2025; 36:2446251. [PMID: 39791493 DOI: 10.1080/10495398.2024.2446251] [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: 06/27/2023] [Accepted: 12/18/2024] [Indexed: 01/12/2025]
Abstract
Copy number variations (CNVs) have become widely acknowledged as a significant source of genomic variability and phenotypic variance. To understand the genetic variants in horses, CNVs from six Indian horse breeds, namely, Manipuri, Zanskari, Bhutia, Spiti, Kathiawari and Marwari were discovered using Axiom™ Equine Genotyping Array. These breeds differed in agro-climatic adaptation with distinct phenotypic characters. A total of 2668 autosomal CNVs and 381 CNV regions (CNVRs) were identified with PennCNV tool. DeepCNV was employed to re-validate to get 883 autosomal CNVs, of which 9.06% were singleton type. A total of 180 CNVRs were identified after DeepCNV filtering with the estimated length of 3.12 Kb-4.90 Mb. The functional analysis showed the majority of the CNVRs genes enriched for sensory perception and olfactory receptor activity. An Equine CNVs database, EqCNVdb (http://backlin.cabgrid.res.in/eqcnvdb/) was developed which catalogues detailed information on the horse CNVs, CNVRs and gene content within CNVRs. Also, three random CNVRs were validated with real-time polymerase chain reaction. These findings will aid in the understanding the horse genome and serve as a preliminary foundation for future CNV association research with commercially significant equine traits. The identification of CNVs and CNVRs would lead to better insights into genetic basis of important traits.
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Affiliation(s)
- Nitesh Kumar Sharma
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
- The Graduate School, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Prashant Singh
- ICAR-National Research Centre on Equines, Hisar, Haryana, India
| | - Bibek Saha
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | - Mir Asif Iquebal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Yash Pal
- ICAR-National Research Centre on Equines, Hisar, Haryana, India
| | - Varij Nayan
- ICAR-Central Institute for Research on Buffaloes, Hisar, Haryana, India
| | - Sarika Jaiswal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Shiv Kumar Giri
- Department of Biotechnology, Maharaja Agrasen University, Baddi (Solan), Himachal Pradesh, India
| | | | | | - Dinesh Kumar
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anil Rai
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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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.
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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
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Hartasánchez DA, Dumond M, Dubrulle N, Monéger F, Boudaoud A. Highly expressed cell wall genes contribute to robustness of sepal size. PLANT SIGNALING & BEHAVIOR 2025; 20:2446858. [PMID: 39739543 DOI: 10.1080/15592324.2024.2446858] [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: 11/04/2024] [Revised: 12/18/2024] [Accepted: 12/19/2024] [Indexed: 01/02/2025]
Abstract
Reproducibility in organ size and shape is a fascinating trait of living organisms. The mechanisms underlying such robustness remain, however, to be elucidated. Taking the sepal of Arabidopsis as a model, we investigated whether variability of gene expression plays a role in variation of organ size and shape. Previous work from our team identified cell-wall related genes as being enriched among the genes whose expression is highly variable. We then hypothesized that the variation of measured morphological parameters in cell-wall related single knockout mutants could be correlated with the variation in gene expression of the corresponding gene (the knocked-out gene) in wild-type plants. We analyzed sepal size and shape from 16 cell-wall mutants and found that sepal size variability correlates positively, not with gene expression variation, but with mean gene expression of the corresponding gene in wild type. These findings support a contribution of cell-wall related genes to the robustness of sepal size.
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Affiliation(s)
- Diego A Hartasánchez
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, UCBL, Lyon, France
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Mathilde Dumond
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, UCBL, Lyon, France
| | - Nelly Dubrulle
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, UCBL, Lyon, France
| | - Françoise Monéger
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, UCBL, Lyon, France
| | - Arezki Boudaoud
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, UCBL, Lyon, France
- LadHyX, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau Cedex, France
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9
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Li D, Chu X, Liu W, Ma Y, Tian X, Yang Y. The regulatory roles of RNA-binding proteins in the tumour immune microenvironment of gastrointestinal malignancies. RNA Biol 2025; 22:1-14. [PMID: 39718205 DOI: 10.1080/15476286.2024.2440683] [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: 11/03/2024] [Accepted: 12/04/2024] [Indexed: 12/25/2024] Open
Abstract
The crosstalk between the tumour immune microenvironment (TIME) and tumour cells promote immune evasion and resistance to immunotherapy in gastrointestinal (GI) tumours. Post-transcriptional regulation of genes is pivotal to GI tumours progression, and RNA-binding proteins (RBPs) serve as key regulators via their RNA-binding domains. RBPs may exhibit either anti-tumour or pro-tumour functions by influencing the TIME through the modulation of mRNAs and non-coding RNAs expression, as well as post-transcriptional modifications, primarily N6-methyladenosine (m6A). Aberrant regulation of RBPs, such as HuR and YBX1, typically enhances tumour immune escape and impacts prognosis of GI tumour patients. Further, while targeting RBPs offers a promising strategy for improving immunotherapy in GI cancers, the mechanisms by which RBPs regulate the TIME in these tumours remain poorly understood, and the therapeutic application is still in its early stages. This review summarizes current advances in exploring the roles of RBPs in regulating genes expression and their effect on the TIME of GI tumours, then providing theoretical insights for RBP-targeted cancer therapies.
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Affiliation(s)
- Dongqi Li
- Department of Hepatobiliary and Pancreatic Surgery, Peking University First Hospital, Beijing, China
| | - Xiangyu Chu
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Weikang Liu
- Department of Hepatobiliary and Pancreatic Surgery, Peking University First Hospital, Beijing, China
| | - Yongsu Ma
- Department of Hepatobiliary and Pancreatic Surgery, Peking University First Hospital, Beijing, China
| | - Xiaodong Tian
- Department of Hepatobiliary and Pancreatic Surgery, Peking University First Hospital, Beijing, China
| | - Yinmo Yang
- Department of Hepatobiliary and Pancreatic Surgery, Peking University First Hospital, Beijing, China
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10
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Li L, Xu X, Cheng P, Yu Z, Li M, Yu Z, Cheng W, Zhang W, Sun H, Song X. Klebsiella pneumoniae derived outer membrane vesicles mediated bacterial virulence, antibiotic resistance, host immune responses and clinical applications. Virulence 2025; 16:2449722. [PMID: 39792030 PMCID: PMC11730361 DOI: 10.1080/21505594.2025.2449722] [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: 07/01/2024] [Revised: 11/14/2024] [Accepted: 12/28/2024] [Indexed: 01/12/2025] Open
Abstract
Klebsiella pneumoniae is a gram-negative pathogen that can cause multiple diseases including sepsis, urinary tract infections, and pneumonia. The escalating detections of hypervirulent and antibiotic-resistant isolates are giving rise to growing public concerns. Outer membrane vesicles (OMVs) are spherical vesicles containing bioactive substances including lipopolysaccharides, peptidoglycans, periplasmic and cytoplasmic proteins, and nucleic acids. Emerging studies have reported various roles of OMVs in bacterial virulence, antibiotic resistance, stress adaptation, and host interactions, whereas knowledge on their roles in K. pneumoniae is currently unclear. In this review, we summarized recent progress on the biogenesis, components, and biological function of K. pneumoniae OMVs, the impact and action mechanism in virulence, antibiotic resistance, and host immune response. We also deliberated on the potential of K. pneumoniae OMVs in vaccine development, as diagnostic biomarkers, and as drug nanocarriers. In conclusion, K. pneumoniae OMVs hold great promise in the prevention and control of infectious diseases, which merits further investigation.
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Affiliation(s)
- Lifeng Li
- Henan International Joint Laboratory of Children’s Infectious Diseases, Department of Neonatology, Henan Province Engineering Research Center of Diagnosis and Treatment of Pediatric Infection and Critical Care, Children’s Hospital Affiliated to Zhengzhou University, Henan Children’s Hospital, Zhengzhou Children’s Hospital, Zhengzhou, China
| | - Xinxiu Xu
- Department of Neurology, Qingdao Hospital, University of Health and Rehabilitation Sciences, Qingdao, China
| | - Ping Cheng
- Henan International Joint Laboratory of Children’s Infectious Diseases, Department of Neonatology, Henan Province Engineering Research Center of Diagnosis and Treatment of Pediatric Infection and Critical Care, Children’s Hospital Affiliated to Zhengzhou University, Henan Children’s Hospital, Zhengzhou Children’s Hospital, Zhengzhou, China
| | - Zengyuan Yu
- Henan International Joint Laboratory of Children’s Infectious Diseases, Department of Neonatology, Henan Province Engineering Research Center of Diagnosis and Treatment of Pediatric Infection and Critical Care, Children’s Hospital Affiliated to Zhengzhou University, Henan Children’s Hospital, Zhengzhou Children’s Hospital, Zhengzhou, China
| | - Mingchao Li
- Henan International Joint Laboratory of Children’s Infectious Diseases, Department of Neonatology, Henan Province Engineering Research Center of Diagnosis and Treatment of Pediatric Infection and Critical Care, Children’s Hospital Affiliated to Zhengzhou University, Henan Children’s Hospital, Zhengzhou Children’s Hospital, Zhengzhou, China
| | - Zhidan Yu
- Henan International Joint Laboratory of Children’s Infectious Diseases, Department of Neonatology, Henan Province Engineering Research Center of Diagnosis and Treatment of Pediatric Infection and Critical Care, Children’s Hospital Affiliated to Zhengzhou University, Henan Children’s Hospital, Zhengzhou Children’s Hospital, Zhengzhou, China
| | - Weyland Cheng
- Henan International Joint Laboratory of Children’s Infectious Diseases, Department of Neonatology, Henan Province Engineering Research Center of Diagnosis and Treatment of Pediatric Infection and Critical Care, Children’s Hospital Affiliated to Zhengzhou University, Henan Children’s Hospital, Zhengzhou Children’s Hospital, Zhengzhou, China
| | - Wancun Zhang
- Henan International Joint Laboratory of Children’s Infectious Diseases, Department of Neonatology, Henan Province Engineering Research Center of Diagnosis and Treatment of Pediatric Infection and Critical Care, Children’s Hospital Affiliated to Zhengzhou University, Henan Children’s Hospital, Zhengzhou Children’s Hospital, Zhengzhou, China
| | - Huiqing Sun
- Henan International Joint Laboratory of Children’s Infectious Diseases, Department of Neonatology, Henan Province Engineering Research Center of Diagnosis and Treatment of Pediatric Infection and Critical Care, Children’s Hospital Affiliated to Zhengzhou University, Henan Children’s Hospital, Zhengzhou Children’s Hospital, Zhengzhou, China
| | - Xiaorui Song
- Henan International Joint Laboratory of Children’s Infectious Diseases, Department of Neonatology, Henan Province Engineering Research Center of Diagnosis and Treatment of Pediatric Infection and Critical Care, Children’s Hospital Affiliated to Zhengzhou University, Henan Children’s Hospital, Zhengzhou Children’s Hospital, Zhengzhou, China
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11
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Herzog MKM, Peters A, Shayya N, Cazzaniga M, Kaka Bra K, Arora T, Barthel M, Gül E, Maurer L, Kiefer P, Christen P, Endhardt K, Vorholt JA, Frankel G, Heimesaat MM, Bereswill S, Gahan CGM, Claesson MJ, Domingo-Almenara X, Hardt WD. Comparing Campylobacter jejuni to three other enteric pathogens in OligoMM 12 mice reveals pathogen-specific host and microbiota responses. Gut Microbes 2025; 17:2447832. [PMID: 39835346 DOI: 10.1080/19490976.2024.2447832] [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: 10/02/2024] [Revised: 12/13/2024] [Accepted: 12/23/2024] [Indexed: 01/22/2025] Open
Abstract
Campylobacter jejuni, non-typhoidal Salmonella spp., Listeria monocytogenes and enteropathogenic/enterohemorrhagic Escherichia coli (EPEC/EHEC) are leading causes of food-borne illness worldwide. Citrobacter rodentium has been used to model EPEC and EHEC infection in mice. The gut microbiome is well-known to affect gut colonization and host responses to many food-borne pathogens. Recent progress has established gnotobiotic mice as valuable models to study how microbiota affect the enteric infections by S. Typhimurium, C. rodentium and L. monocytogenes. However, for C. jejuni, we are still lacking a suitable gnotobiotic mouse model. Moreover, the limited comparability of data across laboratories is often negatively affected by variations between different research facilities or murine microbiotas. In this study, we applied the standardized gnotobiotic OligoMM12 microbiota mouse model and compared the infections in the same facility. We provide evidence of robust colonization and significant pathological changes in OligoMM12 mice following infection with these pathogens. Moreover, we offer insights into pathogen-specific host responses and metabolite signatures, highlighting the advantages of a standardized mouse model for direct comparisons of factors influencing the pathogenesis of major food-borne pathogens. Notably, we reveal for the first time that C. jejuni stably colonizes OligoMM12 mice, triggering inflammation. Additionally, our comparative approach successfully identifies pathogen-specific responses, including the detection of genes uniquely associated with C. jejuni infection in humans. These findings underscore the potential of the OligoMM12 model as a versatile tool for advancing our understanding of food-borne pathogen interactions.
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Affiliation(s)
- Mathias K-M Herzog
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Audrey Peters
- Department of Life Sciences, MRC Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Nizar Shayya
- Gastrointestinal Microbiology Research Group, Institute of Microbiology, Infectious Diseases and Immunology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Monica Cazzaniga
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Kardokh Kaka Bra
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Trisha Arora
- Omic Sciences Unit, EURECAT - Technology Centre of Catalonia, Reus, Spain
| | - Manja Barthel
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Ersin Gül
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Luca Maurer
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Patrick Kiefer
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Philipp Christen
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Katharina Endhardt
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Julia A Vorholt
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Gad Frankel
- Department of Life Sciences, MRC Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Markus M Heimesaat
- Gastrointestinal Microbiology Research Group, Institute of Microbiology, Infectious Diseases and Immunology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Stefan Bereswill
- Gastrointestinal Microbiology Research Group, Institute of Microbiology, Infectious Diseases and Immunology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Cormac G M Gahan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
- School of Pharmacy, University College Cork, Cork, Ireland
| | - Marcus J Claesson
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | | | - Wolf-Dietrich Hardt
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
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12
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Yang Y, Zhong Y, Chen L. EIciRNAs in focus: current understanding and future perspectives. RNA Biol 2025; 22:1-12. [PMID: 39711231 DOI: 10.1080/15476286.2024.2443876] [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: 11/14/2024] [Accepted: 12/09/2024] [Indexed: 12/24/2024] Open
Abstract
Circular RNAs (circRNAs) are a unique class of covalently closed single-stranded RNA molecules that play diverse roles in normal physiology and pathology. Among the major types of circRNA, exon-intron circRNA (EIciRNA) distinguishes itself by its sequence composition and nuclear localization. Recent RNA-seq technologies and computational methods have facilitated the detection and characterization of EIciRNAs, with features like circRNA intron retention (CIR) and tissue-specificity being characterized. EIciRNAs have been identified to exert their functions via mechanisms such as regulating gene transcription, and the physiological relevance of EIciRNAs has been reported. Within this review, we present a summary of the current understanding of EIciRNAs, delving into their identification and molecular functions. Additionally, we emphasize factors regulating EIciRNA biogenesis and the physiological roles of EIciRNAs based on recent research. We also discuss the future challenges in EIciRNA exploration, underscoring the potential for novel functions and functional mechanisms of EIciRNAs for further investigation.
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Affiliation(s)
- Yan Yang
- Department of Cardiology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
- Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, China
| | - Yinchun Zhong
- Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, China
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
| | - Liang Chen
- Department of Cardiology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
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13
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Khan W, Kanwar S, Mannan MM, Kabir F, Iqbal N, Nadeem Rajab Ali M, Zia SR, Mian S, Aziz F, Muneer S, Kalam A, Hussain A, Javed I, Qazi MF, Khalid J, Nisar MI, Jehan F. Identification of differentially expressed non-coding RNAs in the plasma of women with preterm birth. RNA Biol 2025; 22:1-8. [PMID: 39804675 PMCID: PMC11730358 DOI: 10.1080/15476286.2024.2449278] [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: 12/24/2024] [Accepted: 12/27/2024] [Indexed: 01/16/2025] Open
Abstract
This study aimed to identify differentially expressed non-coding RNAs (ncRNAs) associated with preterm birth (PTB) and determine biological pathways being influenced in the context of PTB. We processed cell-free RNA sequencing data and identified seventeen differentially expressed (DE) ncRNAs that could be involved in the onset of PTB. Per the validation via customized RT-qPCR, the recorded variations in expressions of eleven ncRNAs were concordant with the in-silico analyses. The results of this study provide insights into the role of DE ncRNAs and their impact on pregnancy-related biological pathways that could lead to PTB. Further studies are required to elucidate the precise mechanisms by which these DE ncRNAs contribute to adverse pregnancy outcomes (APOs) and their potential as diagnostic biomarkers.
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Affiliation(s)
- Waqasuddin Khan
- Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Pakistan
| | - Samiah Kanwar
- Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Pakistan
| | - Mohammad Mohsin Mannan
- Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Pakistan
| | - Furqan Kabir
- Infectious Diseases Research Lab (IDRL), Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Pakistan
| | - Naveed Iqbal
- Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Pakistan
| | - Mehdia Nadeem Rajab Ali
- Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Pakistan
| | - Syeda Rehana Zia
- Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Pakistan
| | - Sharmeen Mian
- Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Pakistan
| | - Fatima Aziz
- Infectious Diseases Research Lab (IDRL), Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Pakistan
| | - Sahrish Muneer
- Infectious Diseases Research Lab (IDRL), Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Pakistan
| | - Adil Kalam
- Infectious Diseases Research Lab (IDRL), Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Pakistan
| | - Akram Hussain
- Infectious Diseases Research Lab (IDRL), Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Pakistan
| | - Iqra Javed
- Infectious Diseases Research Lab (IDRL), Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Pakistan
| | - Muhammad Farrukh Qazi
- Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Pakistan
| | - Javairia Khalid
- Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Pakistan
| | - Muhammad Imran Nisar
- Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Pakistan
| | - Fyezah Jehan
- Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Pakistan
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14
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Prince N, Peralta Marzal LN, Roussin L, Monnoye M, Philippe C, Maximin E, Ahmed S, Salenius K, Lin J, Autio R, Adolfs Y, Pasterkamp RJ, Garssen J, Naudon L, Rabot S, Kraneveld AD, Perez-Pardo P. Mouse strain-specific responses along the gut-brain axis upon fecal microbiota transplantation from children with autism. Gut Microbes 2025; 17:2447822. [PMID: 39773319 PMCID: PMC11730631 DOI: 10.1080/19490976.2024.2447822] [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: 07/18/2024] [Revised: 12/03/2024] [Accepted: 12/23/2024] [Indexed: 01/11/2025] Open
Abstract
Several factors are linked to the pathophysiology of autism spectrum disorders (ASD); however, the molecular mechanisms of the condition remain unknown. As intestinal problems and gut microbiota dysbiosis are associated with ASD development and severity, recent studies have focused on elucidating the microbiota-gut-brain axis' involvement. This study aims to explore mechanisms through which gut microbiota might influence ASD. Briefly, we depleted the microbiota of conventional male BALB/cAnNCrl (Balb/c) and C57BL/6J (BL/6) mice prior to human fecal microbiota transplantation (hFMT) with samples from children with ASD or their neurotypical siblings. We found mouse strain-specific responses to ASD hFMT. Notably, Balb/c mice exhibit decreased exploratory and social behavior, and show evidence of intestinal, systemic, and central inflammation accompanied with metabolic shifts. BL/6 mice show less changes after hFMT. Our results reveal that gut microbiota alone induce changes in ASD-like behavior, and highlight the importance of mouse strain selection when investigating multifactorial conditions like ASD.
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Affiliation(s)
- Naika Prince
- Division of Pharmacology, Faculty of Science, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Lucia N. Peralta Marzal
- Division of Pharmacology, Faculty of Science, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Léa Roussin
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Magali Monnoye
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Catherine Philippe
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Elise Maximin
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Sabbir Ahmed
- Division of Pharmacology, Faculty of Science, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Karoliina Salenius
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - Jake Lin
- Health Sciences, Faculty of Social Sciences, Tampere University, Tampere, Finland
| | - Reija Autio
- Health Sciences, Faculty of Social Sciences, Tampere University, Tampere, Finland
| | - Youri Adolfs
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, Netherlands
| | - R. Jeroen Pasterkamp
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, Netherlands
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