Article
Biochemistry & Molecular Biology
Giuseppina Covello, Gehan H. Ibrahim, Niccolo Bacchi, Simona Casarosa, Michela Alessandra Denti
Summary: Inherited retinal dystrophies are caused by mutations in more than 250 genes, each carrying several types of mutations that can lead to different clinical phenotypes. This study developed an antisense RNA-based therapeutic approach to correct a specific mutation in the RPGR gene, by skipping an alternatively spliced isoform of the mRNA. The results showed the efficacy of U1 antisense snRNAs in mediating exon skipping and correcting the genetic defect in different cell lines, highlighting the importance of choosing appropriate preclinical model systems for testing RNA splicing-correcting therapies.
NUCLEIC ACID THERAPEUTICS
(2022)
Article
Biochemistry & Molecular Biology
Andrew M. Jobbins, Sebastien Campagne, Robert Weinmeister, Christian M. Lucas, Alison R. Gosliga, Antoine Clery, Li Chen, Lucy P. Eperon, Mark J. Hodson, Andrew J. Hudson, Frederic H. T. Allain, Ian C. Eperon
Summary: SRSF1 protein and U1 snRNPs are splicing factors closely related and involved in exon inclusion. SRSF1 can be recruited by U1 snRNP for splicing, regardless of exon sequences, indicating a key role of U1 snRNPs in exon definition in mammalian splicing.
Review
Oncology
Carlos A. Nino, Rossella Scotto di Perrotolo, Simona Polo
Summary: This review summarizes the cancer hotspot mutations in spliceosome components, focusing on the effects of mutations in U1 snRNA, SF3B1, and U2AF1 on splice site selection and cancer development.
Article
Biochemistry & Molecular Biology
Anouk M. Olthof, Alisa K. White, Stephen Mieruszynski, Karen Doggett, Madisen F. Lee, Almahdi Chakroun, Alice K. Abdel Aleem, Justine Rousseau, Cinzia Magnani, Chaim M. Roifman, Philippe M. Campeau, Joan K. Heath, Rahul N. Kanadia
Summary: The study found that the minor spliceosome protein U11-59K binds to the major spliceosome U2AF complex, supporting a model in which the minor spliceosome interacts with the major spliceosome across an exon to regulate splicing. Inhibition of the minor spliceosome leads to exon skipping and formation of aberrant transcripts with premature stop codons, which are not subjected to nonsense-mediated decay. Elevated levels of these alternatively spliced transcripts were detected in individuals with minor spliceosome-related diseases.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biotechnology & Applied Microbiology
Annette D'Arqom, Tiwaporn Nualkaew, Natee Jearawiriyapaisarn, Ryszard Kole, Saovaros Svasti
Summary: Restoration of correct splicing of beta(IVS2-654)-globin pre-mRNA was successfully achieved in thalassemic mice using engineered U7.BP+623 snRNA, but a high level of truncated U7.BP+623 snRNA was also observed. Differences in the processing of modified U7 snRNA between human and mouse constructs hindered the evaluation of pathological improvement in the mouse model.
HUMAN GENE THERAPY
(2021)
Article
Geriatrics & Gerontology
Zhi Cheng, Yingchun Shang, Xinxin Xu, Zhiqiang Dong, Yongwang Zhang, Zhanqiang Du, Xinyi Lu, Tao Zhang
Summary: The study shows that overexpression of U1 snRNA can lead to the formation of aggregates in neurons, causing widespread changes in RNA splicing and impairments in synaptic plasticity and spatial memory. Additionally, U1 snRNA overexpression regulates RNA splicing and gene expression in neurons, potentially by manipulating the recruitment of U1 snRNA to nascent transcripts.
NEUROBIOLOGY OF AGING
(2021)
Article
Biochemical Research Methods
Samuel T. Hatch, Aaron A. Smargon, Gene W. Yeo
Summary: Alternative splicing is an important aspect of transcriptomic diversity, but errors in splicing patterns can have pathological consequences. U1 snRNA has been proposed as a therapeutic and research tool for correcting splicing errors. This study demonstrates a methodological toolkit for perturbing alternative splicing using engineered U1 snRNAs, showing their effectiveness in controlling targeted exons. These findings contribute to the usability and accessibility of U1 snRNA for investigating splicing modulation in eukaryotic cells.
Article
Genetics & Heredity
Olga Artemyeva-Isman, Andrew C. G. Porter
Summary: The imperfect conservation of human pre-mRNA splice sites is necessary for producing alternative isoforms, and U5 plays a significant role in splicing precision and the mechanism of conserved guanines in the pre-catalytic spliceosome. Statistical analyses indicate that U5 snRNA stabilizes the pre-catalytic complex cooperatively with U6 and U2 snRNAs. This new understanding could have potential applications in snRNA therapeutics and gene repair strategies.
FRONTIERS IN GENETICS
(2021)
Review
Cell Biology
Tetsuro Hirose, Kensuke Ninomiya, Shinichi Nakagawa, Tomohiro Yamazaki
Summary: Membraneless organelles (MLOs) are mesoscopic structures detected as dots in cells, which contribute to the compartmentalization of specific biological functions. MLOs undergo phase separation into liquid-like or gel-like phases and contain specific proteins, including intrinsically disordered regions (1DRs), and nucleic acids, primarily RNA. They promote biochemical reactions by sequestering specific factors and simultaneously concentrating substrates and enzymes. MLOs also contribute to the biogenesis of macromolecular machineries essential for gene expression and are functionally interconnected. Understanding MLOs is important for gene regulation and disease therapeutics.
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2023)
Article
Biology
Sarah R. Hansen, David S. White, Mark Scalf, Ivan R. Correa, Lloyd M. Smith, Aaron A. Hoskins, Jonathan P. Staley
Summary: This study investigated the pathway of 5' SS selection by purified yeast U1 snRNP using colocalization single-molecule spectroscopy. The results revealed a sequence-dependent, two-step mechanism for U1 to reversibly select 5' SS, providing a kinetic basis for how U1 may rapidly surveil nascent transcripts for 5' SS.
Article
Genetics & Heredity
Giulia Romano, Federico Riccardi, Erica Bussani, Simone Vodret, Danilo Licastro, Isabella Ragone, Giuseppe Ronzitti, Elisabetta Morini, Susan A. Slaugenhaupt, Franco Pagani
Summary: This study successfully delivered ExSpeU1 small nuclear RNA using AAV9-U1-FD vector in a mouse model of FD, which increased the inclusion of ELP1 exon 20 and production of functional protein. The treatment rescued the majority of FD mouse mortality and improved motor function, renal function, and cardiac function. RNA-seq analysis showed minimal global changes in gene expression and splicing. This therapeutic strategy shows high specificity and potential for treating FD.
AMERICAN JOURNAL OF HUMAN GENETICS
(2022)
Review
Oncology
Yunze Liu, Xin Liu, Changwei Lin, Xianhong Jia, Hongmei Zhu, Jun Song, Yi Zhang
Summary: AS and ncRNAs play crucial roles in cancer by influencing the development of various diseases, especially in different aspects of cancer progression. Acting as regulatory molecules, ncRNAs can affect cell signaling pathways by influencing AS, thus impacting cancer progression.
JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH
(2021)
Article
Multidisciplinary Sciences
Tao Fan, Yu-Zhen Zhao, Jing-Fang Yang, Qin-Lai Liu, Yuan Tian, Das Debatosh, Ying-Gao Liu, Jianhua Zhang, Chen Chen, Mo-Xian Chen, Shao-Ming Zhou
Summary: The study reveals that animal U1-70K genes are conserved in gene and protein structures, expression patterns, and splicing conservation, and may play crucial roles in cancers and juvenile development. Animal U1-70Ks display unique characteristics of single copy number and a splicing isoform, suggesting their specific role in the animal kingdom.
SCIENTIFIC REPORTS
(2021)
Article
Genetics & Heredity
Lise L. Holm, Thomas K. Doktor, Michael B. Hansen, Ulrika S. S. Petersen, Brage S. Andresen
Summary: Study shows that different exons have varying dependencies on splicing regulatory elements and susceptibility to splicing mutations. Factors like balance between enhancers and silencers, intron length, and splice site strength influence exon definition and splicing efficiency. Inherent vulnerabilities of exons should be considered for predicting pathogenic effects of exonic mutations.
Article
Biochemistry & Molecular Biology
Karli A. Lipinski, Jing Chi, Xin Chen, Aaron A. Hoskins, David A. Brow
Summary: U6 small nuclear RNA (snRNA) is a highly conserved component of spliceosomes. It has been traditionally thought that U6 snRNA is synthesized by RNA polymerase III (RNAP III). However, this study demonstrates that U6 snRNA can also be synthesized by RNA polymerase II (RNAP II). The ability to synthesize U6 snRNA with RNAP II provides more flexibility in controlling U6 levels. Furthermore, the formation of U6 snRNPs containing the Sm complex suggests that U6 snRNA synthesized by RNAP II is functional in vivo.
Article
Biochemistry & Molecular Biology
Armin Fuchs, Stefan Riegler, Zahra Ayatollahi, Nicola Cavallari, Luciana E. Giono, Barbara A. Nimeth, Krishna Mutanwad, Alois Schweighofer, Doris Lucyshyn, Andrea Barta, Ezequiel Petrillo, Maria Kalyna
Summary: The study revealed the importance of RNA interference in regulating gene expression, while its interactions with alternative splicing were not well understood. By using amiRNA to knockdown various splice variants of target genes, it was found that some transcript isoforms escaped degradation due to their nuclear localization. The isoforms of alternatively spliced genes that are nuclear localized and sensitive to NMD mask the action of RNA interference.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Genetics & Heredity
Silvia Lombardi, Gabriele Leo, Simone Merlin, Antonia Follenzi, John H. McVey, Iva Maestri, Francesco Bernardi, Mirko Pinotti, Dario Balestra
Summary: This study focused on the pathogenic significance of nucleotide variants within the F8 gene associated with hemophilia A, exploring their pleiotropic effects on protein biology and mRNA splicing. By combining in silico and recombinant expression analyses, the study characterized a large panel of hemophilia A-causing variants within F8 exon 19. The research findings allowed for precise classification of affected individuals and development of personalized therapeutic approaches.
AMERICAN JOURNAL OF HUMAN GENETICS
(2021)
Article
Pharmacology & Pharmacy
Hardy Mitdank, Simko Sama, Meike Troeger, Maria Francesca Testa, Mattia Ferrarese, Dario Balestra, Mirko Pinotti, Alexander Weng
Summary: Minicircle DNA is a promising tool in gene therapy with advantages such as higher transfection efficiency and longer expression time, but its cost-intensive production limits broader use. An optimized production method can lead to high-quality minicircle DNA, which has been investigated for pharmaceutical potential in vitro in a tumor cell model.
INTERNATIONAL JOURNAL OF PHARMACEUTICS
(2021)
Article
Biochemistry & Molecular Biology
Elena Martin, Claudia Vivori, Malgorzata Rogalska, Jorge Herrero-Vicente, Juan Valcarcel
Summary: A study has identified a complex comprising three splicing factors that regulates various alternative splicing events by repressing short exons with suboptimal splice sites. Knockdown of these factors leads to cell apoptosis and growth arrest, indicating their role in efficient cell proliferation through alternative splicing regulation.
Article
Hematology
Barbara Lunghi, Massimo Morfini, Nicola Martinelli, Dario Balestra, Silvia Linari, Sabrina Frusconi, Alessio Branchini, Christian F. Cervellera, Giovanna Marchetti, Giancarlo Castaman, Francesco Bernardi
Summary: The study found that ASGR2 genotypes significantly impact the variability of FVIII PK outcomes, particularly in regulating the distribution of FVIII; frequent ASGR2 genotypes lead to differences in FVIII PK parameters among different genotypes; ASGR2 genotypes still significantly explain a certain proportion of FVIII PK parameter variability even after adjustment.
THROMBOSIS AND HAEMOSTASIS
(2022)
Article
Biochemistry & Molecular Biology
Claudia Sacchetto, Laura Peretto, Francisco Baralle, Iva Maestri, Francesca Tassi, Francesco Bernardi, Stan F. J. van de Graaf, Franco Pagani, Mirko Pinotti, Dario Balestra
Summary: The study revealed that OTC splicing patterns driven by the c.386G>A mutation are influenced by subtle intronic variations, resulting in species-specific effects on splicing and differential responsiveness to engineered U1snRNAs. Before proposing translation of tailored therapeutics from animal models to humans, careful elucidation of molecular mechanisms is essential.
MOLECULAR MEDICINE
(2021)
Article
Genetics & Heredity
Angelisa Frasca, Efterpi Pavlidou, Matteo Bizzotto, Yunan Gao, Dario Balestra, Mirko Pinotti, Hans Atli Dahl, Nicholas D. Mazarakis, Nicoletta Landsberger, Maria Kinali
Summary: CDKL5 deficiency disorder is a neurodevelopmental disorder caused by variations in the X-linked CDKL5 gene, with clinical consequences generally attributed to loss-of-function variations. We identified a female patient with mild epilepsy carrying a novel nucleotide substitution that leads to hyperactivation of CDKL5. This highlights the importance of tight control of CDKL5 activity in the brain.
NEUROLOGY-GENETICS
(2022)
Article
Genetics & Heredity
Giulia Romano, Federico Riccardi, Erica Bussani, Simone Vodret, Danilo Licastro, Isabella Ragone, Giuseppe Ronzitti, Elisabetta Morini, Susan A. Slaugenhaupt, Franco Pagani
Summary: This study successfully delivered ExSpeU1 small nuclear RNA using AAV9-U1-FD vector in a mouse model of FD, which increased the inclusion of ELP1 exon 20 and production of functional protein. The treatment rescued the majority of FD mouse mortality and improved motor function, renal function, and cardiac function. RNA-seq analysis showed minimal global changes in gene expression and splicing. This therapeutic strategy shows high specificity and potential for treating FD.
AMERICAN JOURNAL OF HUMAN GENETICS
(2022)
Review
Genetics & Heredity
Malgorzata Ewa Rogalska, Claudia Vivori, Juan Valcarcel
Summary: This paper reviews the recent progress in understanding the splicing mechanism, discusses the challenges in predicting splice sites, understanding the regulation of splicing, and utilizing this knowledge for exploring gene function and disease treatment.
NATURE REVIEWS GENETICS
(2023)
Review
Immunology
Xing Zhang, Xiao Chen, Zhongliang Wang, Xuanyi Meng, Karin Hoffmann-Sommergruber, Nicola Cavallari, Yong Wu, Jinyan Gao, Xin Li, Hongbing Chen
Summary: Effective delivery of luminal antigens to the underlying immune system is crucial in generating antigen-specific responses in the gut. Goblet cells have been found to form goblet cell-associated antigen passages, allowing luminal antigens to reach subepithelial immune cells and induce specific immune responses. This review summarizes recent research on intestinal GAPs formation and their role in mucosal immunity, providing valuable insights for clinicians and researchers interested in studying the intestinal immune system.
Article
Biochemistry & Molecular Biology
Laura Peretto, Elena Tonetto, Iva Maestri, Valentino Bezzerri, Roberto Valli, Marco Cipolli, Mirko Pinotti, Dario Balestra
Summary: Shwachman-Diamond syndrome (SDS) is a common inherited bone marrow failure syndrome caused by SBDS gene mutations. The mutation in the SBDS c.258+2T>C variant affects splicing, but some correct transcripts can still be produced, explaining the survival of SDS patients. Correction approaches at the RNA and DNA levels, such as engineered U1snRNA, trans-splicing, and base/prime editors, can partially counteract the mutation effect and lead to correctly spliced transcripts. DNA editors, in particular, may offer a potential innovative therapy for SDS by reverting the mutation and potentially selecting bone-marrow cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Barbara Lunghi, Nicole Ziliotto, Dario Balestra, Lucrezia Rossi, Patrizia Della Valle, Pasquale Pignatelli, Mirko Pinotti, Armando D'Angelo, Giovanna Marchetti, Francesco Bernardi
Summary: Whole-exome sequencing in families with unexplained venous thromboembolism can detect low-frequency variants in genes related to hemostasis, providing insights into disease susceptibility.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Vasiliki Papadaki, Zoi Erpapazoglou, Maria Kokkori, Malgorzata Ewa Rogalska, Myrto Potiri, Andrada Birladeanu, Eleni N. Tsakiri, Hassan Ashktorab, Duane T. Smoot, Katerina Papanikolopoulou, Martina Samiotaki, Panagiota Kafasla
Summary: Constant communication between mitochondria and nucleus is crucial for cellular homeostasis and adaptation to mitochondrial stress. This study uncovers a novel regulatory mechanism involving alternative splicing (AS) of the mitochondrial respiratory chain complex I (CI) subunit NDUFS4, controlled by the scaffold protein IQGAP1, which affects mitochondrial respiration in gastric cancer cells. Understanding this mechanism is significant for unraveling mitochondrial quality control in gastric cancer.
Meeting Abstract
Hematology
S. Lombardi, L. Peretto, S. Merlin, A. Follenzi, J. H. Mcvey, I Maestri, F. Bernardi, M. Pinotti, D. Balestra