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
Cell Biology
Sebastian Swirski, Oliver May, Malte Ahlers, Bernd Wissinger, Martin Greschner, Christoph Jueschke, John Neidhardt
Summary: This study evaluated the efficacy and safety of splice factor-based treatments for mutation-induced splice defects in Opa1 mutant mice. The treatment involved using adeno-associated viruses to deliver an engineered U1 snRNA splice factor to retinal cells, resulting in increased wild-type Opa1 transcripts and protein levels without observable side-effects. These findings suggest that U1 snRNA-based therapies hold promise as in vivo therapeutics for inherited retinal diseases.
Article
Multidisciplinary Sciences
Jason Wong, William Martelly, Shalini Sharma
Summary: The protocol describes a cellular assay for monitoring splicing efficiency, which can be applied to study fundamental splicing mechanisms and related diseases. Disease-associated 5' splice-site mutations can be introduced into the reporter to determine their impact, and these mutations can be suppressed by co-transfection with U1 snRNA construct carrying compensatory mutations.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2021)
Article
Multidisciplinary Sciences
Luba Farberov, Daphna Weissglas-Volkov, Guy Shapira, Yazeed Zoabi, Chen Schiff, Barbara Kloeckener-Gruissem, John Neidhardt, Noam Shomron
Summary: The splicing of transcripts is catalyzed by the spliceosome, and can be modulated by pre-microRNAs interacting with U1 snRNA. This interaction reduces the binding affinity of U1 snRNA to 5'SS, leading to the inclusion of exons containing 5'SS.
Article
Oncology
Mateo Paz-Cabezas, Tania Calvo-Lopez, Alejandro Romera-Lopez, Daniel Tabas-Madrid, Jesus Ogando, Maria-Jesus Fernandez-Acenero, Javier Sastre, Alberto Pascual-Montano, Santos Manes, Eduardo Diaz-Rubio, Beatriz Perez-Villamil
Summary: This study demonstrates the potential of microRNA profiling in defining colorectal cancer subtypes and identifies microRNA targets associated with a specific subtype. The findings highlight the importance of miRNAs in colorectal cancer stratification and treatment.
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)
Article
Oncology
Fazlur Rahman Talukdar, Sheila C. Soares Lima, Rita Khoueiry, Ruhina Shirin Laskar, Cyrille Cuenin, Bruna Pereira Sorroche, Anne-Claire Boisson, Behnoush Abedi-Ardekani, Christine Carreira, Diana Menya, Charles P. Dzamalala, Mathewos Assefa, Abraham Aseffa, Vera Miranda-Goncalves, Carmen Jeronimo, Rui M. Henrique, Ramin Shakeri, Reza Malekzadeh, Nagla Gasmelseed, Mona Ellaithi, Nitin Gangane, Daniel R. S. Middleton, Florence Le Calvez-Kelm, Akram Ghantous, Maria Leon Roux, Joachim Schuz, Valerie McCormack, M. Iqbal Parker, Luis Felipe Ribeiro Pinto, Zdenko Herceg
Summary: This study investigated tumor-specific DNA methylation in ESCC cases from high-incidence countries, identifying thousands of differentially methylated positions and regions, particularly in gene regions associated with transcription activation. Prioritized genes for replication showed consistent methylation differences and downregulation in tumors. The study highlights the potential of these DNA methylation events as tumor-specific markers for further biomarker discovery.
Article
Gastroenterology & Hepatology
Jessica Roelands, Manon Van der Ploeg, Marieke E. Ijsselsteijn, Hao Dang, Jurjen J. Boonstra, James C. H. Hardwick, Lukas J. A. C. Hawinkels, Hans Morreau, Noel F. C. C. de Miranda
Summary: Spatial profiling of pT1 CRC samples revealed the molecular and immunological landscape of early-stage colorectal cancer, identifying biomarkers associated with disease progression and targetable immune processes applicable in a clinical setting.
Article
Chemistry, Multidisciplinary
Eric Rovira, Beatriz Moreno, Nerea Razquin, Lorea Blazquez, Ruben Hernandez-Alcoceba, Puri Fortes, Fernando Pastor
Summary: Synthetic riboswitches are promising regulatory devices that can finely tune gene expression without the need for external factors. By engineering tetracycline-inducible riboswitches and using a technique called SEREX, we were able to achieve significant inductions in gene expression. Multiplexing riboswitches further enhanced inductions. These U1i-based riboswitches are reversible and dose-dependent, making them attractive tools for gene therapy applications.
Article
Oncology
Birandra K. Sinha, Erik J. Tokar, Jianying Li, Pierre R. Bushel
Summary: The nitric oxide donor NCX4040 exhibits cytotoxicity towards ovarian tumor cells by generating reactive oxygen species and inducing DNA damage. It also depletes cellular glutathione and induces oxidative stress, resulting in tumor cell death. NCX4040 treatment leads to the induction of oxidative stress genes, inflammatory response genes, DNA damage response genes, and MAP kinase response genes.
Article
Biotechnology & Applied Microbiology
Dania Vazquez-Blomquist, Ailyn C. Ramon, Mauro Rosales, George V. Perez, Ailenis Rosales, Daniel Palenzuela, Yasser Perera, Silvio E. Perea
Summary: This study analyzed the gene expression profile regulated by CIGB-300 peptide in HL-60 and OCI-AML3 cell lines using Clariom S HT assay. The results showed that the effect of CIGB-300 on cells is dependent on cell type and treatment duration, influencing biological processes and pathways such as apoptosis, cell cycle, leukocyte differentiation, signaling by cytokines/interleukins, and NF-kB and TNF signaling pathways.
Review
Biochemistry & Molecular Biology
Rania Bassiouni, Lee D. Gibbs, David W. Craig, John D. Carpten, Troy A. McEachron
Summary: Spatial transcriptional profiling is a method that provides gene expression information within tissue architecture, making it well suited for studying solid tumors. It can investigate spatial relationships among cell populations and reveal spatial patterns of relevant oncogenic genetic events. The broad utility and flexibility of this approach have been reflected in the development of various strategies and commercial platforms, allowing its widespread applicability in research settings.
Article
Veterinary Sciences
Nilendu Paul, Arumugam Kumaresan, Mohua Das Gupta, Pradeep Nag, Pushpa Rani Guvvala, Channareddi Kuntareddi, Ankur Sharma, Sellappan Selvaraju, Tirtha Kumar Datta
Summary: This study identified significant differences in sperm functional attributes and transcriptomic profiles between high- and low-fertile buffalo bulls. Low-fertile bulls exhibited lower sperm membrane and acrosomal integrity, higher protamine deficiency and lipid peroxidation. Transcriptomic analysis revealed dysregulation of transcripts related to binding activity, transcription, translation, and metabolic processes in low-fertile bull spermatozoa, with pathways like MAPK signaling, ribosome pathway, and oxidative phosphorylation being affected. Validation of the results was conducted through real-time qPCR expression analysis of selected genes.
FRONTIERS IN VETERINARY SCIENCE
(2021)
Article
Health Care Sciences & Services
Rassanee Bissanum, Sitthichok Chaichulee, Rawikant Kamolphiwong, Raphatphorn Navakanitworakul, Kanyanatt Kanokwiroon
Summary: TNBC lacks well-defined molecular targets and is highly heterogeneous, making treatment challenging. This study attempted to define gene signatures for each TNBC subtype and develop a classification method using machine learning. SVM algorithm achieved the highest accuracy in classifying TNBC into four subtypes, but some samples could not be classified.
JOURNAL OF PERSONALIZED MEDICINE
(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
Biochemistry & Molecular Biology
Zhi Cheng, Zhanqiang Du, Yingchun Shang, Yuling Zhang, Tao Zhang
JOURNAL OF MOLECULAR NEUROSCIENCE
(2017)
Article
Genetics & Heredity
Zhi Cheng, Yingchun Shang, Shan Gao, Tao Zhang
JOURNAL OF NEUROGENETICS
(2017)
Article
Multidisciplinary Sciences
Ze Chen, Yu Sun, Xiaojun Yang, Zhenfeng Wu, Kaifei Guo, Xiaoran Niu, Qingsong Wang, Jishou Ruan, Wenjun Bu, Shan Gao
Article
Genetics & Heredity
Xiaoran Niu, Yu Sun, Ze Chen, Rugang Li, Chellappan Padmanabhan, Jishou Ruan, Jan F. Kreuze, KaiShu Ling, ZhangJun Fei, Shan Gao
Letter
Biochemistry & Molecular Biology
Qi Zhao, Yu Sun, Dawei Wang, Hongwan Zhang, Kai Yu, Jian Zheng, Zhixiang Zuo
JOURNAL OF GENETICS AND GENOMICS
(2018)
Article
Cell Biology
Shan Gao, Xiaoxuan Tian, Hong Chang, Yu Sun, Zhenfeng Wu, Zhi Cheng, Pengzhi Dong, Qiang Zhao, Jishou Ruan, Wenjun Bu
Article
Neurosciences
Zhi Cheng, Zhanqiang Du, Baohui Zhai, Zhuo Yang, Tao Zhang
NEUROSCIENCE RESEARCH
(2018)
Article
Biochemical Research Methods
Qi Zhao, Yu Sun, Zekun Liu, Hongwan Zhang, Xingyang Li, Kaiyu Zhu, Ze-Xian Liu, Jian Ren, Zhixiang Zuo
BRIEFINGS IN BIOINFORMATICS
(2020)
Article
Biochemistry & Molecular Biology
Xiufeng Jin, Zhi Cheng, Bo Wang, Tung On Yau, Ze Chen, Stephen C. Barker, Defu Chen, Wenjun Bu, Daqing Sun, Shan Gao
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)
Review
Microbiology
Zhiwei Liang, Michael Siegert, Wenwen Fang, Yu Sun, Feng Jiang, Hui Lu, Guang-Hao Chen, Shanquan Wang
FEMS MICROBIOLOGY ECOLOGY
(2018)
Article
Biology
Hua Wang, Kunshan Zhang, Yifei Liu, Yudong Fu, Shan Gao, Peng Gong, Haiying Wang, Zhongcheng Zhou, Ming Zeng, Zhenfeng Wu, Yu Sun, Tong Chen, Siguang Li, Lin Liu