Article
Biochemistry & Molecular Biology
Karan Bedi, Brian Magnuson, Ishwarya Venkata Narayanan, Michelle T. Paulsen, Thomas E. Wilson, Mats Ljungman
Summary: This study investigated cotranscriptional splicing efficiencies of 17,000 introns expressed across six human cell lines using Bru-seq and BruChase-seq. Less than half of all introns were found to be cotranscriptionally spliced. The efficiency of splicing varied across cell lines and within genes, and was not correlated with gene length, intron position, splice site strengths, or GC content. Binding signals from RNA-binding proteins were found to correlate with splicing efficiency, suggesting their important roles in determining splicing outcomes in a cell type- and intron-specific manner.
Article
Biochemistry & Molecular Biology
Xianhui Ruan, Yue Huang, Lin Geng, Mengran Tian, Yu Liu, Mei Tao, Xiangqian Zheng, Peng Li, Min Zhao
Summary: Single-cell transcriptome sequencing provides higher resolution for cellular differences in papillary thyroid carcinoma. Through integrative analysis of two datasets, we identified 31 consistently differentially expressed genes across multiple cell types, which are related to adaptive immune response and autoimmune thyroid diseases. Experimental validation suggests that KRT7 may be a potential biomarker for PTC epithelial cells.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Hematology
Tobias Kull, Arne Wehling, Martin Etzrodt, Markus Auler, Philip Dettinger, Nicola Aceto, Timm Schroeder
Summary: This research discovers the heterogeneous signaling dynamics response in primary hematopoietic stem and progenitor cells, and different cell types show specific responses to the same signaling inputs. Additionally, oscillatory signaling dynamics can influence cell behavior.
Article
Biochemistry & Molecular Biology
Lingyu Qiu, Chen Liang, Yidong Zheng, Huayu Kang, Aiyue Chen, Chunlin Chen, Xinlong Wang, Jielin Yang, Qiongfang Fang, Xinjie Hui, Yueming Hu, Zewei Chen, Ou Sha, Wei-Guo Zhu, Yejun Wang
Summary: This research systematically investigates stable expressed genes (SEGs) in humans at the single-cell level and observes their specificity in development, tissue, and cell types. The study identifies a list of 408 spatial-temporal SEGs and finds development-specific SEGs as well as tissue-specific SEGs with immune and RNA splicing functions. The research also explores the application of SEGs in cell decomposition and accurately predicts the proportions of major immune cells in peripheral blood samples.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biology
Davia Blake, Caleb M. Radens, Max B. Ferretti, Matthew R. Gazzara, Kristen W. Lynch
Summary: The study investigates the impact of CD28 costimulation on alternative splicing in T cells activated through the T cell receptor (TCR). It is found that CD28 signaling has minimal impact on splicing alone but enhances the extent of change in TCR-induced alternative splicing events. Interestingly, enhanced splicing events occur within genes encoding key components of the apoptotic signaling pathway. Experimental evidence shows that isoforms induced by CD3/CD28 costimulation promote resistance to apoptosis and changes in these genes function combinatorially to further promote cell viability. The JNK signaling pathway is also found to be required for these splicing events, highlighting their co-regulation.
Article
Genetics & Heredity
Shunuo Zhang, Yixin Zhang, Peiru Min
Summary: In this study, the biological characteristics during Hypertrophic scar (HS) formation were investigated through the integrative analysis of single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq data. The study revealed that FB-1 fibroblasts were significantly expanded in HS, while the proportion of KC-2 keratinocytes was reduced. Cell-cell communication analysis showed changes in the autocrine signaling of HB-1 and the intercellular contacts between FB-1/FB-5 and KC-2 in HS. The transcriptionally regulatory network involved CREB3L1 and TWIST2 as critical transcription factors in myofibroblast formation in HS.
FRONTIERS IN GENETICS
(2022)
Article
Biology
Gonzalo Benegas, Jonathan Fischer, Yun S. Song
Summary: This study investigates alternative splicing in diverse murine cell types using two large-scale single-cell datasets and accounting for technical artifacts and unannotated events. The study finds that alternative splicing is prevalent and cell-type-specific, complementary to total gene expression, and identifies a large number of novel splicing events. The study also builds a predictive model based on splicing factor activity, revealing known interactions and suggesting regulatory roles for novel alternative splicing events in critical genes.
Article
Biology
Julia Eve Olivieri, Roozbeh Dehghannasiri, Peter L. Wang, SoRi Jang, Antoine de Morree, Serena Y. Tan, Jingsi Ming, Angela Ruohao Wu, Tabula Sapiens Consortium, Stephen R. Quake, Mark A. Krasnow, Julia Salzman
Summary: The study utilized a new statistical approach called SpliZ to detect and validate cell-type-specific splicing in multiple human tissues, demonstrating that splicing is regulated at the level of cell type.
Article
Biochemistry & Molecular Biology
Mai Baker, Mayra Petasny, Nadeen Taqatqa, Mercedes Bentata, Gillian Kay, Eden Engal, Yuval Nevo, Ahmad Siam, Sara Dahan, Maayan Salton
Summary: Changes in the cellular environment lead to alterations in chromatin structure, impacting gene expression and alternative splicing. KDM3A, as a chromatin sensor, plays a crucial role in regulating gene expression and splicing factor binding in response to environmental cues.
Article
Nanoscience & Nanotechnology
Xiangfei Guo, Linbang Wang, Honghao Yang, Guanping He
Summary: This study investigates the potential biological mechanisms involved in the treatment of osteosarcoma (OS) using zinc oxide nanoparticles (ZnO NPs). Through RNA-seq analysis, we identified differentially expressed genes (DEGs) in ZnO NPs-treated OS cell lines. Gene Ontology (GO) analysis revealed the regulation of transcription factors and extracellular space in both OS cell lines. KEGG analysis showed the enrichment of MAPK, Toll-like receptor, and NF-kappa B pathways. PPI analysis highlighted the involvement of HMOX1, MAFB, CXCL10, and CXCL11 in OS cells treated with ZnO NPs. This study sheds light on the potential antitumor mechanisms and provides more targets for the treatment of OS.
JOURNAL OF BIOMEDICAL NANOTECHNOLOGY
(2023)
Article
Nanoscience & Nanotechnology
Ufafa Anggarini, Liang Yu, Hiroki Nagasawa, Masakoto Kanezashi, Toshinori Tsuru
Summary: In this study, nickel-doped aminosilica membranes were prepared using different terminal amine ligands, and the differences in ligand structures significantly affected the formation of coordinated structures. The coordination of short and rigid pendant amino groups with nickel resulted in the formation of subnanopores, while longer and sterically hindered aminosilica precursors likely underwent an ion-exchange interaction. The basicity of amine precursors also influenced the development of a coordinated network.
ACS APPLIED MATERIALS & INTERFACES
(2022)
Article
Multidisciplinary Sciences
Rebecca L. Wilson, Victor Yuan, Jennifer A. Courtney, Alyssa Tipler, James F. Cnota, Helen N. Jones
Summary: This study identified commonly expressed genes between first trimester fetal heart and placenta cells using single cell sequencing data, and found enrichment in pathways related to vasculature development and angiogenesis. Additionally, common genes and biological processes were discovered between specific types of placenta cells and cardiomyocytes.
SCIENTIFIC REPORTS
(2022)
Article
Biotechnology & Applied Microbiology
Yong Liu, Jing Huang, Rajan Pandey, Pengyuan Liu, Bhavika Therani, Qiongzi Qiu, Sridhar Rao, Aron M. Geurts, Allen W. Cowley Jr, Andrew S. Greene, Mingyu Liang
Summary: This study found that in order to accurately identify differentially expressed genes (DEGs) with various characteristics in single-cell clusters, there need to be at least 2000 cells. However, for the majority of DEGs with extremely small p values or transcript abundance greater than a few hundred transcripts per million in bulk RNA-seq analysis, clusters with as few as 50-100 cells may be sufficient.
Article
Oncology
Yeongjoo Kim, Seungjae Shin, Sunyoung Kwon, Kisung Moon, Su -Vin Baek, Ahyoung Jo, Hyung-Sik Kim, Gue-Ho Hwang, Sangsu Bae, Yun Hak Kim, Sung-Yup Cho, Jung-Min Oh
Summary: N-6-methyladenosine (m6A) modification in RNA affects gene expression and RNA metabolism. This modification is regulated by various proteins, including writers, erasers, and readers. In this study, the authors investigated the effects of m6A modification on alternative splicing in cancer cells and found that METTL3 regulates m6A-dependent alternative splicing, particularly in cell cycle-related genes, through the modulation of splicing factors such as SFPQ.
AMERICAN JOURNAL OF CANCER RESEARCH
(2023)
Article
Biotechnology & Applied Microbiology
Carrie A. Whittle, Arpita Kulkarni, Nina Chung, Cassandra G. Extavour
Summary: This study in crickets revealed that optimal codons are commonly shared among different tissue types and sexes, with the highest frequency in gonadal genes. The use of non-optimal codons was found to be elevated in genes with specialized functions, potentially promoting translational upregulation. Furthermore, the interdependent evolution of amino acid frequency, tRNA gene copy number, and amino acid biosynthetic costs was observed, indicating potential translational optimization in this insect model.
Review
Ophthalmology
Edward H. Wood, Alexander Kreymerman, Tia Kowal, David Buickians, Yang Sun, Stephanie Muscat, Mark Mercola, Darius M. Moshfeghi, Jeffrey L. Goldberg
Summary: Optogenetics is a technique that combines genetics and optics to manipulate specific events in cells, tissues, or animals. While its primary application in ophthalmology is for treating inherited retinal diseases, it also holds promise for other eye diseases such as cellular regeneration, mitochondrial and metabolism modulation, intraocular pressure regulation, and pain control.
PROGRESS IN RETINAL AND EYE RESEARCH
(2023)
Article
Ophthalmology
Arthur Brant, Natasha Kolomeyer, Jeffrey L. Goldberg, Julia Haller, Cecilia S. Lee, Aaron Y. Lee, Alice C. Lorch, Flora Lum, Joan W. Miller, David W. Parke II, Leslie Hyman, Suzann Pershing
Summary: This study evaluates the associations between patient characteristics and United States eye care use and likelihood of blindness. It found that visual impairment and blindness are related to age, geographical location, insurance, and ethnicity. Minorities and Black individuals may be underrepresented among ophthalmology patients, highlighting the need for initiatives to address disparities in use and blindness.
Article
Ophthalmology
Yang Sun, David Wirta, Wendy Murahashi, Vidhu Mathur, Sethu Sankaranarayanan, Lori K. Taylor, Ted Yednock, Donald S. Fong, Jeffrey L. Goldberg
Summary: This study evaluated the safety, tolerability, ocular pharmacokinetics, and pharmacodynamics of ANX007 in glaucoma patients. The results showed that ANX007 injections were safe, well-tolerated, and effectively blocked the activation of the complement system. This study provides important guidance for further treatment of neurodegenerative eye diseases.
OPHTHALMOLOGY SCIENCE
(2023)
Article
Ophthalmology
Ying Zhu, Julian Garcia-Sanchez, Roopa Dalal, Yang Sun, Michael S. Kapiloff, Jeffrey L. Goldberg, Wendy W. Liu
Summary: PIEZO1 and PIEZO2 are mechanosensitive ion channels that may play important roles in ocular function and intraocular pressure regulation. This study used single-molecule fluorescence in situ hybridization (smFISH) and transgenic reporter mice to compare the expression and localization of PIEZO1 and PIEZO2 in mouse ocular tissues relevant to glaucoma. The results suggest that PIEZO1 and PIEZO2 are differentially expressed and may have distinct roles as mechanosensors in glaucoma-relevant ocular tissues.
EXPERIMENTAL EYE RESEARCH
(2023)
Article
Ophthalmology
Michelle T. Sun, Suzann Pershing, Jeffrey L. Goldberg, Sophia Y. Wang
Summary: The study found that in patients with Primary Open-Angle Glaucoma (POAG), those with Type 2 Diabetes Mellitus (T2DM) required more glaucoma surgeries, especially with higher baseline HbA1c levels and insulin use.
Review
Neurosciences
Jonathan R. Soucy, Erika A. Aguzzi, Julie Cho, Michael James Gilhooley, Casey Keuthan, Ziming Luo, Aboozar Monavarfeshani, Meher A. Saleem, Xue-Wei Wang, Juilette Wohlschlegel, Petr Baranov, Adriana Di Polo, Brad Fortune, Kimberly K. Gokoffski, Jeffrey L. Goldberg, William Guido, Alex L. Kolodkin, Carol A. Mason, Yvonne Ou, Thomas A. Reh, Ahmara G. Ross, Brian C. Samuels, Derek Welsbie, Donald J. Zack, Thomas V. Johnson
Summary: This article discusses the key questions and challenges in restoring vision through RGC repopulation and proposes a multidisciplinary approach to advance the field. The efforts of the RReSTORe Consortium provide a comprehensive roadmap for treating patients with optic neuropathies.
MOLECULAR NEURODEGENERATION
(2023)
Article
Ophthalmology
Jeffrey L. Goldberg, Gala Beykin, Kellie R. Satterfield, Mariana Nunez, Byron L. Lam, Thomas A. Albini
Summary: This study evaluated the safety and efficacy of a ciliary neurotrophic factor (CNTF) intraocular implant in patients with glaucoma. The implant was well tolerated and showed improvements in both structural and functional outcomes.
OPHTHALMOLOGY SCIENCE
(2023)
Article
Ophthalmology
Anthony M. Norcia, Alexandra Yakovleva, Naz Jehangir, Jeffrey L. Goldberg
Summary: This study found that glaucoma in human patients preferentially damages OFF visual pathways, which is consistent with previous findings from animal experimental models, patient electroretinogram (ERG), and retinal imaging data.
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2022)
Meeting Abstract
Ophthalmology
Ziming Luo, Kun-Che Chang, Bogdan Tanasa, Jeffrey L. Goldberg
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2022)
Meeting Abstract
Ophthalmology
Niranchana Manivannan, Gary C. Lee, Thomas Callan, Birgit Sandhoefner, Kyung Rim Sung, Gala Beykin, Kenny Trang, Gilda Lai, Gadi Wollstein, Hiroshi Ishikawa, Ronald Zambrano, Ezekiel Ede, Christopher Leung, Jeffrey L. Goldberg, Joel S. Schuman
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2022)
Meeting Abstract
Ophthalmology
Bryan Dev Gopal, Tingwei Zhang, Anthony Norcia, Jeffrey L. Goldberg, Alfredo Dubra, Hao Zhang, Brian Soetikno
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2022)
Meeting Abstract
Ophthalmology
Luciano Custo Greig, Mollie Woodworth, Jeffrey L. Goldberg, Sui Wang
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2022)
Meeting Abstract
Ophthalmology
Kathleen Heng, BaoXiang Li, Xin Xia, Rain Wen, Ashley Nies, Albert Y. Wu, Jeffrey L. Goldberg
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2022)
Meeting Abstract
Ophthalmology
Trent Mangubat Jarin, Ke Ning, Ziming Luo, Tia Kowal, BaoXiang Li, Yang Hu, Albert Y. Wu, Jeffrey L. Goldberg, Yang Sun
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2022)
Meeting Abstract
Ophthalmology
Minjuan Bian, Emma Huie, Michael Nahmou, Jeffrey L. Goldberg
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2022)