1
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Edman NI, Phal A, Redler RL, Schlichthaerle T, Srivatsan SR, Ehnes DD, Etemadi A, An SJ, Favor A, Li Z, Praetorius F, Gordon M, Vincent T, Marchiano S, Blakely L, Lin C, Yang W, Coventry B, Hicks DR, Cao L, Bethel N, Heine P, Murray A, Gerben S, Carter L, Miranda M, Negahdari B, Lee S, Trapnell C, Zheng Y, Murry CE, Schweppe DK, Freedman BS, Stewart L, Ekiert DC, Schlessinger J, Shendure J, Bhabha G, Ruohola-Baker H, Baker D. Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies. Cell 2024; 187:3726-3740.e43. [PMID: 38861993 PMCID: PMC11246234 DOI: 10.1016/j.cell.2024.05.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/14/2024] [Accepted: 05/13/2024] [Indexed: 06/13/2024]
Abstract
Many growth factors and cytokines signal by binding to the extracellular domains of their receptors and driving association and transphosphorylation of the receptor intracellular tyrosine kinase domains, initiating downstream signaling cascades. To enable systematic exploration of how receptor valency and geometry affect signaling outcomes, we designed cyclic homo-oligomers with up to 8 subunits using repeat protein building blocks that can be modularly extended. By incorporating a de novo-designed fibroblast growth factor receptor (FGFR)-binding module into these scaffolds, we generated a series of synthetic signaling ligands that exhibit potent valency- and geometry-dependent Ca2+ release and mitogen-activated protein kinase (MAPK) pathway activation. The high specificity of the designed agonists reveals distinct roles for two FGFR splice variants in driving arterial endothelium and perivascular cell fates during early vascular development. Our designed modular assemblies should be broadly useful for unraveling the complexities of signaling in key developmental transitions and for developing future therapeutic applications.
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Affiliation(s)
- Natasha I Edman
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98195, USA; Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Ashish Phal
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Rachel L Redler
- Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA
| | - Thomas Schlichthaerle
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Sanjay R Srivatsan
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Devon Duron Ehnes
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Ali Etemadi
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Medical Biotechnology Department, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Seong J An
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Andrew Favor
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Zhe Li
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Florian Praetorius
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Max Gordon
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Thomas Vincent
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Division of Nephrology, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Silvia Marchiano
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Leslie Blakely
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Chuwei Lin
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Wei Yang
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Brian Coventry
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Derrick R Hicks
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Longxing Cao
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Neville Bethel
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Piper Heine
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Analisa Murray
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Stacey Gerben
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Marcos Miranda
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Babak Negahdari
- Medical Biotechnology Department, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Sangwon Lee
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Allen Discovery Center for Cell Lineage Tracing, Seattle, WA 98109, USA
| | - Ying Zheng
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Center for Cardiovascular Biology, University of Washington, Seattle WA 98109, USA
| | - Charles E Murry
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Center for Cardiovascular Biology, University of Washington, Seattle WA 98109, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA; Department of Medicine/Cardiology, University of Washington, Seattle WA 98195, USA
| | - Devin K Schweppe
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Benjamin S Freedman
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Division of Nephrology, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA; Kidney Research Institute, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Lance Stewart
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Damian C Ekiert
- Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA; Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA
| | - Joseph Schlessinger
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Allen Discovery Center for Cell Lineage Tracing, Seattle, WA 98109, USA
| | - Gira Bhabha
- Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA
| | - Hannele Ruohola-Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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2
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Jiang J, Wu H, Ji Y, Han K, Tang JM, Hu S, Lei W. Development and disease-specific regulation of RNA splicing in cardiovascular system. Front Cell Dev Biol 2024; 12:1423553. [PMID: 39045460 PMCID: PMC11263117 DOI: 10.3389/fcell.2024.1423553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 06/17/2024] [Indexed: 07/25/2024] Open
Abstract
Alternative splicing is a complex gene regulatory process that distinguishes itself from canonical splicing by rearranging the introns and exons of an immature pre-mRNA transcript. This process plays a vital role in enhancing transcriptomic and proteomic diversity from the genome. Alternative splicing has emerged as a pivotal mechanism governing complex biological processes during both heart development and the development of cardiovascular diseases. Multiple alternative splicing factors are involved in a synergistic or antagonistic manner in the regulation of important genes in relevant physiological processes. Notably, circular RNAs have only recently garnered attention for their tissue-specific expression patterns and regulatory functions. This resurgence of interest has prompted a reevaluation of the topic. Here, we provide an overview of our current understanding of alternative splicing mechanisms and the regulatory roles of alternative splicing factors in cardiovascular development and pathological process of different cardiovascular diseases, including cardiomyopathy, myocardial infarction, heart failure and atherosclerosis.
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Affiliation(s)
- Jinxiu Jiang
- Department of Cardiovascular Surgery of the First Affiliated Hospital and Institute for Cardiovascular Science, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College, Soochow University, Suzhou, China
| | - Hongchun Wu
- Department of Cardiovascular Surgery of the First Affiliated Hospital and Institute for Cardiovascular Science, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College, Soochow University, Suzhou, China
| | - Yabo Ji
- Department of Cardiovascular Surgery of the First Affiliated Hospital and Institute for Cardiovascular Science, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College, Soochow University, Suzhou, China
| | - Kunjun Han
- Department of Cardiovascular Surgery of the First Affiliated Hospital and Institute for Cardiovascular Science, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College, Soochow University, Suzhou, China
| | - Jun-Ming Tang
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Shijun Hu
- Department of Cardiovascular Surgery of the First Affiliated Hospital and Institute for Cardiovascular Science, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College, Soochow University, Suzhou, China
| | - Wei Lei
- Department of Cardiovascular Surgery of the First Affiliated Hospital and Institute for Cardiovascular Science, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College, Soochow University, Suzhou, China
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3
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Mi Y, Dong M, Zuo X, Cao Q, Gu X, Mi H, Xiao F. Genome-wide identification and analysis of epithelial-mesenchymal transition-related RNA-binding proteins and alternative splicing in a human breast cancer cell line. Sci Rep 2024; 14:11753. [PMID: 38783078 PMCID: PMC11116388 DOI: 10.1038/s41598-024-62681-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024] Open
Abstract
Exploring the mechanism of breast cancer metastasis and searching for new drug therapeutic targets are still the focuses of current research. RNA-binding proteins (RBPs) may affect breast cancer metastasis by regulating alternative splicing (AS) during epithelial-mesenchymal transition (EMT). We hypothesised that during EMT development in breast cancer cells, the expression level of RBPs and the gene AS pattern in the cell were significantly changed on a genome-wide scale. Using GEO database, this study identified differentially expressed RBPs and differential AS events at different stages of EMT in breast cancer cells. By establishing the correlation network of differential RBPs and differential AS events, we found that RBM47, PCBP3, FRG1, SRP72, RBMS3 and other RBPs may regulate the AS of ITGA6, ADGRE5, TNC, COL6A3 and other cell adhesion genes. By further analysing above EMT-related RBPs and AS in breast cancer tissues in TCGA, it was found that the expression levels of ADAT2, C2orf15, SRP72, PAICS, RBMS3, APOBEC3G, NOA1, ACO1 and the AS of TNC and COL6A3 were significantly correlated with the prognosis of breast cancer patients. The expression levels of all 8 RBPs were significantly different in breast cancer tissues without metastasis compared with normal breast tissues. Conclusively, eight RBPs such as RBMS3 and AS of TNC and COL6A3 could be used as predictors of breast cancer prognosis. These findings need to be further explored as possible targets for breast cancer treatment.
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Affiliation(s)
- Yin Mi
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe Road, Zhengzhou, 450052, China.
| | - Meilian Dong
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe Road, Zhengzhou, 450052, China
| | - Xiaoxiao Zuo
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe Road, Zhengzhou, 450052, China
| | - Qinchen Cao
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe Road, Zhengzhou, 450052, China
| | - Xiaobin Gu
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe Road, Zhengzhou, 450052, China
| | - Hailong Mi
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Fankai Xiao
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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4
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Sakamuri SSVP, Sure VN, Oruganti L, Wisen W, Chandra PK, Liu N, Fonseca VA, Wang X, Klein J, Katakam PVG. Acute severe hypoglycemia alters mouse brain microvascular proteome. J Cereb Blood Flow Metab 2024; 44:556-572. [PMID: 37944245 PMCID: PMC10981402 DOI: 10.1177/0271678x231212961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 09/12/2023] [Accepted: 10/05/2023] [Indexed: 11/12/2023]
Abstract
Hypoglycemia increases the risk related to stroke and neurodegenerative diseases, however, the underlying mechanisms are unclear. For the first time, we studied the effect of a single episode (acute) of severe (ASH) and mild (AMH) hypoglycemia on mouse brain microvascular proteome. After four-hour fasting, insulin was administered (i.p) to lower mean blood glucose in mice and induce ∼30 minutes of ASH (∼30 mg/dL) or AMH (∼75 mg/dL), whereas a similar volume of saline was given to control mice (∼130 mg/dL). Blood glucose was allowed to recover over 60 minutes either spontaneously or by 20% dextrose administration (i.p). Twenty-four hours later, the brain microvessels (BMVs) were isolated, and tandem mass tag (TMT)-based quantitative proteomics was performed using liquid chromatography-mass spectrometry (LC/MS). When compared to control, ASH significantly downregulated 13 proteins (p ≤ 0.05) whereas 23 proteins showed a strong trend toward decrease (p ≤ 0.10). When compared to AMH, ASH significantly induced the expression of 35 proteins with 13 proteins showing an increasing trend. AMH downregulated only 3 proteins. ASH-induced downregulated proteins are involved in actin cytoskeleton maintenance needed for cell shape and migration which are critical for blood-brain barrier maintenance and angiogenesis. In contrast, ASH-induced upregulated proteins are RNA-binding proteins involved in RNA splicing, transport, and stability. Thus, ASH alters BMV proteomics to impair cytoskeletal integrity and RNA processing which are critical for cerebrovascular function.
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Affiliation(s)
- Siva SVP Sakamuri
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Venkata N Sure
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Lokanatha Oruganti
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA
| | - William Wisen
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Partha K Chandra
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA
- Neuroscience Program, Tulane Brain Institute, Tulane University, New Orleans, LA, USA
| | - Ning Liu
- Neuroscience Program, Tulane Brain Institute, Tulane University, New Orleans, LA, USA
- Clinical Neuroscience Research Center, New Orleans, LA, USA
- Department of Neurosurgery, Tulane University School of Medicine, New Orleans, LA, USA
| | - Vivian A Fonseca
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA
- Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Xiaoying Wang
- Neuroscience Program, Tulane Brain Institute, Tulane University, New Orleans, LA, USA
- Clinical Neuroscience Research Center, New Orleans, LA, USA
- Department of Neurosurgery, Tulane University School of Medicine, New Orleans, LA, USA
| | - Jennifer Klein
- Department of Biochemistry & Molecular Biology, Louisiana State University School of Medicine, New Orleans, LA, USA
| | - Prasad VG Katakam
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA
- Neuroscience Program, Tulane Brain Institute, Tulane University, New Orleans, LA, USA
- Clinical Neuroscience Research Center, New Orleans, LA, USA
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5
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Edman NI, Redler RL, Phal A, Schlichthaerle T, Srivatsan SR, Etemadi A, An SJ, Favor A, Ehnes D, Li Z, Praetorius F, Gordon M, Yang W, Coventry B, Hicks DR, Cao L, Bethel N, Heine P, Murray A, Gerben S, Carter L, Miranda M, Negahdari B, Lee S, Trapnell C, Stewart L, Ekiert DC, Schlessinger J, Shendure J, Bhabha G, Ruohola-Baker H, Baker D. Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.14.532666. [PMID: 36993355 PMCID: PMC10055045 DOI: 10.1101/2023.03.14.532666] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Growth factors and cytokines signal by binding to the extracellular domains of their receptors and drive association and transphosphorylation of the receptor intracellular tyrosine kinase domains, initiating downstream signaling cascades. To enable systematic exploration of how receptor valency and geometry affects signaling outcomes, we designed cyclic homo-oligomers with up to 8 subunits using repeat protein building blocks that can be modularly extended. By incorporating a de novo designed fibroblast growth-factor receptor (FGFR) binding module into these scaffolds, we generated a series of synthetic signaling ligands that exhibit potent valency- and geometry-dependent Ca2+ release and MAPK pathway activation. The high specificity of the designed agonists reveal distinct roles for two FGFR splice variants in driving endothelial and mesenchymal cell fates during early vascular development. The ability to incorporate receptor binding domains and repeat extensions in a modular fashion makes our designed scaffolds broadly useful for probing and manipulating cellular signaling pathways.
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Affiliation(s)
- Natasha I Edman
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98195, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Rachel L Redler
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Ashish Phal
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Thomas Schlichthaerle
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Sanjay R Srivatsan
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Ali Etemadi
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Medical Biotechnology Department, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Seong J An
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
| | - Andrew Favor
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Devon Ehnes
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Zhe Li
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Florian Praetorius
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Max Gordon
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Wei Yang
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Brian Coventry
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Derrick R. Hicks
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Longxing Cao
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Neville Bethel
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Piper Heine
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Analisa Murray
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Stacey Gerben
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Marcos Miranda
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Babak Negahdari
- Medical Biotechnology Department, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Sangwon Lee
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - Lance Stewart
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Damian C. Ekiert
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA
- Department of Microbiology, New York University School of Medicine, New York, United States
| | - Joseph Schlessinger
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - Gira Bhabha
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Hannele Ruohola-Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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6
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Malespín-Bendaña W, Alpízar-Alpízar W, Figueroa-Protti L, Reyes L, Molina-Castro S, Une C, Ramírez-Mayorga V. Helicobacter pylori infection induces gastric precancerous lesions and persistent expression of Angpt2, Vegf-A and Tnf-A in a mouse model. Front Oncol 2023; 13:1072802. [PMID: 36874142 PMCID: PMC9975564 DOI: 10.3389/fonc.2023.1072802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/26/2023] [Indexed: 02/17/2023] Open
Abstract
Introduction Helicobacter pylori colonizes the gastric mucosa and induces chronic inflammation. Methods Using a mouse model of H. pylori-induced gastritis, we evaluated the mRNA and protein expression levels of proinflammatory and proangiogenic factors, as well as the histopathological changes in gastric mucosa in response to infection. Five- to six-week-old female C57BL/6N mice were challenged with H. pylori SS1 strain. Animals were euthanized after 5-, 10-, 20-, 30-, 40- and 50-weeks post infection. mRNA and protein expression of Angpt1, Angpt2, VegfA, Tnf-α, bacterial colonization, inflammatory response and gastric lesions were evaluated. Results A robust bacterial colonization was observed in 30 to 50 weeks-infected mice, which was accompanied by immune cell infiltration in the gastric mucosa. Compared to non-infected animals, H. pylori-colonized animals showed an upregulation in the expression of Tnf-A, Angpt2 and VegfA at the mRNA and protein levels. In contrast, Angpt1 mRNA and protein expression was downregulated in H. pylori-colonized mice. Conclusion Our data show that H. pylori infection induces the expression of Angpt2, Tnf-A and Vegf-A in murine gastric epithelium. This may contribute to the pathogenesis of H. pylori-associated gastritis, however the significance of this should be further addressed.
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Affiliation(s)
| | - Warner Alpízar-Alpízar
- Centre for Research on Microscopic Structures (CIEMic), University of Costa Rica, San José, Costa Rica.,Department of Biochemistry, School of Medicine, University of Costa Rica, San José, Costa Rica
| | - Lucía Figueroa-Protti
- Centre for Research on Microscopic Structures (CIEMic), University of Costa Rica, San José, Costa Rica.,Faculty of Microbiology, University of Costa Rica, San José, Costa Rica
| | - Ledis Reyes
- Laboratory for Biological Assays (LEBi), University of Costa Rica, San José, Costa Rica
| | - Silvia Molina-Castro
- Institute of Health Research (INISA), University of Costa Rica, San José, Costa Rica.,Department of Biochemistry, School of Medicine, University of Costa Rica, San José, Costa Rica
| | - Clas Une
- Institute of Health Research (INISA), University of Costa Rica, San José, Costa Rica
| | - Vanessa Ramírez-Mayorga
- Institute of Health Research (INISA), University of Costa Rica, San José, Costa Rica.,Department Public Nutrition, School of Nutrition, University of Costa Rica, San José, Costa Rica
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7
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TARDBP promotes ovarian cancer progression by altering vascular endothelial growth factor splicing. Oncogene 2023; 42:49-61. [PMID: 36369320 DOI: 10.1038/s41388-022-02539-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 10/26/2022] [Accepted: 10/31/2022] [Indexed: 11/13/2022]
Abstract
Disruptions in alternative splicing regulation play an essential role in ovarian cancer progression. However, the underlying mechanism remains unclear. TAR DNA-binding protein (TARDBP) plays a crucial role in alternative splicing regulation. Herein we found that TARDBP expression was significantly upregulated in OC tissue samples, particularly in cases of metastasis; further, TARDBP expression was markedly upregulated in OC patients with poor prognosis. These findings were validated by extensive tissue microarray data. TARDBP was also found to promote tumorigenesis and metastasis of OC cells in vitro and in vivo. Mechanistically, TARDBP increased the binding of the splicing factor serine/arginine-rich splicing factor 1 (SRSF1) to intron 7 of vascular endothelial growth factor (VEGF), increasing the formation of the proangiogenic VEGF165 isoform and decreasing that of the antiangiogenic VEGF165b isoform. The abnormal alternative splicing event was responsible for the activation of angiogenesis and contributed to the progression of OC. To conclude, TARDBP was found to regulate the alternative splicing of VEGF via SRSF1, induce the formation of VEGF165 but inhibit that of VEGF165b, and promote OC angiogenesis. Hence, TARDBP can serve as an independent prognostic factor and new target for OC cancer therapy.
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8
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Li H, Liu P, Li D, Wang Z, Ding Z, Zhou M, Chen X, Miao M, Ding J, Lin W, Liu Y, Zha X. STAT3/miR-130b-3p/MBNL1 feedback loop regulated by mTORC1 signaling promotes angiogenesis and tumor growth. J Exp Clin Cancer Res 2022; 41:297. [PMID: 36217202 PMCID: PMC9552455 DOI: 10.1186/s13046-022-02513-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/04/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Aberrantly activated mammalian target of rapamycin complex 1 (mTORC1) plays a vital role in tumor angiogenesis, but its precise mechanisms are still unclear. METHODS Micro-RNA-130b-3p (miR-130b-3p) expression in mTORC1-activated and control cells was examined by quantitative real-time PCR (qRT-PCR). MiR-130b-3p levels and their correlation with mTORC1 activity were evaluated by analyzing publicly available databases and in-house head and neck squamous cell carcinoma (HNSCC) tissues. The role of miR-130b-3p in mTORC1-mediated angiogenesis and tumor growth was examined using tube formation assay, chicken chorioallantoic membrane assay, cell line - derived xenograft models, and an HNSCC patient-derived xenograft (PDX) model. The regulatory mechanisms among signal transducer and activator of transcription 3 (STAT3), miR-130b-3p, and muscleblind-like protein 1 (MBNL1) were investigated via bioinformatics analyses, qRT-PCR, western blot, RNA immunoprecipitation, immunofluorescence, luciferase reporter assay, and chromatin immunoprecipitation assay. RESULTS Elevated miR-130b-3p enhanced the angiogenic and tumorigenic abilities of mTORC1-activated cells both in vitro and in vivo. STAT3, a downstream effector of mTORC1, transactivated miR-130b-3p by direct binding promoter of the miR-130b gene. MBNL1 was identified as a direct target of miR-130b-3p. MBNL1 depletion rescued the compromised angiogenesis and tumor growth caused by miR-130b-3p inhibition. MiR-130b-3p levels were significantly upregulated and positively correlated with mTORC1 signaling in multiple cancers. MiR-130b-3p inhibition attenuated tumor angiogenesis and growth in an HNSCC PDX model. MBNL1 feedback inhibited STAT3 activation in mTORC1-activated cells. CONCLUSIONS The STAT3/miR-130b-3p/MBNL1 feedback loop plays a vital role in mTORC1-mediated angiogenesis and tumor progression. This pathway could be targeted for therapeutic intervention of mTORC1-related cancers.
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Affiliation(s)
- Hongwu Li
- Department of Otorhinolaryngology, Head & Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, China
- Anhui Public Health Clinical Center, Hefei, 230032, China
- Department of Biochemistry & Molecular Biology, School of Basic Medicine, Anhui Medical University, Hefei, 230032, China
| | - Ping Liu
- Department of Otorhinolaryngology, Head & Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, China
- Anhui Public Health Clinical Center, Hefei, 230032, China
- Department of Biochemistry & Molecular Biology, School of Basic Medicine, Anhui Medical University, Hefei, 230032, China
| | - Dapeng Li
- Department of Otorhinolaryngology, Head & Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, China
| | - Zixi Wang
- Department of Biochemistry & Molecular Biology, School of Basic Medicine, Anhui Medical University, Hefei, 230032, China
| | - Zhao Ding
- Department of Otorhinolaryngology, Head & Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, China
| | - Meng Zhou
- Department of Pharmacy, Genertec Universal Medical Maanshan Shiqiye Hospital, Maanshan, 243000, Anhui Province, China
| | - Xu Chen
- Department of Biochemistry & Molecular Biology, School of Basic Medicine, Anhui Medical University, Hefei, 230032, China
| | - Manli Miao
- Department of Biochemistry & Molecular Biology, School of Basic Medicine, Anhui Medical University, Hefei, 230032, China
| | - Junli Ding
- Department of Pediatrics, The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, China
| | - Wei Lin
- Department of Stomatology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, China.
| | - Yehai Liu
- Department of Otorhinolaryngology, Head & Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, China.
| | - Xiaojun Zha
- Department of Biochemistry & Molecular Biology, School of Basic Medicine, Anhui Medical University, Hefei, 230032, China.
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9
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Sui YB, Zhang KK, Ling LY, Fan R, Liu L. Preclinical study of Shen Qi Li Xin formula in improving the development of chronic heart failure. Histol Histopathol 2022; 37:803-812. [PMID: 35333374 DOI: 10.14670/hh-18-454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Chronic heart failure (CHF) is a common clinical heart disease. In recent years, traditional Chinese medicines have shown good outcomes in CHF treatment. We aimed to explore the therapeutic effect of Shen Qi Li Xin formula (SQLXF) in CHF. CHF rats were treated with SQLXF at the doses of 8.48, 16.96, and 33.92 g/kg/d once a day for 4 weeks by intragastric administration. The hemodynamic and cardiac function parameters of the rats were monitored by conduction echocardiography. In our results, SQLXF treatment at the doses of 16.96 and 33.92 g/kg/d significantly improved the haemodynamics and cardiac function of CHF rats by enhancing the levels of LVSP, +dp/dtmax, -dp/dtmax, LVEF and LVFS and reducing the levels of LVEDP, LVEDD and LVESD. SQLXF treatment at 16.96 and 33.92 g/kg/d also attenuated the damage of myocardial tissues in CHF rats. In addition, compared with normal rats, the number of pericytes was reduced in myocardial tissues of CHF rats. SQLXF treatment at the doses of 16.96 and 33.92 g/kg/d obviously increased the number of pericytes and proliferation of endothelial cells and promoted angiogenesis in myocardial tissues of CHF rats. In vitro, SQLXF impaired low-oxygen-induced inhibition of cell viability and promotion of apoptosis in primary pericytes. Importantly, SQLXF enhanced the adhesion ability of pericytes to endothelial cells. In conclusion, SQLXF improved myocardial injury in CHF rats by enhancing the interaction between pericytes and endothelial cells, suggesting that SQLXF may be a potential drug for CHF treatment.
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Affiliation(s)
- Yan-Bo Sui
- Department of Cardiology, First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Xiangfang District, Harbin, China
- Department of Cardiology, Heilongjiang University of Chinese Medicine, Xiangfang District, Harbin, China
| | - Kui-Kui Zhang
- Department of Cardiology, First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Xiangfang District, Harbin, China.
| | - Li-Yun Ling
- Department of Cardiology, Heilongjiang University of Chinese Medicine, Xiangfang District, Harbin, China
| | - Rui Fan
- Department of Cardiology, Heilongjiang University of Chinese Medicine, Xiangfang District, Harbin, China
| | - Li Liu
- Department of Cardiology, First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Xiangfang District, Harbin, China
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10
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Bao G, Li T, Guan X, Yao Y, Liang J, Xiang Y, Zhong X. Development of a Prognostic Alternative Splicing Signature Associated With Tumor Microenvironment Immune Profiles in Lung Adenocarcinoma. Front Oncol 2022; 12:880478. [PMID: 35832557 PMCID: PMC9271776 DOI: 10.3389/fonc.2022.880478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 05/24/2022] [Indexed: 12/24/2022] Open
Abstract
Background Alternative splicing (AS), a pivotal post-transcriptional process across more than 95% of human transcripts, is involved in transcript structural variations and protein complexity. Clinical implications of AS events and their interaction with tumor immunity were systematically analyzed in lung adenocarcinoma (LUAD). Methods Transcriptome profiling as well as AS data of LUAD were retrospectively curated. Then, the network of the overall survival (OS)-relevant AS events with splicing factors was established. After screening OS-relevant AS events, a LASSO prognostic model was conducted and evaluated with ROC curves. A nomogram that integrated independent prognostic indicators was created. Immune response and immune cell infiltration were estimated with ESTIMATE, CIBERSORT, and ssGSEA algorithms. Drug sensitivity was inferred with pRRophetic package. Results In total, 2415 OS-relevant AS events were identified across LUAD patients. The interaction network of splicing factors with OS-relevant AS events uncovered the underlying regulatory mechanisms of AS events in LUAD. Thereafter, a prognostic model containing 12 AS events was developed, which acted as a reliable and independent prognostic indicator following verification. A nomogram that constituted stage and risk score displayed great effectiveness in evaluating the survival likelihood. Moreover, the AS-based prognostic model was in relation to immune response and immune cell infiltration. Patients with a high-risk score displayed therapeutic superiority to cisplatin, erlotinib, gefitinib, and gemcitabine. Finally, three AS-relevant genes (CDKN2A, TTC39C, and PKIB) were identified as prognostic markers. Conclusion Collectively, our findings developed an AS event signature with powerful prognostic predictive efficacy in LUAD.
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Affiliation(s)
- Guangyao Bao
- Department of Thoracic Surgery, First Affiliated Hospital, China Medical University, Shenyang, China
| | - Tian Li
- School of Basic Medicine, Fourth Military Medical University, Xi’an, China
| | - Xiaojiao Guan
- Department of Pathology, Shengjing Hospital, China Medical University, Shenyang, China
| | - Yao Yao
- Department of Thoracic Surgery, First Affiliated Hospital, China Medical University, Shenyang, China
| | - Jie Liang
- Department of Thoracic Surgery, First Affiliated Hospital, China Medical University, Shenyang, China
| | - Yifan Xiang
- Department of Thoracic Surgery, First Affiliated Hospital, China Medical University, Shenyang, China
| | - Xinwen Zhong
- Department of Thoracic Surgery, First Affiliated Hospital, China Medical University, Shenyang, China
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11
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Systematic Review: Targeted Molecular Imaging of Angiogenesis and Its Mediators in Rheumatoid Arthritis. Int J Mol Sci 2022; 23:ijms23137071. [PMID: 35806074 PMCID: PMC9267012 DOI: 10.3390/ijms23137071] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/23/2022] [Accepted: 06/23/2022] [Indexed: 12/14/2022] Open
Abstract
Extensive angiogenesis is a characteristic feature in the synovial tissue of rheumatoid arthritis (RA) from a very early stage of the disease onward and constitutes a crucial event for the development of the proliferative synovium. This process is markedly intensified in patients with prolonged disease duration, high disease activity, disease severity, and significant inflammatory cell infiltration. Angiogenesis is therefore an interesting target for the development of new therapeutic approaches as well as disease monitoring strategies in RA. To this end, nuclear imaging modalities represent valuable non-invasive tools that can selectively target molecular markers of angiogenesis and accurately and quantitatively track molecular changes in multiple joints simultaneously. This systematic review summarizes the imaging markers used for single photon emission computed tomography (SPECT) and/or positron emission tomography (PET) approaches, targeting pathways and mediators involved in synovial neo-angiogenesis in RA.
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12
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Clinical Significance and Regulation of ERK5 Expression and Function in Cancer. Cancers (Basel) 2022; 14:cancers14020348. [PMID: 35053510 PMCID: PMC8773716 DOI: 10.3390/cancers14020348] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/08/2022] [Accepted: 01/08/2022] [Indexed: 02/06/2023] Open
Abstract
Extracellular signal-regulated kinase 5 (ERK5) is a unique kinase among MAPKs family members, given its large structure characterized by the presence of a unique C-terminal domain. Despite increasing data demonstrating the relevance of the ERK5 pathway in the growth, survival, and differentiation of normal cells, ERK5 has recently attracted the attention of several research groups given its relevance in inflammatory disorders and cancer. Accumulating evidence reported its role in tumor initiation and progression. In this review, we explore the gene expression profile of ERK5 among cancers correlated with its clinical impact, as well as the prognostic value of ERK5 and pERK5 expression levels in tumors. We also summarize the importance of ERK5 in the maintenance of a cancer stem-like phenotype and explore the major known contributions of ERK5 in the tumor-associated microenvironment. Moreover, although several questions are still open concerning ERK5 molecular regulation, different ERK5 isoforms derived from the alternative splicing process are also described, highlighting the potential clinical relevance of targeting ERK5 pathways.
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13
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Niño CA, Scotto di Perrotolo R, Polo S. Recurrent Spliceosome Mutations in Cancer: Mechanisms and Consequences of Aberrant Splice Site Selection. Cancers (Basel) 2022; 14:281. [PMID: 35053445 PMCID: PMC8773931 DOI: 10.3390/cancers14020281] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/30/2021] [Accepted: 01/04/2022] [Indexed: 12/21/2022] Open
Abstract
Splicing alterations have been widely documented in tumors where the proliferation and dissemination of cancer cells is supported by the expression of aberrant isoform variants. Splicing is catalyzed by the spliceosome, a ribonucleoprotein complex that orchestrates the complex process of intron removal and exon ligation. In recent years, recurrent hotspot mutations in the spliceosome components U1 snRNA, SF3B1, and U2AF1 have been identified across different tumor types. Such mutations in principle are highly detrimental for cells as all three spliceosome components are crucial for accurate splice site selection: the U1 snRNA is essential for 5′ splice site recognition, and SF3B1 and U2AF1 are important for 3′ splice site selection. Nonetheless, they appear to be selected to promote specific types of cancers. Here, we review the current molecular understanding of these mutations in cancer, focusing on how they influence splice site selection and impact on cancer development.
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Affiliation(s)
- Carlos A. Niño
- Fondazione Istituto FIRC di Oncologia Molecolare (IFOM), 20139 Milan, Italy;
| | | | - Simona Polo
- Fondazione Istituto FIRC di Oncologia Molecolare (IFOM), 20139 Milan, Italy;
- Dipartimento di Oncologia ed Emato-Oncologia, Università degli Studi di Milano, 20122 Milan, Italy
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14
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Mehlferber MM, Jeffery ED, Saquing J, Jordan BT, Sheynkman L, Murali M, Genet G, Acharya BR, Hirschi KK, Sheynkman GM. Characterization of protein isoform diversity in human umbilical vein endothelial cells via long-read proteogenomics. RNA Biol 2022; 19:1228-1243. [PMID: 36457147 PMCID: PMC9721438 DOI: 10.1080/15476286.2022.2141938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Endothelial cells (ECs) comprise the lumenal lining of all blood vessels and are critical for the functioning of the cardiovascular system. Their phenotypes can be modulated by alternative splicing of RNA to produce distinct protein isoforms. To characterize the RNA and protein isoform landscape within ECs, we applied a long read proteogenomics approach to analyse human umbilical vein endothelial cells (HUVECs). Transcripts delineated from PacBio sequencing serve as the basis for a sample-specific protein database used for downstream mass-spectrometry (MS) analysis to infer protein isoform expression. We detected 53,863 transcript isoforms from 10,426 genes, with 22,195 of those transcripts being novel. Furthermore, the predominant isoform in HUVECs does not correspond with the accepted "reference isoform" 25% of the time, with vascular pathway-related genes among this group. We found 2,597 protein isoforms supported through unique peptides, with an additional 2,280 isoforms nominated upon incorporation of long-read transcript evidence. We characterized a novel alternative acceptor for endothelial-related gene CDH5, suggesting potential changes in its associated signalling pathways. Finally, we identified novel protein isoforms arising from a diversity of RNA splicing mechanisms supported by uniquely mapped novel peptides. Our results represent a high-resolution atlas of known and novel isoforms of potential relevance to endothelial phenotypes and function.[Figure: see text].
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Affiliation(s)
- Madison M. Mehlferber
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Erin D. Jeffery
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Jamie Saquing
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Ben T. Jordan
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Leon Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Mayank Murali
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Gael Genet
- Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Bipul R. Acharya
- Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, VA, USA,Cardiovascular Research Center, University of Virginia, Charlottesville, VA, USA,Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, the University of Manchester, UK
| | - Karen K. Hirschi
- Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, VA, USA,Cardiovascular Research Center, University of Virginia, Charlottesville, VA, USA
| | - Gloria M. Sheynkman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA,Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA,UVA Comprehensive Cancer Center, University of Virginia, Charlottesville, Virginia, USA,CONTACT Gloria M. Sheynkman The Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
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15
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A ligand-insensitive UNC5B splicing isoform regulates angiogenesis by promoting apoptosis. Nat Commun 2021; 12:4872. [PMID: 34381052 PMCID: PMC8358048 DOI: 10.1038/s41467-021-24998-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 07/16/2021] [Indexed: 12/12/2022] Open
Abstract
The Netrin-1 receptor UNC5B is an axon guidance regulator that is also expressed in endothelial cells (ECs), where it finely controls developmental and tumor angiogenesis. In the absence of Netrin-1, UNC5B induces apoptosis that is blocked upon Netrin-1 binding. Here, we identify an UNC5B splicing isoform (called UNC5B-Δ8) expressed exclusively by ECs and generated through exon skipping by NOVA2, an alternative splicing factor regulating vascular development. We show that UNC5B-Δ8 is a constitutively pro-apoptotic splicing isoform insensitive to Netrin-1 and required for specific blood vessel development in an apoptosis-dependent manner. Like NOVA2, UNC5B-Δ8 is aberrantly expressed in colon cancer vasculature where its expression correlates with tumor angiogenesis and poor patient outcome. Collectively, our data identify a mechanism controlling UNC5B’s necessary apoptotic function in ECs and suggest that the NOVA2/UNC5B circuit represents a post-transcriptional pathway regulating angiogenesis. UNC5B is a Netrin-1 receptor expressed in endothelial cells that in the absence of ligand induces apoptosis. Here the authors identify an UNC5B splicing isoform that is insensitive to the pro-survival ligand Netrin-1 and is required for apoptosis-dependent blood vessel development.
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16
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Oh J, Pradella D, Kim Y, Shao C, Li H, Choi N, Ha J, Di Matteo A, Fu XD, Zheng X, Ghigna C, Shen H. Global Alternative Splicing Defects in Human Breast Cancer Cells. Cancers (Basel) 2021; 13:cancers13123071. [PMID: 34202984 PMCID: PMC8235023 DOI: 10.3390/cancers13123071] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/09/2021] [Accepted: 06/16/2021] [Indexed: 12/21/2022] Open
Abstract
Simple Summary Aberrant alternative splicing (AS) regulation plays a pivotal role in breast cancer development, progression, and resistance to therapeutical interventions. Indeed, cancer cells can adapt their own transcriptome by changing different AS programs, thus generating cancer-specific AS isoforms involved in every hallmark of cancer. Here, we investigated global AS errors occurring in human breast cancer cells by using RNA-mediated oligonucleotide annealing, selection, and ligation coupled with next-generation sequencing. Our results identified several dysregulated AS events potentially relevant for breast cancer-related biological processes and that provide a better comprehension of the molecular mechanisms that orchestrate the malignant transformation. Abstract Breast cancer is the most frequently occurred cancer type and the second cause of death in women worldwide. Alternative splicing (AS) is the process that generates more than one mRNA isoform from a single gene, and it plays a major role in expanding the human protein diversity. Aberrant AS contributes to breast cancer metastasis and resistance to chemotherapeutic interventions. Therefore, identifying cancer-specific isoforms is the prerequisite for therapeutic interventions intended to correct aberrantly expressed AS events. Here, we performed RNA-mediated oligonucleotide annealing, selection, and ligation coupled with next-generation sequencing (RASL-seq) in breast cancer cells, to identify global breast cancer-specific AS defects. By RT-PCR validation, we demonstrate the high accuracy of RASL-seq results. In addition, we analyzed identified AS events using the Cancer Genome Atlas (TCGA) database in a large number of non-pathological and breast tumor specimens and validated them in normal and breast cancer samples. Interestingly, aberrantly regulated AS cassette exons in cancer tissues do not encode for known functional domains but instead encode for amino acids constituting regions of intrinsically disordered protein portions characterized by high flexibility and prone to be subjected to post-translational modifications. Collectively, our results reveal novel AS errors occurring in human breast cancer, potentially affecting breast cancer-related biological processes.
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Affiliation(s)
- Jagyeong Oh
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea; (J.O.); (Y.K.); (N.C.); (J.H.); (X.Z.)
| | - Davide Pradella
- Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza”, National Research Council, Via Abbiategrasso 207, 27100 Pavia, Italy; (D.P.); (A.D.M.)
| | - Yoonseong Kim
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea; (J.O.); (Y.K.); (N.C.); (J.H.); (X.Z.)
| | - Changwei Shao
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; (C.S.); (H.L.); (X.-D.F.)
| | - Hairi Li
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; (C.S.); (H.L.); (X.-D.F.)
| | - Namjeong Choi
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea; (J.O.); (Y.K.); (N.C.); (J.H.); (X.Z.)
| | - Jiyeon Ha
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea; (J.O.); (Y.K.); (N.C.); (J.H.); (X.Z.)
| | - Anna Di Matteo
- Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza”, National Research Council, Via Abbiategrasso 207, 27100 Pavia, Italy; (D.P.); (A.D.M.)
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; (C.S.); (H.L.); (X.-D.F.)
| | - Xuexiu Zheng
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea; (J.O.); (Y.K.); (N.C.); (J.H.); (X.Z.)
| | - Claudia Ghigna
- Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza”, National Research Council, Via Abbiategrasso 207, 27100 Pavia, Italy; (D.P.); (A.D.M.)
- Correspondence: (C.G.); (H.S.); Tel.: +39-0382-546324 (C.G.); +82-62-715-2507 (H.S.); Fax: +82-62-715-2484 (H.S.)
| | - Haihong Shen
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea; (J.O.); (Y.K.); (N.C.); (J.H.); (X.Z.)
- Correspondence: (C.G.); (H.S.); Tel.: +39-0382-546324 (C.G.); +82-62-715-2507 (H.S.); Fax: +82-62-715-2484 (H.S.)
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17
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Natua S, Dhamdhere SG, Mutnuru SA, Shukla S. Interplay within tumor microenvironment orchestrates neoplastic RNA metabolism and transcriptome diversity. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1676. [PMID: 34109748 DOI: 10.1002/wrna.1676] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/03/2021] [Accepted: 05/25/2021] [Indexed: 12/11/2022]
Abstract
The heterogeneous population of cancer cells within a tumor mass interacts intricately with the multifaceted aspects of the surrounding microenvironment. The reciprocal crosstalk between cancer cells and the tumor microenvironment (TME) shapes the cancer pathophysiome in a way that renders it uniquely suited for immune tolerance, angiogenesis, metastasis, and therapy resistance. This dynamic interaction involves a dramatic reconstruction of the transcriptomic landscape of tumors by altering the synthesis, modifications, stability, and processing of gene readouts. In this review, we categorically evaluate the influence of TME components, encompassing a myriad of resident and infiltrating cells, signaling molecules, extracellular vesicles, extracellular matrix, and blood vessels, in orchestrating the cancer-specific metabolism and diversity of both mRNA and noncoding RNA, including micro RNA, long noncoding RNA, circular RNA among others. We also highlight the transcriptomic adaptations in response to the physicochemical idiosyncrasies of TME, which include tumor hypoxia, extracellular acidosis, and osmotic stress. Finally, we provide a nuanced analysis of existing and prospective therapeutics targeting TME to ameliorate cancer-associated RNA metabolism, consequently thwarting the cancer progression. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing RNA Turnover and Surveillance > Regulation of RNA Stability RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Subhashis Natua
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, Madhya Pradesh, 462066, India
| | - Shruti Ganesh Dhamdhere
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, Madhya Pradesh, 462066, India
| | - Srinivas Abhishek Mutnuru
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, Madhya Pradesh, 462066, India
| | - Sanjeev Shukla
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, Madhya Pradesh, 462066, India
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18
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Long noncoding RNA DGCR5 involves in tumorigenesis of esophageal squamous cell carcinoma via SRSF1-mediated alternative splicing of Mcl-1. Cell Death Dis 2021; 12:587. [PMID: 34099633 PMCID: PMC8184765 DOI: 10.1038/s41419-021-03858-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 05/16/2021] [Accepted: 05/17/2021] [Indexed: 02/06/2023]
Abstract
Long noncoding RNAs (lncRNAs) emerge as essential roles in the regulation of alternative splicing (AS) in various malignancies. Serine- and arginine-rich splicing factor 1 (SRSF1)-mediated AS events are the most important molecular hallmarks in cancer. Nevertheless, the biological mechanism underlying tumorigenesis of lncRNAs correlated with SRSF1 in esophageal squamous cell carcinoma (ESCC) remains elusive. In this study, we found that lncRNA DiGeorge syndrome critical region gene 5 (DGCR5) was upregulated in ESCC clinical samples, which associated with poor prognosis. Through RNA interference and overexpression approaches, we confirmed that DGCR5 contributed to promote ESCC cell proliferation, migration, and invasion while inhibited apoptosis in vitro. Mechanistically, DGCR5 could directly bind with SRSF1 to increase its stability and thus stimulate alternative splicing events. Furthermore, we clarified that SRSF1 regulated the aberrant splicing of myeloid cell leukemia-1 (Mcl-1) and initiated a significant Mcl-1L (antiapoptotic) isoform switch, which contributed to the expression of the full length of Mcl-1. Moreover, the cell-derived xenograft (CDX) model was validated that DGCR5 could facilitate the tumorigenesis of ESCC in vivo. Collectively, our findings identified that the key biological role of lncRNA DGCR5 in alternative splicing regulation and emphasized DGCR5 as a potential biomarker and therapeutic target for ESCC.
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19
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Li S. Anlotinib: A Novel Targeted Drug for Bone and Soft Tissue Sarcoma. Front Oncol 2021; 11:664853. [PMID: 34094958 PMCID: PMC8173120 DOI: 10.3389/fonc.2021.664853] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 04/22/2021] [Indexed: 12/13/2022] Open
Abstract
Bone and soft tissue sarcomas account for approximately 15% of pediatric solid malignant tumors and 1% of adult solid malignant tumors. There are over 50 subtypes of sarcomas, each of which is notably heterogeneous and manifested by remarkable phenotypic and morphological variability. Anlotinib is a novel oral tyrosine kinase inhibitor (TKI) targeting c-kit, platelet-derived growth factor receptors, fibroblast growth factor receptor, and vascular endothelial growth factor receptor. In comparison with the placebo, anlotinib was associated with better overall survival and progression-free survival (PFS) in a phase III trial of patients with advanced non-small cell lung cancer (NSCLC), albeit with cancer progression after two previous lines of treatment. Recently, the National Medical Products Administration approved anlotinib monotherapy as a third-line treatment for patients with advanced NSCLC. Additionally, a phase IIB randomized trial substantiated that anlotinib is associated with a significant longer median PFS in patients with advanced soft tissue sarcoma. Moreover, anlotinib is also effective in patients with advanced medullary thyroid carcinoma and metastatic renal cell carcinoma. Anlotinib has similar tolerability to other TKIs targeting vascular endothelial growth factor receptors and other tyrosine kinase-mediated pathways. However, anlotinib has a notably lower rate of side effects ≥grade 3 relative to sunitinib. This review discussed the remarkable characteristics and major dilemmas of anlotinib as a targeted therapy for sarcomas.
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Affiliation(s)
- Shenglong Li
- Department of Bone and Soft Tissue Tumor Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, China.,Department of Tissue Engineering, Center of 3D Printing & Organ Manufacturing, School of Fundamental Sciences, China Medical University (CMU), Shenyang, China
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