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Tao Y, Zhang Q, Wang H, Yang X, Mu H. Alternative splicing and related RNA binding proteins in human health and disease. Signal Transduct Target Ther 2024; 9:26. [PMID: 38302461 PMCID: PMC10835012 DOI: 10.1038/s41392-024-01734-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 12/18/2023] [Accepted: 12/27/2023] [Indexed: 02/03/2024] Open
Abstract
Alternative splicing (AS) serves as a pivotal mechanism in transcriptional regulation, engendering transcript diversity, and modifications in protein structure and functionality. Across varying tissues, developmental stages, or under specific conditions, AS gives rise to distinct splice isoforms. This implies that these isoforms possess unique temporal and spatial roles, thereby associating AS with standard biological activities and diseases. Among these, AS-related RNA-binding proteins (RBPs) play an instrumental role in regulating alternative splicing events. Under physiological conditions, the diversity of proteins mediated by AS influences the structure, function, interaction, and localization of proteins, thereby participating in the differentiation and development of an array of tissues and organs. Under pathological conditions, alterations in AS are linked with various diseases, particularly cancer. These changes can lead to modifications in gene splicing patterns, culminating in changes or loss of protein functionality. For instance, in cancer, abnormalities in AS and RBPs may result in aberrant expression of cancer-associated genes, thereby promoting the onset and progression of tumors. AS and RBPs are also associated with numerous neurodegenerative diseases and autoimmune diseases. Consequently, the study of AS across different tissues holds significant value. This review provides a detailed account of the recent advancements in the study of alternative splicing and AS-related RNA-binding proteins in tissue development and diseases, which aids in deepening the understanding of gene expression complexity and offers new insights and methodologies for precision medicine.
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Affiliation(s)
- Yining Tao
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Qi Zhang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
| | - Haoyu Wang
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Xiyu Yang
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Haoran Mu
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China.
- Shanghai Bone Tumor Institution, 200000, Shanghai, China.
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Du L, Deng H, Wu X, Liu F, Yin T, Zheng J. Relationship Between Spleen Pathologic Changes and Spleen Stiffness in Portal Hypertension Rat Model. ULTRASOUND IN MEDICINE & BIOLOGY 2024; 50:216-223. [PMID: 37919143 DOI: 10.1016/j.ultrasmedbio.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/16/2023] [Accepted: 10/01/2023] [Indexed: 11/04/2023]
Abstract
OBJECTIVE The aim of the study described here was to explore the influence of splenic pathology and hemodynamic parameters on spleen stiffness in portal hypertension (PH). METHODS A Sprague‒Dawley rat model of PH (n = 34) induced by CCl4 was established, and 9 normal rats were used as controls. All animals underwent a routine ultrasound examination, spleen stiffness measurement (SSM), liver stiffness measurement (LSM), portal vein pressure (PVP) measurement and histopathologic assessment. The diagnostic performance of SSM and LSM in PH was evaluated. SSMs were compared among the groups at different pathologic and hemodynamic levels. Multiple linear regression was used to analyze the factors affecting SSM. RESULTS SSM had excellent diagnostic efficacy for PH (area under the receiver operating characteristic curve [AUC] = 0.900) and was superior to LSM (AUC = 0.794). In a rat model of PH, pathologic changes such as splenic sinus widening, thickening of the splenic capsule and an increase in collagen fibers were observed in the spleen. There were significant differences in SSM at different splenic capsule thicknesses and splenic sinus widths (all p values <0.05), but there were no significant differences in the SSM at different levels of the splenic collagen fiber area and red pulp area (all p values >0.05). In addition, there were significant differences in SSM at different levels of portal vein diameter, blood flow and congestion index (all p values <0.05). Multiple linear regression analysis revealed that PVP, portal vein congestion index and splenic capsule thickness were significantly associated with SSM. CONCLUSION SSM is a good non-invasive way to assess PH. PVP, splenic capsule thickness and portal vein congestion index are responsible for spleen stiffness but not the proliferation of splenic fibrous tissue.
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Affiliation(s)
- Lingyue Du
- Department of Second Affiliated Hospital, School of Medicine, Chinese University of Hong Kong, Shenzhen & Longgang District People's Hospital of Shenzhen, Shenzhen, China; Department of Ultrasound, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Huan Deng
- Department of Ultrasound, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Xiaoting Wu
- Department of Second Affiliated Hospital, School of Medicine, Chinese University of Hong Kong, Shenzhen & Longgang District People's Hospital of Shenzhen, Shenzhen, China
| | - Fan Liu
- Department of Second Affiliated Hospital, School of Medicine, Chinese University of Hong Kong, Shenzhen & Longgang District People's Hospital of Shenzhen, Shenzhen, China
| | - Tinghui Yin
- Department of Ultrasound, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Jian Zheng
- Department of Second Affiliated Hospital, School of Medicine, Chinese University of Hong Kong, Shenzhen & Longgang District People's Hospital of Shenzhen, Shenzhen, China; Department of Ultrasound, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China.
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Oliveira RFD, Stoltz IR, Gonçalves PG, Echevarria A, Taborda L, Lepinsk Lopes RH, Pereira LF, Elifio-Esposito S. Evaluation of the antitumoral effects of the mesoionic compound MI-D: Implications for endothelial cells viability and angiogenesis inhibition. Chem Biol Interact 2024; 387:110796. [PMID: 37951333 DOI: 10.1016/j.cbi.2023.110796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 10/19/2023] [Accepted: 11/03/2023] [Indexed: 11/13/2023]
Abstract
Angiogenesis is considered one of the hallmarks of cancer, assisting tumor progression and metastasis. The mesoionic compound, MI-D, can induce cell death and provoke cytoskeletal and metabolic changes in cancer cells. Using in vitro and in vivo models, this study aimed to evaluate the effects of MI-D on the viability of human endothelial cells (EC) and its ability to inhibit tumor-induced angiogenesis induced by tumoral cells. For in vitro analysis, colon carcinoma (HT29) and endothelial (EA.hy926) cells were used as the tumoral and angiogenesis models, respectively. To evaluate cytotoxicity, methylene blue viability stain and annexin-V/7AAD tests were performed with both cell types. For the angiogenesis experiments, scratch wound healing and capillary tube-like formation assays were performed with the EC. The in vivo tests were performed with the chorioallantoic membrane (HET-CAM) methodology, wherein gelatin sponge implants containing MI-D (5, 25, and 50 μM), HT29 cells, or both were grafted in the CAM. Our data showed that MI-D induced apoptosis in both endothelial and colon carcinoma cells, with a strong cytotoxic effect on the tumoral lineage. The drug inhibited the EC's migration and capillary-like structure formation in vitro. In the HET-CAM assays, MI-D reduced the number of blood vessels in the membrane when grafted alone and accompanied by tumor cells. In this study, MI-D interfered in important steps of angiogenesis, such as maintenance of endothelial cell viability, migration, formation of capillary-like structures, as well tumor-induced neovascularization, reinforcing the hypothesis that MI-D might act as an inhibitor of angiogenesis, and a potential antitumor agent.
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Affiliation(s)
- Ronaldo Figueira de Oliveira
- Post Graduate Program in Health Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, PR, Brazil; School of Medicine and Life Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, PR, Brazil
| | - Ian Rodrigo Stoltz
- School of Medicine and Life Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, PR, Brazil
| | - Paola Gyuliane Gonçalves
- School of Medicine and Life Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, PR, Brazil
| | - Aurea Echevarria
- Institute of Chemistry, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, Brazil
| | - Leandro Taborda
- School of Medicine and Life Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, PR, Brazil
| | | | - Luiz Fernando Pereira
- School of Medicine and Life Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, PR, Brazil
| | - Selene Elifio-Esposito
- Post Graduate Program in Health Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, PR, Brazil.
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Hou X, Li Y, Song J, Peng L, Zhang W, Liu R, Yuan H, Feng T, Li J, Li W, Zhu C. METTL14 reverses liver fibrosis by inhibiting NOVA2 through an m6A-YTHDF2-dependent mechanism. Hepatol Commun 2023; 7:e0199. [PMID: 37534933 PMCID: PMC10409442 DOI: 10.1097/hc9.0000000000000199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/15/2023] [Indexed: 08/04/2023] Open
Abstract
BACKGROUND N6-methyladenosine (m6A), the most prevalent internal RNA modification in eukaryotic cells, is dynamically regulated in response to a wide range of physiological and pathological states. Nonetheless, the involvement of METTL14-induced m6A in liver fibrosis (LF) has yet to be established. METHODS In vitro, HSC cell lines with knock-down and overexpression of METTL14 were constructed, and the effects of METTL14 gene on the phenotypic function of activated HSCs were observed. The proliferation rate was measured by CCK8 and EDU, the cell proliferation cycle was measured by flow detector, the migration rate was measured by Transwell, and the contractility of F-actin was observed after phalloidin staining. The downstream target gene NOVA2 of METTL14 was screened by combined sequencing of MeRIP-seq and RNA-seq, combined with signal analysis. Adeno-associated virus (AAV) was injected into the tail vein in vivo to knock down the expression of METTL14, so as to further observe the role of METTL14 in the progress of LF. RESULTS our research showed that the methylase METTL14 content was decreased in hepatic tissue from patients with LF, leading to a lowered degree of m6A modification. Functionally, we discovered that knocking down m6A methyltransferase METTL14 led to increased HSC activation and a substantial worsening of LF. Mechanically, as shown in a multiomics study of HSCs, depleting METTL14 levels decreased m6A deposition onNOVA2 mRNA transcripts, which prompted the activation of YTHDF2 to detect and degrade the decrease of NOVA2 mRNA. CONCLUSIONS METTL14 functioned as a profibrotic gene by suppressing NOVA2 activity in a mechanism dependent on m6A-YTHDF2. Moreover, knocking down METTL14 exacerbated LF, while NOVA2 prevented its development and partly reversed the damage.
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Affiliation(s)
- Xiaoxue Hou
- Department of Infectious Disease, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yuwen Li
- Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jiali Song
- Department of Infectious Disease, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Linya Peng
- Department of Infectious Disease, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wen Zhang
- Department of Infectious Disease, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Rui Liu
- Department of Tropical Diseases of the Second Affiliated Hospital, Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Control of Tropical Diseases, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, China
| | - Hui Yuan
- Department of Infectious Disease, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Tiantong Feng
- Department of Infectious Disease, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jieying Li
- Department of Tropical Diseases of the Second Affiliated Hospital, Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Control of Tropical Diseases, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, China
| | - Wenting Li
- Department of Tropical Diseases of the Second Affiliated Hospital, Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Control of Tropical Diseases, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, China
| | - Chuanlong Zhu
- Department of Infectious Disease, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Department of Tropical Diseases of the Second Affiliated Hospital, Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Control of Tropical Diseases, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, China
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Li S, Qi Y, Yu J, Hao Y, Xu L, Ding X, Zhang M, Geng J. Aurora kinase A regulates cancer-associated RNA aberrant splicing in breast cancer. Heliyon 2023; 9:e17386. [PMID: 37415951 PMCID: PMC10320321 DOI: 10.1016/j.heliyon.2023.e17386] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 06/03/2023] [Accepted: 06/15/2023] [Indexed: 07/08/2023] Open
Abstract
The contribution of oncogenes to tumor-associated RNA splicing and the relevant molecular mechanisms therein require further elaboration. Here, we show that oncogenic Aurora kinase A (AURKA) promotes breast cancer-related RNA aberrant splicing in a context-dependent manner. AURKA regulated pan-breast cancer-associated RNA splicing events including GOLGA4, RBM4 and UBQLN1. Aberrant splicing of GOLGA4 and RBM4 was closely related to breast cancer development. Mechanistically, AURKA interacted with the splicing factor YBX1 and promoted AURKA-YBX1 complex-mediated GOLGA4 exon inclusion. AURKA binding to the splicing factor hnRNPK promoted AURKA-hnRNPK complex-mediated RBM4 exon skipping. Analysis of clinical data identified an association between the AURKA-YBX1/hnRNPK complex and poor prognosis in breast cancer. Blocking AURKA nuclear translocation with small molecule drugs partially reversed the oncogenic splicing of RBM4 and GOLGA4 in breast cancer cells. In summary, oncogenic AURKA executes its function on modulating breast cancer-related RNA splicing, and nuclear AURKA is distinguished as a hopeful target in the case of treating breast cancer.
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Affiliation(s)
- Sisi Li
- Department of Pathology, Harbin Medical University Cancer Hospital, Harbin, China
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Yangfan Qi
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Jiachuan Yu
- Department of Anesthesiology, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Yuchao Hao
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Lingzhi Xu
- Department of Oncology, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Xudong Ding
- Department of Pathology, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Minghui Zhang
- Department of Oncology, Chifeng City Hospital, Chifeng, China
| | - Jingshu Geng
- Department of Pathology, Harbin Medical University Cancer Hospital, Harbin, China
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Di Matteo A, Belloni E, Pradella D, Chiaravalli AM, Pini GM, Bugatti M, Alfieri R, Barzan C, Franganillo Tena E, Bione S, Terenzani E, Sessa F, Wyatt CDR, Vermi W, Ghigna C. Alternative Splicing Changes Promoted by NOVA2 Upregulation in Endothelial Cells and Relevance for Gastric Cancer. Int J Mol Sci 2023; 24:ijms24098102. [PMID: 37175811 PMCID: PMC10178952 DOI: 10.3390/ijms24098102] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
Angiogenesis is crucial for cancer progression. While several anti-angiogenic drugs are in use for cancer treatment, their clinical benefits are unsatisfactory. Thus, a deeper understanding of the mechanisms sustaining cancer vessel growth is fundamental to identify novel biomarkers and therapeutic targets. Alternative splicing (AS) is an essential modifier of human proteome diversity. Nevertheless, AS contribution to tumor vasculature development is poorly known. The Neuro-Oncological Ventral Antigen 2 (NOVA2) is a critical AS regulator of angiogenesis and vascular development. NOVA2 is upregulated in tumor endothelial cells (ECs) of different cancers, thus representing a potential driver of tumor blood vessel aberrancies. Here, we identified novel AS transcripts generated upon NOVA2 upregulation in ECs, suggesting a pervasive role of NOVA2 in vascular biology. In addition, we report that NOVA2 is also upregulated in ECs of gastric cancer (GC), and its expression correlates with poor overall survival of GC patients. Finally, we found that the AS of the Rap Guanine Nucleotide Exchange Factor 6 (RapGEF6), a newly identified NOVA2 target, is altered in GC patients and associated with NOVA2 expression, tumor angiogenesis, and poor patient outcome. Our findings provide a better understanding of GC biology and suggest that AS might be exploited to identify novel biomarkers and therapeutics for anti-angiogenic GC treatments.
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Affiliation(s)
- Anna Di Matteo
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", Consiglio Nazionale delle Ricerche, 27100 Pavia, Italy
| | - Elisa Belloni
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", Consiglio Nazionale delle Ricerche, 27100 Pavia, Italy
| | - Davide Pradella
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", Consiglio Nazionale delle Ricerche, 27100 Pavia, Italy
| | | | - Giacomo Maria Pini
- Department of Pathology, Ospedale di Circolo, ASST-Sette Laghi, 21100 Varese, Italy
| | - Mattia Bugatti
- Department of Molecular and Translational Medicine, University of Brescia, 25100 Brescia, Italy
| | - Roberta Alfieri
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", Consiglio Nazionale delle Ricerche, 27100 Pavia, Italy
| | - Chiara Barzan
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", Consiglio Nazionale delle Ricerche, 27100 Pavia, Italy
- Istituto Universitario di Studi Superiori (IUSS), Università degli Studi di Pavia, 27100 Pavia, Italy
| | - Elena Franganillo Tena
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", Consiglio Nazionale delle Ricerche, 27100 Pavia, Italy
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università degli Studi di Pavia, 27100 Pavia, Italy
| | - Silvia Bione
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", Consiglio Nazionale delle Ricerche, 27100 Pavia, Italy
| | - Elisa Terenzani
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", Consiglio Nazionale delle Ricerche, 27100 Pavia, Italy
| | - Fausto Sessa
- Department of Pathology, Ospedale di Circolo, ASST-Sette Laghi, 21100 Varese, Italy
- Department of Medicine and Surgery, Università degli Studi dell'Insubria, 21100 Varese, Italy
| | - Christopher D R Wyatt
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, 08036 Barcelona, Spain
| | - William Vermi
- Department of Molecular and Translational Medicine, University of Brescia, 25100 Brescia, Italy
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110-1010, USA
| | - Claudia Ghigna
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", Consiglio Nazionale delle Ricerche, 27100 Pavia, Italy
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Kim SH, Nichols KD, Anderson EN, Liu Y, Ramesh N, Jia W, Kuerbis CJ, Scalf M, Smith LM, Pandey UB, Tibbetts RS. Axon guidance genes modulate neurotoxicity of ALS-associated UBQLN2. eLife 2023; 12:e84382. [PMID: 37039476 PMCID: PMC10147378 DOI: 10.7554/elife.84382] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 04/06/2023] [Indexed: 04/12/2023] Open
Abstract
Mutations in the ubiquitin (Ub) chaperone Ubiquilin 2 (UBQLN2) cause X-linked forms of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) through unknown mechanisms. Here, we show that aggregation-prone, ALS-associated mutants of UBQLN2 (UBQLN2ALS) trigger heat stress-dependent neurodegeneration in Drosophila. A genetic modifier screen implicated endolysosomal and axon guidance genes, including the netrin receptor, Unc-5, as key modulators of UBQLN2 toxicity. Reduced gene dosage of Unc-5 or its coreceptor Dcc/frazzled diminished neurodegenerative phenotypes, including motor dysfunction, neuromuscular junction defects, and shortened lifespan, in flies expressing UBQLN2ALS alleles. Induced pluripotent stem cells (iPSCs) harboring UBQLN2ALS knockin mutations exhibited lysosomal defects while inducible motor neurons (iMNs) expressing UBQLN2ALS alleles exhibited cytosolic UBQLN2 inclusions, reduced neurite complexity, and growth cone defects that were partially reversed by silencing of UNC5B and DCC. The combined findings suggest that altered growth cone dynamics are a conserved pathomechanism in UBQLN2-associated ALS/FTD.
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Affiliation(s)
- Sang Hwa Kim
- Department of Human Oncology, University of Wisconsin School of Medicine and Public HealthMadisonUnited States
| | - Kye D Nichols
- Department of Human Oncology, University of Wisconsin School of Medicine and Public HealthMadisonUnited States
| | - Eric N Anderson
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical CenterPittsburghUnited States
| | - Yining Liu
- Department of Human Oncology, University of Wisconsin School of Medicine and Public HealthMadisonUnited States
| | - Nandini Ramesh
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical CenterPittsburghUnited States
| | - Weiyan Jia
- Department of Human Oncology, University of Wisconsin School of Medicine and Public HealthMadisonUnited States
| | - Connor J Kuerbis
- Department of Human Oncology, University of Wisconsin School of Medicine and Public HealthMadisonUnited States
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin-MadisonMadisonUnited States
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-MadisonMadisonUnited States
| | - Udai Bhan Pandey
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical CenterPittsburghUnited States
| | - Randal S Tibbetts
- Department of Human Oncology, University of Wisconsin School of Medicine and Public HealthMadisonUnited States
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Abstract
Alternative splicing (AS) of mRNAs is an essential regulatory mechanism in eukaryotic gene expression. AS misregulation, caused by either dysregulation or mutation of splicing factors, has been shown to be involved in cancer development and progression, making splicing factors suitable targets for cancer therapy. In recent years, various types of pharmacological modulators, such as small molecules and oligonucleotides, targeting distinct components of the splicing machinery, have been under development to treat multiple disorders. Although these approaches have promise, targeting the core spliceosome components disrupts the early stages of spliceosome assembly and can lead to nonspecific and toxic effects. New research directions have been focused on targeting specific splicing factors for a more precise effect. In this Perspective, we will highlight several approaches for targeting splicing factors and their functions and suggest ways to improve their specificity.
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Affiliation(s)
- Ariel Bashari
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel-Canada, Hebrew University Hadassah Medical School, Jerusalem 9112001, Israel
| | - Zahava Siegfried
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel-Canada, Hebrew University Hadassah Medical School, Jerusalem 9112001, Israel
| | - Rotem Karni
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel-Canada, Hebrew University Hadassah Medical School, Jerusalem 9112001, Israel
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Zargar S, Wani TA. Food Toxicity of Mycotoxin Citrinin and Molecular Mechanisms of Its Potential Toxicity Effects through the Implicated Targets Predicted by Computer-Aided Multidimensional Data Analysis. Life (Basel) 2023; 13:life13040880. [PMID: 37109409 PMCID: PMC10142723 DOI: 10.3390/life13040880] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 03/16/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
The mycotoxin citrinin, which can contaminate food, is a major global concern. Citrinin is regarded as an inevitable pollutant in foods and feed since fungi are widely present in the environment. To identify contentious toxicity and lessen its severity by understanding the targets of citrinin in the human body and the impacted biosynthetic pathways, we analyzed the production of citrinin from Aspergillus flavus and Penicillium notatum and used a thorough bioinformatics analysis to characterize the toxicity and predict genes and protein targets for it. The predicted median fatal dosage (LD50) for citrinin was 105 mg/kg weight, and it belonged to toxicity class 3 (toxic if swallowed). Citrinin was found to be well absorbed by human intestinal epithelium and was a Pgp nonsubstrate (permeability glycoprotein), which means that once it is absorbed, it cannot be pumped out, hence leading to bioconcentration or biomagnification in the human body. The main targets of toxicity were casp3, TNF, IL10, IL1B, BAG3, CCNB1, CCNE1, and CDC25A, and the biological pathways implicated were signal transduction involved in DNA damage checkpoints, cellular and chemical responses to oxidative stress, DNA damage response signal transduction by P53, stress-activated protein kinase signaling cascade, netrin–UNC5B signaling, PTEN gene regulation, and immune response. Citrinin was linked to neutrophilia, squamous cell carcinoma, Fanconi anemia, leukemia, hepatoblastoma, and fatty liver diseases. The transcription factors E2F1, HSF1, SIRT1, RELA, NFKB, JUN, and MYC were found to be responsible. When data mining was performed on citrinin targets, the top five functional descriptions were a cell’s response to an organic cyclic compound, the netrin–UNC5B signaling pathway, lipids and atherosclerosis, thyroid cancer, and controlling the transcription of the PTEN gene.
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Neogenin suppresses tumor progression and metastasis via inhibiting Merlin/YAP signaling. Cell Death Dis 2023; 9:47. [PMID: 36746934 PMCID: PMC9902585 DOI: 10.1038/s41420-023-01345-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 01/24/2023] [Accepted: 01/26/2023] [Indexed: 02/08/2023]
Abstract
From in situ growth to invasive dissemination is the most lethal attribute of various tumor types. This transition is majorly mediated by the dynamic interplay between two cancer hallmarks, EMT and cell cycle. In this study, we applied nonlinear association analysis in 33 cancer types and found that most signaling receptors simultaneously associating with EMT and cell cycle are potential tumor suppressors. Here we find that a top co-associated receptor, Neogenin (NEO1), inhibits colorectal cancer (CRC) and Glioma in situ growth and metastasis by forming a complex with Merlin (NF2), and subsequent simultaneous promoting the phosphorylation of YAP. Furthermore, Neogenin protein level is associated with good prognosis and correlates with Merlin status in CRC and Glioma. Collectively, our results define Neogenin as a tumor suppressor in CRC and Glioma that acts by restricting oncogenic signaling by the Merlin-YAP pathway, and suggest Neogenin as a candidate therapeutic agent for CRC and Glioma.
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Kremer V, Oppelaar JJ, Gimbel T, Koziarek S, Ganzevoort W, van Pampus MG, van den Born BJ, Vogt L, de Groot C, Boon RA. Neuro-oncological Ventral Antigen 2 Regulates Splicing of Vascular Endothelial Growth Factor Receptor 1 and Is Required for Endothelial Function. Reprod Sci 2023; 30:678-689. [PMID: 35927413 PMCID: PMC9988812 DOI: 10.1007/s43032-022-01044-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 07/16/2022] [Indexed: 11/24/2022]
Abstract
Pre-eclampsia (PE) affects 2-8% of pregnancies and is responsible for significant morbidity and mortality. The maternal clinical syndrome (defined by hypertension, proteinuria, and organ dysfunction) is the result of endothelial dysfunction. The endothelial response to increased levels of soluble FMS-like Tyrosine Kinase 1 (sFLT1) is thought to play a central role. sFLT1 is released from multiple tissues and binds VEGF with high affinity and antagonizes VEGF. Expression of soluble variants of sFLT1 is a result of alternative splicing; however, the mechanism is incompletely understood. We hypothesize that neuro-oncological ventral antigen 2 (NOVA2) contributes to this. NOVA2 was inhibited in human umbilical vein endothelial cells (HUVECs) and multiple cellular functions were assessed. NOVA2 and FLT1 expression in the placenta of PE, pregnancy-induced hypertension, and normotensive controls was measured by RT-qPCR. Loss of NOVA2 in HUVECs resulted in significantly increased levels of sFLT1, but did not affect expression of membrane-bound FLT1. NOVA2 protein was shown to directly interact with FLT1 mRNA. Loss of NOVA2 was also accompanied by impaired endothelial functions such as sprouting. We were able to restore sprouting capacity by exogenous VEGF. We did not observe statistically significant regulation of NOVA2 or sFLT1 in the placenta. However, we observed a negative correlation between sFLT1 and NOVA2 expression levels. In conclusion, NOVA2 was found to regulate FLT1 splicing in the endothelium. Loss of NOVA2 resulted in impaired endothelial function, at least partially dependent on VEGF. In PE patients, we observed a negative correlation between NOVA2 and sFLT1.
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Affiliation(s)
- Veerle Kremer
- Department of Physiology, Amsterdam Cardiovascular Sciences, VU Medical Center, Amsterdam UMC, Amsterdam, The Netherlands.,Department of Medical Chemistry, Academic Medical Center, Amsterdam UMC, Amsterdam, The Netherlands.,Amsterdam Cardiovascular Sciences, Microcirculation, Amsterdam, The Netherlands
| | - Jetta J Oppelaar
- Department of Internal Medicine, Section of Nephrology, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Theresa Gimbel
- Institute of Cardiovascular Regeneration, Goethe University, Frankfurt am Main, Germany.,German Centre for Cardiovascular Research DZHK, Partner Site Frankfurt Rhein/Main, Frankfurt am Main, Germany
| | - Susanne Koziarek
- Institute of Cardiovascular Regeneration, Goethe University, Frankfurt am Main, Germany.,German Centre for Cardiovascular Research DZHK, Partner Site Frankfurt Rhein/Main, Frankfurt am Main, Germany
| | - Wessel Ganzevoort
- Department of Obstetrics and Gynecology, Amsterdam Reproduction & Development, Amsterdam UMC University of Amsterdam, Amsterdam, The Netherlands
| | | | - Bert-Jan van den Born
- Department of Internal Medicine, Section of Vascular Medicine, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands.,Amsterdam Cardiovascular Sciences, Atherosclerosis and Ischemic Syndromes, Amsterdam, The Netherlands
| | - Liffert Vogt
- Amsterdam Cardiovascular Sciences, Microcirculation, Amsterdam, The Netherlands.,Department of Internal Medicine, Section of Nephrology, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Christianne de Groot
- Department of Obstetrics and Gynaecology, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Reinier A Boon
- Department of Physiology, Amsterdam Cardiovascular Sciences, VU Medical Center, Amsterdam UMC, Amsterdam, The Netherlands. .,Institute of Cardiovascular Regeneration, Goethe University, Frankfurt am Main, Germany. .,German Centre for Cardiovascular Research DZHK, Partner Site Frankfurt Rhein/Main, Frankfurt am Main, Germany. .,Amsterdam UMC, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands.
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12
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Weng Y, Qian H, Hong L, Zhao S, Deng X, Shen B. Identification of EMT-related alternative splicing event of TMC7 to promote invasion and migration of pancreatic cancer. Front Immunol 2023; 13:1089008. [PMID: 36713450 PMCID: PMC9878378 DOI: 10.3389/fimmu.2022.1089008] [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: 11/03/2022] [Accepted: 12/21/2022] [Indexed: 01/15/2023] Open
Abstract
Objective Epithelial-to-mesenchymal transition (EMT) is tightly associated with the invasion and metastasis of pancreatic cancer with rapid progression and poor prognosis. Notably, gene alternative splicing (AS) event plays a critical role in regulating the progression of pancreatic cancer. Therefore, this study aims to identify the EMT-related AS event in pancreatic cancer. Methods The EMT-related gene sets, transcriptomes, and matched clinical data were obtained from the MSigDB, The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC), and Gene Expression Omnibus (GEO) databases. Key gene AS events associated with liver metastasis were identified by prognostic analysis, gene set variation analysis (GSVA), and correlation analysis in pancreatic cancer. The cell line and organoid model was constructed to evaluate these key gene AS events in regulating pancreatic cancer in vitro. Furthermore, we established an EMT-related gene set consisting of 13 genes by prognostic analysis, the role of which was validated in two other databases. Finally, the human pancreatic cancer tissue and organoid model was used to evaluate the correlation between the enrichment of this gene set and liver metastasis. Results Prognostic analysis and correlation analysis revealed that eight AS events were closely associated with the prognosis of pancreatic cancer. Furthermore, the expression of TMC7 and CHECK1 AS events was increased in the metastatic lesions of the human tissue and organoid model. Additionally, the knockdown of exon 17 of TMC7 significantly inhibited the proliferation, invasion, and migration of pancreatic cancer cells in 2D and 3D cell experiments. Finally, the expression of exon 17 of TMC17 exhibited a significant correlation with the poor prognosis in pancreatic ductal adenocarcinoma (PDAC). Conclusion The AS events of TMC7 and CHECK1 were associated with liver metastasis in pancreatic cancer. Moreover, exon 17 of TMC7 could be a potential therapeutic target in pancreatic cancer.
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Affiliation(s)
- Yuanchi Weng
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hao Qian
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Liwen Hong
- Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shulin Zhao
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaxing Deng
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China,*Correspondence: Xiaxing Deng, ; Baiyong Shen,
| | - Baiyong Shen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China,*Correspondence: Xiaxing Deng, ; Baiyong Shen,
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13
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Goeppert B, Roessler S. New kid on the block: Netrin-1 as a novel player in the delicate molecular network of hepatic inflammation. Hepatology 2022; 76:1237-1239. [PMID: 35384001 DOI: 10.1002/hep.32509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 03/25/2022] [Indexed: 12/08/2022]
Affiliation(s)
- Benjamin Goeppert
- Institute of Pathology and Liver Cancer Center Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
| | - Stephanie Roessler
- Institute of Pathology and Liver Cancer Center Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
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Zhou R, Gao Z, Ju Y. Novel six-gene prognostic signature based on colon adenocarcinoma immune-related genes. BMC Bioinformatics 2022; 23:418. [PMID: 36221049 PMCID: PMC9552517 DOI: 10.1186/s12859-022-04909-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/23/2022] [Indexed: 12/05/2022] Open
Abstract
Background Colon adenocarcinoma (COAD) is one of the most common gastrointestinal tumors worldwide, and immunotherapy is one of the most promising treatments for it. Identifying immune genes involved in the development and maintenance of cancer is key to the use of tumor immunotherapy. This study aimed to determine the prognostic value of immune genes in patients with COAD and to establish an immune-related gene signature. Differentially expressed genes, immune-related genes (DEIGs), and transcription factors (DETFs) were screened using the following databases: Cistrome, The Cancer Genome Atlas (TCGA), the Immunology Database and Analysis Portal, and InnateDB. We constructed a network showing the regulation of DEIGs by DETFs. Using weighted gene co-expression network analysis, we prepared 5 co-expressed gene modules; 6 hub genes (CD1A, CD1B, FGF9, GRP, SERPINE1, and F2RL2) obtained using univariate and multivariate regression analysis were used to construct a risk model. Patients from TCGA database were divided into high- and low-risk groups based on whether their risk score was greater or less than the mean; the public dataset GSE40967, which contains gene expression profiles of 566 colon cancer patients, was used for validation. Results Survival analysis, somatic gene mutations, and tumor-infiltrating immune cells differed significantly between the high- and low-risk groups. Conclusions This immune-related gene signature could play an important role in guiding treatment, making prognoses, and potentially developing future clinical applications. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04909-2.
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Affiliation(s)
- Rui Zhou
- Surgical Department of Gastrointestinal Surgery, Shunde Hospital of Southern Medical University, No. 1 Jiazi Road, Shunde District, Foshan, 528399, Guangdong, China
| | - Zhuowei Gao
- Medical Department of Traditional Chinese Medicine, Shunde Hospital of Guangzhou University of Traditional Chinese Medicine, No. 12, Jinsha Avenue, Shunde District, Foshan, 510006, Guangdong, China
| | - Yongle Ju
- Surgical Department of Gastrointestinal Surgery, Shunde Hospital of Southern Medical University, No. 1 Jiazi Road, Shunde District, Foshan, 528399, Guangdong, China.
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Ye Z, Bing A, Zhao S, Yi S, Zhan X. Comprehensive analysis of spliceosome genes and their mutants across 27 cancer types in 9070 patients: clinically relevant outcomes in the context of 3P medicine. EPMA J 2022; 13:335-350. [DOI: 10.1007/s13167-022-00279-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 04/25/2022] [Indexed: 12/19/2022]
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Analysis of Gene Expression Microarray Data Reveals Androgen-Responsive Genes of Muscles in Polycystic Ovarian Syndrome Patients. Processes (Basel) 2022. [DOI: 10.3390/pr10020387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Polycystic ovarian syndrome (PCOS) is an endocrine disorder that is characterized by hyperandrogenism. Therefore, information about androgen-induced molecular changes can be obtained using the tissues of patients with PCOS. We analyzed two microarray datasets of normal and PCOS muscle samples (GSE8157 and GSE6798) to identify androgen-responsive genes (ARGs). Differentially expressed genes were determined using the t-test and a meta-analysis of the datasets. The overlap between significant results of the meta-analysis and ARGs predicted from an external database was determined, and differential coexpression analysis was then applied between these genes and the other genes. We found 313 significant genes in the meta-analysis using the Benjamini–Hochberg multiple testing correction. Of these genes, 61 were in the list of predicted ARGs. When the differential coexpression between these 61 genes and 13,545 genes filtered by variance was analyzed, 540 significant gene pairs were obtained using the Benjamini–Hochberg correction. While no significant results were obtained regarding the functional enrichment of the differentially expressed genes, top-level gene ontology terms were significantly enriched in the list of differentially coexpressed genes, which indicates that a broad range of cellular processes is affected by androgen administration. Our findings provide valuable information for the identification of ARGs.
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