1
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Marx OM, Mankarious MM, Koltun WA, Yochum GS. Identification of differentially expressed genes and splicing events in early-onset colorectal cancer. Front Oncol 2024; 14:1365762. [PMID: 38680862 PMCID: PMC11047122 DOI: 10.3389/fonc.2024.1365762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/27/2024] [Indexed: 05/01/2024] Open
Abstract
Background The incidence of colorectal cancer (CRC) has been steadily increasing in younger individuals over the past several decades for reasons that are incompletely defined. Identifying differences in gene expression profiles, or transcriptomes, in early-onset colorectal cancer (EOCRC, < 50 years old) patients versus later-onset colorectal cancer (LOCRC, > 50 years old) patients is one approach to understanding molecular and genetic features that distinguish EOCRC. Methods We performed RNA-sequencing (RNA-seq) to characterize the transcriptomes of patient-matched tumors and adjacent, uninvolved (normal) colonic segments from EOCRC (n=21) and LOCRC (n=22) patients. The EOCRC and LOCRC cohorts were matched for demographic and clinical characteristics. We used The Cancer Genome Atlas Colon Adenocarcinoma (TCGA-COAD) database for validation. We used a series of computational and bioinformatic tools to identify EOCRC-specific differentially expressed genes, molecular pathways, predicted cell populations, differential gene splicing events, and predicted neoantigens. Results We identified an eight-gene signature in EOCRC comprised of ALDOB, FBXL16, IL1RN, MSLN, RAC3, SLC38A11, WBSCR27 and WNT11, from which we developed a score predictive of overall CRC patient survival. On the entire set of genes identified in normal tissues and tumors, cell type deconvolution analysis predicted a differential abundance of immune and non-immune populations in EOCRC versus LOCRC. Gene set enrichment analysis identified increased expression of splicing machinery in EOCRC. We further found differences in alternative splicing (AS) events, including one within the long non-coding RNA, HOTAIRM1. Additional analysis of AS found seven events specific to EOCRC that encode potential neoantigens. Conclusion Our transcriptome analyses identified genetic and molecular features specific to EOCRC which may inform future screening, development of prognostic indicators, and novel drug targets.
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Affiliation(s)
- Olivia M. Marx
- Koltun and Yochum Laboratory, Department of Surgery, Division of Colon & Rectal Surgery, Pennsylvania State University College of Medicine, Hershey, PA, United States
- Department of Biochemistry & Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - Marc M. Mankarious
- Koltun and Yochum Laboratory, Department of Surgery, Division of Colon & Rectal Surgery, Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - Walter A. Koltun
- Koltun and Yochum Laboratory, Department of Surgery, Division of Colon & Rectal Surgery, Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - Gregory S. Yochum
- Koltun and Yochum Laboratory, Department of Surgery, Division of Colon & Rectal Surgery, Pennsylvania State University College of Medicine, Hershey, PA, United States
- Department of Biochemistry & Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, United States
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2
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Singla RK, Wang X, Gundamaraju R, Joon S, Tsagkaris C, Behzad S, Khan J, Gautam R, Goyal R, Rakmai J, Dubey AK, Simal-Gandara J, Shen B. Natural products derived from medicinal plants and microbes might act as a game-changer in breast cancer: a comprehensive review of preclinical and clinical studies. Crit Rev Food Sci Nutr 2023; 63:11880-11924. [PMID: 35838143 DOI: 10.1080/10408398.2022.2097196] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Breast cancer (BC) is the most prevalent neoplasm among women. Genetic and environmental factors lead to BC development and on this basis, several preventive - screening and therapeutic interventions have been developed. Hormones, both in the form of endogenous hormonal signaling or hormonal contraceptives, play an important role in BC pathogenesis and progression. On top of these, breast microbiota includes both species with an immunomodulatory activity enhancing the host's response against cancer cells and species producing proinflammatory cytokines associated with BC development. Identification of novel multitargeted therapeutic agents with poly-pharmacological potential is a dire need to combat advanced and metastatic BC. A growing body of research has emphasized the potential of natural compounds derived from medicinal plants and microbial species as complementary BC treatment regimens, including dietary supplements and probiotics. In particular, extracts from plants such as Artemisia monosperma Delile, Origanum dayi Post, Urtica membranacea Poir. ex Savigny, Krameria lappacea (Dombey) Burdet & B.B. Simpson and metabolites extracted from microbes such as Deinococcus radiodurans and Streptomycetes strains as well as probiotics like Bacillus coagulans and Lactobacillus brevis MK05 have exhibited antitumor effects in the form of antiproliferative and cytotoxic activity, increase in tumors' chemosensitivity, antioxidant activity and modulation of BC - associated molecular pathways. Further, bioactive compounds like 3,3'-diindolylmethane, epigallocatechin gallate, genistein, rutin, resveratrol, lycopene, sulforaphane, silibinin, rosmarinic acid, and shikonin are of special interest for the researchers and clinicians because these natural agents have multimodal action and act via multiple ways in managing the BC and most of these agents are regularly available in our food and fruit diets. Evidence from clinical trials suggests that such products had major potential in enhancing the effectiveness of conventional antitumor agents and decreasing their side effects. We here provide a comprehensive review of the therapeutic effects and mechanistic underpinnings of medicinal plants and microbial metabolites in BC management. The future perspectives on the translation of these findings to the personalized treatment of BC are provided and discussed.
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Affiliation(s)
- Rajeev K Singla
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- iGlobal Research and Publishing Foundation, New Delhi, India
| | - Xiaoyan Wang
- Department of Pathology, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Rohit Gundamaraju
- ER Stress and Mucosal Immunology Lab, School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston, Tasmania, Australia
| | - Shikha Joon
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- iGlobal Research and Publishing Foundation, New Delhi, India
| | | | - Sahar Behzad
- Evidence-based Phytotherapy and Complementary Medicine Research Center, Alborz University of Medical Sciences, Karaj, Iran
- Department of Pharmacognosy, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Johra Khan
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah, Saudi Arabia
- Health and Basic Sciences Research Center, Majmaah University, Majmaah, Saudi Arabia
| | - Rupesh Gautam
- Department of Pharmacology, MM School of Pharmacy, MM University, Sadopur, Haryana, India
| | - Rajat Goyal
- Department of Pharmacology, MM School of Pharmacy, MM University, Sadopur, Haryana, India
| | - Jaruporn Rakmai
- Kasetsart Agricultural and Agro-Industrial Product Improvement Institute (KAPI), Kasetsart University, Bangkok, Thailand
| | | | - Jesus Simal-Gandara
- Nutrition and Bromatology Group, Department of Analytical Chemistry and Food Science, Faculty of Science, Universidade de Vigo, Ourense, Spain
| | - Bairong Shen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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3
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Popli P, Chadchan SB, Dias M, Deng X, Gunderson SJ, Jimenez P, Yalamanchili H, Kommagani R. SF3B1-dependent alternative splicing is critical for maintaining endometrial homeostasis and the establishment of pregnancy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.20.541590. [PMID: 37292891 PMCID: PMC10245700 DOI: 10.1101/2023.05.20.541590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The remarkable potential of human endometrium to undergo spontaneous remodeling is shaped by controlled spatiotemporal gene expression patterns. Although hormone-driven transcription shown to govern these patterns, the post-transcriptional processing of these mRNA transcripts, including the mRNA splicing in the endometrium is not studied yet. Here, we report that the splicing factor, SF3B1 is central in driving alternative splicing (AS) events that are vital for physiological responses of the endometrium. We show that loss of SF3B1 splicing activity impairs stromal cell decidualization as well as embryo implantation. Transcriptomic analysis revealed that SF3B1 depletion decidualizing stromal cells led to differential mRNA splicing. Specifically, a significant upregulation in mutually exclusive AS events (MXEs) with SF3B1 loss resulted in the generation of aberrant transcripts. Further, we found that some of these candidate genes phenocopy SF3B1 function in decidualization. Importantly, we identify progesterone as a potential upstream regulator of SF3B1-mediated functions in endometrium possibly via maintaining its persistently high levels, in coordination with deubiquitinating enzymes. Collectively, our data suggest that SF3B1-driven alternative splicing plays a critical role in mediating the endometrial-specific transcriptional paradigms. Thus, the identification of novel mRNA variants associated with successful pregnancy establishment may help to develop new strategies to diagnose or prevent early pregnancy loss.
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Alles J, Legnini I, Pacelli M, Rajewsky N. Rapid nuclear deadenylation of mammalian messenger RNA. iScience 2022; 26:105878. [PMID: 36691625 PMCID: PMC9860345 DOI: 10.1016/j.isci.2022.105878] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 06/13/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022] Open
Abstract
Poly(A) tails protect RNAs from degradation and their deadenylation rates determine RNA stability. Although poly(A) tails are generated in the nucleus, deadenylation of tails has mostly been investigated within the cytoplasm. Here, we combined long-read sequencing with metabolic labeling, splicing inhibition and cell fractionation experiments to quantify, separately, the genesis and trimming of nuclear and cytoplasmic tails in vitro and in vivo. We present evidence for genome-wide, nuclear synthesis of tails longer than 200 nt, which are rapidly shortened after transcription. Our data suggests that rapid deadenylation is a nuclear process, and that different classes of transcripts and even transcript isoforms have distinct nuclear tail lengths. For example, many long-noncoding RNAs retain long poly(A) tails. Modeling deadenylation dynamics predicts nuclear deadenylation about 10 times faster than cytoplasmic deadenylation. In summary, our data suggests that nuclear deadenylation might be a key mechanism for regulating mRNA stability, abundance, and subcellular localization.
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Affiliation(s)
- Jonathan Alles
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Laboratory for Systems Biology of Gene Regulatory Elements, Hannoversche Str. 28, 10115 Berlin, Germany,Humboldt-Universität zu Berlin, Institute of Biology, Unter den Linden 6, 10099 Berlin, Germany
| | - Ivano Legnini
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Laboratory for Systems Biology of Gene Regulatory Elements, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Maddalena Pacelli
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Laboratory for Systems Biology of Gene Regulatory Elements, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Nikolaus Rajewsky
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Laboratory for Systems Biology of Gene Regulatory Elements, Hannoversche Str. 28, 10115 Berlin, Germany,Humboldt-Universität zu Berlin, Institute of Biology, Unter den Linden 6, 10099 Berlin, Germany,Corresponding author
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5
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Singh N, Tapader R, Chatterjee S, Pal A, Pal A. Subtilisin from Bacillus amyloliquefaciens induces apoptosis in breast cancer cells through ubiquitin-proteasome-mediated tubulin degradation. Int J Biol Macromol 2022; 220:852-865. [PMID: 35985398 DOI: 10.1016/j.ijbiomac.2022.08.086] [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: 05/05/2022] [Revised: 07/20/2022] [Accepted: 08/11/2022] [Indexed: 11/05/2022]
Abstract
To search for novel proteases from environmental isolates which can induce apoptosis in cancer cells, we have purified subtilisin from Bacillus amyloliquefaciens and studied its anti-cancer properties. Subtilisin induced apoptosis in colon (HT29) and breast (MCF7) cancer cells but showed no effect on mouse peritoneal macrophages and normal breast cells (MCF10A). Western blot analysis showed that Bax, Bcl-2 level remained unchanged but tubulin level decreased significantly. Subtilisin does not induce the intrinsic pathway of apoptosis, rather it induced tubulin degradation in MCF-7 cells, whereas in normal cells (MCF-10A) tubulin degradation was not observed. Subtilisin activates ubiquitination and proteasomal-mediated tubulin degradation which was completely restored in presence of proteasome inhibitor MG-132. We further observed PARKIN, one of the known E3-ligase, is overexpressed and interacts with tubulin in subtilisin treated cells. Knockdown of PARKIN effectively downregulates ubiquitination and inhibits degradation of tubulin. PARKIN activation and tubulin degradation lead to ER-stress which in turn activates caspase-7 and PARP cleavage, thus guiding the subtilisin treated cells towards apoptosis. To our knowledge this is the first report of subtilisin induced apoptosis in cancer cells by proteasomal degradation of tubulin.
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Affiliation(s)
- Nanda Singh
- Division of Pathophysiology, ICMR-National Institute of Cholera and Enteric Diseases (NICED), Kolkata 700010, India
| | - Rima Tapader
- Division of Pathophysiology, ICMR-National Institute of Cholera and Enteric Diseases (NICED), Kolkata 700010, India
| | - Shruti Chatterjee
- Division of Biotechnology and Phycology, CSIR-Central Salt & Marine Chemical Research Institute, Bhavnagar 364002, India
| | - Ananda Pal
- Division of Clinical Medicine, ICMR-National Institute of Cholera and Enteric Diseases (NICED), Kolkata 700010, India
| | - Amit Pal
- Division of Pathophysiology, ICMR-National Institute of Cholera and Enteric Diseases (NICED), Kolkata 700010, India.
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Jemmy Christy H, Vasudevan S, Sudha S, Kandeel M, Subramanian K, Pugazhvendan SR, Ronald Ross P, Velmurugan. Targeting Streptomyces-Derived Streptenol Derivatives against Gynecological Cancer Target PIK3CA: An In Silico Approach. BIOMED RESEARCH INTERNATIONAL 2022; 2022:6600403. [PMID: 35860806 PMCID: PMC9293527 DOI: 10.1155/2022/6600403] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/10/2022] [Accepted: 06/15/2022] [Indexed: 01/21/2023]
Abstract
Streptomyces is amongst the most amenable genera for biotechnological applications, and it is extensively used as a scaffold for drug development. One of the most effective therapeutic applications in the treatment of cancer is targeted therapy. Small molecule therapy is one of them, and it has gotten a lot of attention recently. Streptomyces derived compounds namely streptenols A, C, and F-I and streptazolin were subjected for ADMET property assessment. Our computational studies based on molecular docking effectively displayed the synergistic effect of streptomyces-derived compounds on the gynecological cancer target PIK3CA. These compounds were observed with the highest docking scores as well as promising intermolecular interaction stability throughout the molecular dynamic simulation. Molecular docking and molecular dynamic modeling techniques were utilized to investigate the binding mode stability of drugs using a pharmacophore scaffold, as well as physicochemical and pharmacokinetic aspects linked to alpelisib. With a root mean square fluctuation of the protein backbone of less than 0.7 nm, they demonstrated a steady binding mode in the target binding pocket. They have also prompted hydrogen bonding throughout the simulations, implying that the chemicals have firmly occupied the active site. A comprehensive study showed that streptenol D, streptenol E, streptenol C, streptenol G, streptenol F, and streptenol B can be considered as lead compounds for PIK3CA-based inhibitor design. To warrant the treatment efficacy against cancer, comprehensive computational research based on proposed chemicals must be assessed through in vitro studies.
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Affiliation(s)
- H. Jemmy Christy
- Department of Bioinformatics, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Swetha Vasudevan
- Department of Bioinformatics, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - S. Sudha
- Department of Biotechnology, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Mahmoud Kandeel
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-Ahsa, Saudi Arabia
- Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelshikh University, Kafrelshikh, Egypt
| | - Kumaran Subramanian
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - S. R. Pugazhvendan
- Department of Zoology, Arignar Anna Government Arts College, Cheyyar, Tamil Nadu, India
- Department of Zoology, Annamalai University, Annamalai Nagar, Cuddalore, Tamil Nadu, India
| | - P. Ronald Ross
- Department of Zoology, Annamalai University, Annamalai Nagar, Cuddalore, Tamil Nadu, India
| | - Velmurugan
- Department of Biology, School of Natural Science, Madda Walabu University, Oromiya Region, Ethiopia
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7
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Murphy AJ, Li AH, Li P, Sun H. Therapeutic Targeting of Alternative Splicing: A New Frontier in Cancer Treatment. Front Oncol 2022; 12:868664. [PMID: 35463320 PMCID: PMC9027816 DOI: 10.3389/fonc.2022.868664] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/11/2022] [Indexed: 01/05/2023] Open
Abstract
The ability for cells to harness alternative splicing enables them to diversify their proteome in order to carry out complex biological functions and adapt to external and internal stimuli. The spliceosome is the multiprotein-RNA complex charged with the intricate task of alternative splicing. Aberrant splicing can arise from abnormal spliceosomes or splicing factors and drive cancer development and progression. This review will provide an overview of the alternative splicing process and aberrant splicing in cancer, with a focus on serine/arginine-rich (SR) proteins and their recently reported roles in cancer development and progression and beyond. Recent mapping of the spliceosome, its associated splicing factors, and their relationship to cancer have opened the door to novel therapeutic approaches that capitalize on the widespread influence of alternative splicing. We conclude by discussing small molecule inhibitors of the spliceosome that have been identified in an evolving era of cancer treatment.
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Affiliation(s)
- Anthony J. Murphy
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, United States
| | - Alex H. Li
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, United States
| | - Peichao Li
- Department of Thoracic Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Hong Sun
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, United States
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8
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Zhang S, Wang Y, Sun Y, Zhao G, Wang J, Liu L, Liu F, Wang P, Xu X. 4′,7-Di-O-methylnaringenin (DMNG), a naringenin derivative, activates p53 signal pathway through down-regulating MDM2. J Funct Foods 2022. [DOI: 10.1016/j.jff.2022.104962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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9
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Kobayashi A, Clément MJ, Craveur P, El Hage K, Salone JDM, Bollot G, Pastré D, Maucuer A. Identification of a small molecule splicing inhibitor targeting UHM domains. FEBS J 2021; 289:682-698. [PMID: 34520118 DOI: 10.1111/febs.16199] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/10/2021] [Accepted: 09/13/2021] [Indexed: 01/07/2023]
Abstract
Splicing factor mutations are frequent in myeloid neoplasms, blood cancers, and solid tumors. Cancer cells harboring these mutations present a particular vulnerability to drugs that target splicing factors such as SF3b155 or CAPERα. Still, the arsenal of chemical probes that target the spliceosome is very limited. U2AF homology motifs (UHMs) are common protein interaction domains among splicing factors. They present a hydrophobic pocket ideally suited to anchor small molecules with the aim to inhibit protein-protein interaction. Here, we combined a virtual screening of a small molecules database and an in vitro competition assay and identified a small molecule, we named UHMCP1 that prevents the SF3b155/U2AF65 interaction. NMR analyses and molecular dynamics simulations confirmed the binding of this molecule in the hydrophobic pocket of the U2AF65 UHM domain. We further provide evidence that UHMCP1 impacts RNA splicing and cell viability and is therefore an interesting novel compound targeting an UHM domain with potential anticancer properties.
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Affiliation(s)
- Asaki Kobayashi
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, Evry, France.,SYNSIGHT, Genopole Entreprises, Evry, France
| | | | | | - Krystel El Hage
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, Evry, France
| | | | | | - David Pastré
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, Evry, France
| | - Alexandre Maucuer
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, Evry, France
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10
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Nichols RG, Davenport ER. The relationship between the gut microbiome and host gene expression: a review. Hum Genet 2021; 140:747-760. [PMID: 33221945 PMCID: PMC7680557 DOI: 10.1007/s00439-020-02237-0] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/06/2020] [Indexed: 12/13/2022]
Abstract
Despite the growing knowledge surrounding host-microbiome interactions, we are just beginning to understand how the gut microbiome influences-and is influenced by-host gene expression. Here, we review recent literature that intersects these two fields, summarizing themes across studies. Work in model organisms, human biopsies, and cell culture demonstrate that the gut microbiome is an important regulator of several host pathways relevant for disease, including immune development and energy metabolism, and vice versa. The gut microbiome remodels host chromatin, causes differential splicing, alters the epigenetic landscape, and directly interrupts host signaling cascades. Emerging techniques like single-cell RNA sequencing and organoid generation have the potential to refine our understanding of the relationship between the gut microbiome and host gene expression in the future. By intersecting microbiome and host gene expression, we gain a window into the physiological processes important for fostering the extensive cross-kingdom interactions and ultimately our health.
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Affiliation(s)
- Robert G. Nichols
- Department of Biology, The Pennsylvania State University, University Park, PA 16802 USA
| | - Emily R. Davenport
- Department of Biology, The Pennsylvania State University, University Park, PA 16802 USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802 USA
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11
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Ghidini A, Cléry A, Halloy F, Allain FHT, Hall J. RNA-PROTACs: Degraders of RNA-Binding Proteins. Angew Chem Int Ed Engl 2021; 60:3163-3169. [PMID: 33108679 PMCID: PMC7898822 DOI: 10.1002/anie.202012330] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/08/2020] [Indexed: 12/19/2022]
Abstract
Defects in the functions of RNA binding proteins (RBPs) are at the origin of many diseases; however, targeting RBPs with conventional drugs has proven difficult. PROTACs are a new class of drugs that mediate selective degradation of a target protein through a cell's ubiquitination machinery. PROTACs comprise a moiety that binds the selected protein, conjugated to a ligand of an E3 ligase. Herein, we introduce RNA-PROTACs as a new concept in the targeting of RBPs. These chimeric structures employ small RNA mimics as targeting groups that dock the RNA-binding site of the RBP, whereupon a conjugated E3-recruiting peptide derived from the HIF-1α protein directs the RBP for proteasomal degradation. We performed a proof-of-concept demonstration with the degradation of two RBPs-a stem cell factor LIN28 and a splicing factor RBFOX1-and showed their use in cancer cell lines. The RNA-PROTAC approach opens the way to rapid, selective targeting of RBPs in a rational and general fashion.
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Affiliation(s)
- Alice Ghidini
- Department of Chemistry and Applied BiosciencesETH ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
| | - Antoine Cléry
- Department of BiologyETH ZurichHönggerbergring 648093ZurichSwitzerland
| | - François Halloy
- Department of Chemistry and Applied BiosciencesETH ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
| | | | - Jonathan Hall
- Department of Chemistry and Applied BiosciencesETH ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
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12
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Xia Y, Liu S, Li C, Ai Z, Shen W, Ren W, Yang X. Discovery of a novel ferroptosis inducer-talaroconvolutin A-killing colorectal cancer cells in vitro and in vivo. Cell Death Dis 2020; 11:988. [PMID: 33203867 PMCID: PMC7673992 DOI: 10.1038/s41419-020-03194-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 02/07/2023]
Abstract
Ferropotsis is among the most important mechanisms of cancer suppression, which could be harnessed for cancer therapy. However, no natural small-molecule compounds with cancer inhibitory activity have been identified to date. In the present study, we reported the discovery of a novel ferroptosis inducer, talaroconvolutin A (TalaA), and the underlying molecular mechanism. We discovered that TalaA killed colorectal cancer cells in dose-dependent and time-dependent manners. Interestingly, TalaA did not induce apoptosis, but strongly triggered ferroptosis. Notably, TalaA was significantly more effective than erastin (a well-known ferroptosis inducer) in suppressing colorectal cancer cells via ferroptosis. We revealed a dual mechanism of TalaA’ action against cancer. On the one hand, TalaA considerably increased reactive oxygen species levels to a certain threshold, the exceeding of which induced ferroptosis. On the other hand, this compound downregulated the expression of the channel protein solute carrier family 7 member 11 (SLC7A11) but upregulated arachidonate lipoxygenase 3 (ALOXE3), promoting ferroptosis. Furthermore, in vivo experiments in mice evidenced that TalaA effectively suppressed the growth of xenografted colorectal cancer cells without obvious liver and kidney toxicities. The findings of this study indicated that TalaA could be a new potential powerful drug candidate for colorectal cancer therapy due to its outstanding ability to kill colorectal cancer cells via ferroptosis induction.
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Affiliation(s)
- Yong Xia
- Key Laboratory of Precision Oncology of Shandong Higher Education, Institute of Precision Medicine, Jining Medical University, 272067, Jining, Shandong, P.R. China. .,Departments of Urology, New York University School of Medicine, New York, NY, 10016, USA.
| | - Shuzhi Liu
- The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central University for Nationalities, 430074, Wuhan, P.R. China
| | - Changlin Li
- Key Laboratory of Precision Oncology of Shandong Higher Education, Institute of Precision Medicine, Jining Medical University, 272067, Jining, Shandong, P.R. China
| | - Zhiying Ai
- Key Laboratory of Precision Oncology of Shandong Higher Education, Institute of Precision Medicine, Jining Medical University, 272067, Jining, Shandong, P.R. China
| | - Wenzhi Shen
- Key Laboratory of Precision Oncology of Shandong Higher Education, Institute of Precision Medicine, Jining Medical University, 272067, Jining, Shandong, P.R. China
| | - Wenqi Ren
- Key Laboratory of Precision Oncology of Shandong Higher Education, Institute of Precision Medicine, Jining Medical University, 272067, Jining, Shandong, P.R. China
| | - Xiaolong Yang
- The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central University for Nationalities, 430074, Wuhan, P.R. China.
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Law JWF, Law LNS, Letchumanan V, Tan LTH, Wong SH, Chan KG, Ab Mutalib NS, Lee LH. Anticancer Drug Discovery from Microbial Sources: The Unique Mangrove Streptomycetes. Molecules 2020; 25:E5365. [PMID: 33212836 PMCID: PMC7698459 DOI: 10.3390/molecules25225365] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/08/2020] [Accepted: 11/13/2020] [Indexed: 02/07/2023] Open
Abstract
Worldwide cancer incidence and mortality have always been a concern to the community. The cancer mortality rate has generally declined over the years; however, there is still an increased mortality rate in poorer countries that receives considerable attention from healthcare professionals. This suggested the importance of the prompt detection, effective treatment, and prevention strategies. The genus Streptomyces has been documented as a prolific producer of biologically active secondary metabolites. Streptomycetes from mangrove environments attract researchers' attention due to their ability to synthesize diverse, interesting bioactive metabolites. The present review highlights research on mangrove-derived streptomycetes and the production of anticancer-related compounds from these microorganisms. Research studies conducted between 2008 and 2019, specifically mentioning the isolation of streptomycetes from mangrove areas and described the successful purification of compound(s) or generation of crude extracts with cytotoxic activity against human cancer cell lines, were compiled in this review. It is anticipated that there will be an increase in prospects for mangrove-derived streptomycetes as one of the natural resources for the isolation of chemotherapeutic agents.
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Affiliation(s)
- Jodi Woan-Fei Law
- Novel Bacteria and Drug Discovery (NBDD) Research Group, Microbiome and Bioresource Research Strength, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Selangor Darul Ehsan, Malaysia; (J.W.-F.L.); (V.L.); (L.T.-H.T.)
| | - Lydia Ngiik-Shiew Law
- Monash Credentialed Pharmacy Clinical Educator, Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville 3052, VIC, Australia;
| | - Vengadesh Letchumanan
- Novel Bacteria and Drug Discovery (NBDD) Research Group, Microbiome and Bioresource Research Strength, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Selangor Darul Ehsan, Malaysia; (J.W.-F.L.); (V.L.); (L.T.-H.T.)
| | - Loh Teng-Hern Tan
- Novel Bacteria and Drug Discovery (NBDD) Research Group, Microbiome and Bioresource Research Strength, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Selangor Darul Ehsan, Malaysia; (J.W.-F.L.); (V.L.); (L.T.-H.T.)
| | - Sunny Hei Wong
- Li Ka Shing Institute of Health Sciences, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong, China;
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
- International Genome Centre, Jiangsu University, Zhenjiang 212013, China
| | - Nurul-Syakima Ab Mutalib
- UKM Medical Molecular Biology Institute (UMBI), UKM Medical Centre, Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia
| | - Learn-Han Lee
- Novel Bacteria and Drug Discovery (NBDD) Research Group, Microbiome and Bioresource Research Strength, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Selangor Darul Ehsan, Malaysia; (J.W.-F.L.); (V.L.); (L.T.-H.T.)
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14
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Popli P, Richters MM, Chadchan SB, Kim TH, Tycksen E, Griffith O, Thaker PH, Griffith M, Kommagani R. Splicing factor SF3B1 promotes endometrial cancer progression via regulating KSR2 RNA maturation. Cell Death Dis 2020; 11:842. [PMID: 33040078 PMCID: PMC7548007 DOI: 10.1038/s41419-020-03055-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 09/21/2020] [Accepted: 09/25/2020] [Indexed: 02/06/2023]
Abstract
Although endometrial cancer is the most common cancer of the female reproductive tract, we have little understanding of what controls endometrial cancer beyond the transcriptional effects of steroid hormones such as estrogen. As a result, we have limited therapeutic options for the ~62,000 women diagnosed with endometrial cancer each year in the United States. Here, in an attempt to identify new prognostic and therapeutic targets, we focused on a new area for this cancer—alternative mRNA splicing—and investigated whether splicing factor, SF3B1, plays an important role in endometrial cancer pathogenesis. Using a tissue microarray, we found that human endometrial tumors expressed more SF3B1 protein than non-cancerous tissues. Furthermore, SF3B1 knockdown reduced in vitro proliferation, migration, and invasion of the endometrial cancer cell lines Ishikawa and AN3CA. Similarly, the SF3B1 inhibitor, Pladienolide-B (PLAD-B), reduced the Ishikawa and AN3CA cell proliferation and invasion in vitro. Moreover, PLAD-B reduced tumor growth in an orthotopic endometrial cancer mouse model. Using RNA-Seq approach, we identified ~2000 differentially expressed genes (DEGs) with SF3B1 knockdown in endometrial cancer cells. Additionally, alternative splicing (AS) events analysis revealed that SF3B1 depletion led to alteration in multiple categories of AS events including alternative exon skipping (ES), transcript start site usage (TSS), and transcript termination site (TTS) usage. Subsequently, bioinformatics analysis showed KSR2 as a potential candidate for SF3B1-mediated functions in endometrial cancer. Specifically, loss of SF3B1 led to decrease in KSR2 expression, owing to reduced maturation of KSR2 pre-mRNA to a mature RNA. Importantly, we found rescuing the KSR2 expression with SF3B1 knockdown partially restored the cell growth of endometrial cancer cells. Taken together, our data suggest that SF3B1 plays a crucial oncogenic role in the tumorigenesis of endometrial cancer and hence may support the development of SF3B1 inhibitors to treat this disease.
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Affiliation(s)
- Pooja Popli
- Department of Obstetrics and Gynecology, Center for Reproductive Health Sciences, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Megan M Richters
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Genome Technology Access Center, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Sangappa B Chadchan
- Department of Obstetrics and Gynecology, Center for Reproductive Health Sciences, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Tae Hoon Kim
- Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University, Grand Rapids, MI, 48824, USA
| | - Eric Tycksen
- Genome Technology Access Center, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Obi Griffith
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Genome Technology Access Center, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Premal H Thaker
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Malachi Griffith
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Genome Technology Access Center, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Ramakrishna Kommagani
- Department of Obstetrics and Gynecology, Center for Reproductive Health Sciences, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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15
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Xu Q, Deng B, Li M, Chen Y, Zhuan L. circRNA-UBAP2 promotes the proliferation and inhibits apoptosis of ovarian cancer though miR-382-5p/PRPF8 axis. J Ovarian Res 2020; 13:81. [PMID: 32690086 PMCID: PMC7372761 DOI: 10.1186/s13048-020-00685-w] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 07/13/2020] [Indexed: 01/08/2023] Open
Abstract
Objective circular RNAs (circRNAs) have been reported to be essential regulators of multiple malignant cancers. However, the functions of circRNAs in ovarian cancer need to be further explored. The aim of our study is to explore the role of circRNA-UBAP2 in ovarian cancer and its mechanism. Results circRNA-UBAP2 was upregulated in ovarian cancer tissues and cell lines. Knockdown of circRNA-UBAP2 inhibited cell proliferation and promoted cell apoptosis, but circRNA-UBAP2 overexpressed got opposite results. In addition, circRNA-UBAP2 targeted miR-382-5p and downregulated its expression, PRPF8 was a target gene of miR-382-5p. Furthemore, circRNA-UBAP2/miR-382-5p/PRPF8 axis affected the proliferation, apoptosis and cell cycle of ovarian cancer through the mechanism of competing endogenous RNAs (ceRNA). Conclusion circRNA-UBAP2 acted as a ceRNA to sponged miR-382-5p, increased the expression level of PRPF8, and prompted proliferation and inhibited apoptosis in ovarian cancer cells.
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Affiliation(s)
- Qin Xu
- Department of Reproductive Medicine, Reproductive Medical Centre, The First People's Hospital of Yunnan Province, No. 157 Jin Bi Road, Kunming, People's Republic of China
| | - Bo Deng
- Department of Reproductive Medicine, Reproductive Medical Centre, The First People's Hospital of Yunnan Province, No. 157 Jin Bi Road, Kunming, People's Republic of China
| | - Manlin Li
- Kunming University of Science and Technology, Kunming, People's Republic of China
| | - Yang Chen
- Kunming University of Science and Technology, Kunming, People's Republic of China
| | - Li Zhuan
- Department of Reproductive Medicine, Reproductive Medical Centre, The First People's Hospital of Yunnan Province, No. 157 Jin Bi Road, Kunming, People's Republic of China.
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Abstract
While recognized as a therapeutic target, the spliceosome may offer a robust vector to improve established therapeutics against other protein targets. Here, we describe how modulating the spliceosome using small molecule splice modulators (SPLMs) can prime a cell for sensitivity to a target-specific drug. Using the cell cycle regulators aurora kinase and polo-like kinase as models, this study demonstrates how the combination of SPLM treatment in conjunction with kinase inhibition offers synergy for antitumor activity using reduced, sublethal levels of SPLM and kinase inhibitors. This concept of splice-modulated drug attenuation suggests a possible approach to enhance therapeutic agents that have shown limited applicability due to high toxicity or low efficacy.
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Affiliation(s)
- Kelsey A. Trieger
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0358, United States
| | - James J. La Clair
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0358, United States
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0358, United States
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17
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Yang YK, Shen DD, He P, Du LD, Wan DJ, Wang P, Wang T, Feng MQ. Chemically synthesized LYRM03 could inhibit the metastasis of human breast cancer MDA-MB-231 cells in vitro and in vivo. Bioorg Med Chem Lett 2019; 29:1719-1726. [PMID: 31126854 DOI: 10.1016/j.bmcl.2019.05.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/09/2019] [Accepted: 05/15/2019] [Indexed: 02/02/2023]
Abstract
Aminopeptidase N (APN) belongs to the aminopeptidase family, which is widely distributed throughout the animal and plant kingdoms. APN is thought to be a very important target for cancer therapy as it is linked to cancer progression and metastasis. However, bestatin (Ubenimex) is the only approved drug that targets various aminopeptidases for the treatment of acute myelocytic leukemia and lymphedema. A compound 3-amino-2-hydroxy-4-phenylbutanoylvalylisoleucine (also known as LYRM03), isolated from a Streptomyces strain HCCB10043, exhibited more potent inhibitory activity than bestatin. In this work, we applied a chemical synthesis strategy to generate LYRM03 to overcome the low yields typically achieved from fermentation. Finally, we explored a suite of experiments to determine the bioactivity of LYRM03 and revealed that the metastasis of MDA-MB-231 cells was significantly restrained with LYRM03 treatment or injection both in vitro and in vivo. Because of its anti-metastasis capacity, further structure modifications of LYRM03 will be of interest for its use alone or in combination as a therapy in cancer.
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Affiliation(s)
- Yun-Kai Yang
- Department of Microbiology and Biochemical Pharmacy, School of Pharmacy, Fudan University, Shanghai 201203, PR China
| | - Da-Dong Shen
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310032, Zhejiang, PR China
| | - Peng He
- Department of Microbiology and Biochemical Pharmacy, School of Pharmacy, Fudan University, Shanghai 201203, PR China
| | - Liang-Dong Du
- Shanghai Laiyi Center for Biopharmaceuticals R&D, 5B, Building 8 200 Niudun Road Pudong District, Shanghai 201203, PR China
| | - Ding-Jian Wan
- Shanghai Laiyi Center for Biopharmaceuticals R&D, 5B, Building 8 200 Niudun Road Pudong District, Shanghai 201203, PR China
| | - Pu Wang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310032, Zhejiang, PR China
| | - Tao Wang
- Shanghai Laiyi Center for Biopharmaceuticals R&D, 5B, Building 8 200 Niudun Road Pudong District, Shanghai 201203, PR China.
| | - Mei-Qing Feng
- Department of Microbiology and Biochemical Pharmacy, School of Pharmacy, Fudan University, Shanghai 201203, PR China.
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18
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Targeting the spliceosome for cutaneous squamous cell carcinoma therapy: a role for c-MYC and wild-type p53 in determining the degree of tumour selectivity. Oncotarget 2018; 9:23029-23046. [PMID: 29796170 PMCID: PMC5955416 DOI: 10.18632/oncotarget.25196] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 04/04/2018] [Indexed: 12/25/2022] Open
Abstract
We show that suppression of the spliceosome has potential for the treatment of cutaneous squamous cell carcinoma (cSCC). The small-molecule inhibitors of the spliceosome at the most advanced stage of development target the splicing factor SF3B1/SF3b155. The majority of cSCC cell lines are more sensitive than normal skin cells to death induced by the SF3B1 inhibitor pladienolide B. Knockdown of SF3B1 and a range of other splicing factors with diverse roles in the spliceosome can also selectively kill cSCC cells. We demonstrate that endogenous c-MYC participates in conferring sensitivity to spliceosome inhibition. c-MYC expression is elevated in cSCC lines and its knockdown reduces alterations in mRNA splicing and attenuates cell death caused by interference with the spliceosome. In addition, this study provides further support for a key role of the p53 pathway in the response to spliceosome disruption. SF3B1 inhibition causes wild-type p53 upregulation associated with altered mRNA splicing and reduced protein expression of both principal p53 negative regulators MDMX/MDM4 and MDM2. We observed that wild-type p53 can promote pladienolide B-induced death in tumour cells. However, p53 is commonly inactivated by mutation in cSCCs and p53 participates in killing normal skin cells at high concentrations of pladienolide B. This may limit the therapeutic window of SF3B1 inhibitors for cSCC. We provide evidence that, while suppression of SF3B1 has promise for treating cSCCs with mutant p53, inhibitors which target the spliceosome through SF3B1-independent mechanisms could have greater cSCC selectivity as a consequence of reduced p53 upregulation in normal cells.
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19
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Antimicrobial peptides, nanotechnology, and natural metabolites as novel approaches for cancer treatment. Pharmacol Ther 2018; 183:160-176. [DOI: 10.1016/j.pharmthera.2017.10.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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20
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Alternative Splicing as a Target for Cancer Treatment. Int J Mol Sci 2018; 19:ijms19020545. [PMID: 29439487 PMCID: PMC5855767 DOI: 10.3390/ijms19020545] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 01/29/2018] [Accepted: 01/29/2018] [Indexed: 02/06/2023] Open
Abstract
Alternative splicing is a key mechanism determinant for gene expression in metazoan. During alternative splicing, non-coding sequences are removed to generate different mature messenger RNAs due to a combination of sequence elements and cellular factors that contribute to splicing regulation. A different combination of splicing sites, exonic or intronic sequences, mutually exclusive exons or retained introns could be selected during alternative splicing to generate different mature mRNAs that could in turn produce distinct protein products. Alternative splicing is the main source of protein diversity responsible for 90% of human gene expression, and it has recently become a hallmark for cancer with a full potential as a prognostic and therapeutic tool. Currently, more than 15,000 alternative splicing events have been associated to different aspects of cancer biology, including cell proliferation and invasion, apoptosis resistance and susceptibility to different chemotherapeutic drugs. Here, we present well established and newly discovered splicing events that occur in different cancer-related genes, their modification by several approaches and the current status of key tools developed to target alternative splicing with diagnostic and therapeutic purposes.
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21
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Alternative Splicing in Breast Cancer and the Potential Development of Therapeutic Tools. Genes (Basel) 2017; 8:genes8100217. [PMID: 28981467 PMCID: PMC5664086 DOI: 10.3390/genes8100217] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 08/22/2017] [Accepted: 08/22/2017] [Indexed: 12/19/2022] Open
Abstract
Alternative splicing is a key molecular mechanism now considered as a hallmark of cancer that has been associated with the expression of distinct isoforms during the onset and progression of the disease. The leading cause of cancer-related deaths in women worldwide is breast cancer, and even when the role of alternative splicing in this type of cancer has been established, the function of this mechanism in breast cancer biology is not completely decoded. In order to gain a comprehensive view of the role of alternative splicing in breast cancer biology and development, we summarize here recent findings regarding alternative splicing events that have been well documented for breast cancer evolution, considering its prognostic and therapeutic value. Moreover, we analyze how the response to endocrine and chemical therapies could be affected due to alternative splicing and differential expression of variant isoforms. With all this knowledge, it becomes clear that targeting alternative splicing represents an innovative approach for breast cancer therapeutics and the information derived from current studies could guide clinical decisions with a direct impact in the clinical advances for breast cancer patients nowadays.
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22
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Armstrong RN, Steeples V, Singh S, Sanchi A, Boultwood J, Pellagatti A. Splicing factor mutations in the myelodysplastic syndromes: target genes and therapeutic approaches. Adv Biol Regul 2017; 67:13-29. [PMID: 28986033 DOI: 10.1016/j.jbior.2017.09.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 09/19/2017] [Accepted: 09/21/2017] [Indexed: 10/25/2022]
Abstract
Mutations in splicing factor genes (SF3B1, SRSF2, U2AF1 and ZRSR2) are frequently found in patients with myelodysplastic syndromes (MDS), suggesting that aberrant spliceosome function plays a key role in the pathogenesis of MDS. Splicing factor mutations have been shown to result in aberrant splicing of many downstream target genes. Recent functional studies have begun to characterize the splicing dysfunction in MDS, identifying some key aberrantly spliced genes that are implicated in disease pathophysiology. These findings have led to the development of therapeutic strategies using splicing-modulating agents and rapid progress is being made in this field. Splicing inhibitors are promising agents that exploit the preferential sensitivity of splicing factor-mutant cells to these compounds. Here, we review the known target genes associated with splicing factor mutations in MDS, and discuss the potential of splicing-modulating therapies for these disorders.
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Affiliation(s)
- Richard N Armstrong
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and Oxford BRC Haematology Theme, Oxford, UK
| | - Violetta Steeples
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and Oxford BRC Haematology Theme, Oxford, UK
| | - Shalini Singh
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and Oxford BRC Haematology Theme, Oxford, UK
| | - Andrea Sanchi
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and Oxford BRC Haematology Theme, Oxford, UK
| | - Jacqueline Boultwood
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and Oxford BRC Haematology Theme, Oxford, UK.
| | - Andrea Pellagatti
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and Oxford BRC Haematology Theme, Oxford, UK.
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23
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Gallego-Paez LM, Bordone MC, Leote AC, Saraiva-Agostinho N, Ascensão-Ferreira M, Barbosa-Morais NL. Alternative splicing: the pledge, the turn, and the prestige : The key role of alternative splicing in human biological systems. Hum Genet 2017; 136:1015-1042. [PMID: 28374191 PMCID: PMC5602094 DOI: 10.1007/s00439-017-1790-y] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/25/2017] [Indexed: 02/06/2023]
Abstract
Alternative pre-mRNA splicing is a tightly controlled process conducted by the spliceosome, with the assistance of several regulators, resulting in the expression of different transcript isoforms from the same gene and increasing both transcriptome and proteome complexity. The differences between alternative isoforms may be subtle but enough to change the function or localization of the translated proteins. A fine control of the isoform balance is, therefore, needed throughout developmental stages and adult tissues or physiological conditions and it does not come as a surprise that several diseases are caused by its deregulation. In this review, we aim to bring the splicing machinery on stage and raise the curtain on its mechanisms and regulation throughout several systems and tissues of the human body, from neurodevelopment to the interactions with the human microbiome. We discuss, on one hand, the essential role of alternative splicing in assuring tissue function, diversity, and swiftness of response in these systems or tissues, and on the other hand, what goes wrong when its regulatory mechanisms fail. We also focus on the possibilities that splicing modulation therapies open for the future of personalized medicine, along with the leading techniques in this field. The final act of the spliceosome, however, is yet to be fully revealed, as more knowledge is needed regarding the complex regulatory network that coordinates alternative splicing and how its dysfunction leads to disease.
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Affiliation(s)
- L M Gallego-Paez
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - M C Bordone
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - A C Leote
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - N Saraiva-Agostinho
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - M Ascensão-Ferreira
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - N L Barbosa-Morais
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.
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