1
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Fischer M. Gene regulation by the tumor suppressor p53 - The omics era. Biochim Biophys Acta Rev Cancer 2024; 1879:189111. [PMID: 38740351 DOI: 10.1016/j.bbcan.2024.189111] [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: 11/27/2023] [Revised: 05/08/2024] [Accepted: 05/10/2024] [Indexed: 05/16/2024]
Abstract
The transcription factor p53 is activated in response to a variety of cellular stresses and serves as a prominent and potent tumor suppressor. Since its discovery, we have sought to understand how p53 functions as both a transcription factor and a tumor suppressor. Two decades ago, the field of gene regulation entered the omics era and began to study the regulation of entire genomes. The omics perspective has greatly expanded our understanding of p53 functions and has begun to reveal its gene regulatory network. In this mini-review, I discuss recent insights into the p53 transcriptional program from high-throughput analyses.
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Affiliation(s)
- Martin Fischer
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany.
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2
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Liu Y, Su Z, Tavana O, Gu W. Understanding the complexity of p53 in a new era of tumor suppression. Cancer Cell 2024; 42:946-967. [PMID: 38729160 PMCID: PMC11190820 DOI: 10.1016/j.ccell.2024.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/15/2024] [Accepted: 04/16/2024] [Indexed: 05/12/2024]
Abstract
p53 was discovered 45 years ago as an SV40 large T antigen binding protein, coded by the most frequently mutated TP53 gene in human cancers. As a transcription factor, p53 is tightly regulated by a rich network of post-translational modifications to execute its diverse functions in tumor suppression. Although early studies established p53-mediated cell-cycle arrest, apoptosis, and senescence as the classic barriers in cancer development, a growing number of new functions of p53 have been discovered and the scope of p53-mediated anti-tumor activity is largely expanded. Here, we review the complexity of different layers of p53 regulation, and the recent advance of the p53 pathway in metabolism, ferroptosis, immunity, and others that contribute to tumor suppression. We also discuss the challenge regarding how to activate p53 function specifically effective in inhibiting tumor growth without harming normal homeostasis for cancer therapy.
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Affiliation(s)
- Yanqing Liu
- Institute for Cancer Genetics, and Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Zhenyi Su
- Institute for Cancer Genetics, and Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Omid Tavana
- Institute for Cancer Genetics, and Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Wei Gu
- Institute for Cancer Genetics, and Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA; Department of Pathology and Cell Biology, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA.
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3
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Xu Y, Bai Z, Lan T, Fu C, Cheng P. CD44 and its implication in neoplastic diseases. MedComm (Beijing) 2024; 5:e554. [PMID: 38783892 PMCID: PMC11112461 DOI: 10.1002/mco2.554] [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: 08/01/2023] [Revised: 03/20/2024] [Accepted: 04/01/2024] [Indexed: 05/25/2024] Open
Abstract
CD44, a nonkinase single span transmembrane glycoprotein, is a major cell surface receptor for many other extracellular matrix components as well as classic markers of cancer stem cells and immune cells. Through alternative splicing of CD44 gene, CD44 is divided into two isoforms, the standard isoform of CD44 (CD44s) and the variant isoform of CD44 (CD44v). Different isoforms of CD44 participate in regulating various signaling pathways, modulating cancer proliferation, invasion, metastasis, and drug resistance, with its aberrant expression and dysregulation contributing to tumor initiation and progression. However, CD44s and CD44v play overlapping or contradictory roles in tumor initiation and progression, which is not fully understood. Herein, we discuss the present understanding of the functional and structural roles of CD44 in the pathogenic mechanism of multiple cancers. The regulation functions of CD44 in cancers-associated signaling pathways is summarized. Moreover, we provide an overview of the anticancer therapeutic strategies that targeting CD44 and preclinical and clinical trials evaluating the pharmacokinetics, efficacy, and drug-related toxicity about CD44-targeted therapies. This review provides up-to-date information about the roles of CD44 in neoplastic diseases, which may open new perspectives in the field of cancer treatment through targeting CD44.
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Affiliation(s)
- Yiming Xu
- Department of BiotherapyLaboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan UniversityChengduSichuanChina
| | - Ziyi Bai
- Department of BiotherapyLaboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan UniversityChengduSichuanChina
| | - Tianxia Lan
- Department of BiotherapyLaboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan UniversityChengduSichuanChina
| | - Chenying Fu
- Laboratory of Aging and Geriatric Medicine, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan UniversityChengduSichuanChina
| | - Ping Cheng
- Department of Biotherapy, Cancer Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan UniversityChengduChina
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4
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Xu Z. CRISPR/Cas9-mediated silencing of CD44: unveiling the role of hyaluronic acid-mediated interactions in cancer drug resistance. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:2849-2876. [PMID: 37991544 DOI: 10.1007/s00210-023-02840-8] [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: 10/13/2023] [Accepted: 11/07/2023] [Indexed: 11/23/2023]
Abstract
A comprehensive overview of CD44 (CD44 Molecule (Indian Blood Group)), a cell surface glycoprotein, and its interaction with hyaluronic acid (HA) in drug resistance mechanisms across various types of cancer is provided, where CRISPR/Cas9 gene editing was utilized to silence CD44 expression and examine its impact on cancer cell behavior, migration, invasion, proliferation, and drug sensitivity. The significance of the HA-CD44 axis in tumor microenvironment (TME) delivery and its implications in specific cancer types, the influence of CD44 variants and the KHDRBS3 (KH RNA Binding Domain Containing, Signal Transduction Associated 3) gene on cancer progression and drug resistance, and the potential of targeting HA-mediated pathways using CRISPR/Cas9 gene editing technology to overcome drug resistance in cancer were also highlighted.
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Affiliation(s)
- Zhujun Xu
- Wuhan No.1 Hospital, Wuhan, 430022, Hubei, China.
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5
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Howard GC, Wang J, Rose KL, Jones C, Patel P, Tsui T, Florian AC, Vlach L, Lorey SL, Grieb BC, Smith BN, Slota MJ, Reynolds EM, Goswami S, Savona MR, Mason FM, Lee T, Fesik S, Liu Q, Tansey WP. Ribosome subunit attrition and activation of the p53-MDM4 axis dominate the response of MLL-rearranged cancer cells to WDR5 WIN site inhibition. eLife 2024; 12:RP90683. [PMID: 38682900 PMCID: PMC11057873 DOI: 10.7554/elife.90683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024] Open
Abstract
The chromatin-associated protein WD Repeat Domain 5 (WDR5) is a promising target for cancer drug discovery, with most efforts blocking an arginine-binding cavity on the protein called the 'WIN' site that tethers WDR5 to chromatin. WIN site inhibitors (WINi) are active against multiple cancer cell types in vitro, the most notable of which are those derived from MLL-rearranged (MLLr) leukemias. Peptidomimetic WINi were originally proposed to inhibit MLLr cells via dysregulation of genes connected to hematopoietic stem cell expansion. Our discovery and interrogation of small-molecule WINi, however, revealed that they act in MLLr cell lines to suppress ribosome protein gene (RPG) transcription, induce nucleolar stress, and activate p53. Because there is no precedent for an anticancer strategy that specifically targets RPG expression, we took an integrated multi-omics approach to further interrogate the mechanism of action of WINi in human MLLr cancer cells. We show that WINi induce depletion of the stock of ribosomes, accompanied by a broad yet modest translational choke and changes in alternative mRNA splicing that inactivate the p53 antagonist MDM4. We also show that WINi are synergistic with agents including venetoclax and BET-bromodomain inhibitors. Together, these studies reinforce the concept that WINi are a novel type of ribosome-directed anticancer therapy and provide a resource to support their clinical implementation in MLLr leukemias and other malignancies.
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Affiliation(s)
- Gregory Caleb Howard
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | - Jing Wang
- Department of Biostatistics, Vanderbilt University Medical CenterNashvilleUnited States
- Center for Quantitative Sciences, Vanderbilt University Medical CenterNashvilleUnited States
| | - Kristie L Rose
- Mass Spectrometry Research Center, Vanderbilt University School of MedicineNashvilleUnited States
- Department of Biochemistry, Vanderbilt University School of MedicineNashvilleUnited States
| | - Camden Jones
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | - Purvi Patel
- Mass Spectrometry Research Center, Vanderbilt University School of MedicineNashvilleUnited States
| | - Tina Tsui
- Mass Spectrometry Research Center, Vanderbilt University School of MedicineNashvilleUnited States
| | - Andrea C Florian
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | - Logan Vlach
- Department of Medicine, Vanderbilt University Medical CenterNashvilleUnited States
| | - Shelly L Lorey
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | - Brian C Grieb
- Department of Medicine, Vanderbilt University Medical CenterNashvilleUnited States
| | - Brianna N Smith
- Department of Medicine, Vanderbilt University Medical CenterNashvilleUnited States
| | - Macey J Slota
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | - Elizabeth M Reynolds
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | - Soumita Goswami
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | - Michael R Savona
- Department of Medicine, Vanderbilt University Medical CenterNashvilleUnited States
| | - Frank M Mason
- Department of Medicine, Vanderbilt University Medical CenterNashvilleUnited States
| | - Taekyu Lee
- Department of Biochemistry, Vanderbilt University School of MedicineNashvilleUnited States
| | - Stephen Fesik
- Department of Biochemistry, Vanderbilt University School of MedicineNashvilleUnited States
- Department of Pharmacology, Vanderbilt University School of MedicineNashvilleUnited States
- Department of Chemistry, Vanderbilt UniversityNashvilleUnited States
| | - Qi Liu
- Department of Biostatistics, Vanderbilt University Medical CenterNashvilleUnited States
- Center for Quantitative Sciences, Vanderbilt University Medical CenterNashvilleUnited States
| | - William P Tansey
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
- Department of Biochemistry, Vanderbilt University School of MedicineNashvilleUnited States
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6
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Kaller M, Forné I, Imhof A, Hermeking H. LINC01021 Attenuates Expression and Affects Alternative Splicing of a Subset of p53-Regulated Genes. Cancers (Basel) 2024; 16:1639. [PMID: 38730591 PMCID: PMC11083319 DOI: 10.3390/cancers16091639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/18/2024] [Accepted: 04/21/2024] [Indexed: 05/13/2024] Open
Abstract
BACKGROUND Loss of the p53-inducible LINC01021 in p53-proficient CRC cell lines results in increased sensitivity to DNA-damaging chemotherapeutics. Here, we comprehensively analyze how LINC01021 affects the p53-induced transcriptional program. METHODS Using a CRISPR/Cas9-approach, we deleted the p53 binding site in the LINC01021 promoter of SW480 colorectal cancer cells and subjected them to RNA-Seq analysis after the activation of ectopic p53. RNA affinity purification followed by mass spectrometry was used to identify proteins associated with LINC01021. RESULTS Loss of the p53-inducibility of LINC01021 resulted in an ~1.8-fold increase in the number of significantly regulated mRNAs compared to LINC01021 wild-type cells after ectopic activation of p53. A subset of direct p53 target genes, such as NOXA and FAS, displayed significantly stronger induction when the p53-inducibility of LINC01021 was abrogated. Loss of the p53-inducibility of LINC01021 resulted in alternative splicing of a small number of mRNAs, such as ARHGAP12, HSF2, and LYN. Several RNA binding proteins involved in pre-mRNA splicing were identified as interaction partners of LINC01021 by mass spectrometry. CONCLUSIONS Our results suggest that LINC01021 may restrict the extent and strength of p53-mediated transcriptional changes via context-dependent regulation of the expression and splicing of a subset of p53-regulated genes.
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Affiliation(s)
- Markus Kaller
- Experimental and Molecular Pathology, Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Thalkirchner Strasse 36, D-80337 Munich, Germany
| | - Ignasi Forné
- BioMedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 9, D-82152 Planegg-Martinsried, Germany
| | - Axel Imhof
- BioMedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 9, D-82152 Planegg-Martinsried, Germany
| | - Heiko Hermeking
- Experimental and Molecular Pathology, Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Thalkirchner Strasse 36, D-80337 Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, D-69120 Heidelberg, Germany
- German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
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7
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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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Brennan MS, Brinkmann K, Romero Sola G, Healey G, Gibson L, Gangoda L, Potts MA, Lieschke E, Wilcox S, Strasser A, Herold MJ, Janic A. Combined absence of TRP53 target genes ZMAT3, PUMA and p21 cause a high incidence of cancer in mice. Cell Death Differ 2024; 31:159-169. [PMID: 38110554 PMCID: PMC10850490 DOI: 10.1038/s41418-023-01250-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 12/20/2023] Open
Abstract
Transcriptional activation of target genes is essential for TP53-mediated tumour suppression, though the roles of the diverse TP53-activated target genes in tumour suppression remains poorly understood. Knockdown of ZMAT3, an RNA-binding zinc-finger protein involved in regulating alternative splicing, in haematopoietic cells by shRNA caused leukaemia only with the concomitant absence of the PUMA and p21, the critical effectors of TRP53-mediated apoptosis and cell cycle arrest respectively. We were interested to further investigate the role of ZMAT3 in tumour suppression beyond the haematopoietic system. Therefore, we generated Zmat3 knockout and compound gene knockout mice, lacking Zmat3 and p21, Zmat3 and Puma or all three genes. Puma-/-p21-/-Zmat3-/- triple knockout mice developed tumours at a significantly higher frequency compared to wild-type, Puma-/-Zmat3-/- or p21-/-Zmat3-/-deficient mice. Interestingly, we observed that the triple knockout and Puma-/-Zmat3-/- double deficient animals succumbed to lymphoma, while p21-/-Zmat3-/- animals developed mainly solid cancers. This analysis suggests that in addition to ZMAT3 loss, additional TRP53-regulated processes must be disabled simultaneously for TRP53-mediated tumour suppression to fail. Our findings reveal that the absence of different TRP53 regulated tumour suppressive processes changes the tumour spectrum, indicating that different TRP53 tumour suppressive pathways are more critical in different tissues.
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Affiliation(s)
- Margs S Brennan
- The Walter and Eliza Hall Institute of Medical Research (WEHI), 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
- Department of Medicine Huddinge, Centre for Haematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Kerstin Brinkmann
- The Walter and Eliza Hall Institute of Medical Research (WEHI), 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Gerard Romero Sola
- Department of Medicine and Life Sciences, Universidad Pompeu Fabra, Barcelona, Spain
| | - Geraldine Healey
- The Walter and Eliza Hall Institute of Medical Research (WEHI), 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia
- Genome Engineering and Cancer Modelling Program, Olivia Newton-John Cancer Research Institute, Melbourne, VIC, Australia
| | - Leonie Gibson
- The Walter and Eliza Hall Institute of Medical Research (WEHI), 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia
| | - Lahiru Gangoda
- The Walter and Eliza Hall Institute of Medical Research (WEHI), 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Margaret A Potts
- The Walter and Eliza Hall Institute of Medical Research (WEHI), 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Elizabeth Lieschke
- The Walter and Eliza Hall Institute of Medical Research (WEHI), 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Stephen Wilcox
- The Walter and Eliza Hall Institute of Medical Research (WEHI), 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia
| | - Andreas Strasser
- The Walter and Eliza Hall Institute of Medical Research (WEHI), 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia.
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia.
| | - Marco J Herold
- The Walter and Eliza Hall Institute of Medical Research (WEHI), 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia.
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia.
- Genome Engineering and Cancer Modelling Program, Olivia Newton-John Cancer Research Institute, Melbourne, VIC, Australia.
- School of Cancer Medicine, La Trobe University, Melbourne, VIC, Australia.
| | - Ana Janic
- Department of Medicine and Life Sciences, Universidad Pompeu Fabra, Barcelona, Spain.
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9
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Howard GC, Wang J, Rose KL, Jones C, Patel P, Tsui T, Florian AC, Vlach L, Lorey SL, Grieb BC, Smith BN, Slota MJ, Reynolds EM, Goswami S, Savona MR, Mason FM, Lee T, Fesik SW, Liu Q, Tansey WP. Ribosome subunit attrition and activation of the p53-MDM4 axis dominate the response of MLL-rearranged cancer cells to WDR5 WIN site inhibition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.26.550648. [PMID: 37546802 PMCID: PMC10402127 DOI: 10.1101/2023.07.26.550648] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The chromatin-associated protein WD Repeat Domain 5 (WDR5) is a promising target for cancer drug discovery, with most efforts blocking an arginine-binding cavity on the protein called the "WIN" site that tethers WDR5 to chromatin. WIN site inhibitors (WINi) are active against multiple cancer cell types in vitro, the most notable of which are those derived from MLL-rearranged (MLLr) leukemias. Peptidomimetic WINi were originally proposed to inhibit MLLr cells via dysregulation of genes connected to hematopoietic stem cell expansion. Our discovery and interrogation of small molecule WIN site inhibitors, however, revealed that they act in MLLr cell lines to suppress ribosome protein gene (RPG) transcription, induce nucleolar stress, and activate p53. Because there is no precedent for an anti-cancer strategy that specifically targets RPG expression, we took an integrated multi-omics approach to further interrogate the mechanism of action of WINi in MLLr cancer cells. We show that WINi induce depletion of the stock of ribosomes, accompanied by a broad yet modest translational choke and changes in alternative mRNA splicing that inactivate the p53 antagonist MDM4. We also show that WINi are synergistic with agents including venetoclax and BET-bromodomain inhibitors. Together, these studies reinforce the concept that WINi are a novel type of ribosome-directed anti-cancer therapy and provide a resource to support their clinical implementation in MLLr leukemias and other malignancies.
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Affiliation(s)
- Gregory C. Howard
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jing Wang
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Kristie Lindsey Rose
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Camden Jones
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Purvi Patel
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Tina Tsui
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Andrea C. Florian
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Current address: Department of Biology, Belmont University, Nashville, TN 37212, USA
| | - Logan Vlach
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Shelly L. Lorey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Brian C. Grieb
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Brianna N. Smith
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Macey J. Slota
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Current address: Department of Urology, University of California San Francisco, San Francisco CA 94143, USA
| | - Elizabeth M. Reynolds
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Soumita Goswami
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Michael R. Savona
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Frank M. Mason
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Taekyu Lee
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Stephen W. Fesik
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Qi Liu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - William P. Tansey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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10
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Zhou Y, Nakajima R, Shirasawa M, Fikriyanti M, Zhao L, Iwanaga R, Bradford AP, Kurayoshi K, Araki K, Ohtani K. Expanding Roles of the E2F-RB-p53 Pathway in Tumor Suppression. BIOLOGY 2023; 12:1511. [PMID: 38132337 PMCID: PMC10740672 DOI: 10.3390/biology12121511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/03/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023]
Abstract
The transcription factor E2F links the RB pathway to the p53 pathway upon loss of function of pRB, thereby playing a pivotal role in the suppression of tumorigenesis. E2F fulfills a major role in cell proliferation by controlling a variety of growth-associated genes. The activity of E2F is controlled by the tumor suppressor pRB, which binds to E2F and actively suppresses target gene expression, thereby restraining cell proliferation. Signaling pathways originating from growth stimulative and growth suppressive signals converge on pRB (the RB pathway) to regulate E2F activity. In most cancers, the function of pRB is compromised by oncogenic mutations, and E2F activity is enhanced, thereby facilitating cell proliferation to promote tumorigenesis. Upon such events, E2F activates the Arf tumor suppressor gene, leading to activation of the tumor suppressor p53 to protect cells from tumorigenesis. ARF inactivates MDM2, which facilitates degradation of p53 through proteasome by ubiquitination (the p53 pathway). P53 suppresses tumorigenesis by inducing cellular senescence or apoptosis. Hence, in almost all cancers, the p53 pathway is also disabled. Here we will introduce the canonical functions of the RB-E2F-p53 pathway first and then the non-classical functions of each component, which may be relevant to cancer biology.
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Affiliation(s)
- Yaxuan Zhou
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo 669-1330, Japan; (Y.Z.); (R.N.); (M.S.); (M.F.); (L.Z.)
| | - Rinka Nakajima
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo 669-1330, Japan; (Y.Z.); (R.N.); (M.S.); (M.F.); (L.Z.)
| | - Mashiro Shirasawa
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo 669-1330, Japan; (Y.Z.); (R.N.); (M.S.); (M.F.); (L.Z.)
| | - Mariana Fikriyanti
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo 669-1330, Japan; (Y.Z.); (R.N.); (M.S.); (M.F.); (L.Z.)
| | - Lin Zhao
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo 669-1330, Japan; (Y.Z.); (R.N.); (M.S.); (M.F.); (L.Z.)
| | - Ritsuko Iwanaga
- Department of Obstetrics and Gynecology, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO 80045, USA; (R.I.); (A.P.B.)
| | - Andrew P. Bradford
- Department of Obstetrics and Gynecology, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO 80045, USA; (R.I.); (A.P.B.)
| | - Kenta Kurayoshi
- Division of Molecular Genetics, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan;
| | - Keigo Araki
- Department of Morphological Biology, Ohu University School of Dentistry, 31-1 Misumido Tomitamachi, Koriyama, Fukushima 963-8611, Japan;
| | - Kiyoshi Ohtani
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo 669-1330, Japan; (Y.Z.); (R.N.); (M.S.); (M.F.); (L.Z.)
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11
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Maltseva D, Tonevitsky A. RNA-binding proteins regulating the CD44 alternative splicing. Front Mol Biosci 2023; 10:1326148. [PMID: 38106992 PMCID: PMC10722200 DOI: 10.3389/fmolb.2023.1326148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 11/15/2023] [Indexed: 12/19/2023] Open
Abstract
Alternative splicing is often deregulated in cancer, and cancer-specific isoform switches are part of the oncogenic transformation of cells. Accumulating evidence indicates that isoforms of the multifunctional cell-surface glycoprotein CD44 play different roles in cancer cells as compared to normal cells. In particular, the shift of CD44 isoforms is required for epithelial to mesenchymal transition (EMT) and is crucial for the maintenance of pluripotency in normal human cells and the acquisition of cancer stem cells phenotype for malignant cells. The growing and seemingly promising use of splicing inhibitors for treating cancer and other pathologies gives hope for the prospect of using such an approach to regulate CD44 alternative splicing. This review integrates current knowledge about regulating CD44 alternative splicing by RNA-binding proteins.
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Affiliation(s)
- Diana Maltseva
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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12
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Lin W, Fang J, Wei S, He G, Liu J, Li X, Peng X, Li D, Yang S, Li X, Yang L, Li H. Extracellular vesicle-cell adhesion molecules in tumours: biofunctions and clinical applications. Cell Commun Signal 2023; 21:246. [PMID: 37735659 PMCID: PMC10512615 DOI: 10.1186/s12964-023-01236-8] [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: 04/09/2023] [Accepted: 07/18/2023] [Indexed: 09/23/2023] Open
Abstract
Cell adhesion molecule (CAM) is an umbrella term for several families of molecules, including the cadherin family, integrin family, selectin family, immunoglobulin superfamily, and some currently unclassified adhesion molecules. Extracellular vesicles (EVs) are important information mediators in cell-to-cell communication. Recent evidence has confirmed that CAMs transported by EVs interact with recipient cells to influence EV distribution in vivo and regulate multiple cellular processes. This review focuses on the loading of CAMs onto EVs, the roles of CAMs in regulating EV distribution, and the known and possible mechanisms of these actions. Moreover, herein, we summarize the impacts of CAMs transported by EVs to the tumour microenvironment (TME) on the malignant behaviour of tumour cells (proliferation, metastasis, immune escape, and so on). In addition, from the standpoint of clinical applications, the significance and challenges of using of EV-CAMs in the diagnosis and therapy of tumours are discussed. Finally, considering recent advances in the understanding of EV-CAMs, we outline significant challenges in this field that require urgent attention to advance research and promote the clinical applications of EV-CAMs. Video Abstract.
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Affiliation(s)
- Weikai Lin
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
- Shenyang Clinical Medical Research Center for Diagnosis, Treatment and Health Management of Early Digestive Cancer, Shenyang, 110032, China
| | - Jianjun Fang
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
- Shenyang Clinical Medical Research Center for Diagnosis, Treatment and Health Management of Early Digestive Cancer, Shenyang, 110032, China
| | - Shibo Wei
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
- Shenyang Clinical Medical Research Center for Diagnosis, Treatment and Health Management of Early Digestive Cancer, Shenyang, 110032, China
| | - Guangpeng He
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
- Shenyang Clinical Medical Research Center for Diagnosis, Treatment and Health Management of Early Digestive Cancer, Shenyang, 110032, China
| | - Jiaxing Liu
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
- Shenyang Clinical Medical Research Center for Diagnosis, Treatment and Health Management of Early Digestive Cancer, Shenyang, 110032, China
| | - Xian Li
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
- Shenyang Clinical Medical Research Center for Diagnosis, Treatment and Health Management of Early Digestive Cancer, Shenyang, 110032, China
| | - Xueqiang Peng
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
- Shenyang Clinical Medical Research Center for Diagnosis, Treatment and Health Management of Early Digestive Cancer, Shenyang, 110032, China
| | - Dai Li
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
- Shenyang Clinical Medical Research Center for Diagnosis, Treatment and Health Management of Early Digestive Cancer, Shenyang, 110032, China
| | - Shuo Yang
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
- Shenyang Clinical Medical Research Center for Diagnosis, Treatment and Health Management of Early Digestive Cancer, Shenyang, 110032, China
| | - Xinyu Li
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
- Shenyang Clinical Medical Research Center for Diagnosis, Treatment and Health Management of Early Digestive Cancer, Shenyang, 110032, China
| | - Liang Yang
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China.
- Shenyang Clinical Medical Research Center for Diagnosis, Treatment and Health Management of Early Digestive Cancer, Shenyang, 110032, China.
| | - Hangyu Li
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China.
- Shenyang Clinical Medical Research Center for Diagnosis, Treatment and Health Management of Early Digestive Cancer, Shenyang, 110032, China.
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13
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Manabile MA, Hull R, Khanyile R, Molefi T, Damane BP, Mongan NP, Bates DO, Dlamini Z. Alternative Splicing Events and Their Clinical Significance in Colorectal Cancer: Targeted Therapeutic Opportunities. Cancers (Basel) 2023; 15:3999. [PMID: 37568815 PMCID: PMC10417810 DOI: 10.3390/cancers15153999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/28/2023] [Accepted: 08/04/2023] [Indexed: 08/13/2023] Open
Abstract
Colorectal cancer (CRC) ranks as one of the top causes of cancer mortality worldwide and its incidence is on the rise, particularly in low-middle-income countries (LMICs). There are several factors that contribute to the development and progression of CRC. Alternative splicing (AS) was found to be one of the molecular mechanisms underlying the development and progression of CRC. With the advent of genome/transcriptome sequencing and large patient databases, the broad role of aberrant AS in cancer development and progression has become clear. AS affects cancer initiation, proliferation, invasion, and migration. These splicing changes activate oncogenes or deactivate tumor suppressor genes by producing altered amounts of normally functional or new proteins with different, even opposing, functions. Thus, identifying and characterizing CRC-specific alternative splicing events and variants might help in designing new therapeutic splicing disrupter drugs. CRC-specific splicing events can be used as diagnostic and prognostic biomarkers. In this review, alternatively spliced events and their role in CRC development will be discussed. The paper also reviews recent research on alternatively spliced events that might be exploited as prognostic, diagnostic, and targeted therapeutic indicators. Of particular interest is the targeting of protein arginine methyltransferase (PMRT) isoforms for the development of new treatments and diagnostic tools. The potential challenges and limitations in translating these discoveries into clinical practice will also be addressed.
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Affiliation(s)
- Mosebo Armstrong Manabile
- SAMRC Precision Oncology Research Unit (PORU), DSI/NRF SARChI Chair in Precision Oncology and Cancer Prevention (POCP), Pan African Cancer Research Institute (PACRI), University of Pretoria, Pretoria 0028, South Africa; (M.A.M.); (R.H.); (R.K.); (T.M.); (D.O.B.)
- Department of Medical Oncology, Faculty of Health Sciences, Steve Biko Academic Hospital, University of Pretoria, Pretoria 0028, South Africa
| | - Rodney Hull
- SAMRC Precision Oncology Research Unit (PORU), DSI/NRF SARChI Chair in Precision Oncology and Cancer Prevention (POCP), Pan African Cancer Research Institute (PACRI), University of Pretoria, Pretoria 0028, South Africa; (M.A.M.); (R.H.); (R.K.); (T.M.); (D.O.B.)
| | - Richard Khanyile
- SAMRC Precision Oncology Research Unit (PORU), DSI/NRF SARChI Chair in Precision Oncology and Cancer Prevention (POCP), Pan African Cancer Research Institute (PACRI), University of Pretoria, Pretoria 0028, South Africa; (M.A.M.); (R.H.); (R.K.); (T.M.); (D.O.B.)
- Department of Medical Oncology, Faculty of Health Sciences, Steve Biko Academic Hospital, University of Pretoria, Pretoria 0028, South Africa
| | - Thulo Molefi
- SAMRC Precision Oncology Research Unit (PORU), DSI/NRF SARChI Chair in Precision Oncology and Cancer Prevention (POCP), Pan African Cancer Research Institute (PACRI), University of Pretoria, Pretoria 0028, South Africa; (M.A.M.); (R.H.); (R.K.); (T.M.); (D.O.B.)
- Department of Medical Oncology, Faculty of Health Sciences, Steve Biko Academic Hospital, University of Pretoria, Pretoria 0028, South Africa
| | - Botle Precious Damane
- Department of Surgery, Steve Biko Academic Hospital, University of Pretoria, Pretoria 0028, South Africa;
| | - Nigel Patrick Mongan
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham NG7 2QL, UK;
| | - David Owen Bates
- SAMRC Precision Oncology Research Unit (PORU), DSI/NRF SARChI Chair in Precision Oncology and Cancer Prevention (POCP), Pan African Cancer Research Institute (PACRI), University of Pretoria, Pretoria 0028, South Africa; (M.A.M.); (R.H.); (R.K.); (T.M.); (D.O.B.)
- Centre for Cancer Sciences, Division of Cancer and Stem Cells, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK
| | - Zodwa Dlamini
- SAMRC Precision Oncology Research Unit (PORU), DSI/NRF SARChI Chair in Precision Oncology and Cancer Prevention (POCP), Pan African Cancer Research Institute (PACRI), University of Pretoria, Pretoria 0028, South Africa; (M.A.M.); (R.H.); (R.K.); (T.M.); (D.O.B.)
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14
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Wang M, Cheng L, Gao Z, Li J, Ding Y, Shi R, Xiang Q, Chen X. Investigation of the shared molecular mechanisms and hub genes between myocardial infarction and depression. Front Cardiovasc Med 2023; 10:1203168. [PMID: 37547246 PMCID: PMC10401437 DOI: 10.3389/fcvm.2023.1203168] [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: 04/17/2023] [Accepted: 07/06/2023] [Indexed: 08/08/2023] Open
Abstract
Background The pathogenesis of myocardial infarction complicating depression is still not fully understood. Bioinformatics is an effective method to study the shared pathogenesis of multiple diseases and has important application value in myocardial infarction complicating depression. Methods The differentially expressed genes (DEGs) between control group and myocardial infarction group (M-DEGs), control group and depression group (D-DEGs) were identified in the training set. M-DEGs and D-DEGs were intersected to obtain DEGs shared by the two diseases (S-DEGs). The GO, KEGG, GSEA and correlation analysis were conducted to analyze the function of DEGs. The biological function differences of myocardial infarction and depression were analyzed by GSVA and immune cell infiltration analysis. Four machine learning methods, nomogram, ROC analysis, calibration curve and decision curve were conducted to identify hub S-DEGs and predict depression risk. The unsupervised cluster analysis was constructed to identify myocardial infarction molecular subtype clusters based on hub S-DEGs. Finally, the value of these genes was verified in the validation set, and blood samples were collected for RT-qPCR experiments to further verify the changes in expression levels of these genes in myocardial infarction and depression. Results A total of 803 M-DEGs, 214 D-DEGs, 13 S-DEGs and 6 hub S-DEGs (CD24, CSTA, EXTL3, RPS7, SLC25A5 and ZMAT3) were obtained in the training set and they were all involved in immune inflammatory response. The GSVA and immune cell infiltration analysis results also suggested that immune inflammation may be the shared pathogenesis of myocardial infarction and depression. The diagnostic models based on 6 hub S-DEGs found that these genes showed satisfactory combined diagnostic performance for depression. Then, two molecular subtypes clusters of myocardial infarction were identified, many differences in immune inflammation related-biological functions were found between them, and the hub S-DEGs had satisfactory molecular subtypes identification performance. Finally, the analysis results of the validation set further confirmed the value of these hub genes, and the RT-qPCR results of blood samples further confirmed the expression levels of these hub genes in myocardial infarction and depression. Conclusion Immune inflammation may be the shared pathogenesis of myocardial infarction and depression. Meanwhile, hub S-DEGs may be potential biomarkers for the diagnosis and molecular subtype identification of myocardial infarction and depression.
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Affiliation(s)
- Mengxi Wang
- Department of Cardiology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
- Department of Cardiology, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
- First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China
| | - Liying Cheng
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Ziwei Gao
- Department of Cardiology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
- Department of Cardiology, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
- First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jianghong Li
- Department of Cardiology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
- Department of Cardiology, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
- First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yuhan Ding
- Department of Cardiology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
- Department of Cardiology, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
- First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China
| | - Ruijie Shi
- Department of Cardiology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
- Department of Cardiology, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
- First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China
| | - Qian Xiang
- Department of Cardiology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
- Department of Cardiology, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
- First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xiaohu Chen
- Department of Cardiology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
- Department of Cardiology, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
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15
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Liu B, Song A, Gui P, Wang J, Pan Y, Li C, Li S, Zhang Y, Jiang T, Xu Y, Pei D, Song J. Long noncoding RNA LINC01594 inhibits the CELF6-mediated splicing of oncogenic CD44 variants to promote colorectal cancer metastasis. Cell Death Dis 2023; 14:427. [PMID: 37452042 PMCID: PMC10349055 DOI: 10.1038/s41419-023-05924-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 06/16/2023] [Accepted: 06/23/2023] [Indexed: 07/18/2023]
Abstract
Long noncoding RNAs (lncRNAs) play critical roles in tumorigenesis and tumor metastasis. However, the underlying mechanisms of lncRNAs in colorectal cancer (CRC) need further exploration. By using data from The Cancer Genome Atlas (TCGA) and GEO databases, we identified a novel CRC-related lncRNA, LINC01594, that is significantly upregulated in CRC and associated with poor prognosis. In vitro and in vivo, gain- and loss-of-function experiments demonstrated that LINC01594 promotes metastasis in CRC. LINC01594 functions as a DNMT1 scaffold, increasing the level of CELF6 promoter methylation. LINC01594 also competitively binds the transcription factor p53, decreasing CELF6 expression. This inhibited the exon skipping of CD44 V4-V7 induced by CELF6. In summary, this study highlights a novel CRC biomarker and therapeutic target, LINC01594, and the findings suggest that the LINC01594-CELF6-CD44 axis might serve as a biomarker and therapeutic target in CRC.
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Affiliation(s)
- Bowen Liu
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University. No. 99, Huaihai West Road, Quanshan District, Xuzhou, 221006, China
- Institute of Digestive Diseases, Xuzhou Medical University. No. 84, Huaihai West Road, Quanshan District, Xuzhou, 221002, China
| | - Angxi Song
- Institute of Digestive Diseases, Xuzhou Medical University. No. 84, Huaihai West Road, Quanshan District, Xuzhou, 221002, China
| | - Pengkun Gui
- Institute of Digestive Diseases, Xuzhou Medical University. No. 84, Huaihai West Road, Quanshan District, Xuzhou, 221002, China
| | - Jin Wang
- Department of Pathology, Xuzhou Medical University. No. 209, Tongshan Road, Yunlong District, Xuzhou, 221004, China
| | - Yaojie Pan
- Department of Medical Oncology, Zhejiang Provincial People's Hospital. No. 158, Shangtang Road, Xiacheng District, Zhejiang, 310000, China
| | - Chao Li
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University. No. 99, Huaihai West Road, Quanshan District, Xuzhou, 221006, China
- Institute of Digestive Diseases, Xuzhou Medical University. No. 84, Huaihai West Road, Quanshan District, Xuzhou, 221002, China
| | - Shuai Li
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University. No. 99, Huaihai West Road, Quanshan District, Xuzhou, 221006, China
- Institute of Digestive Diseases, Xuzhou Medical University. No. 84, Huaihai West Road, Quanshan District, Xuzhou, 221002, China
| | - Yi Zhang
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University. No. 99, Huaihai West Road, Quanshan District, Xuzhou, 221006, China
- Institute of Digestive Diseases, Xuzhou Medical University. No. 84, Huaihai West Road, Quanshan District, Xuzhou, 221002, China
| | - Tao Jiang
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University. No. 99, Huaihai West Road, Quanshan District, Xuzhou, 221006, China
- Institute of Digestive Diseases, Xuzhou Medical University. No. 84, Huaihai West Road, Quanshan District, Xuzhou, 221002, China
| | - Yixin Xu
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University. No. 99, Huaihai West Road, Quanshan District, Xuzhou, 221006, China
- Institute of Digestive Diseases, Xuzhou Medical University. No. 84, Huaihai West Road, Quanshan District, Xuzhou, 221002, China
| | - Dongsheng Pei
- Department of Pathology, Xuzhou Medical University. No. 209, Tongshan Road, Yunlong District, Xuzhou, 221004, China.
| | - Jun Song
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University. No. 99, Huaihai West Road, Quanshan District, Xuzhou, 221006, China.
- Institute of Digestive Diseases, Xuzhou Medical University. No. 84, Huaihai West Road, Quanshan District, Xuzhou, 221002, China.
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16
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Nguyen SV, Shamoun L, Landerholm K, Wågsäter D, Dimberg J. Clinicopathological and prognostic value of CD44 gene polymorphism (rs187115) in Swedish patients with colorectal cancer. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2023; 42:807-817. [PMID: 37074032 DOI: 10.1080/15257770.2023.2200419] [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: 09/14/2022] [Revised: 04/03/2023] [Accepted: 04/03/2023] [Indexed: 04/20/2023]
Abstract
Cluster of differentiation (CD) 44 plays a crucial role in apoptosis, cell-cell interactions, angiogenesis, metastasis and proliferation. The aim of the present study was to examine the influence of CD44 gene polymorphism rs187115 on colorectal cancer (CRC) susceptibility and the association with various clinical features including long-term survival in Swedish patients with CRC. Genotypes were screened, using TaqMan single nucleotide polymorphism (SNP) assays based on polymerase chain reaction, in 612 CRC patients and 575 healthy controls.The carriers of G allele, genotypes (AG + GG), were found to be associated with an increased risk of CRC with an odds ratio (OR) of 1.35 (95% confidence interval (CI) = 1.01-1.81; p = 0.039) and found to be more common in patients with mucinous cancer compared with non-mucinous cancer, OR = 1.69 (95% CI = 1.02-2.80; p = 0.011). By using Kaplan-Meier analysis, the patients with genotype GG showed shorter cancer-specific and recurrence free survival with a hazard ratio (HR) of 1.25 (95% CI = 1.02-1.54; p = 0.036) and 1.52 (95% CI = 1.12-2.06; p = 0.007), respectively, in comparison with the carriers of A allele (AG + AA). The present findings demonstrated that the variant G allele of CD44 gene polymorphism rs187115 was related to risk for CRC and associated to mucinous cancer and predict worse prognosis in Swedish patients with CRC.
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Affiliation(s)
- Song Van Nguyen
- Department of Medical Laboratory, Da Nang University of Medical Technology and Pharmacy, Da Nang, Vietnam
| | - Levar Shamoun
- Department of Laboratory Medicine and Pathology, Region Jönköping County, Jönköping, Sweden
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Kalle Landerholm
- Department of Surgery, Region Jönköping County, Jönköping, Sweden
- Department of Biomedical and Clinical Science, Linköping University, Linköping, Sweden
| | - Dick Wågsäter
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Jan Dimberg
- Department of Natural Science and Biomedicine, School of Health and Welfare, Jönköping University, Jönköping, Sweden
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17
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Muys BR, Shrestha RL, Anastasakis DG, Pongor L, Li XL, Grammatikakis I, Polash A, Chari R, Gorospe M, Harris CC, Aladjem MI, Basrai MA, Hafner M, Lal A. Matrin3 regulates mitotic spindle dynamics by controlling alternative splicing of CDC14B. Cell Rep 2023; 42:112260. [PMID: 36924503 PMCID: PMC10132239 DOI: 10.1016/j.celrep.2023.112260] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 02/03/2023] [Accepted: 02/28/2023] [Indexed: 03/17/2023] Open
Abstract
Matrin3 is an RNA-binding protein that regulates diverse RNA-related processes, including mRNA splicing. Although Matrin3 has been intensively studied in neurodegenerative diseases, its function in cancer remains unclear. Here, we report Matrin3-mediated regulation of mitotic spindle dynamics in colorectal cancer (CRC) cells. We comprehensively identified RNAs bound and regulated by Matrin3 in CRC cells and focused on CDC14B, one of the top Matrin3 targets. Matrin3 knockdown results in increased inclusion of an exon containing a premature termination codon in the CDC14B transcript and simultaneous down-regulation of the standard CDC14B transcript. Knockdown of CDC14B phenocopies the defects in mitotic spindle dynamics upon Matrin3 knockdown, and the elongated and misoriented mitotic spindle observed upon Matrin3 knockdown are rescued upon overexpression of CDC14B, suggesting that CDC14B is a key downstream effector of Matrin3. Collectively, these data reveal a role for the Matrin3/CDC14B axis in control of mitotic spindle dynamics.
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Affiliation(s)
- Bruna R Muys
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), Bethesda, MD 20892, USA
| | | | - Dimitrios G Anastasakis
- RNA Molecular Biology Laboratory, National Institute for Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD 20892, USA
| | - Lorinc Pongor
- Developmental Therapeutics Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Xiao Ling Li
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), Bethesda, MD 20892, USA
| | - Ioannis Grammatikakis
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), Bethesda, MD 20892, USA
| | - Ahsan Polash
- RNA Molecular Biology Laboratory, National Institute for Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD 20892, USA
| | - Raj Chari
- Genome Modification Core, Frederick National Lab for Cancer Research, Frederick, MD 21701, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging, Baltimore, MD 21224, USA
| | - Curtis C Harris
- Laboratory of Human Carcinogenesis, CCR, NCI, Bethesda, MD 20892, USA
| | - Mirit I Aladjem
- Developmental Therapeutics Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | | | - Markus Hafner
- RNA Molecular Biology Laboratory, National Institute for Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD 20892, USA.
| | - Ashish Lal
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), Bethesda, MD 20892, USA.
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18
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Yu S, Zhang J, Ding Y, Kang X, Pu X. Genome-wide identification of alternative splicing associated with histone deacetylase inhibitor in cutaneous T-cell lymphomas. Front Genet 2022; 13:937623. [PMID: 36147491 PMCID: PMC9485882 DOI: 10.3389/fgene.2022.937623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 08/19/2022] [Indexed: 11/18/2022] Open
Abstract
Cutaneous T-cell lymphomas (CTCLs) are a kind of non-Hodgkin lymphoma that originates from skin, which is difficult to treat with traditional drugs. Human histone deacetylase inhibitors (HDACi) targeted therapy has become a promising treatment strategy in recent years, but some patients can develop resistance to the drug, leading to treatment failure. There are no public reports on whether alternative splicing (AS) and RNA binding proteins (RBP) affect the efficacy of targeted therapy. Using data from the Gene Expression Omnibus (GEO) database, we established a co-change network of AS events and RBP in CTCLs for the first time, and analyzed the potential regulatory effects of RBP on HDACi-related AS events. The dataset GSE132053, which contained the RNA sequence data for 17 HDACi samples, was downloaded and clean reads were aligned to the human GRCh38 genome by hierarchical indexing for spliced alignment of the transcripts, allowing four mismatches. Gene expression levels were evaluated using exons per million fragments mapped for each gene. Student’s t-tests were performed to evaluate the significance of changes in ratios for AS events, and regulated alternative splicing events (RASEs) were defined as events with p values less than 0.05. To sort the differentially expressed genes functional categories, Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways were identified using the KOBAS 2.0 server. The regulatory mechanisms of the RASEs and RBPs were evaluated using Pearson’s correlation coefficient. Seven indirect events of HDACi resistance or sensitivity were identified: NIR_5151_RP11-977G19.10, NIR_4557_IRAG2, NIR_11870_SUMO1, NIR_5347_ING4, NIR_17935_DNAJC2, NIR_17974_CBLL1, and NIR_422_SLC50A1. The potential regulatory relationships between RBPs and HDACi-sensitive RASEs were also analyzed. LEPR and HNRNPAO significantly affected NIR_11870_SUMO1, suggesting a potential regulatory relationship. Additionally, CNN1 may regulate NIR_5347_ING4, CNOT3 may regulate NIR_17935_DNAJC2, and DQX1 and LENG9 may regulate NIR_422_SLC5A1. Overall, our findings establish a theoretical foundation for the precise targeted treatment of CTCLs with HDACi.
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Affiliation(s)
- Shirong Yu
- Xinjiang Medical University, Urumqi, China
| | | | - Yuan Ding
- Department of Dermatology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
- Xinjiang Clinical Research Center for Dermatologic Diseases, Urumqi, China
- Xinjiang Key Laboratory of Dermatology Research, Urumqi, China
| | - Xiaojing Kang
- Department of Dermatology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
- Xinjiang Clinical Research Center for Dermatologic Diseases, Urumqi, China
- Xinjiang Key Laboratory of Dermatology Research, Urumqi, China
| | - Xiongming Pu
- Department of Dermatology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
- Xinjiang Clinical Research Center for Dermatologic Diseases, Urumqi, China
- Xinjiang Key Laboratory of Dermatology Research, Urumqi, China
- *Correspondence: Xiongming Pu,
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19
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CD44a functions as a regulator of p53 signaling, apoptosis and autophagy in the antibacterial immune response. Commun Biol 2022; 5:889. [PMID: 36042265 PMCID: PMC9427754 DOI: 10.1038/s42003-022-03856-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 08/17/2022] [Indexed: 11/26/2022] Open
Abstract
The cell adhesion molecule CD44 has been implicated in diverse biological functions including the pathological responses to infections and inflammatory diseases. The variable forms of CD44 contribute to functional variations, which are not yet defined in teleost. Here, we show that zebrafish CD44a plays a protective role in the host defense against Edwardsiella piscicida infection. Zebrafish CD44a deficiency inhibits cell growth and proliferation, impairs cell growth and death pathways, and regulates the expression levels of many genes involved in p53 signaling, apoptosis and autophagy. In addition, CD44a gene disruption in zebrafish leads to inhibition of apoptosis and induction of autophagy, with the increased susceptibility to E. piscicida infection. Furthermore, we show that zebrafish CD44a variants including CD44a_tv1 and CD44a_tv2 promote the translocation of p53 from the nucleus to the cytoplasm and interact with p53 in the cytoplasm. Mechanistically, zebrafish CD44a_tv1 mediates the beneficial effect for larvae survival infected with E. piscicida is depending on the CASP8-mediated apoptosis. However, the antibacterial effect of zebrafish CD44a_tv2 depends on the cytoplasmic p53-mediated inhibition of autophagy. Collectively, our results identify that different mechanisms regulate CD44a variants-mediated antibacterial responses. The adhesion molecule CD44 drives host defence in zebrafish by regulating apoptosis and autophagy.
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20
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Craniofacial Defects in Embryos with Homozygous Deletion of Eftud2 in Their Neural Crest Cells Are Not Rescued by Trp53 Deletion. Int J Mol Sci 2022; 23:ijms23169033. [PMID: 36012294 PMCID: PMC9409426 DOI: 10.3390/ijms23169033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/27/2022] [Accepted: 07/29/2022] [Indexed: 12/12/2022] Open
Abstract
Embryos with homozygous mutation of Eftud2 in their neural crest cells (Eftud2ncc−/−) have brain and craniofacial malformations, hyperactivation of the P53-pathway and die before birth. Treatment of Eftud2ncc−/− embryos with pifithrin-α, a P53-inhibitor, partly improved brain and craniofacial development. To uncover if craniofacial malformations and death were indeed due to P53 hyperactivation we generated embryos with homozygous loss of function mutations in both Eftud2 and Trp53 in the neural crest cells. We evaluated the molecular mechanism underlying craniofacial development in pifithrin-α-treated embryos and in Eftud2; Trp53 double homozygous (Eftud2ncc−/−; Trp53ncc−/−) mutant embryos. Eftud2ncc−/− embryos that were treated with pifithrin-α or homozygous mutant for Trp53 in their neural crest cells showed reduced apoptosis in their neural tube and reduced P53-target activity. Furthermore, although the number of SOX10 positive cranial neural crest cells was increased in embryonic day (E) 9.0 Eftud2ncc−/−; Trp53ncc−/− embryos compared to Eftud2ncc−/− mutants, brain and craniofacial development, and survival were not improved in double mutant embryos. Furthermore, mis-splicing of both P53-regulated transcripts, Mdm2 and Foxm1, and a P53-independent transcript, Synj2bp, was increased in the head of Eftud2ncc−/−; Trp53ncc−/− embryos. While levels of Zmat3, a P53- regulated splicing factor, was similar to those of wild-type. Altogether, our data indicate that both P53-regulated and P53-independent pathways contribute to craniofacial malformations and death of Eftud2ncc−/− embryos.
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21
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David G, Reboutier D, Deschamps S, Méreau A, Taylor W, Padilla-Parra S, Tramier M, Audic Y, Paillard L. The RNA-binding proteins CELF1 and ELAVL1 cooperatively control the alternative splicing of CD44. Biochem Biophys Res Commun 2022; 626:79-84. [DOI: 10.1016/j.bbrc.2022.07.073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 11/29/2022]
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22
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Yang L, Yang J, Jacobson B, Gilbertsen A, Smith K, Higgins L, Guerrero C, Xia H, Henke CA, Lin J. SFPQ Promotes Lung Cancer Malignancy via Regulation of CD44 v6 Expression. Front Oncol 2022; 12:862250. [PMID: 35707369 PMCID: PMC9190464 DOI: 10.3389/fonc.2022.862250] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/06/2022] [Indexed: 11/13/2022] Open
Abstract
Mesenchymal stem cells (MSCs) contribute to tumor pathogenesis and elicit antitumor immune responses in tumor microenvironments. Nuclear proteins might be the main players in these processes. In the current study, combining spatial proteomics with ingenuity pathway analysis (IPA) in lung non-small cell (NSC) cancer MSCs, we identify a key nuclear protein regulator, SFPQ (Splicing Factor Proline and Glutamine Rich), which is overexpressed in lung cancer MSCs and functions to promote MSCs proliferation, chemical resistance, and invasion. Mechanistically, the knockdown of SFPQ reduces CD44v6 expression to inhibit lung cancer MSCs stemness, proliferation in vitro, and metastasis in vivo. The data indicates that SFPQ may be a potential therapeutic target for limiting growth, chemotherapy resistance, and metastasis of lung cancer.
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Affiliation(s)
- Libang Yang
- Department of Medicine, University of Minnesota, Minneapolis, MN, United States
| | - Jianbo Yang
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Minneapolis, Minneapolis, MN, United States.,The Cancer Center, Fujian Medical University Union Hospital, Fuzhou, China
| | - Blake Jacobson
- Hematology, Oncology and Transplantation, School of Medicine, University of Minnesota, Minneapolis, MN, United States
| | - Adam Gilbertsen
- Department of Medicine, University of Minnesota, Minneapolis, MN, United States
| | - Karen Smith
- Department of Medicine, University of Minnesota, Minneapolis, MN, United States
| | - LeeAnn Higgins
- Center for Mass Spectrometry and Proteomics, University of Minnesota, St. Paul, MN, United States
| | - Candace Guerrero
- Center for Mass Spectrometry and Proteomics, University of Minnesota, St. Paul, MN, United States
| | - Hong Xia
- Department of Medicine, University of Minnesota, Minneapolis, MN, United States
| | - Craig A Henke
- Department of Medicine, University of Minnesota, Minneapolis, MN, United States
| | - Jizhen Lin
- The Cancer Center, Fujian Medical University Union Hospital, Fuzhou, China.,The Immunotherapy Research Laboratory, Department of Otolaryngology, Cancer Center, University of Minnesota, Minneapolis, MN, United States
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23
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Chen X, Wu J, Li Z, Han J, Xia P, Shen Y, Ma J, Liu X, Zhang J, Yu P. Advances in The Study of RNA-binding Proteins in Diabetic Complications. Mol Metab 2022; 62:101515. [PMID: 35597446 PMCID: PMC9168169 DOI: 10.1016/j.molmet.2022.101515] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/21/2022] [Accepted: 05/12/2022] [Indexed: 12/18/2022] Open
Abstract
Background It has been reported that diabetes mellitus affects 435 million people globally as a primary health care problem. Despite many therapies available, many diabetes remains uncontrolled, giving rise to irreversible diabetic complications that pose significant risks to patients’ wellbeing and survival. Scope of Review In recent years, as much effort is put into elucidating the posttranscriptional gene regulation network of diabetes and diabetic complications; RNA binding proteins (RBPs) are found to be vital. RBPs regulate gene expression through various post-transcriptional mechanisms, including alternative splicing, RNA export, messenger RNA translation, RNA degradation, and RNA stabilization. Major Conclusions Here, we summarized recent studies on the roles and mechanisms of RBPs in mediating abnormal gene expression in diabetes and its complications. Moreover, we discussed the potential and theoretical basis of RBPs to treat diabetes and its complications. • Mechanisms of action of RBPs involved in diabetic complications are summarized and elucidated. • We discuss the theoretical basis and potential of RBPs for the treatment of diabetes and its complications. • We summarize the possible effective drugs for diabetes based on RBPs promoting the development of future therapeutic drugs.
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Affiliation(s)
- Xinyue Chen
- The Second Clinical Medical College of Nanchang University, the Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jiaqiang Wu
- The Second Clinical Medical College of Nanchang University, the Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhangwang Li
- The Second Clinical Medical College of Nanchang University, the Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jiashu Han
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Beijing 100730, China
| | - Panpan Xia
- Department of Metabolism and Endocrinology, the Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yunfeng Shen
- Department of Metabolism and Endocrinology, the Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jianyong Ma
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, USA
| | - Xiao Liu
- Department of Cardiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jing Zhang
- The Second Clinical Medical College of Nanchang University, the Second Affiliated Hospital of Nanchang University, Nanchang, China; Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Jiangxi, Nanchang 330006, China.
| | - Peng Yu
- The Second Clinical Medical College of Nanchang University, the Second Affiliated Hospital of Nanchang University, Nanchang, China; Department of Metabolism and Endocrinology, the Second Affiliated Hospital of Nanchang University, Nanchang, China.
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24
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Thomas AF, Kelly GL, Strasser A. Of the many cellular responses activated by TP53, which ones are critical for tumour suppression? Cell Death Differ 2022; 29:961-971. [PMID: 35396345 PMCID: PMC9090748 DOI: 10.1038/s41418-022-00996-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 03/24/2022] [Accepted: 03/28/2022] [Indexed: 12/12/2022] Open
Abstract
The tumour suppressor TP53 is a master regulator of several cellular processes that collectively suppress tumorigenesis. The TP53 gene is mutated in ~50% of human cancers and these defects usually confer poor responses to therapy. The TP53 protein functions as a homo-tetrameric transcription factor, directly regulating the expression of ~500 target genes, some of them involved in cell death, cell cycling, cell senescence, DNA repair and metabolism. Originally, it was thought that the induction of apoptotic cell death was the principal mechanism by which TP53 prevents the development of tumours. However, gene targeted mice lacking the critical effectors of TP53-induced apoptosis (PUMA and NOXA) do not spontaneously develop tumours. Indeed, even mice lacking the critical mediators for TP53-induced apoptosis, G1/S cell cycle arrest and cell senescence, namely PUMA, NOXA and p21, do not spontaneously develop tumours. This suggests that TP53 must activate additional cellular responses to mediate tumour suppression. In this review, we will discuss the processes by which TP53 regulates cell death, cell cycling/cell senescence, DNA damage repair and metabolic adaptation, and place this in context of current understanding of TP53-mediated tumour suppression.
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Affiliation(s)
- Annabella F Thomas
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,The Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Gemma L Kelly
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,The Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Andreas Strasser
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia. .,The Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia.
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25
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Spinelli R, Florese P, Parrillo L, Zatterale F, Longo M, D’Esposito V, Desiderio A, Nerstedt A, Gustafson B, Formisano P, Miele C, Raciti GA, Napoli R, Smith U, Beguinot F. ZMAT3 hypomethylation contributes to early senescence of preadipocytes from healthy first-degree relatives of type 2 diabetics. Aging Cell 2022; 21:e13557. [PMID: 35146866 PMCID: PMC8920444 DOI: 10.1111/acel.13557] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 12/16/2021] [Accepted: 01/09/2022] [Indexed: 12/18/2022] Open
Abstract
Senescence of adipose precursor cells (APC) impairs adipogenesis, contributes to the age-related subcutaneous adipose tissue (SAT) dysfunction, and increases risk of type 2 diabetes (T2D). First-degree relatives of T2D individuals (FDR) feature restricted adipogenesis, reflecting the detrimental effects of APC senescence earlier in life and rendering FDR more vulnerable to T2D. Epigenetics may contribute to these abnormalities but the underlying mechanisms remain unclear. In previous methylome comparison in APC from FDR and individuals with no diabetes familiarity (CTRL), ZMAT3 emerged as one of the top-ranked senescence-related genes featuring hypomethylation in FDR and associated with T2D risk. Here, we investigated whether and how DNA methylation changes at ZMAT3 promote early APC senescence. APC from FDR individuals revealed increases in multiple senescence markers compared to CTRL. Senescence in these cells was accompanied by ZMAT3 hypomethylation, which caused ZMAT3 upregulation. Demethylation at this gene in CTRL APC led to increased ZMAT3 expression and premature senescence, which were reverted by ZMAT3 siRNA. Furthermore, ZMAT3 overexpression in APC determined senescence and activation of the p53/p21 pathway, as observed in FDR APC. Adipogenesis was also inhibited in ZMAT3-overexpressing APC. In FDR APC, rescue of ZMAT3 methylation through senolytic exposure simultaneously downregulated ZMAT3 expression and improved adipogenesis. Interestingly, in human SAT, aging and T2D were associated with significantly increased expression of both ZMAT3 and the P53 senescence marker. Thus, DNA hypomethylation causes ZMAT3 upregulation in FDR APC accompanied by acquisition of the senescence phenotype and impaired adipogenesis, which may contribute to FDR predisposition for T2D.
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Affiliation(s)
- Rosa Spinelli
- Department of Translational Medical Sciences Federico II University of Naples Naples Italy
- URT Genomics of Diabetes Institute of Experimental Endocrinology and Oncology National Research Council Naples Italy
| | - Pasqualina Florese
- Department of Translational Medical Sciences Federico II University of Naples Naples Italy
- URT Genomics of Diabetes Institute of Experimental Endocrinology and Oncology National Research Council Naples Italy
| | - Luca Parrillo
- Department of Translational Medical Sciences Federico II University of Naples Naples Italy
- URT Genomics of Diabetes Institute of Experimental Endocrinology and Oncology National Research Council Naples Italy
| | - Federica Zatterale
- Department of Translational Medical Sciences Federico II University of Naples Naples Italy
- URT Genomics of Diabetes Institute of Experimental Endocrinology and Oncology National Research Council Naples Italy
| | - Michele Longo
- Department of Translational Medical Sciences Federico II University of Naples Naples Italy
- URT Genomics of Diabetes Institute of Experimental Endocrinology and Oncology National Research Council Naples Italy
| | - Vittoria D’Esposito
- Department of Translational Medical Sciences Federico II University of Naples Naples Italy
- URT Genomics of Diabetes Institute of Experimental Endocrinology and Oncology National Research Council Naples Italy
| | - Antonella Desiderio
- Department of Translational Medical Sciences Federico II University of Naples Naples Italy
- URT Genomics of Diabetes Institute of Experimental Endocrinology and Oncology National Research Council Naples Italy
| | - Annika Nerstedt
- Lundberg Laboratory for Diabetes Research Department of Molecular and Clinical Medicine Sahlgrenska Academy University of Gothenburg Gothenburg Sweden
| | - Birgit Gustafson
- Lundberg Laboratory for Diabetes Research Department of Molecular and Clinical Medicine Sahlgrenska Academy University of Gothenburg Gothenburg Sweden
| | - Pietro Formisano
- Department of Translational Medical Sciences Federico II University of Naples Naples Italy
- URT Genomics of Diabetes Institute of Experimental Endocrinology and Oncology National Research Council Naples Italy
| | - Claudia Miele
- Department of Translational Medical Sciences Federico II University of Naples Naples Italy
- URT Genomics of Diabetes Institute of Experimental Endocrinology and Oncology National Research Council Naples Italy
| | - Gregory Alexander Raciti
- Department of Translational Medical Sciences Federico II University of Naples Naples Italy
- URT Genomics of Diabetes Institute of Experimental Endocrinology and Oncology National Research Council Naples Italy
| | - Raffaele Napoli
- Department of Translational Medical Sciences Federico II University of Naples Naples Italy
| | - Ulf Smith
- Lundberg Laboratory for Diabetes Research Department of Molecular and Clinical Medicine Sahlgrenska Academy University of Gothenburg Gothenburg Sweden
| | - Francesco Beguinot
- Department of Translational Medical Sciences Federico II University of Naples Naples Italy
- URT Genomics of Diabetes Institute of Experimental Endocrinology and Oncology National Research Council Naples Italy
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26
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Wang M, Attardi LD. A Balancing Act: p53 Activity from Tumor Suppression to Pathology and Therapeutic Implications. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2021; 17:205-226. [PMID: 34699262 DOI: 10.1146/annurev-pathol-042320-025840] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
TP53, encoding the p53 transcription factor, is the most frequently mutated tumor suppressor gene across all human cancer types. While p53 has long been appreciated to induce antiproliferative cell cycle arrest, apoptosis, and senescence programs in response to diverse stress signals, various studies in recent years have revealed additional important functions for p53 that likely also contribute to tumor suppression, including roles in regulating tumor metabolism, ferroptosis, signaling in the tumor microenvironment, and stem cell self-renewal/differentiation. Not only does p53 loss or mutation cause cancer, but hyperactive p53 also drives various pathologies, including developmental phenotypes, premature aging, neurodegeneration, and side effects of cancer therapies. These findings underscore the importance of balanced p53 activity and influence our thinking of how to best develop cancer therapies based on modulating the p53 pathway. Expected final online publication date for the Annual Review of Pathology: Mechanisms of Disease, Volume 17 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Mengxiong Wang
- Department of Radiation Oncology, Division of Radiation and Cancer Biology, Stanford University School of Medicine, Stanford, California 94305, USA;
| | - Laura D Attardi
- Department of Radiation Oncology, Division of Radiation and Cancer Biology, Stanford University School of Medicine, Stanford, California 94305, USA; .,Department of Genetics and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California 94305, USA
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27
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Barnoud T, Indeglia A, Murphy ME. Shifting the paradigms for tumor suppression: lessons from the p53 field. Oncogene 2021; 40:4281-4290. [PMID: 34103683 PMCID: PMC8238873 DOI: 10.1038/s41388-021-01852-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/05/2021] [Accepted: 05/20/2021] [Indexed: 01/20/2023]
Abstract
The TP53 gene continues to hold distinction as the most frequently mutated gene in cancer. Since its discovery in 1979, hundreds of research groups have devoted their efforts toward understanding why this gene is so frequently selected against by tumors, with the hopes of harnessing this information toward improved therapy of cancer. The result is that this protein has been meticulously analyzed in tumor and normal cells, resulting in over one hundred thousand publications, with an average of five thousand papers published on p53 every year for the past decade. The journey toward understanding p53 function has been anything but straightforward; in fact, the field is notable for the numerous times that established paradigms not only have been shifted, but in fact have been shattered or reversed. In this review, we will discuss the manuscripts, or series of manuscripts, that have most radically changed our thinking about how this tumor suppressor functions, and we will delve into the emerging challenges for the future in this important area of research. It is hoped that this review will serve as a useful historical reference for those interested in p53, and a useful lesson on the need to be flexible in the face of established paradigms.
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Affiliation(s)
- Thibaut Barnoud
- Program in Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, PA, USA
| | - Alexandra Indeglia
- Program in Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, PA, USA.,Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Maureen E Murphy
- Program in Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, PA, USA.
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28
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Abstract
The tumor protein p53 (TP53, best known as p53) transcription factor is a critical tumor suppressor, but those p53-inducible genes most important for tumor suppression have remained unclear. Using unbiased RNA interference and CRISPR (Clustered Regularly Interspersed Palindromic Repeats)/Cas9 (CRISPR-associated protein 9) screens, genetically engineered mouse models, human cancer genome analysis, and integrative eCLIP-sequencing and RNA-sequencing analyses, we reveal a new branch of p53-mediated tumor suppression involving the RNA splicing regulator Zinc finger Matrin-type 3, Zmat3.
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Affiliation(s)
- Kathryn T Bieging-Rolett
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Laura D Attardi
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
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29
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Alternative splicing perturbation landscape identifies RNA binding proteins as potential therapeutic targets in cancer. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 24:792-806. [PMID: 33996260 PMCID: PMC8099609 DOI: 10.1016/j.omtn.2021.04.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 04/03/2021] [Indexed: 02/07/2023]
Abstract
Alternative splicing (AS) plays an important role in gene regulation, and AS perturbations are frequently observed in cancer. RNA binding protein (RBP) is one of the molecular determinants of AS, and perturbations in RBP-gene network activity are causally associated with cancer development. Here, we performed a systematic analysis to characterize the perturbations in AS events across 18 cancer types. We showed that AS alterations were prevalent in cancer and involved in cancer-related pathways. Given that the extent of AS perturbation was associated with disease severity, we proposed a computational pipeline to identify RBP regulators. Pan-cancer analysis identified a number of conserved RBP regulators, which play important roles in regulating AS of genes involved in cancer hallmark pathways. Our application analysis revealed that the expression of 68 RBP regulators helped in cancer subtyping. Specifically, we identified four subtypes of kidney cancer with differences in cancer hallmark pathway activities and prognosis. Finally, we identified the small molecules that can potentially target the RBP genes and suggested potential candidates for cancer therapy. In summary, our comprehensive AS perturbation landscape analysis identified RBPs as potential therapeutic targets in cancer and provided novel insights into the regulatory functions of RBPs in cancer.
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30
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Thyroid Cancer Stem-Like Cells: From Microenvironmental Niches to Therapeutic Strategies. J Clin Med 2021; 10:jcm10071455. [PMID: 33916320 PMCID: PMC8037626 DOI: 10.3390/jcm10071455] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/25/2021] [Accepted: 03/29/2021] [Indexed: 02/08/2023] Open
Abstract
Thyroid cancer (TC) is the most common endocrine malignancy. Recent progress in thyroid cancer biology revealed a certain degree of intratumoral heterogeneity, highlighting the coexistence of cellular subpopulations with distinct proliferative capacities and differentiation abilities. Among those subpopulations, cancer stem-like cells (CSCs) are hypothesized to drive TC heterogeneity, contributing to its metastatic potential and therapy resistance. CSCs principally exist in tumor areas with specific microenvironmental conditions, the so-called stem cell niches. In particular, in thyroid cancer, CSCs' survival is enhanced in the hypoxic niche, the immune niche, and some areas with specific extracellular matrix composition. In this review, we summarize the current knowledge about thyroid CSCs, the tumoral niches that allow their survival, and the implications for TC therapy.
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31
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Boutelle AM, Attardi LD. p53 and Tumor Suppression: It Takes a Network. Trends Cell Biol 2021; 31:298-310. [PMID: 33518400 DOI: 10.1016/j.tcb.2020.12.011] [Citation(s) in RCA: 142] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/22/2020] [Accepted: 12/28/2020] [Indexed: 02/07/2023]
Abstract
The TP53 tumor suppressor is the most frequently mutated gene in human cancer. p53 suppresses tumorigenesis by transcriptionally regulating a network of target genes that play roles in various cellular processes. Though originally characterized as a critical regulator for responses to acute DNA damage (activation of apoptosis and cell cycle arrest), recent studies have highlighted new pathways and transcriptional targets downstream of p53 regulating genomic integrity, metabolism, redox biology, stemness, and non-cell autonomous signaling in tumor suppression. Here, we summarize our current understanding of p53-mediated tumor suppression, situating recent findings from mouse models and unbiased screens in the context of previous studies and arguing for the importance of the pleiotropic effects of the p53 transcriptional network in inhibiting cancer.
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Affiliation(s)
- Anthony M Boutelle
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Laura D Attardi
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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