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George JW, Cancino RA, Griffin Miller JL, Qiu F, Lin Q, Rowley MJ, Chennathukuzhi VM, Davis JS. Characterization of m6A Modifiers and RNA Modifications in Uterine Fibroids. Endocrinology 2024; 165:bqae074. [PMID: 38946397 PMCID: PMC11222979 DOI: 10.1210/endocr/bqae074] [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: 09/02/2023] [Revised: 06/07/2024] [Accepted: 06/20/2024] [Indexed: 07/02/2024]
Abstract
Uterine leiomyoma or fibroids are prevalent noncancerous tumors of the uterine muscle layer, yet their origin and development remain poorly understood. We analyzed RNA expression profiles of 15 epigenetic mediators in uterine fibroids compared to myometrium using publicly available RNA sequencing (RNA-seq) data. To validate our findings, we performed RT-qPCR on a separate cohort of uterine fibroids targeting these modifiers confirming our RNA-seq data. We then examined protein profiles of key N6-methyladenosine (m6A) modifiers in fibroids and their matched myometrium, showing no significant differences in concordance with our RNA expression profiles. To determine RNA modification abundance, mRNA and small RNA from fibroids and matched myometrium were analyzed by ultra-high performance liquid chromatography-mass spectrometry identifying prevalent m6A and 11 other known modifiers. However, no aberrant expression in fibroids was detected. We then mined a previously published dataset and identified differential expression of m6A modifiers that were specific to fibroid genetic subtype. Our analysis also identified m6A consensus motifs on genes previously identified to be dysregulated in uterine fibroids. Overall, using state-of-the-art mass spectrometry, RNA expression, and protein profiles, we characterized and identified differentially expressed m6A modifiers in relation to driver mutations. Despite the use of several different approaches, we identified limited differential expression of RNA modifiers and associated modifications in uterine fibroids. However, considering the highly heterogenous genomic and cellular nature of fibroids, and the possible contribution of single molecule m6A modifications to fibroid pathology, there is a need for greater in-depth characterization of m6A marks and modifiers in a larger and diverse patient cohort.
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Affiliation(s)
- Jitu W George
- Olson Center for Women's Health, Department of Obstetrics and Gynecology, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Veterans Affairs Nebraska Western Iowa Health Care System, Omaha, NE 68105, USA
| | - Rosa A Cancino
- Olson Center for Women's Health, Department of Obstetrics and Gynecology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Jennifer L Griffin Miller
- Olson Center for Women's Health, Department of Obstetrics and Gynecology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Fang Qiu
- Department of Biostatistics, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Qishan Lin
- RNA Epitranscriptomics and Proteomics Resource, Department of Chemistry, University at Albany, Albany, NY 12222, USA
| | - M Jordan Rowley
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Varghese M Chennathukuzhi
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - John S Davis
- Olson Center for Women's Health, Department of Obstetrics and Gynecology, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Veterans Affairs Nebraska Western Iowa Health Care System, Omaha, NE 68105, USA
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2
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Jowhar Z, Xu A, Venkataramanan S, Dossena F, Hoye ML, Silver DL, Floor SN, Calviello L. A ubiquitous GC content signature underlies multimodal mRNA regulation by DDX3X. Mol Syst Biol 2024; 20:276-290. [PMID: 38273160 PMCID: PMC10912769 DOI: 10.1038/s44320-024-00013-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/21/2023] [Accepted: 01/03/2024] [Indexed: 01/27/2024] Open
Abstract
The road from transcription to protein synthesis is paved with many obstacles, allowing for several modes of post-transcriptional regulation of gene expression. A fundamental player in mRNA biology is DDX3X, an RNA binding protein that canonically regulates mRNA translation. By monitoring dynamics of mRNA abundance and translation following DDX3X depletion, we observe stabilization of translationally suppressed mRNAs. We use interpretable statistical learning models to uncover GC content in the coding sequence as the major feature underlying RNA stabilization. This result corroborates GC content-related mRNA regulation detectable in other studies, including hundreds of ENCODE datasets and recent work focusing on mRNA dynamics in the cell cycle. We provide further evidence for mRNA stabilization by detailed analysis of RNA-seq profiles in hundreds of samples, including a Ddx3x conditional knockout mouse model exhibiting cell cycle and neurogenesis defects. Our study identifies a ubiquitous feature underlying mRNA regulation and highlights the importance of quantifying multiple steps of the gene expression cascade, where RNA abundance and protein production are often uncoupled.
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Affiliation(s)
- Ziad Jowhar
- Department of Cell and Tissue Biology, UCSF, San Francisco, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, 94158, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Albert Xu
- Department of Cell and Tissue Biology, UCSF, San Francisco, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, 94158, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, 94158, USA
| | | | | | - Mariah L Hoye
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, USA
| | - Debra L Silver
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, USA
- Department of Cell Biology, Duke University Medical Center, Durham, USA
- Duke Regeneration Center, Duke University Medical Center, Durham, USA
- Department of Neurobiology, Duke University Medical Center, Durham, USA
- Duke Institute for Brain Sciences, Duke University Medical Center, Durham, USA
| | - Stephen N Floor
- Department of Cell and Tissue Biology, UCSF, San Francisco, USA.
- Helen Diller Family Comprehensive Cancer Center, San Francisco, USA.
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3
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Ghoshdastider U, Sendoel A. Exploring the pan-cancer landscape of posttranscriptional regulation. Cell Rep 2023; 42:113172. [PMID: 37742190 DOI: 10.1016/j.celrep.2023.113172] [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: 03/29/2023] [Revised: 07/28/2023] [Accepted: 09/07/2023] [Indexed: 09/26/2023] Open
Abstract
Understanding the mechanisms underlying cancer gene expression is critical for precision oncology. Posttranscriptional regulation is a key determinant of protein abundance and cancer cell behavior. However, to what extent posttranscriptional regulatory mechanisms impact protein levels and cancer progression is an ongoing question. Here, we exploit cancer proteogenomics data to systematically compare mRNA-protein correlations across 14 different human cancer types. We identify two clusters of genes with particularly low mRNA-protein correlations across all cancer types, shed light on the role of posttranscriptional regulation of cancer driver genes and drug targets, and unveil a cohort of 55 mutations that alter systems-wide posttranscriptional regulation. Surprisingly, we find that decreased levels of posttranscriptional control in patients correlate with shorter overall survival across multiple cancer types, prompting further mechanistic studies into how posttranscriptional regulation affects patient outcomes. Our findings underscore the importance of a comprehensive understanding of the posttranscriptional regulatory landscape for predicting cancer progression.
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Affiliation(s)
- Umesh Ghoshdastider
- Institute for Regenerative Medicine (IREM), University of Zurich, Wagistrasse 12, 8952 Schlieren-Zurich, Switzerland
| | - Ataman Sendoel
- Institute for Regenerative Medicine (IREM), University of Zurich, Wagistrasse 12, 8952 Schlieren-Zurich, Switzerland.
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4
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Aksoylu IS, Martin P, Robert F, Szkop KJ, Redmond NE, Bhattacharyya S, Wang J, Chen S, Beauchamp RL, Nobeli I, Pelletier J, Larsson O, Ramesh V. Translatome analysis of tuberous sclerosis complex 1 patient-derived neural progenitor cells reveals rapamycin-dependent and independent alterations. Mol Autism 2023; 14:39. [PMID: 37880800 PMCID: PMC10601155 DOI: 10.1186/s13229-023-00572-3] [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: 05/16/2023] [Accepted: 10/13/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND Tuberous sclerosis complex (TSC) is an inherited neurocutaneous disorder caused by mutations in the TSC1 or TSC2 genes, with patients often exhibiting neurodevelopmental (ND) manifestations termed TSC-associated neuropsychiatric disorders (TAND) including autism spectrum disorder (ASD) and intellectual disability. Hamartin (TSC1) and tuberin (TSC2) proteins form a complex inhibiting mechanistic target of rapamycin complex 1 (mTORC1) signaling. Loss of TSC1 or TSC2 activates mTORC1 that, among several targets, controls protein synthesis by inhibiting translational repressor eIF4E-binding proteins. Using TSC1 patient-derived neural progenitor cells (NPCs), we recently reported early ND phenotypic changes, including increased cell proliferation and altered neurite outgrowth in TSC1-null NPCs, which were unaffected by the mTORC1 inhibitor rapamycin. METHODS Here, we used polysome profiling, which quantifies changes in mRNA abundance and translational efficiencies at a transcriptome-wide level, to compare CRISPR-edited TSC1-null with CRISPR-corrected TSC1-WT NPCs generated from one TSC donor (one clone/genotype). To assess the relevance of identified gene expression alterations, we performed polysome profiling in postmortem brains from ASD donors and age-matched controls. We further compared effects on translation of a subset of transcripts and rescue of early ND phenotypes in NPCs following inhibition of mTORC1 using the allosteric inhibitor rapamycin versus a third-generation bi-steric, mTORC1-selective inhibitor RMC-6272. RESULTS Polysome profiling of NPCs revealed numerous TSC1-associated alterations in mRNA translation that were largely recapitulated in human ASD brains. Moreover, although rapamycin treatment partially reversed the TSC1-associated alterations in mRNA translation, most genes related to neural activity/synaptic regulation or ASD were rapamycin-insensitive. In contrast, treatment with RMC-6272 inhibited rapamycin-insensitive translation and reversed TSC1-associated early ND phenotypes including proliferation and neurite outgrowth that were unaffected by rapamycin. CONCLUSIONS Our work reveals ample mRNA translation alterations in TSC1 patient-derived NPCs that recapitulate mRNA translation in ASD brain samples. Further, suppression of TSC1-associated but rapamycin-insensitive translation and ND phenotypes by RMC-6272 unveils potential implications for more efficient targeting of mTORC1 as a superior treatment strategy for TAND.
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Affiliation(s)
- Inci S Aksoylu
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, 171 77, Stockholm, Sweden
| | - Pauline Martin
- Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
| | - Francis Robert
- Department of Biochemistry and Goodman Cancer Research Institute, McGill University, Montreal, PQ, H3G1Y6, Canada
| | - Krzysztof J Szkop
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, 171 77, Stockholm, Sweden
| | - Nicholas E Redmond
- Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
| | - Srirupa Bhattacharyya
- Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
| | - Jennifer Wang
- Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
| | - Shan Chen
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, 171 77, Stockholm, Sweden
| | - Roberta L Beauchamp
- Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
| | - Irene Nobeli
- Institute of Structural and Molecular Biology, Department of Biological Sciences,, Birkbeck, University of London, London, WC1E 7HX, UK
| | - Jerry Pelletier
- Department of Biochemistry and Goodman Cancer Research Institute, McGill University, Montreal, PQ, H3G1Y6, Canada
| | - Ola Larsson
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, 171 77, Stockholm, Sweden.
| | - Vijaya Ramesh
- Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA.
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Zhao H, Shi C, Zhao G, Liu J, Wang X, Liang J, Li F. RNA modification regulator DDC in endometrial cancer affects the tumor microenvironment and patient prognosis. Sci Rep 2023; 13:18057. [PMID: 37872211 PMCID: PMC10593861 DOI: 10.1038/s41598-023-44269-2] [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: 06/21/2023] [Accepted: 10/05/2023] [Indexed: 10/25/2023] Open
Abstract
Uterine corpus endometrial carcinoma (UCEC) is infiltrated by immune cells, which are involved in the growth and proliferation of malignant tumors and resistance to immunotherapy. This study suggested that RNA modification regulators played an important role in the development and prognosis of UCEC. Many studies confirmed that RNA modification played an essential role in tumor immune regulation, and abnormal RNA modification contributed to tumorigenesis and cancer progression. Based on the RNA modification regulatory factors, the UCEC samples from TCGA (The Cancer Genome Atlas) were classified into two clusters, namely Cluster A and Cluster B, using unsupervised consensus clustering. We obtained DEG (differentially expressed genes) between the two clusters, and constructed a risk model of RNA modification-related genes using DEGs. Cluster A had lower RNA modification regulatory factors, richer immune cell infiltration, and better prognosis. The differentially expressed genes between the two clusters were obtained, and these genes were used for modeling. This model divided patients with UCEC into two groups. The low-risk group had better immune infiltration, and the ROC (receiver operating characteristic) curve showed that this model had good predictive efficacy. The low-risk group had a better response to immunotherapy by immune checkpoint prediction. We obtained the key gene L-dopa decarboxylase (DDC) through the intersection of LASSO model genes and GEO dataset GSE17025. We evaluated the potential biological functions of DDC. The differences in the expression of DDC were verified by immunohistochemistry. We evaluated the relationship between DDC and immune cell infiltration and verified this difference using immunofluorescence. Cluster A with low expression of RNA modification regulators has better prognosis and richer immune cell infiltration, therefore, we believed that RNA modification regulators in UCEC were closely related to the tumor microenvironment. Also, the risk score could well predict the prognosis of patients and guide immunotherapy, which might benefit patients with UCEC.
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Affiliation(s)
- Huai Zhao
- Shengjing Hospital of China Medical University, 110001, Shenyang, Liaoning, China
| | - Chuang Shi
- Guangming Community Health Service Center, 101127, Shunyi District, Beijing, China
| | - Guoguang Zhao
- Shengjing Hospital of China Medical University, 110001, Shenyang, Liaoning, China
| | - Jiamin Liu
- Zigong First People's Hospital, 643099, Zigong, Sichuan, China
| | - Xi Wang
- The First Hospital of China Medical University, 110001, Shenyang, Liaoning, China
| | - Jie Liang
- The First Hospital of China Medical University, 110001, Shenyang, Liaoning, China.
| | - Fangmei Li
- The First Hospital of China Medical University, 110001, Shenyang, Liaoning, China.
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6
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Rao A, Lyu B, Jahan I, Lubertozzi A, Zhou G, Tedeschi F, Jankowsky E, Kang J, Carstens B, Poss KD, Baskin K, Goldman JA. The translation initiation factor homolog eif4e1c regulates cardiomyocyte metabolism and proliferation during heart regeneration. Development 2023; 150:dev201376. [PMID: 37306388 PMCID: PMC10281269 DOI: 10.1242/dev.201376] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 04/28/2023] [Indexed: 05/25/2023]
Abstract
The eIF4E family of translation initiation factors bind 5' methylated caps and act as the limiting step for mRNA translation. The canonical eIF4E1A is required for cell viability, yet other related eIF4E families exist and are utilized in specific contexts or tissues. Here, we describe a family called Eif4e1c, for which we find roles during heart development and regeneration in zebrafish. The Eif4e1c family is present in all aquatic vertebrates but is lost in all terrestrial species. A core group of amino acids shared over 500 million years of evolution forms an interface along the protein surface, suggesting that Eif4e1c functions in a novel pathway. Deletion of eif4e1c in zebrafish caused growth deficits and impaired survival in juveniles. Mutants surviving to adulthood had fewer cardiomyocytes and reduced proliferative responses to cardiac injury. Ribosome profiling of mutant hearts demonstrated changes in translation efficiency of mRNA for genes known to regulate cardiomyocyte proliferation. Although eif4e1c is broadly expressed, its disruption had most notable impact on the heart and at juvenile stages. Our findings reveal context-dependent requirements for translation initiation regulators during heart regeneration.
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Affiliation(s)
- Anupama Rao
- Department of Biological Chemistry and Pharmacology, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Baken Lyu
- Department of Biological Chemistry and Pharmacology, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Ishrat Jahan
- Department of Biological Chemistry and Pharmacology, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Anna Lubertozzi
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Gao Zhou
- Center for RNA Molecular Biology, Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106USA
| | - Frank Tedeschi
- Center for RNA Molecular Biology, Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106USA
| | - Eckhard Jankowsky
- Center for RNA Molecular Biology, Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106USA
| | - Junsu Kang
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Bryan Carstens
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Kenneth D. Poss
- Department of Cell Biology, Duke Regeneration Center, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kedryn Baskin
- Department of Cell Biology and Physiology, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Joseph Aaron Goldman
- Department of Biological Chemistry and Pharmacology, The Ohio State University Medical Center, Columbus, OH 43210, USA
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George JW, Cancino RA, Miller JLG, Qiu F, Lin Q, Rowley MJ, Chennathukuzhi VM, Davis JS. Characterization of m 6A modifiers and RNA modifications in uterine fibroids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.07.552278. [PMID: 37609293 PMCID: PMC10441280 DOI: 10.1101/2023.08.07.552278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Uterine leiomyoma or fibroids are the most common prevalent noncancerous tumors of the uterine muscle layer. Common symptoms associated with fibroids include pelvic pain, heavy menstrual bleeding, anemia, and pelvic pressure. These tumors are a leading cause of gynecological care but lack long-term therapy as the origin and development of fibroids are not well understood. Several next-generation sequencing technologies have been performed to identify the underlying genetic and epigenetic basis of fibroids. However, there remains a systemic gap in our understanding of molecular and biological process that define uterine fibroids. Recent epitranscriptomics studies have unraveled RNA modifications that are associated with all forms of RNA and are thought to influence both normal physiological functions and the progression of diseases. We quantified RNA expression profiles by analyzing publicly available RNA-seq data for 15 known epigenetic mediators to identify their expression profile in uterine fibroids compared to myometrium. To validate our findings, we performed RT-qPCR on a separate cohort of uterine fibroids targeting these modifiers confirming our RNA-seq data. We then examined protein profiles of key m6A modifiers in fibroids and their matched myometrium. In concordance with our RNA expression profiles, no significant differences were observed in these proteins in uterine fibroids compared to myometrium. To determine abundance of RNA modifications, mRNA and small RNA from fibroids and matched myometrium were analyzed by UHPLC MS/MS. In addition to the prevalent N6-methyladenosine (m6A), we identified 11 other known modifiers but did not identify any aberrant expression in fibroids. We then mined a previously published dataset and identified differential expression of m6A modifiers that were specific to fibroid genetic sub-type. Our analysis also identified m6A consensus motifs on genes previously identified to be dysregulated in uterine fibroids. Overall, using state-of-the-art mass spectrometry, RNA expression and protein profiles, we characterized and identified differentially expressed m6A modifiers in relation to driver mutations. Despite the use of several different approaches, we identified limited differential expression of RNA modifiers and associated modifications in uterine fibroids. However, considering the highly heterogenous genomic and cellular nature of fibroids, and the possible contribution of single molecule m6A modifications to fibroid pathology, there is a need for greater in-depth characterization of m6A marks and modifiers in a larger and varied patient cohort.
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Affiliation(s)
- Jitu W. George
- Olson Center for Women’s Health, Department of Obstetrics and Gynecology, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Veterans Affairs Nebraska Western Iowa Health Care System, 4101 Woolworth Ave, Omaha, NE 68105, USA
| | - Rosa A. Cancino
- Olson Center for Women’s Health, Department of Obstetrics and Gynecology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Jennifer L. Griffin Miller
- Olson Center for Women’s Health, Department of Obstetrics and Gynecology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Fang Qiu
- Department of Biostatistics, University of Nebraska Medical Center, Omaha, NE, USA
| | - Qishan Lin
- RNA Epitranscriptomics and Proteomics Resource, Department of Chemistry, University at Albany, Albany, NY, United States
| | - M Jordan Rowley
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
| | - Varghese M. Chennathukuzhi
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - John S. Davis
- Olson Center for Women’s Health, Department of Obstetrics and Gynecology, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Veterans Affairs Nebraska Western Iowa Health Care System, 4101 Woolworth Ave, Omaha, NE 68105, USA
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8
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Perez-Pepe M, Desotell AW, Li H, Li W, Han B, Lin Q, Klein DE, Liu Y, Goodarzi H, Alarcón CR. 7SK methylation by METTL3 promotes transcriptional activity. SCIENCE ADVANCES 2023; 9:eade7500. [PMID: 37163588 PMCID: PMC10171809 DOI: 10.1126/sciadv.ade7500] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 04/07/2023] [Indexed: 05/12/2023]
Abstract
A fundamental feature of cell signaling is the conversion of extracellular signals into adaptive transcriptional responses. The role of RNA modifications in this process is poorly understood. The small nuclear RNA 7SK prevents transcriptional elongation by sequestering the cyclin dependent kinase 9/cyclin T1 (CDK9/CCNT1) positive transcription elongation factor (P-TEFb) complex. We found that epidermal growth factor signaling induces phosphorylation of the enzyme methyltransferase 3 (METTL3), leading to METTL3-mediated methylation of 7SK. 7SK methylation enhanced its binding to heterogeneous nuclear ribonucleoproteins, causing the release of the HEXIM1 P-TEFb complex subunit1 (HEXIM1)/P-TEFb complex and inducing transcriptional elongation. Our findings establish the mechanism underlying 7SK activation and uncover a previously unknown function for the m6A modification in converting growth factor signaling events into a regulatory transcriptional response via an RNA methylation-dependent switch.
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Affiliation(s)
- Marcelo Perez-Pepe
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Anthony W. Desotell
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Hengyi Li
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Wenxue Li
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Bing Han
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Qishan Lin
- RNA Epitranscriptomics and Proteomics Resource, University at Albany, Albany, NY 12222, USA
| | - Daryl E. Klein
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Yansheng Liu
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Claudio R. Alarcón
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
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9
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Aksoylu IS, Martin P, Robert F, Szkop KJ, Redmond NE, Chen S, Beauchamp RL, Nobeli I, Pelletier J, Larsson O, Ramesh V. Translatome analysis of Tuberous Sclerosis Complex-1 patient-derived neural progenitor cells reveal rapamycin-dependent and independent alterations. RESEARCH SQUARE 2023:rs.3.rs-2702044. [PMID: 37034588 PMCID: PMC10081384 DOI: 10.21203/rs.3.rs-2702044/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Tuberous sclerosis complex (TSC) is an inherited neurocutaneous disorder caused by mutations in TSC1 or TSC2 genes, with patients often exhibiting neurodevelopmental (ND) manifestations termed TSC-associated neuropsychiatric disorders (TAND) including autism spectrum disorder (ASD). The hamartin-tuberin (TSC1-TSC2) protein complex inactivates mechanistic target of rapamycin complex 1 (mTORC1) signaling, leading to increased protein synthesis via inactivation of translational repressor eIF4E-binding proteins (4E-BPs). In TSC1-null neural progenitor cells (NPCs), we previously reported early ND phenotypic changes, including increased proliferation/altered neurite outgrowth, which were unaffected by mTORC1-inhibitor rapamycin. Here, using polysome-profiling to quantify translational efficiencies at a transcriptome-wide level, we observed numerous TSC1-dependent alterations in NPCs, largely recapitulated in post-mortem brains from ASD donors. Although rapamycin partially reversed TSC1-associated alterations, most neural activity/synaptic- or ASD-related genes remained insensitive but were inhibited by third-generation bi-steric, mTORC1-selective inhibitor RMC-6272, which also reversed altered ND phenotypes. Together these data reveal potential implications for treatment of TAND.
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Affiliation(s)
- Inci S. Aksoylu
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
- These authors contributed equally to this work
| | - Pauline Martin
- Ctr. for Genomic Med., Department of Neurology, Massachusetts Gen. Hosp., Boston, MA
- These authors contributed equally to this work
| | - Francis Robert
- Department of Biochem. and Goodman Cancer Res. Ctr., McGill Univ., Montreal, QC, Canada
- These authors contributed equally to this work
| | - Krzysztof J. Szkop
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
- These authors contributed equally to this work
| | - Nicholas E. Redmond
- Ctr. for Genomic Med., Department of Neurology, Massachusetts Gen. Hosp., Boston, MA
| | - Shan Chen
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Roberta L. Beauchamp
- Ctr. for Genomic Med., Department of Neurology, Massachusetts Gen. Hosp., Boston, MA
| | - Irene Nobeli
- Department of Biol. Sciences, Inst. of Structural and Mol. Biology, Birkbeck, Univ. of London, London, United Kingdom
| | - Jerry Pelletier
- Department of Biochem. and Goodman Cancer Res. Ctr., McGill Univ., Montreal, QC, Canada
| | - Ola Larsson
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Vijaya Ramesh
- Ctr. for Genomic Med., Department of Neurology, Massachusetts Gen. Hosp., Boston, MA
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10
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Zeid D, Gould TJ. Chronic nicotine exposure alters sperm small RNA content in C57BL/6J mouse model. Dev Psychobiol 2023; 65:e22367. [PMID: 36811365 PMCID: PMC9978956 DOI: 10.1002/dev.22367] [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: 07/15/2022] [Revised: 11/10/2022] [Accepted: 12/19/2022] [Indexed: 01/15/2023]
Abstract
Multigenerational inheritance is a nongenomic form of heritability characterized by altered phenotypes in the first generation born from the exposed parent. Multigenerational factors may account for inconsistencies and gaps in heritable nicotine addiction vulnerability. Our lab previously found that F1 offspring of male C57BL/6J mice chronically exposed to nicotine exhibited altered hippocampus functioning and related learning, nicotine-seeking, nicotine metabolism, and basal stress hormones. In an effort to identify germline mechanisms underlying these multigenerational phenotypes, the current study sequenced small RNA extracted from sperm of males chronically administered nicotine using our previously established exposure model. We identified 16 miRNAs whose expression in sperm was dysregulated by nicotine exposure. A literature review of previous research on these transcripts suggested an enrichment for regulation of psychological stress and learning. mRNAs predicted to be regulated by differentially expressed sperm small RNAs were further analyzed using exploratory enrichment analysis, which suggested potential modulation of pathways related to learning, estrogen signaling, and hepatic disease, among other findings. Overall, our findings point to links between nicotine-exposed F0 sperm miRNA and altered F1 phenotypes in this multigenerational inheritance model, particularly F1 memory, stress, and nicotine metabolism. These findings provide a valuable foundation for future functional validation of these hypotheses and characterization of mechanisms underlying male-line multigenerational inheritance.
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Affiliation(s)
- Dana Zeid
- Department of Psychology, Temple University, Philadelphia PA, USA
| | - Thomas J. Gould
- Department of Biobehavioral Health, Penn State University, University Park PA, USA
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11
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Schroader JH, Jones LA, Meng R, Shorrock HK, Richardson J, Shaughnessy S, Lin Q, Begley T, Berglund J, Fuchs G, Handley M, Reddy K. Disease-associated inosine misincorporation into RNA hinders translation. Nucleic Acids Res 2022; 50:9306-9318. [PMID: 35979951 PMCID: PMC9458462 DOI: 10.1093/nar/gkac709] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 07/08/2022] [Accepted: 08/06/2022] [Indexed: 12/24/2022] Open
Abstract
Failure to prevent accumulation of the non-canonical nucleotide inosine triphosphate (ITP) by inosine triphosphate pyrophosphatase (ITPase) during nucleotide synthesis results in misincorporation of inosine into RNA and can cause severe and fatal developmental anomalies in humans. While the biochemical activity of ITPase is well understood, the pathogenic basis of ITPase deficiency and the molecular and cellular consequences of ITP misincorporation into RNA remain cryptic. Here, we demonstrate that excess ITP in the nucleotide pool during in vitro transcription results in T7 polymerase-mediated inosine misincorporation in luciferase RNA. In vitro translation of inosine-containing luciferase RNA reduces resulting luciferase activity, which is only partly explained by reduced abundance of the luciferase protein produced. Using Oxford Nanopore Direct RNA sequencing, we reveal inosine misincorporation to be stochastic but biased largely towards misincorporation in place of guanosine, with evidence for misincorporation also in place of cytidine, adenosine and uridine. Inosine misincorporation into RNA is also detected in Itpa-null mouse embryonic heart tissue as an increase in relative variants compared with the wild type using Illumina RNA sequencing. By generating CRISPR/Cas9 rat H9c2 Itpa-null cardiomyoblast cells, we validate a translation defect in cells that accumulate inosine within endogenous RNA. Furthermore, we observe hindered cellular translation of transfected luciferase RNA containing misincorporated inosine in both wild-type and Itpa-null cells. We therefore conclude that inosine misincorporation into RNA perturbs translation, thus providing mechanistic insight linking ITPase deficiency, inosine accumulation and pathogenesis.
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Affiliation(s)
| | | | - Ryan Meng
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Hannah K Shorrock
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Jared I Richardson
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA,Department of Biochemistry and Molecular Biology, Center for NeuroGenetics, University of Florida, Gainesville, FL 32611, USA
| | - Sharon M Shaughnessy
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Qishan Lin
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA,RNA Epitranscriptomics & Proteomics Resource, University at Albany, Albany, NY 12222, USA
| | - Thomas J Begley
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA,Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USA,RNA Epitranscriptomics & Proteomics Resource, University at Albany, Albany, NY 12222, USA
| | - J Andrew Berglund
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA,Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USA,Department of Biochemistry and Molecular Biology, Center for NeuroGenetics, University of Florida, Gainesville, FL 32611, USA
| | - Gabriele Fuchs
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA,Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Mark T Handley
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Kaalak Reddy
- *To whom correspondence should be addressed. Tel: +1 518 442 1464;
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12
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Smith LK, Parmenter T, Kleinschmidt M, Kusnadi EP, Kang J, Martin CA, Lau P, Patel R, Lorent J, Papadopoli D, Trigos A, Ward T, Rao AD, Lelliott EJ, Sheppard KE, Goode D, Hicks RJ, Tiganis T, Simpson KJ, Larsson O, Blythe B, Cullinane C, Wickramasinghe VO, Pearson RB, McArthur GA. Adaptive translational reprogramming of metabolism limits the response to targeted therapy in BRAF V600 melanoma. Nat Commun 2022; 13:1100. [PMID: 35232962 PMCID: PMC8888590 DOI: 10.1038/s41467-022-28705-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 02/07/2022] [Indexed: 12/26/2022] Open
Abstract
Despite the success of therapies targeting oncogenes in cancer, clinical outcomes are limited by residual disease that ultimately results in relapse. This residual disease is often characterized by non-genetic adaptive resistance, that in melanoma is characterised by altered metabolism. Here, we examine how targeted therapy reprograms metabolism in BRAF-mutant melanoma cells using a genome-wide RNA interference (RNAi) screen and global gene expression profiling. Using this systematic approach we demonstrate post-transcriptional regulation of metabolism following BRAF inhibition, involving selective mRNA transport and translation. As proof of concept we demonstrate the RNA processing kinase U2AF homology motif kinase 1 (UHMK1) associates with mRNAs encoding metabolism proteins and selectively controls their transport and translation during adaptation to BRAF-targeted therapy. UHMK1 inactivation induces cell death by disrupting therapy induced metabolic reprogramming, and importantly, delays resistance to BRAF and MEK combination therapy in multiple in vivo models. We propose selective mRNA processing and translation by UHMK1 constitutes a mechanism of non-genetic resistance to targeted therapy in melanoma by controlling metabolic plasticity induced by therapy. Different adaptive mechanisms have been reported to reduce the efficacy of mutant BRAF inhibition in melanoma. Here, the authors show BRAF inhibition induces the translational regulation of metabolic genes leading to acquired therapy resistance.
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Affiliation(s)
- Lorey K Smith
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia. .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia.
| | - Tiffany Parmenter
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia
| | | | - Eric P Kusnadi
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Jian Kang
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Claire A Martin
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Peter Lau
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Riyaben Patel
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Julie Lorent
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - David Papadopoli
- Lady Davis Institute for Medical Research and Gerald Bronfman Department of Oncology, McGill University, Montreal, Canada
| | - Anna Trigos
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Teresa Ward
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Aparna D Rao
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Emily J Lelliott
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Karen E Sheppard
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia.,Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, Australia
| | - David Goode
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Rodney J Hicks
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Tony Tiganis
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Kaylene J Simpson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Ola Larsson
- Lady Davis Institute for Medical Research and Gerald Bronfman Department of Oncology, McGill University, Montreal, Canada
| | - Benjamin Blythe
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Carleen Cullinane
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Vihandha O Wickramasinghe
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Richard B Pearson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia.,Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, Australia
| | - Grant A McArthur
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia. .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia. .,Department of Medicine, St. Vincent's Hospital, University of Melbourne, Melbourne, Australia.
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13
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Oertlin C, Watt K, Ristau J, Larsson O. Anota2seq Analysis for Transcriptome-Wide Studies of mRNA Translation. Methods Mol Biol 2022; 2418:243-268. [PMID: 35119670 DOI: 10.1007/978-1-0716-1920-9_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
mRNA translation plays a critical role in determining proteome composition. In health, regulation of mRNA translation facilitates rapid gene expression responses to intra- and extracellular signals. Moreover, dysregulated mRNA translation is a common feature in disease states, including neurological disorders and cancer. Yet, most studies of gene expression focus on analysis of mRNA levels, leaving variations in translational efficiencies largely uncharacterized. Here, we outline procedures to identify mRNA-selective alterations in translational efficiencies on a transcriptome-wide scale using the anota2seq package. Anota2seq compares expression data originating from translated mRNA to data from matched total mRNA to identify changes in translated mRNA not paralleled by corresponding changes in total mRNA (interpreted as changes in translational efficiencies impacting protein levels), congruent changes in total and translated mRNA (interpreted as changes in transcription and/or mRNA stability), and changes in total mRNA not paralleled by corresponding alterations in translated mRNA (interpreted as translational buffering). To illustrate the functionality of the anota2seq analysis package, we demonstrate a detailed analysis using a polysome-profiling data set quantified by RNA sequencing, revealing that estrogen receptor α modulates gene expression via a type of translational buffering termed offsetting. Notably, this anota2seq analysis procedure is also applicable to ribosome-profiling (RiboSeq) data sets and can be adapted to a variety of other data types and experimental contexts. Finally, we provide guidance for extending anota2seq analysis to examine associations between untranslated regions and altered translational efficiencies as well as targeted cellular functions to gain insights into mechanisms and phenotypic consequences of altered mRNA translation. Thus, this step-by-step manual allows users to interrogate selective changes in mRNA translation on a transcriptome-wide scale using the Bioconductor package anota2seq.
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Affiliation(s)
- Christian Oertlin
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Kathleen Watt
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Johannes Ristau
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Ola Larsson
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden.
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14
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Ristau J, Watt K, Oertlin C, Larsson O. Polysome Fractionation for Transcriptome-Wide Studies of mRNA Translation. Methods Mol Biol 2022; 2418:223-241. [PMID: 35119669 DOI: 10.1007/978-1-0716-1920-9_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Protein synthesis and degradation determine the relationship between mRNA and corresponding protein amounts. This relationship can change in a dynamic and selective fashion when translational efficiencies of transcript subsets are altered downstream of, for example, translation factors and/or RNA binding proteins. Notably, even transcription factors such as estrogen receptor alpha (ERα) can modulate mRNA translation in a transcript-selective manner. Yet, despite ample evidence suggesting a key role for mRNA translation in shaping the proteome in health and disease, it remains largely unexplored. Here, we present a guide for the extraction of mRNA engaged in translation using polysome fractionation with linear and optimized sucrose gradients. The isolated polysome-associated RNA is then quantified, in parallel with total mRNA from the same conditions, using methods such as RNA sequencing; and the resulting data set is analyzed to derive transcriptome-wide insights into how mRNA translation is modulated. The methods we describe are applicable to cultured cells, small numbers of FACS-isolated primary cells, and small tissue samples from biobanks or animal studies. Accordingly, this approach can be applied to study in detail how ERα and other factors control gene expression by selectively modulating mRNA translation both in vitro and in vivo.
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Affiliation(s)
- Johannes Ristau
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Kathleen Watt
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Christian Oertlin
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Ola Larsson
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden.
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15
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The Estrogen Receptor α Signaling Pathway Controls Alternative Splicing in the Absence of Ligands in Breast Cancer Cells. Cancers (Basel) 2021; 13:cancers13246261. [PMID: 34944881 PMCID: PMC8699117 DOI: 10.3390/cancers13246261] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/30/2021] [Accepted: 12/10/2021] [Indexed: 12/21/2022] Open
Abstract
Background: The transcriptional activity of estrogen receptor α (ERα) in breast cancer (BC) is extensively characterized. Our group has previously shown that ERα controls the expression of a number of genes in its unliganded form (apoERα), among which a large group of RNA-binding proteins (RBPs) encode genes, suggesting its role in the control of co- and post-transcriptional events. Methods: apoERα-mediated RNA processing events were characterized by the analysis of transcript usage and alternative splicing changes in an RNA-sequencing dataset from MCF-7 cells after siRNA-induced ERα downregulation. Results: ApoERα depletion induced an expression change of 681 RBPs, including 84 splicing factors involved in translation, ribonucleoprotein complex assembly, and 3′end processing. ApoERα depletion results in 758 isoform switching events with effects on 3′end length and the splicing of alternative cassette exons. The functional enrichment of these events shows that post-transcriptional regulation is part of the mechanisms by which apoERα controls epithelial-to-mesenchymal transition and BC cell proliferation. In primary BCs, the inclusion levels of the experimentally identified alternatively spliced exons are associated with overall and disease-free survival. Conclusion: Our data supports the role of apoERα in maintaining the luminal phenotype of BC cells by extensively regulating gene expression at the alternative splicing level.
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16
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Gillen SL, Waldron JA, Bushell M. Codon optimality in cancer. Oncogene 2021; 40:6309-6320. [PMID: 34584217 PMCID: PMC8585667 DOI: 10.1038/s41388-021-02022-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/24/2021] [Accepted: 09/10/2021] [Indexed: 12/14/2022]
Abstract
A key characteristic of cancer cells is their increased proliferative capacity, which requires elevated levels of protein synthesis. The process of protein synthesis involves the translation of codons within the mRNA coding sequence into a string of amino acids to form a polypeptide chain. As most amino acids are encoded by multiple codons, the nucleotide sequence of a coding region can vary dramatically without altering the polypeptide sequence of the encoded protein. Although mutations that do not alter the final amino acid sequence are often thought of as silent/synonymous, these can still have dramatic effects on protein output. Because each codon has a distinct translation elongation rate and can differentially impact mRNA stability, each codon has a different degree of 'optimality' for protein synthesis. Recent data demonstrates that the codon preference of a transcriptome matches the abundance of tRNAs within the cell and that this supply and demand between tRNAs and mRNAs varies between different cell types. The largest observed distinction is between mRNAs encoding proteins associated with proliferation or differentiation. Nevertheless, precisely how codon optimality and tRNA expression levels regulate cell fate decisions and their role in malignancy is not fully understood. This review describes the current mechanistic understanding on codon optimality, its role in malignancy and discusses the potential to target codon optimality therapeutically in the context of cancer.
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Affiliation(s)
- Sarah L Gillen
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK.
| | - Joseph A Waldron
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - Martin Bushell
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK.
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK, G61 1QH.
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17
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Tang SC, Lion Q, Peulen O, Chariot P, Lavergne A, Mayer A, Fuster PA, Close P, Klein S, Florin A, Büttner R, Nemazanyy I, Shostak K, Chariot A. The E3 ligase COP1 promotes ERα signaling and suppresses EMT in breast cancer. Oncogene 2021; 41:173-190. [PMID: 34716429 DOI: 10.1038/s41388-021-02038-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/14/2021] [Accepted: 09/23/2021] [Indexed: 01/22/2023]
Abstract
ERα signaling drives proliferation, survival and cancer initiation in the mammary gland. Therefore, it is critical to elucidate mechanisms by which ERα expression is regulated. We show that the tumor suppressor E3 ligase COP1 promotes the degradative polyubiquitination of the microtubule-associated protein HPIP. As such, COP1 negatively regulates estrogen-dependent AKT activation in breast cancer cells. However, COP1 also induces ERα expression and ERα-dependent gene transcription, at least through c-Jun degradation. COP1 and ERα levels are positively correlated in clinical cases of breast cancer. COP1 also supports the metabolic reprogramming by estrogens, including glycolysis. On the other hand, COP1 suppresses EMT in breast cancer cells. COP1 deficiency also contributes to Tamoxifen resistance, at least through protective autophagy. Therefore, COP1 acts as an oncogenic E3 ligase by promoting ERα signaling but also acts as a tumor suppressor candidate by preventing EMT, which reflects a dual role of COP1 in breast cancer.
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Affiliation(s)
- Seng Chuan Tang
- Interdisciplinary Cluster for Applied Genoproteomics, University of Liege, CHU, Sart-Tilman, Liège, Belgium.,Laboratory of Medical Chemistry, GIGA Stem Cells, University of Liege, CHU, Sart-Tilman, Liège, Belgium
| | - Quentin Lion
- Interdisciplinary Cluster for Applied Genoproteomics, University of Liege, CHU, Sart-Tilman, Liège, Belgium.,Laboratory of Medical Chemistry, GIGA Stem Cells, University of Liege, CHU, Sart-Tilman, Liège, Belgium
| | - Olivier Peulen
- Interdisciplinary Cluster for Applied Genoproteomics, University of Liege, CHU, Sart-Tilman, Liège, Belgium.,Metastasis Research Laboratory, GIGA Cancer, University of Liege, CHU, Sart-Tilman, Liège, Belgium
| | - Philippe Chariot
- Interdisciplinary Cluster for Applied Genoproteomics, University of Liege, CHU, Sart-Tilman, Liège, Belgium.,Laboratory of Medical Chemistry, GIGA Stem Cells, University of Liege, CHU, Sart-Tilman, Liège, Belgium
| | - Arnaud Lavergne
- Interdisciplinary Cluster for Applied Genoproteomics, University of Liege, CHU, Sart-Tilman, Liège, Belgium.,GIGA Genomics Platform, University of Liege, CHU, Sart-Tilman, Liège, Belgium
| | - Alice Mayer
- Interdisciplinary Cluster for Applied Genoproteomics, University of Liege, CHU, Sart-Tilman, Liège, Belgium.,GIGA Genomics Platform, University of Liege, CHU, Sart-Tilman, Liège, Belgium
| | - Paula Allepuz Fuster
- Interdisciplinary Cluster for Applied Genoproteomics, University of Liege, CHU, Sart-Tilman, Liège, Belgium.,Laboratory of Medical Chemistry, GIGA Stem Cells, University of Liege, CHU, Sart-Tilman, Liège, Belgium
| | - Pierre Close
- Interdisciplinary Cluster for Applied Genoproteomics, University of Liege, CHU, Sart-Tilman, Liège, Belgium.,Laboratory of Cancer Signaling, GIGA Stem Cells, University of Liege, CHU, Sart-Tilman, 4000, Liège, Belgium.,Walloon Excellence in Life Sciences and Biotechnology (WELBIO), Wavres, Belgium
| | - Sebastian Klein
- Institute for Pathology-University Hospital of Cologne, Cologne, Germany
| | - Alexandra Florin
- Institute for Pathology-University Hospital of Cologne, Cologne, Germany
| | - Reinhard Büttner
- Institute for Pathology-University Hospital of Cologne, Cologne, Germany
| | - Ivan Nemazanyy
- Platform for Metabolic Analyses, Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS 3633, Paris, France
| | - Kateryna Shostak
- Interdisciplinary Cluster for Applied Genoproteomics, University of Liege, CHU, Sart-Tilman, Liège, Belgium.,Laboratory of Medical Chemistry, GIGA Stem Cells, University of Liege, CHU, Sart-Tilman, Liège, Belgium
| | - Alain Chariot
- Interdisciplinary Cluster for Applied Genoproteomics, University of Liege, CHU, Sart-Tilman, Liège, Belgium. .,Laboratory of Medical Chemistry, GIGA Stem Cells, University of Liege, CHU, Sart-Tilman, Liège, Belgium. .,Walloon Excellence in Life Sciences and Biotechnology (WELBIO), Wavres, Belgium.
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18
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Kusnadi EP, Timpone C, Topisirovic I, Larsson O, Furic L. Regulation of gene expression via translational buffering. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1869:119140. [PMID: 34599983 DOI: 10.1016/j.bbamcr.2021.119140] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 09/19/2021] [Accepted: 09/21/2021] [Indexed: 12/28/2022]
Abstract
Translation of an mRNA represents a critical step during the expression of protein-coding genes. As mechanisms governing post-transcriptional regulation of gene expression are progressively unveiled, it is becoming apparent that transcriptional programs are not fully reflected in the proteome. Herein, we highlight a previously underappreciated post-transcriptional mode of regulation of gene expression termed translational buffering. In principle, translational buffering opposes the impact of alterations in mRNA levels on the proteome. We further describe three types of translational buffering: compensation, which maintains protein levels e.g. across species or individuals; equilibration, which retains pathway stoichiometry; and offsetting, which acts as a reversible mechanism that maintains the levels of selected subsets of proteins constant despite genetic alteration and/or stress-induced changes in corresponding mRNA levels. While mechanisms underlying compensation and equilibration have been reviewed elsewhere, the principal focus of this review is on the less-well understood mechanism of translational offsetting. Finally, we discuss potential roles of translational buffering in homeostasis and disease.
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Affiliation(s)
- Eric P Kusnadi
- Translational Prostate Cancer Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia; Cancer Program, Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
| | - Clelia Timpone
- Translational Prostate Cancer Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Ivan Topisirovic
- Lady Davis Institute, Gerald Bronfman Department of Oncology and Departments of Biochemistry and Experimental Medicine, McGill University, Montreal, QC, Canada.
| | - Ola Larsson
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden.
| | - Luc Furic
- Translational Prostate Cancer Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia; Cancer Program, Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia.
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19
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Xie J, Kusnadi EP, Furic L, Selth LA. Regulation of mRNA Translation by Hormone Receptors in Breast and Prostate Cancer. Cancers (Basel) 2021; 13:3254. [PMID: 34209750 PMCID: PMC8268847 DOI: 10.3390/cancers13133254] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 12/12/2022] Open
Abstract
Breast and prostate cancer are the second and third leading causes of death amongst all cancer types, respectively. Pathogenesis of these malignancies is characterised by dysregulation of sex hormone signalling pathways, mediated by the estrogen receptor-α (ER) in breast cancer and androgen receptor (AR) in prostate cancer. ER and AR are transcription factors whose aberrant function drives oncogenic transcriptional programs to promote cancer growth and progression. While ER/AR are known to stimulate cell growth and survival by modulating gene transcription, emerging findings indicate that their effects in neoplasia are also mediated by dysregulation of protein synthesis (i.e., mRNA translation). This suggests that ER/AR can coordinately perturb both transcriptional and translational programs, resulting in the establishment of proteomes that promote malignancy. In this review, we will discuss relatively understudied aspects of ER and AR activity in regulating protein synthesis as well as the potential of targeting mRNA translation in breast and prostate cancer.
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Affiliation(s)
- Jianling Xie
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia
| | - Eric P Kusnadi
- Translational Prostate Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
- Cancer Program, Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Luc Furic
- Translational Prostate Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
- Cancer Program, Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Luke A Selth
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia
- Freemasons Centre for Male Health and Wellbeing, Flinders University, Bedford Park, SA 5042, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia
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20
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Lee BJ, Boyer JA, Burnett GL, Thottumkara AP, Tibrewal N, Wilson SL, Hsieh T, Marquez A, Lorenzana EG, Evans JW, Hulea L, Kiss G, Liu H, Lee D, Larsson O, McLaughlan S, Topisirovic I, Wang Z, Wang Z, Zhao Y, Wildes D, Aggen JB, Singh M, Gill AL, Smith JAM, Rosen N. Selective inhibitors of mTORC1 activate 4EBP1 and suppress tumor growth. Nat Chem Biol 2021; 17:1065-1074. [PMID: 34168367 DOI: 10.1038/s41589-021-00813-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 05/07/2021] [Indexed: 12/28/2022]
Abstract
The clinical benefits of pan-mTOR active-site inhibitors are limited by toxicity and relief of feedback inhibition of receptor expression. To address these limitations, we designed a series of compounds that selectively inhibit mTORC1 and not mTORC2. These 'bi-steric inhibitors' comprise a rapamycin-like core moiety covalently linked to an mTOR active-site inhibitor. Structural modification of these components modulated their affinities for their binding sites on mTOR and the selectivity of the bi-steric compound. mTORC1-selective compounds potently inhibited 4EBP1 phosphorylation and caused regressions of breast cancer xenografts. Inhibition of 4EBP1 phosphorylation was sufficient to block cancer cell growth and was necessary for maximal antitumor activity. At mTORC1-selective doses, these compounds do not alter glucose tolerance, nor do they relieve AKT-dependent feedback inhibition of HER3. Thus, in preclinical models, selective inhibitors of mTORC1 potently inhibit tumor growth while causing less toxicity and receptor reactivation as compared to pan-mTOR inhibitors.
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Affiliation(s)
- Bianca J Lee
- Department of Biology, Revolution Medicines, Inc., Redwood City, CA, USA
| | - Jacob A Boyer
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.,Program in Molecular Pharmacology, Department of Medicine, Memorial Sloan-Kettering Cancer Center (MSKCC), New York, NY, USA
| | - G Leslie Burnett
- Department of Chemistry, Revolution Medicines, Inc., Redwood City, CA, USA
| | - Arun P Thottumkara
- Department of Chemistry, Revolution Medicines, Inc., Redwood City, CA, USA
| | - Nidhi Tibrewal
- Department of Discovery Technologies, Revolution Medicines, Inc., Redwood City, CA, USA
| | - Stacy L Wilson
- Department of Biology, Revolution Medicines, Inc., Redwood City, CA, USA
| | - Tientien Hsieh
- Department of Discovery Technologies, Revolution Medicines, Inc., Redwood City, CA, USA
| | - Abby Marquez
- Department of Discovery Technologies, Revolution Medicines, Inc., Redwood City, CA, USA
| | - Edward G Lorenzana
- Department of Biology, Revolution Medicines, Inc., Redwood City, CA, USA
| | - James W Evans
- Department of Biology, Revolution Medicines, Inc., Redwood City, CA, USA
| | - Laura Hulea
- Gerald Bronfman Department of Oncology and Departments of Biochemistry and Experimental Medicine, Lady Davis Institute, McGill University, Montréal, QC, Canada.,Département de Médecine, Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC, Canada.,Maisonneuve-Rosemont Hospital Research Centre, Montréal, QC, Canada
| | - Gert Kiss
- Department of Discovery Technologies, Revolution Medicines, Inc., Redwood City, CA, USA
| | - Hui Liu
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institute, Solna, Sweden
| | - Dong Lee
- Department of Non-clinical Development and Clinical Pharmacology, Revolution Medicines, Inc., Redwood City, CA, USA
| | - Ola Larsson
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institute, Solna, Sweden
| | - Shannon McLaughlan
- Gerald Bronfman Department of Oncology and Departments of Biochemistry and Experimental Medicine, Lady Davis Institute, McGill University, Montréal, QC, Canada
| | - Ivan Topisirovic
- Gerald Bronfman Department of Oncology and Departments of Biochemistry and Experimental Medicine, Lady Davis Institute, McGill University, Montréal, QC, Canada
| | - Zhengping Wang
- Department of Non-clinical Development and Clinical Pharmacology, Revolution Medicines, Inc., Redwood City, CA, USA
| | - Zhican Wang
- Department of Non-clinical Development and Clinical Pharmacology, Revolution Medicines, Inc., Redwood City, CA, USA
| | - Yongyuan Zhao
- Department of Non-clinical Development and Clinical Pharmacology, Revolution Medicines, Inc., Redwood City, CA, USA
| | - David Wildes
- Department of Biology, Revolution Medicines, Inc., Redwood City, CA, USA
| | - James B Aggen
- Department of Chemistry, Revolution Medicines, Inc., Redwood City, CA, USA
| | - Mallika Singh
- Department of Biology, Revolution Medicines, Inc., Redwood City, CA, USA
| | - Adrian L Gill
- Department of Chemistry, Revolution Medicines, Inc., Redwood City, CA, USA
| | | | - Neal Rosen
- Program in Molecular Pharmacology, Department of Medicine, Memorial Sloan-Kettering Cancer Center (MSKCC), New York, NY, USA.
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21
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Casas-Tintó S, Ferrús A. The haplolethality paradox of the wupA gene in Drosophila. PLoS Genet 2021; 17:e1009108. [PMID: 33739971 PMCID: PMC8011728 DOI: 10.1371/journal.pgen.1009108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 03/31/2021] [Accepted: 02/15/2021] [Indexed: 11/18/2022] Open
Abstract
Haplolethals (HL) are regions of diploid genomes that in one dose are fatal for the organism. Their biological meaning is obscure because heterozygous loss-of-function mutations result in dominant lethality (DL) and, consequently, should be under strong negative selection. We report an in depth study of the HL associated to the gene wings up A (wupA). It encodes 13 transcripts (A-M) that yield 11 protein isoforms (A-K) of Troponin I (TnI). They are functionally diverse in their control of muscle contraction, cell polarity and cell proliferation. Isoform K transfers to the nucleus where it increases transcription of the cell proliferation related genes CDK2, CDK4, Rap and Rab5. The nuclear translocation of isoform K is prevented by the co-expression of A or B isoforms, which illustrates isoform interactions. The corresponding DL mutations are, either DNA rearrangements clustered towards the gene 3’ end, thus affecting the genomic organization of all transcripts, or CRISPR-induced mutations in one of the two ATG sites which eliminate a subset of wupA products. The joint elimination of isoforms C, F, G and H, however, do not cause DL phenotypes. Genetically driven expression of single isoforms rescue neither DL nor any of the mutants known in the gene, suggesting that normal function requires properly regulated expression of specific combinations, rather than single, TnI isoforms. We conclude that the wupA associated HL results from the combined haploinsufficiency of a large set of TnI isoforms. The qualitative and quantitative normal expression of which, requires the chromosomal integrity of the wupA genomic region. Since all fly TnI isoforms are encoded in the same gene, its HL condition becomes unavoidable. These wupA features are comparable to those of dpp, the only other HL studied to some extent, and reveal a scenario of strict dosage dependence with implications for gene expression regulation and splitting. Most species contain two copies of their genetic endowment, each received from each progenitor. If one of the duplicated genes is non-functional, the remaining copy may supply enough product as to cover the requirements for normal function or, alternatively, may reflect the insufficiency through a visible phenotype. In rare occasions, however, having one copy is so deleterious that causes lethality. These so called “haplolethal regions”, exist across species and represent an evolutionary paradox since they should have been subject to intense negative selection. The inherent difficulties to study haplolethals have precluded their study so far. Here, we analyzed the case of one of the five haplolethal regions of Drosophila, the one associated to the Troponin I encoding gene wupA, by measuring the transcriptional effects of mutations and chromosomal rearrangements affecting this gene. The data show that this haplolethality results from the combined insufficiency of a large number of Troponin I isoforms, which are functionally specialized, show interference and require the integrity of the native chromatin structure for their quantitatively regulated expression. These features unveil novel aspects of gene expression and, possibly, on evolutionary gene splitting. Also, haplolethals underscore the biological significance of protein dosage, in particular for functionally related products.
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Affiliation(s)
- Sergio Casas-Tintó
- Instituto Cajal, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Alberto Ferrús
- Instituto Cajal, Consejo Superior de Investigaciones Científicas, Madrid, Spain
- * E-mail:
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22
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Ho JJD, Man JHS, Schatz JH, Marsden PA. Translational remodeling by RNA-binding proteins and noncoding RNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1647. [PMID: 33694288 DOI: 10.1002/wrna.1647] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/14/2022]
Abstract
Responsible for generating the proteome that controls phenotype, translation is the ultimate convergence point for myriad upstream signals that influence gene expression. System-wide adaptive translational reprogramming has recently emerged as a pillar of cellular adaptation. As classic regulators of mRNA stability and translation efficiency, foundational studies established the concept of collaboration and competition between RNA-binding proteins (RBPs) and noncoding RNAs (ncRNAs) on individual mRNAs. Fresh conceptual innovations now highlight stress-activated, evolutionarily conserved RBP networks and ncRNAs that increase the translation efficiency of populations of transcripts encoding proteins that participate in a common cellular process. The discovery of post-transcriptional functions for long noncoding RNAs (lncRNAs) was particularly intriguing given their cell-type-specificity and historical definition as nuclear-functioning epigenetic regulators. The convergence of RBPs, lncRNAs, and microRNAs on functionally related mRNAs to enable adaptive protein synthesis is a newer biological paradigm that highlights their role as "translatome (protein output) remodelers" and reinvigorates the paradigm of "RNA operons." Together, these concepts modernize our understanding of cellular stress adaptation and strategies for therapeutic development. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Translation > Translation Regulation Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Affiliation(s)
- J J David Ho
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida, USA.,Division of Hematology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Jeffrey H S Man
- Keenan Research Centre, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada.,Department of Respirology, University Health Network, Latner Thoracic Research Laboratories, University of Toronto, Toronto, Ontario, Canada
| | - Jonathan H Schatz
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida, USA.,Division of Hematology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Philip A Marsden
- Keenan Research Centre, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada
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23
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Hajj GNM, Nunes PBC, Roffe M. Genome-wide translation patterns in gliomas: An integrative view. Cell Signal 2020; 79:109883. [PMID: 33321181 DOI: 10.1016/j.cellsig.2020.109883] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 12/01/2020] [Accepted: 12/11/2020] [Indexed: 02/06/2023]
Abstract
Gliomas are the most frequent tumors of the central nervous system (CNS) and include the highly malignant glioblastoma (GBM). Characteristically, gliomas have translational control deregulation related to overactivation of signaling pathways such as PI3K/AKT/mTORC1 and Ras/ERK1/2. Thus, mRNA translation appears to play a dominant role in glioma gene expression patterns. The, analysis of genome-wide translated transcripts, together known as the translatome, may reveal important information for understanding gene expression patterns in gliomas. This review provides a brief overview of translational control mechanisms altered in gliomas with a focus on the current knowledge related to the translatomes of glioma cells and murine glioma models. We present an integrative meta-analysis of selected glioma translatome data with the aim of identifying recurrent patterns of gene expression preferentially regulated at the level of translation and obtaining clues regarding the pathological significance of these alterations. Re-analysis of several translatome datasets was performed to compare the translatomes of glioma models with those of their non-tumor counterparts and to document glioma cell responses to radiotherapy and MNK modulation. The role of recurrently altered genes in the context of translational control and tumorigenesis are discussed.
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Affiliation(s)
- Glaucia Noeli Maroso Hajj
- International Research Institute, A.C.Camargo Cancer Center, Rua Taguá, 440, São Paulo ZIP Code: 01508-010, Brazil; National Institute of Oncogenomics and Innovation, Brazil.
| | - Paula Borzino Cordeiro Nunes
- International Research Institute, A.C.Camargo Cancer Center, Rua Taguá, 440, São Paulo ZIP Code: 01508-010, Brazil
| | - Martin Roffe
- International Research Institute, A.C.Camargo Cancer Center, Rua Taguá, 440, São Paulo ZIP Code: 01508-010, Brazil; National Institute of Oncogenomics and Innovation, Brazil.
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24
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Cruz-Gordillo P, Honeywell ME, Harper NW, Leete T, Lee MJ. ELP-dependent expression of MCL1 promotes resistance to EGFR inhibition in triple-negative breast cancer cells. Sci Signal 2020; 13:13/658/eabb9820. [PMID: 33203722 DOI: 10.1126/scisignal.abb9820] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Targeted therapeutics for cancer generally exploit "oncogene addiction," a phenomenon in which the growth and survival of tumor cells depend on the activity of a particular protein. However, the efficacy of oncogene-targeted therapies varies substantially. For instance, targeting epidermal growth factor receptor (EGFR) signaling is effective in some non-small cell lung cancer (NSCLC) but not in triple-negative breast cancer (TNBC), although these cancers show a similar degree of increase in EGFR activity. Using a genome-wide CRISPR-Cas9 genetic knockout screen, we found that the Elongator (ELP) complex mediates insensitivity to the EGFR inhibitor erlotinib in TNBC cells by promoting the synthesis of the antiapoptotic protein Mcl-1. Depleting ELP proteins promoted apoptotic cell death in an EGFR inhibition-dependent manner. Pharmacological inhibition of Mcl-1 synergized with EGFR inhibition in a panel of genetically diverse TNBC cells. The findings indicate that TNBC "addiction" to EGFR signaling is masked by the ELP complex and that resistance to EGFR inhibitors in TNBC might be overcome by cotargeting Mcl-1.
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Affiliation(s)
- Peter Cruz-Gordillo
- Program in Systems Biology, University of Massachusetts Medical School, Worcester MA 01605, USA
| | - Megan E Honeywell
- Program in Systems Biology, University of Massachusetts Medical School, Worcester MA 01605, USA
| | - Nicholas W Harper
- Program in Systems Biology, University of Massachusetts Medical School, Worcester MA 01605, USA
| | - Thomas Leete
- Program in Systems Biology, University of Massachusetts Medical School, Worcester MA 01605, USA
| | - Michael J Lee
- Program in Systems Biology, University of Massachusetts Medical School, Worcester MA 01605, USA. .,Program in Molecular Medicine, Department of Molecular, Cell, and Cancer Biology (MCCB), University of Massachusetts Medical School, Worcester MA 01605, USA
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25
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Abstract
Tumor-associated macrophages (TAMs) continuously fine tune their immune modulatory properties, but how gene expression programs coordinate this immune cell plasticity is largely unknown. Selective mRNA translation, controlled by MNK1/MNK2 and mTOR pathways impinging on eIF4E, facilitates reshaping of proteomes without changes in abundance of corresponding mRNAs. Using polysome profiling developed for small samples we show that, during tumor growth, gene expression in TAMs is predominately modulated via mRNA-selective changes in translational efficiencies. These alterations in gene expression paralleled accumulation of antiinflammatory macrophages with augmented phosphorylation of eIF4E, a target of the MNK1 and MNK2 kinases, known to selectively modulate mRNA translation. Furthermore, suppression of the MNK2, but not the mTOR signaling pathway, reprogrammed antiinflammatory macrophages toward a proinflammatory phenotype with the ability to activate CD8+ T cells. Thus, selective changes of mRNA translation depending on MNK2 signaling represents a key node regulating macrophage antiinflammatory functions.
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26
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Kusnadi EP, Trigos AS, Cullinane C, Goode DL, Larsson O, Devlin JR, Chan KT, De Souza DP, McConville MJ, McArthur GA, Thomas G, Sanij E, Poortinga G, Hannan RD, Hannan KM, Kang J, Pearson RB. Reprogrammed mRNA translation drives resistance to therapeutic targeting of ribosome biogenesis. EMBO J 2020; 39:e105111. [PMID: 32945574 PMCID: PMC7604608 DOI: 10.15252/embj.2020105111] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 08/04/2020] [Accepted: 08/08/2020] [Indexed: 12/31/2022] Open
Abstract
Elevated ribosome biogenesis in oncogene‐driven cancers is commonly targeted by DNA‐damaging cytotoxic drugs. Our previous first‐in‐human trial of CX‐5461, a novel, less genotoxic agent that specifically inhibits ribosome biogenesis via suppression of RNA polymerase I (Pol I) transcription, revealed single‐agent efficacy in refractory blood cancers. Despite this clinical response, patients were not cured. In parallel, we demonstrated a marked improvement in the in vivo efficacy of CX‐5461 in combination with PI3K/AKT/mTORC1 pathway inhibitors. Here, we reveal the molecular basis for this improved efficacy observed in vivo, which is associated with specific suppression of translation of mRNAs encoding regulators of cellular metabolism. Importantly, acquired resistance to this cotreatment is driven by translational rewiring that results in dysregulated cellular metabolism and induction of a cAMP‐dependent pathway critical for the survival of blood cancers including lymphoma and acute myeloid leukemia. Our studies thus identify key molecular mechanisms underpinning the response of blood cancers to selective inhibition of ribosome biogenesis and define metabolic vulnerabilities that will facilitate the rational design of more effective regimens for Pol I‐directed therapies.
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Affiliation(s)
- Eric P Kusnadi
- Peter MacCallum Cancer Centre, Melbourne, Vic, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Vic, Australia
| | - Anna S Trigos
- Peter MacCallum Cancer Centre, Melbourne, Vic, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Vic, Australia
| | - Carleen Cullinane
- Peter MacCallum Cancer Centre, Melbourne, Vic, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Vic, Australia
| | - David L Goode
- Peter MacCallum Cancer Centre, Melbourne, Vic, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Vic, Australia
| | - Ola Larsson
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
| | - Jennifer R Devlin
- Peter MacCallum Cancer Centre, Melbourne, Vic, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Vic, Australia
| | - Keefe T Chan
- Peter MacCallum Cancer Centre, Melbourne, Vic, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Vic, Australia
| | - David P De Souza
- Metabolomics Australia, Bio21 Molecular Science and Biotechnology Institute, Parkville, Vic, Australia
| | - Malcolm J McConville
- Metabolomics Australia, Bio21 Molecular Science and Biotechnology Institute, Parkville, Vic, Australia.,Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Vic, Australia
| | - Grant A McArthur
- Peter MacCallum Cancer Centre, Melbourne, Vic, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Vic, Australia
| | - George Thomas
- Metabolism and Cancer Group, Molecular Mechanisms and Experimental Therapy In Oncology Program, Bellvitge Biomedical Research Institute, IDIBELL, Barcelona, Spain
| | - Elaine Sanij
- Peter MacCallum Cancer Centre, Melbourne, Vic, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Vic, Australia.,Department of Clinical Pathology, The University of Melbourne, Parkville, Vic, Australia
| | - Gretchen Poortinga
- Peter MacCallum Cancer Centre, Melbourne, Vic, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Vic, Australia
| | - Ross D Hannan
- Peter MacCallum Cancer Centre, Melbourne, Vic, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Vic, Australia.,Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Vic, Australia.,ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, Acton, ACT, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, Vic, Australia.,School of Biomedical Sciences, University of Queensland, Brisbane, Qld, Australia
| | - Katherine M Hannan
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Vic, Australia.,ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, Acton, ACT, Australia
| | - Jian Kang
- Peter MacCallum Cancer Centre, Melbourne, Vic, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Vic, Australia
| | - Richard B Pearson
- Peter MacCallum Cancer Centre, Melbourne, Vic, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Vic, Australia.,Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Vic, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, Vic, Australia
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27
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Translational profiling of macrophages infected with Leishmania donovani identifies mTOR- and eIF4A-sensitive immune-related transcripts. PLoS Pathog 2020; 16:e1008291. [PMID: 32479529 PMCID: PMC7310862 DOI: 10.1371/journal.ppat.1008291] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 06/23/2020] [Accepted: 05/13/2020] [Indexed: 12/28/2022] Open
Abstract
The protozoan parasite Leishmania donovani (L. donovani) causes visceral leishmaniasis, a chronic infection which is fatal when untreated. Herein, we investigated whether in addition to altering transcription, L. donovani modulates host mRNA translation to establish a successful infection. Polysome-profiling revealed that one third of protein-coding mRNAs expressed in primary mouse macrophages are differentially translated upon infection with L. donovani promastigotes or amastigotes. Gene ontology analysis identified key biological processes enriched for translationally regulated mRNAs and were predicted to be either activated (e.g. chromatin remodeling and RNA metabolism) or inhibited (e.g. intracellular trafficking and antigen presentation) upon infection. Mechanistic in silico and biochemical analyses showed selective activation mTOR- and eIF4A-dependent mRNA translation, including transcripts encoding central regulators of mRNA turnover and inflammation (i.e. PABPC1, EIF2AK2, and TGF-β). L. donovani survival within macrophages was favored under mTOR inhibition but was dampened by pharmacological blockade of eIF4A. Overall, this study uncovers a vast yet selective reprogramming of the host cell translational landscape early during L. donovani infection, and suggests that some of these changes are involved in host defense mechanisms while others are part of parasite-driven survival strategies. Further in vitro and in vivo investigation will shed light on the contribution of mTOR- and eIF4A-dependent translational programs to the outcome of visceral leishmaniasis.
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28
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Kozlovski I, Agami R. More or less - the same? mRNA fluctuations are balanced during translation. EMBO J 2019; 38:e103651. [PMID: 31642082 PMCID: PMC6885732 DOI: 10.15252/embj.2019103651] [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] [Indexed: 11/09/2022] Open
Abstract
Transcription factors have been traditionally studied at the level of transcription, neglecting a potential impact on protein translation. A new study published by Lorent et al (2019) describes a mechanism by which fluctuations in mRNA abundance are counteracted during translation upon estrogen receptor-alpha (ERα) depletion. This phenomenon, termed translational offsetting, is prevalent and programmed to maintain essential proteins at constant levels.
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Affiliation(s)
- Itamar Kozlovski
- Division of OncogenomicsThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Reuven Agami
- Division of OncogenomicsThe Netherlands Cancer InstituteAmsterdamThe Netherlands
- Erasmus MCRotterdam UniversityRotterdamThe Netherlands
- Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
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