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Shade LMP, Katsumata Y, Abner EL, Aung KZ, Claas SA, Qiao Q, Heberle BA, Brandon JA, Page ML, Hohman TJ, Mukherjee S, Mayeux RP, Farrer LA, Schellenberg GD, Haines JL, Kukull WA, Nho K, Saykin AJ, Bennett DA, Schneider JA, Ebbert MTW, Nelson PT, Fardo DW. GWAS of multiple neuropathology endophenotypes identifies new risk loci and provides insights into the genetic risk of dementia. Nat Genet 2024:10.1038/s41588-024-01939-9. [PMID: 39379761 DOI: 10.1038/s41588-024-01939-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/30/2024] [Indexed: 10/10/2024]
Abstract
Genome-wide association studies (GWAS) have identified >80 Alzheimer's disease and related dementias (ADRD)-associated genetic loci. However, the clinical outcomes used in most previous studies belie the complex nature of underlying neuropathologies. Here we performed GWAS on 11 ADRD-related neuropathology endophenotypes with participants drawn from the following three sources: the National Alzheimer's Coordinating Center, the Religious Orders Study and Rush Memory and Aging Project, and the Adult Changes in Thought study (n = 7,804 total autopsied participants). We identified eight independent significantly associated loci, of which four were new (COL4A1, PIK3R5, LZTS1 and APOC2). Separately testing known ADRD loci, 19 loci were significantly associated with at least one neuropathology after false-discovery rate adjustment. Genetic colocalization analyses identified pleiotropic effects and quantitative trait loci. Methylation in the cerebral cortex at two sites near APOC2 was associated with cerebral amyloid angiopathy. Studies that include neuropathology endophenotypes are an important step in understanding the mechanisms underlying genetic ADRD risk.
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Affiliation(s)
- Lincoln M P Shade
- Department of Biostatistics, College of Public Health, University of Kentucky, Lexington, KY, USA
| | - Yuriko Katsumata
- Department of Biostatistics, College of Public Health, University of Kentucky, Lexington, KY, USA
- Sanders-Brown Center on Aging and Alzheimer's Disease Research Center, University of Kentucky, Lexington, KY, USA
| | - Erin L Abner
- Sanders-Brown Center on Aging and Alzheimer's Disease Research Center, University of Kentucky, Lexington, KY, USA
- Department of Epidemiology and Environmental Health, College of Public Health, University of Kentucky, Lexington, KY, USA
| | - Khine Zin Aung
- Department of Biostatistics, College of Public Health, University of Kentucky, Lexington, KY, USA
- Sanders-Brown Center on Aging and Alzheimer's Disease Research Center, University of Kentucky, Lexington, KY, USA
| | - Steven A Claas
- Department of Biostatistics, College of Public Health, University of Kentucky, Lexington, KY, USA
| | - Qi Qiao
- Department of Biostatistics, College of Public Health, University of Kentucky, Lexington, KY, USA
- Sanders-Brown Center on Aging and Alzheimer's Disease Research Center, University of Kentucky, Lexington, KY, USA
| | - Bernardo Aguzzoli Heberle
- Sanders-Brown Center on Aging and Alzheimer's Disease Research Center, University of Kentucky, Lexington, KY, USA
- Department of Neuroscience, University of Kentucky College of Medicine, Lexington, KY, USA
| | - J Anthony Brandon
- Sanders-Brown Center on Aging and Alzheimer's Disease Research Center, University of Kentucky, Lexington, KY, USA
- Department of Neuroscience, University of Kentucky College of Medicine, Lexington, KY, USA
| | - Madeline L Page
- Sanders-Brown Center on Aging and Alzheimer's Disease Research Center, University of Kentucky, Lexington, KY, USA
- Department of Neuroscience, University of Kentucky College of Medicine, Lexington, KY, USA
| | - Timothy J Hohman
- Vanderbilt Memory and Alzheimer's Center, Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Richard P Mayeux
- Department of Neurology, Columbia University, New York City, NY, USA
| | - Lindsay A Farrer
- Department of Medicine (Biomedical Genetics), Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- Department of Neurology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- Department of Ophthalmology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
- Department of Epidemiology, School of Public Health, Boston University, Boston, MA, USA
| | - Gerard D Schellenberg
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jonathan L Haines
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Walter A Kukull
- National Alzheimer's Coordinating Center, Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Kwangsik Nho
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana Alzheimer's Disease Research Center, Indiana University School of Medicine, Indianapolis, IN, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Andrew J Saykin
- Indiana Alzheimer's Disease Research Center, Indiana University School of Medicine, Indianapolis, IN, USA
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
| | - David A Bennett
- Department of Neurological Sciences, Rush Medical College, Chicago, IL, USA
- Rush Alzheimer's Disease Center, Rush Medical College, Chicago, IL, USA
| | - Julie A Schneider
- Department of Neurological Sciences, Rush Medical College, Chicago, IL, USA
- Rush Alzheimer's Disease Center, Rush Medical College, Chicago, IL, USA
- Department of Pathology, Rush Medical College, Chicago, IL, USA
| | - Mark T W Ebbert
- Sanders-Brown Center on Aging and Alzheimer's Disease Research Center, University of Kentucky, Lexington, KY, USA
- Department of Neuroscience, University of Kentucky College of Medicine, Lexington, KY, USA
- Division of Biomedical Informatics, Department of Internal Medicine, University of Kentucky College of Medicine, Lexington, KY, USA
| | - Peter T Nelson
- Sanders-Brown Center on Aging and Alzheimer's Disease Research Center, University of Kentucky, Lexington, KY, USA
- Department of Pathology and Laboratory Medicine, University of Kentucky College of Medicine, Lexington, KY, USA
| | - David W Fardo
- Department of Biostatistics, College of Public Health, University of Kentucky, Lexington, KY, USA.
- Sanders-Brown Center on Aging and Alzheimer's Disease Research Center, University of Kentucky, Lexington, KY, USA.
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2
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Gallardo-Dodd CJ, Kutter C. The regulatory landscape of interacting RNA and protein pools in cellular homeostasis and cancer. Hum Genomics 2024; 18:109. [PMID: 39334294 PMCID: PMC11437681 DOI: 10.1186/s40246-024-00678-6] [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: 04/28/2024] [Accepted: 09/22/2024] [Indexed: 09/30/2024] Open
Abstract
Biological systems encompass intricate networks governed by RNA-protein interactions that play pivotal roles in cellular functions. RNA and proteins constituting 1.1% and 18% of the mammalian cell weight, respectively, orchestrate vital processes from genome organization to translation. To date, disentangling the functional fraction of the human genome has presented a major challenge, particularly for noncoding regions, yet recent discoveries have started to unveil a host of regulatory functions for noncoding RNAs (ncRNAs). While ncRNAs exist at different sizes, structures, degrees of evolutionary conservation and abundances within the cell, they partake in diverse roles either alone or in combination. However, certain ncRNA subtypes, including those that have been described or remain to be discovered, are poorly characterized given their heterogeneous nature. RNA activity is in most cases coordinated through interactions with RNA-binding proteins (RBPs). Extensive efforts are being made to accurately reconstruct RNA-RBP regulatory networks, which have provided unprecedented insight into cellular physiology and human disease. In this review, we provide a comprehensive view of RNAs and RBPs, focusing on how their interactions generate functional signals in living cells, particularly in the context of post-transcriptional regulatory processes and cancer.
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Affiliation(s)
- Carlos J Gallardo-Dodd
- Department of Microbiology, Tumor, and Cell Biology, Science for Life Laboratory, Karolinska Institute, Solna, Sweden
| | - Claudia Kutter
- Department of Microbiology, Tumor, and Cell Biology, Science for Life Laboratory, Karolinska Institute, Solna, Sweden.
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3
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Čelešnik H, Gorenjak M, Krušič M, Crnobrnja B, Sobočan M, Takač I, Arko D, Potočnik U. Isoform-Level Transcriptome Analysis of Peripheral Blood Mononuclear Cells from Breast Cancer Patients Identifies a Disease-Associated RASGEF1A Isoform. Cancers (Basel) 2024; 16:3171. [PMID: 39335143 PMCID: PMC11429621 DOI: 10.3390/cancers16183171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2024] [Revised: 09/11/2024] [Accepted: 09/12/2024] [Indexed: 09/30/2024] Open
Abstract
Background: Breast cancer (BC) comprises multiple subtypes with distinct molecular features, which differ in their interplay with host immunity, prognosis, and treatment. Non-invasive blood analyses can provide valuable insights into systemic immunity during cancer. The aim of this study was to analyze the expression of transcriptional isoforms in peripheral blood mononuclear cells (PBMCs) from BC patients and healthy women to identify potential BC immune biomarkers. Methods: RNA sequencing and isoform-level bioinformatics were performed on PBMCs from 12 triple-negative and 13 luminal A patients. Isoform expression validation by qRT-PCR and clinicopathological correlations were performed in a larger cohort (156 BC patients and 32 healthy women). Results: Transcriptional analyses showed a significant (p < 0.001) decrease in the ENST00000374459 RASGEF1A isoform in PBMCs of BC compared to healthy subjects, indicating disease-related expression changes. The decrease was associated with higher ctDNA and Ki-67 values. Conclusions: The levels of the RASGEF1A transcriptional isoform ENST00000374459 may have the potential to distinguish between BC and healthy subjects. The downregulation of ENST00000374459 in breast cancer is associated with higher proliferation and ctDNA shedding. Specialized bioinformatics analyses such as isoform analyses hold significant promise in the detection of biomarkers, since standard RNA sequencing analyses may overlook specific transcriptional changes that may be disease-associated and biologically important.
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Grants
- P3-0427, P3-0067, J3-4523, J3-3069, I0-0029, J3-9272 and P3-0321 Slovenian Research and Innovation Agency
- IRP-2019/01-05, IRP-2019/02-15, IRP-2021/01-02 Internal University Medical Centre Maribor research funding,
- RIUM Republic of Slovenia, the Ministry of Higher Education, Science and Innovation and the European Union from the European Regional Development Fund
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Affiliation(s)
- Helena Čelešnik
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, 2000 Maribor, Slovenia;
- Faculty of Medicine, University of Maribor, Taborska ulica 8, 2000 Maribor, Slovenia; (M.G.); (M.K.); (M.S.); (I.T.); (D.A.)
| | - Mario Gorenjak
- Faculty of Medicine, University of Maribor, Taborska ulica 8, 2000 Maribor, Slovenia; (M.G.); (M.K.); (M.S.); (I.T.); (D.A.)
| | - Martina Krušič
- Faculty of Medicine, University of Maribor, Taborska ulica 8, 2000 Maribor, Slovenia; (M.G.); (M.K.); (M.S.); (I.T.); (D.A.)
| | - Bojana Crnobrnja
- Division of Gynecology and Perinatology, University Medical Center Maribor, Ljubljanska ulica 5, 2000 Maribor, Slovenia;
| | - Monika Sobočan
- Faculty of Medicine, University of Maribor, Taborska ulica 8, 2000 Maribor, Slovenia; (M.G.); (M.K.); (M.S.); (I.T.); (D.A.)
- Division of Gynecology and Perinatology, University Medical Center Maribor, Ljubljanska ulica 5, 2000 Maribor, Slovenia;
| | - Iztok Takač
- Faculty of Medicine, University of Maribor, Taborska ulica 8, 2000 Maribor, Slovenia; (M.G.); (M.K.); (M.S.); (I.T.); (D.A.)
- Division of Gynecology and Perinatology, University Medical Center Maribor, Ljubljanska ulica 5, 2000 Maribor, Slovenia;
| | - Darja Arko
- Faculty of Medicine, University of Maribor, Taborska ulica 8, 2000 Maribor, Slovenia; (M.G.); (M.K.); (M.S.); (I.T.); (D.A.)
- Division of Gynecology and Perinatology, University Medical Center Maribor, Ljubljanska ulica 5, 2000 Maribor, Slovenia;
| | - Uroš Potočnik
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, 2000 Maribor, Slovenia;
- Faculty of Medicine, University of Maribor, Taborska ulica 8, 2000 Maribor, Slovenia; (M.G.); (M.K.); (M.S.); (I.T.); (D.A.)
- Department for Science and Research, University Medical Centre Maribor, Ljubljanska ulica 5, 2000 Maribor, Slovenia
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4
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O'Donnell BL, Stefan D, Chiu YH, Zeitz MJ, Tang J, Johnston D, Leighton SE, Kessel CV, Barr K, Gyenis L, Freeman TJ, Kelly JJ, Sayedyahossein S, Litchfield DW, Roth K, Smyth JW, Hebb M, Ronald J, Bayliss DA, Penuela S. Novel Pannexin 1 isoform is increased in cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.09.612143. [PMID: 39314291 PMCID: PMC11419113 DOI: 10.1101/2024.09.09.612143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Pannexin 1 (PANX1) is upregulated in many cancers, where its activity and signalling promote tumorigenic properties. Here, we report a novel ∼25 kDa isoform of human PANX1 (hPANX1-25K) which lacks the N-terminus and was detected in several human cancer cell lines including melanoma, osteosarcoma, breast cancer and glioblastoma multiforme. This isoform was increased upon hPANX1 CRISPR/Cas9 deletion targeting the first exon near M1, suggesting a potential alternative translation initiation (ATI) site. hPANX1-25K was confirmed to be a hPANX1 isoform via mass spectrometry, can be N-linked glycosylated at N254, and can interact with both β-catenin and full length hPANX1. A double deletion of hPANX1 and hPANX1-25K reduces cell growth and viability in cancer cells. hPANX1-25K is prevalent throughout melanoma progression, and its levels are increased in squamous cell carcinoma cells and patient-derived tumours, compared to keratinocytes and normal skin, indicating that it may be differentially regulated in normal and cancer cells.
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5
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Yu S, Wu R, Si Y, Fan Z, Wang Y, Yao C, Sun R, Xue Y, Chen Y, Wang Z, Dong S, Wang N, Ling X, Liang Z, Bi C, Yang Y, Dong W, Sun H. Alternative splicing of ALDOA confers tamoxifen resistance in breast cancer. Oncogene 2024; 43:2901-2913. [PMID: 39164523 DOI: 10.1038/s41388-024-03134-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 08/09/2024] [Accepted: 08/12/2024] [Indexed: 08/22/2024]
Abstract
The cancer-associated alternative splicing (AS) events generate cancer-related transcripts which are involved in uncontrolled cell proliferation and drug resistance. However, the key AS variants implicated in tamoxifen (TAM) resistance in breast cancer remain elusive. In the current study, we investigated the landscape of AS events in nine pairs of primary and relapse breast tumors from patients receiving TAM-based therapy. We unrevealed a notable association between the inclusion of exon 7.2 in the 5'untranslated region (5'UTR) of ALDOA mRNA and TAM resistance. Mechanistically, the inclusion of ALDOA exon 7.2 enhances the translation efficiency of the transcript, resulting in increased ALDOA protein expression, mTOR pathway activity, and the promotion of TAM resistance in breast cancer cells. Moreover, the inclusion of exon 7.2 in ALDOA mRNA is mediated by MSI1 via direct interaction. In addition, elevated inclusion of ALDOA exon 7.2 or expression of MSI1 is associated with an unfavorable prognosis in patients undergoing endocrine therapy. Notably, treatment with Aldometanib, an ALDOA inhibitor, effectively restrains the growth of TAM-resistant breast cancer cells in vitro and in vivo. The present study unveils the pivotal role of an AS event in ALDOA, under the regulation of MSI1, in driving TAM resistance in breast cancer. Therefore, this study provides a promising therapeutic avenue targeting ALDOA to combat TAM resistance.
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Affiliation(s)
- Shiyi Yu
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-Coding RNA Research, Yangzhou University, Yangzhou, China
| | - Rui Wu
- School of Life Science, Liaoning Normal University, Dalian, China
| | - Yue Si
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-Coding RNA Research, Yangzhou University, Yangzhou, China
| | - Zhehao Fan
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-Coding RNA Research, Yangzhou University, Yangzhou, China
| | - Ying Wang
- Department of Thyroid and Breast Surgery, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Chang Yao
- The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Rongmao Sun
- Department of Thyroid and Breast Surgery, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Yaji Xue
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-Coding RNA Research, Yangzhou University, Yangzhou, China
| | - Yongli Chen
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-Coding RNA Research, Yangzhou University, Yangzhou, China
| | - Zheng Wang
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Shuangshuang Dong
- Department of Pathology, Northern Jiangsu People's Hospital Affiliated to Yangzhou University/Clinical Medical College, Yangzhou University, Yangzhou, China
| | - Ning Wang
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-Coding RNA Research, Yangzhou University, Yangzhou, China
| | - Xinyue Ling
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-Coding RNA Research, Yangzhou University, Yangzhou, China
| | - Zhengyan Liang
- School of Basic Medical Science, Guangdong Medical University, Dongguan, China
| | - Caili Bi
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-Coding RNA Research, Yangzhou University, Yangzhou, China
| | - Yi Yang
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China.
- Jiangsu Key Laboratory of Experimental & Translational Non-Coding RNA Research, Yangzhou University, Yangzhou, China.
| | - Weibing Dong
- School of Life Science, Liaoning Normal University, Dalian, China.
| | - Haibo Sun
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China.
- Jiangsu Key Laboratory of Experimental & Translational Non-Coding RNA Research, Yangzhou University, Yangzhou, China.
- Haian Hospital of Traditional Chinese Medicine, Haian, China.
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6
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Schlusser N, González A, Pandey M, Zavolan M. Current limitations in predicting mRNA translation with deep learning models. Genome Biol 2024; 25:227. [PMID: 39164757 PMCID: PMC11337900 DOI: 10.1186/s13059-024-03369-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 08/07/2024] [Indexed: 08/22/2024] Open
Abstract
BACKGROUND The design of nucleotide sequences with defined properties is a long-standing problem in bioengineering. An important application is protein expression, be it in the context of research or the production of mRNA vaccines. The rate of protein synthesis depends on the 5' untranslated region (5'UTR) of the mRNAs, and recently, deep learning models were proposed to predict the translation output of mRNAs from the 5'UTR sequence. At the same time, large data sets of endogenous and reporter mRNA translation have become available. RESULTS In this study, we use complementary data obtained in two different cell types to assess the accuracy and generality of currently available models for predicting translational output. We find that while performing well on the data sets on which they were trained, deep learning models do not generalize well to other data sets, in particular of endogenous mRNAs, which differ in many properties from reporter constructs. CONCLUSIONS These differences limit the ability of deep learning models to uncover mechanisms of translation control and to predict the impact of genetic variation. We suggest directions that combine high-throughput measurements and machine learning to unravel mechanisms of translation control and improve construct design.
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Affiliation(s)
- Niels Schlusser
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland.
| | - Asier González
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Spain
| | - Muskan Pandey
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
- Current address: Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, 8093, Zurich, Switzerland
| | - Mihaela Zavolan
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland.
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7
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Renz PF, Ghoshdastider U, Baghai Sain S, Valdivia-Francia F, Khandekar A, Ormiston M, Bernasconi M, Duré C, Kretz JA, Lee M, Hyams K, Forny M, Pohly M, Ficht X, Ellis SJ, Moor AE, Sendoel A. In vivo single-cell CRISPR uncovers distinct TNF programmes in tumour evolution. Nature 2024; 632:419-428. [PMID: 39020166 PMCID: PMC11306103 DOI: 10.1038/s41586-024-07663-y] [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: 06/20/2023] [Accepted: 06/04/2024] [Indexed: 07/19/2024]
Abstract
The tumour evolution model posits that malignant transformation is preceded by randomly distributed driver mutations in cancer genes, which cause clonal expansions in phenotypically normal tissues. Although clonal expansions can remodel entire tissues1-3, the mechanisms that result in only a small number of clones transforming into malignant tumours remain unknown. Here we develop an in vivo single-cell CRISPR strategy to systematically investigate tissue-wide clonal dynamics of the 150 most frequently mutated squamous cell carcinoma genes. We couple ultrasound-guided in utero lentiviral microinjections, single-cell RNA sequencing and guide capture to longitudinally monitor clonal expansions and document their underlying gene programmes at single-cell transcriptomic resolution. We uncover a tumour necrosis factor (TNF) signalling module, which is dependent on TNF receptor 1 and involving macrophages, that acts as a generalizable driver of clonal expansions in epithelial tissues. Conversely, during tumorigenesis, the TNF signalling module is downregulated. Instead, we identify a subpopulation of invasive cancer cells that switch to an autocrine TNF gene programme associated with epithelial-mesenchymal transition. Finally, we provide in vivo evidence that the autocrine TNF gene programme is sufficient to mediate invasive properties and show that the TNF signature correlates with shorter overall survival of patients with squamous cell carcinoma. Collectively, our study demonstrates the power of applying in vivo single-cell CRISPR screening to mammalian tissues, unveils distinct TNF programmes in tumour evolution and highlights the importance of understanding the relationship between clonal expansions in epithelia and tumorigenesis.
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Affiliation(s)
- Peter F Renz
- Institute for Regenerative Medicine (IREM), University of Zurich, Schlieren-Zurich, Switzerland
| | - Umesh Ghoshdastider
- Institute for Regenerative Medicine (IREM), University of Zurich, Schlieren-Zurich, Switzerland
| | - Simona Baghai Sain
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Fabiola Valdivia-Francia
- Institute for Regenerative Medicine (IREM), University of Zurich, Schlieren-Zurich, Switzerland
- Life Science Zurich Graduate School, Molecular Life Science Program, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Ameya Khandekar
- Max Perutz Labs, Vienna BioCenter Campus (VBC), Vienna, Austria
- Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
| | - Mark Ormiston
- Institute for Regenerative Medicine (IREM), University of Zurich, Schlieren-Zurich, Switzerland
| | - Martino Bernasconi
- Institute for Regenerative Medicine (IREM), University of Zurich, Schlieren-Zurich, Switzerland
| | - Clara Duré
- Institute for Regenerative Medicine (IREM), University of Zurich, Schlieren-Zurich, Switzerland
- Life Science Zurich Graduate School, Molecular Life Science Program, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Jonas A Kretz
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Minkyoung Lee
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Katie Hyams
- Institute for Regenerative Medicine (IREM), University of Zurich, Schlieren-Zurich, Switzerland
| | - Merima Forny
- Institute for Regenerative Medicine (IREM), University of Zurich, Schlieren-Zurich, Switzerland
| | - Marcel Pohly
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Xenia Ficht
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Stephanie J Ellis
- Max Perutz Labs, Vienna BioCenter Campus (VBC), Vienna, Austria
- Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
| | - Andreas E Moor
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
| | - Ataman Sendoel
- Institute for Regenerative Medicine (IREM), University of Zurich, Schlieren-Zurich, Switzerland.
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8
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Lama-Diaz T, Blanco MG. Alternative translation initiation by ribosomal leaky scanning produces multiple isoforms of the Pif1 helicase. Nucleic Acids Res 2024; 52:6928-6944. [PMID: 38783074 PMCID: PMC11229318 DOI: 10.1093/nar/gkae400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 04/24/2024] [Accepted: 05/01/2024] [Indexed: 05/25/2024] Open
Abstract
In budding yeast, the integrity of both the nuclear and mitochondrial genomes relies on dual-targeted isoforms of the conserved Pif1 helicase, generated by alternative translation initiation (ATI) of PIF1 mRNA from two consecutive AUG codons flanking a mitochondrial targeting signal. Here, we demonstrate that ribosomal leaky scanning is the specific ATI mechanism that produces not only these, but also novel, previously uncharacterized Pif1 isoforms. Both in-frame, downstream AUGs as well as near-cognate start codons contribute to the generation of these alternative isoforms. This has crucial implications for the rational design of genuine separation-of-function alleles and provides an explanation for the suboptimal behaviour of the widely employed mitochondrial- (pif1-m1) and nuclear-deficient (pif1-m2) alleles, with mutations in the first or second AUG codon, respectively. We have taken advantage of this refined model to develop improved versions of these alleles, which will serve as valuable tools to elucidate novel functions of this helicase and to disambiguate previously described genetic interactions of PIF1 in the context of nuclear and mitochondrial genome stability.
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Affiliation(s)
- Tomas Lama-Diaz
- Department of Biochemistry and Molecular Biology, CIMUS, Universidade de Santiago de Compostela-Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, A Coruña 15782, Spain
| | - Miguel G Blanco
- Department of Biochemistry and Molecular Biology, CIMUS, Universidade de Santiago de Compostela-Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, A Coruña 15782, Spain
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9
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Dasgupta A, Prensner JR. Upstream open reading frames: new players in the landscape of cancer gene regulation. NAR Cancer 2024; 6:zcae023. [PMID: 38774471 PMCID: PMC11106035 DOI: 10.1093/narcan/zcae023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/29/2024] [Accepted: 05/07/2024] [Indexed: 05/24/2024] Open
Abstract
The translation of RNA by ribosomes represents a central biological process and one of the most dysregulated processes in cancer. While translation is traditionally thought to occur exclusively in the protein-coding regions of messenger RNAs (mRNAs), recent transcriptome-wide approaches have shown abundant ribosome activity across diverse stretches of RNA transcripts. The most common type of this kind of ribosome activity occurs in gene leader sequences, also known as 5' untranslated regions (UTRs) of the mRNA, that precede the main coding sequence. Translation of these upstream open reading frames (uORFs) is now known to occur in upwards of 25% of all protein-coding genes. With diverse functions from RNA regulation to microprotein generation, uORFs are rapidly igniting a new arena of cancer biology, where they are linked to cancer genetics, cancer signaling, and tumor-immune interactions. This review focuses on the contributions of uORFs and their associated 5'UTR sequences to cancer biology.
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Affiliation(s)
- Anwesha Dasgupta
- Chad Carr Pediatric Brain Tumor Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - John R Prensner
- Chad Carr Pediatric Brain Tumor Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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10
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Pina C. Contributions of transcriptional noise to leukaemia evolution: KAT2A as a case-study. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230052. [PMID: 38432321 PMCID: PMC10909511 DOI: 10.1098/rstb.2023.0052] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 12/04/2023] [Indexed: 03/05/2024] Open
Abstract
Transcriptional noise is proposed to participate in cell fate changes, but contributions to mammalian cell differentiation systems, including cancer, remain associative. Cancer evolution is driven by genetic variability, with modulatory or contributory participation of epigenetic variants. Accumulation of epigenetic variants enhances transcriptional noise, which can facilitate cancer cell fate transitions. Acute myeloid leukaemia (AML) is an aggressive cancer with strong epigenetic dependencies, characterized by blocked differentiation. It constitutes an attractive model to probe links between transcriptional noise and malignant cell fate regulation. Gcn5/KAT2A is a classical epigenetic transcriptional noise regulator. Its loss increases transcriptional noise and modifies cell fates in stem and AML cells. By reviewing the analysis of KAT2A-depleted pre-leukaemia and leukaemia models, I discuss that the net result of transcriptional noise is diversification of cell fates secondary to alternative transcriptional programmes. Cellular diversification can enable or hinder AML progression, respectively, by differentiation of cell types responsive to mutations, or by maladaptation of leukaemia stem cells. KAT2A-dependent noise-responsive genes participate in ribosome biogenesis and KAT2A loss destabilizes translational activity. I discuss putative contributions of perturbed translation to AML biology, and propose KAT2A loss as a model for mechanistic integration of transcriptional and translational control of noise and fate decisions. This article is part of a discussion meeting issue 'Causes and consequences of stochastic processes in development and disease'.
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Affiliation(s)
- Cristina Pina
- College of Health, Medicine and Life Sciences, Brunel University London, Kingston Lane, Uxbridge, London, UB8 3PH, United Kingdom
- CenGEM – Centre for Genome Engineering and Maintenance, Brunel University London, Kingston Lane, Uxbridge, London, UB8 3PH, United Kingdom
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11
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Alfonso-Gonzalez C, Hilgers V. (Alternative) transcription start sites as regulators of RNA processing. Trends Cell Biol 2024:S0962-8924(24)00033-3. [PMID: 38531762 DOI: 10.1016/j.tcb.2024.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/20/2024] [Accepted: 02/23/2024] [Indexed: 03/28/2024]
Abstract
Alternative transcription start site usage (ATSS) is a widespread regulatory strategy that enables genes to choose between multiple genomic loci for initiating transcription. This mechanism is tightly controlled during development and is often altered in disease states. In this review, we examine the growing evidence highlighting a role for transcription start sites (TSSs) in the regulation of mRNA isoform selection during and after transcription. We discuss how the choice of transcription initiation sites influences RNA processing and the importance of this crosstalk for cell identity and organism function. We also speculate on possible mechanisms underlying the integration of transcriptional and post-transcriptional processes.
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Affiliation(s)
- Carlos Alfonso-Gonzalez
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; Faculty of Biology, Albert Ludwigs University, 79104 Freiburg, Germany; International Max Planck Research School for Molecular and Cellular Biology (IMPRS- MCB), 79108 Freiburg, Germany
| | - Valérie Hilgers
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.
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12
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Lewis CJT, Xie L, Bhandarkar S, Jin D, Abdallah KS, Draycott AS, Chen Y, Thoreen CC, Gilbert WV. Quantitative profiling of human translation initiation reveals regulatory elements that potently affect endogenous and therapeutically modified mRNAs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.28.582532. [PMID: 38463950 PMCID: PMC10925289 DOI: 10.1101/2024.02.28.582532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
mRNA therapeutics offer a potentially universal strategy for the efficient development and delivery of therapeutic proteins. Current mRNA vaccines include chemically modified nucleotides to reduce cellular immunogenicity. Here, we develop an efficient, high-throughput method to measure human translation initiation on therapeutically modified as well as endogenous RNAs. Using systems-level biochemistry, we quantify ribosome recruitment to tens of thousands of human 5' untranslated regions and identify sequences that mediate 250-fold effects. We observe widespread effects of coding sequences on translation initiation and identify small regulatory elements of 3-6 nucleotides that are sufficient to potently affect translational output. Incorporation of N1-methylpseudouridine (m1Ψ) selectively enhances translation by specific 5' UTRs that we demonstrate surpass those of current mRNA vaccines. Our approach is broadly applicable to dissect mechanisms of human translation initiation and engineer more potent therapeutic mRNAs. Highlights Measurement of >30,000 human 5' UTRs reveals a 250-fold range of translation outputSystematic mutagenesis demonstrates the causality of short (3-6nt) regulatory elementsN1-methylpseudouridine alters translation initiation in a sequence-specific mannerOptimal modified 5' UTRs outperform those in the current class of mRNA vaccines.
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13
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Fernández-Parejo N, Lorenzo-Martín LF, García-Pedrero JM, Rodrigo JP, Dosil M, Bustelo XR. VAV2 orchestrates the interplay between regenerative proliferation and ribogenesis in both keratinocytes and oral squamous cell carcinoma. Sci Rep 2024; 14:4060. [PMID: 38374399 PMCID: PMC10876654 DOI: 10.1038/s41598-024-54808-0] [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: 11/22/2023] [Accepted: 02/16/2024] [Indexed: 02/21/2024] Open
Abstract
VAV2 is an activator of RHO GTPases that promotes and maintains regenerative proliferation-like states in normal keratinocytes and oral squamous cell carcinoma (OSCC) cells. Here, we demonstrate that VAV2 also regulates ribosome biogenesis in those cells, a program associated with poor prognosis of human papilloma virus-negative (HPV-) OSCC patients. Mechanistically, VAV2 regulates this process in a catalysis-dependent manner using a conserved pathway comprising the RAC1 and RHOA GTPases, the PAK and ROCK family kinases, and the c-MYC and YAP/TAZ transcription factors. This pathway directly promotes RNA polymerase I activity and synthesis of 47S pre-rRNA precursors. This process is further consolidated by the upregulation of ribosome biogenesis factors and the acquisition of the YAP/TAZ-dependent undifferentiated cell state. Finally, we show that RNA polymerase I is a therapeutic Achilles' heel for both keratinocytes and OSCC patient-derived cells endowed with high VAV2 catalytic activity. Collectively, these findings highlight the therapeutic potential of modulating VAV2 and the ribosome biogenesis pathways in both preneoplastic and late progression stages of OSCC.
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Affiliation(s)
- Natalia Fernández-Parejo
- Centro de Investigación del Cáncer and Instituto de Biología Molecular del Cáncer, CSIC and Universidad de Salamanca, 37007, Salamanca, Spain
- Centro de Investigación Biomédica en Red de Cáncer, 28029, Madrid, Spain
| | - L Francisco Lorenzo-Martín
- Centro de Investigación del Cáncer and Instituto de Biología Molecular del Cáncer, CSIC and Universidad de Salamanca, 37007, Salamanca, Spain
- Centro de Investigación Biomédica en Red de Cáncer, 28029, Madrid, Spain
- Laboratory of Stem Cell Bioengineering, École Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
| | - Juana M García-Pedrero
- Centro de Investigación Biomédica en Red de Cáncer, 28029, Madrid, Spain
- Hospital Universitario Central de Asturias and Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Instituto Universitario de Oncología del Principado de Asturias, University of Oviedo, 33011, Oviedo, Spain
| | - Juan P Rodrigo
- Centro de Investigación Biomédica en Red de Cáncer, 28029, Madrid, Spain
- Hospital Universitario Central de Asturias and Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Instituto Universitario de Oncología del Principado de Asturias, University of Oviedo, 33011, Oviedo, Spain
| | - Mercedes Dosil
- Centro de Investigación del Cáncer and Instituto de Biología Molecular del Cáncer, CSIC and Universidad de Salamanca, 37007, Salamanca, Spain.
- Centro de Investigación Biomédica en Red de Cáncer, 28029, Madrid, Spain.
| | - Xosé R Bustelo
- Centro de Investigación del Cáncer and Instituto de Biología Molecular del Cáncer, CSIC and Universidad de Salamanca, 37007, Salamanca, Spain.
- Centro de Investigación Biomédica en Red de Cáncer, 28029, Madrid, Spain.
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14
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Valdivia-Francia F, Sendoel A. No country for old methods: New tools for studying microproteins. iScience 2024; 27:108972. [PMID: 38333695 PMCID: PMC10850755 DOI: 10.1016/j.isci.2024.108972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024] Open
Abstract
Microproteins encoded by small open reading frames (sORFs) have emerged as a fascinating frontier in genomics. Traditionally overlooked due to their small size, recent technological advancements such as ribosome profiling, mass spectrometry-based strategies and advanced computational approaches have led to the annotation of more than 7000 sORFs in the human genome. Despite the vast progress, only a tiny portion of these microproteins have been characterized and an important challenge in the field lies in identifying functionally relevant microproteins and understanding their role in different cellular contexts. In this review, we explore the recent advancements in sORF research, focusing on the new methodologies and computational approaches that have facilitated their identification and functional characterization. Leveraging these new tools hold great promise for dissecting the diverse cellular roles of microproteins and will ultimately pave the way for understanding their role in the pathogenesis of diseases and identifying new therapeutic targets.
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Affiliation(s)
- Fabiola Valdivia-Francia
- University of Zurich, Institute for Regenerative Medicine (IREM), Wagistrasse 12, 8952 Schlieren-Zurich, Switzerland
- Life Science Zurich Graduate School, Molecular Life Science Program, University of Zurich/ ETH Zurich, Schlieren-Zurich, Switzerland
| | - Ataman Sendoel
- University of Zurich, Institute for Regenerative Medicine (IREM), Wagistrasse 12, 8952 Schlieren-Zurich, Switzerland
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15
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Dueñas Rey A, Del Pozo Valero M, Bouckaert M, Wood KA, Van den Broeck F, Daich Varela M, Thomas HB, Van Heetvelde M, De Bruyne M, Van de Sompele S, Bauwens M, Lenaerts H, Mahieu Q, Josifova D, Rivolta C, O'Keefe RT, Ellingford J, Webster AR, Arno G, Ayuso C, De Zaeytijd J, Leroy BP, De Baere E, Coppieters F. Combining a prioritization strategy and functional studies nominates 5'UTR variants underlying inherited retinal disease. Genome Med 2024; 16:7. [PMID: 38184646 PMCID: PMC10771650 DOI: 10.1186/s13073-023-01277-1] [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: 06/16/2023] [Accepted: 12/15/2023] [Indexed: 01/08/2024] Open
Abstract
BACKGROUND 5' untranslated regions (5'UTRs) are essential modulators of protein translation. Predicting the impact of 5'UTR variants is challenging and rarely performed in routine diagnostics. Here, we present a combined approach of a comprehensive prioritization strategy and functional assays to evaluate 5'UTR variation in two large cohorts of patients with inherited retinal diseases (IRDs). METHODS We performed an isoform-level re-analysis of retinal RNA-seq data to identify the protein-coding transcripts of 378 IRD genes with highest expression in retina. We evaluated the coverage of their 5'UTRs by different whole exome sequencing (WES) kits. The selected 5'UTRs were analyzed in whole genome sequencing (WGS) and WES data from IRD sub-cohorts from the 100,000 Genomes Project (n = 2397 WGS) and an in-house database (n = 1682 WES), respectively. Identified variants were annotated for 5'UTR-relevant features and classified into seven categories based on their predicted functional consequence. We developed a variant prioritization strategy by integrating population frequency, specific criteria for each category, and family and phenotypic data. A selection of candidate variants underwent functional validation using diverse approaches. RESULTS Isoform-level re-quantification of retinal gene expression revealed 76 IRD genes with a non-canonical retina-enriched isoform, of which 20 display a fully distinct 5'UTR compared to that of their canonical isoform. Depending on the probe design, 3-20% of IRD genes have 5'UTRs fully captured by WES. After analyzing these regions in both cohorts, we prioritized 11 (likely) pathogenic variants in 10 genes (ARL3, MERTK, NDP, NMNAT1, NPHP4, PAX6, PRPF31, PRPF4, RDH12, RD3), of which 7 were novel. Functional analyses further supported the pathogenicity of three variants. Mis-splicing was demonstrated for the PRPF31:c.-9+1G>T variant. The MERTK:c.-125G>A variant, overlapping a transcriptional start site, was shown to significantly reduce both luciferase mRNA levels and activity. The RDH12:c.-123C>T variant was found in cis with the hypomorphic RDH12:c.701G>A (p.Arg234His) variant in 11 patients. This 5'UTR variant, predicted to introduce an upstream open reading frame, was shown to result in reduced RDH12 protein but unaltered mRNA levels. CONCLUSIONS This study demonstrates the importance of 5'UTR variants implicated in IRDs and provides a systematic approach for 5'UTR annotation and validation that is applicable to other inherited diseases.
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Affiliation(s)
- Alfredo Dueñas Rey
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Marta Del Pozo Valero
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz, University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Manon Bouckaert
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Katherine A Wood
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
| | - Filip Van den Broeck
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
- Department of Head & Skin, Ghent University, Ghent, Belgium
| | - Malena Daich Varela
- UCL Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital, London, UK
| | - Huw B Thomas
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
| | - Mattias Van Heetvelde
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Marieke De Bruyne
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Stijn Van de Sompele
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Miriam Bauwens
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Hanne Lenaerts
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Quinten Mahieu
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | | | - Carlo Rivolta
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Raymond T O'Keefe
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
| | - Jamie Ellingford
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
- Genomics England, London, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Andrew R Webster
- UCL Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital, London, UK
| | - Gavin Arno
- UCL Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital, London, UK
| | - Carmen Ayuso
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz, University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Julie De Zaeytijd
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
- Department of Head & Skin, Ghent University, Ghent, Belgium
| | - Bart P Leroy
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
- Department of Head & Skin, Ghent University, Ghent, Belgium
- Division of Ophthalmology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elfride De Baere
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Frauke Coppieters
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium.
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium.
- Department of Pharmaceutics, Ghent University, Ghent, Belgium.
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16
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Wragg JW, White PL, Hadzhiev Y, Wanigasooriya K, Stodolna A, Tee L, Barros-Silva JD, Beggs AD, Müller F. Intra-promoter switch of transcription initiation sites in proliferation signaling-dependent RNA metabolism. Nat Struct Mol Biol 2023; 30:1970-1984. [PMID: 37996663 PMCID: PMC10716046 DOI: 10.1038/s41594-023-01156-8] [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: 01/30/2023] [Accepted: 10/19/2023] [Indexed: 11/25/2023]
Abstract
Global changes in transcriptional regulation and RNA metabolism are crucial features of cancer development. However, little is known about the role of the core promoter in defining transcript identity and post-transcriptional fates, a potentially crucial layer of transcriptional regulation in cancer. In this study, we use CAGE-seq analysis to uncover widespread use of dual-initiation promoters in which non-canonical, first-base-cytosine (C) transcription initiation occurs alongside first-base-purine initiation across 59 human cancers and healthy tissues. C-initiation is often followed by a 5' terminal oligopyrimidine (5'TOP) sequence, dramatically increasing the range of genes potentially subjected to 5'TOP-associated post-transcriptional regulation. We show selective, dynamic switching between purine and C-initiation site usage, indicating transcription initiation-level regulation in cancers. We additionally detail global metabolic changes in C-initiation transcripts that mark differentiation status, proliferative capacity, radiosensitivity, and response to irradiation and to PI3K-Akt-mTOR and DNA damage pathway-targeted radiosensitization therapies in colorectal cancer organoids and cancer cell lines and tissues.
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Affiliation(s)
- Joseph W Wragg
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
| | - Paige-Louise White
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Yavor Hadzhiev
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Kasun Wanigasooriya
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Department of Surgery, University Hospitals Birmingham National Health Service (NHS) Foundation Trust, Birmingham, UK
| | - Agata Stodolna
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Louise Tee
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Joao D Barros-Silva
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Andrew D Beggs
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
- Department of Surgery, University Hospitals Birmingham National Health Service (NHS) Foundation Trust, Birmingham, UK.
| | - Ferenc Müller
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
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17
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Reimão-Pinto MM, Castillo-Hair SM, Seelig G, Schier AF. The regulatory landscape of 5' UTRs in translational control during zebrafish embryogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.23.568470. [PMID: 38045294 PMCID: PMC10690280 DOI: 10.1101/2023.11.23.568470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The 5' UTRs of mRNAs are critical for translation regulation, but their in vivo regulatory features are poorly characterized. Here, we report the regulatory landscape of 5' UTRs during early zebrafish embryogenesis using a massively parallel reporter assay of 18,154 sequences coupled to polysome profiling. We found that the 5' UTR is sufficient to confer temporal dynamics to translation initiation, and identified 86 motifs enriched in 5' UTRs with distinct ribosome recruitment capabilities. A quantitative deep learning model, DaniO5P, revealed a combined role for 5' UTR length, translation initiation site context, upstream AUGs and sequence motifs on in vivo ribosome recruitment. DaniO5P predicts the activities of 5' UTR isoforms and indicates that modulating 5' UTR length and motif grammar contributes to translation initiation dynamics. This study provides a first quantitative model of 5' UTR-based translation regulation in early vertebrate development and lays the foundation for identifying the underlying molecular effectors.
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Affiliation(s)
| | - Sebastian M Castillo-Hair
- Department of Electrical & Computer Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Georg Seelig
- Department of Electrical & Computer Engineering, University of Washington, Seattle, Washington 98195, United States
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Alex F Schier
- Biozentrum, University of Basel, 4056 Basel, Switzerland
- Allen Discovery Center for Cell Lineage Tracing, Seattle, Washington 98195, United States
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18
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Lu Y, Wang S, Jiao Y. The Effects of Deregulated Ribosomal Biogenesis in Cancer. Biomolecules 2023; 13:1593. [PMID: 38002277 PMCID: PMC10669593 DOI: 10.3390/biom13111593] [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: 09/13/2023] [Revised: 10/04/2023] [Accepted: 10/22/2023] [Indexed: 11/26/2023] Open
Abstract
Ribosomes are macromolecular ribonucleoprotein complexes assembled from RNA and proteins. Functional ribosomes arise from the nucleolus, require ribosomal RNA processing and the coordinated assembly of ribosomal proteins (RPs), and are frequently hyperactivated to support the requirement for protein synthesis during the self-biosynthetic and metabolic activities of cancer cells. Studies have provided relevant information on targeted anticancer molecules involved in ribosome biogenesis (RiBi), as increased RiBi is characteristic of many types of cancer. The association between unlimited cell proliferation and alterations in specific steps of RiBi has been highlighted as a possible critical driver of tumorigenesis and metastasis. Thus, alterations in numerous regulators and actors involved in RiBi, particularly in cancer, significantly affect the rate and quality of protein synthesis and, ultimately, the transcriptome to generate the associated proteome. Alterations in RiBi in cancer cells activate nucleolar stress response-related pathways that play important roles in cancer-targeted interventions and immunotherapies. In this review, we focus on the association between alterations in RiBi and cancer. Emphasis is placed on RiBi deregulation and its secondary consequences, including changes in protein synthesis, loss of RPs, adaptive transcription and translation, nucleolar stress regulation, metabolic changes, and the impaired ribosome biogenesis checkpoint.
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Affiliation(s)
| | - Shizhuo Wang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang 110055, China;
| | - Yisheng Jiao
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang 110055, China;
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19
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Translational Control of Metabolism and Cell Cycle Progression in Hepatocellular Carcinoma. Int J Mol Sci 2023; 24:ijms24054885. [PMID: 36902316 PMCID: PMC10002961 DOI: 10.3390/ijms24054885] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023] Open
Abstract
The liver is a metabolic hub characterized by high levels of protein synthesis. Eukaryotic initiation factors, eIFs, control the first phase of translation, initiation. Initiation factors are essential for tumor progression and, since they regulate the translation of specific mRNAs downstream of oncogenic signaling cascades, may be druggable. In this review, we address the issue of whether the massive translational machinery of liver cells contributes to liver pathology and to the progression of hepatocellular carcinoma (HCC); it represents a valuable biomarker and druggable target. First, we observe that the common markers of HCC cells, such as phosphorylated ribosomal protein S6, belong to the ribosomal and translational apparatus. This fact is in agreement with observations that demonstrate a huge amplification of the ribosomal machinery during the progression to HCC. Some translation factors, such as eIF4E and eIF6, are then harnessed by oncogenic signaling. In particular, the action of eIF4E and eIF6 is particularly important in HCC when driven by fatty liver pathologies. Indeed, both eIF4E and eIF6 amplify at the translational level the production and accumulation of fatty acids. As it is evident that abnormal levels of these factors drive cancer, we discuss their therapeutic value.
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