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Djajawi TM, Pijpers L, Srivaths A, Chisanga D, Chan KF, Hogg SJ, Neil L, Rivera SM, Bartonicek N, Ellis SL, Lim Kam Sian TCC, Faridi P, Liao Y, Pal B, Behren A, Shi W, Vervoort SJ, Johnstone RW, Kearney CJ. PRMT1 acts as a suppressor of MHC-I and anti-tumor immunity. Cell Rep 2024; 43:113831. [PMID: 38401121 DOI: 10.1016/j.celrep.2024.113831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/31/2023] [Accepted: 02/05/2024] [Indexed: 02/26/2024] Open
Abstract
Cancer immunotherapies have demonstrated remarkable success; however, the majority of patients do not respond or develop resistance. Here, we conduct epigenetic gene-targeted CRISPR-Cas9 screens to identify epigenomic factors that limit CD8+ T cell-mediated anti-tumor immunity. We identify that PRMT1 suppresses interferon gamma (Ifnγ)-induced MHC-I expression, thus dampening CD8+ T cell-mediated killing. Indeed, PRMT1 knockout or pharmacological targeting of type I PRMT with the clinical inhibitor GSK3368715 enhances Ifnγ-induced MHC-I expression through elevated STAT1 expression and activation, while re-introduction of PRMT1 in PRMT1-deficient cells reverses this effect. Importantly, loss of PRMT1 enhances the efficacy of anti-PD-1 immunotherapy, and The Cancer Genome Atlas analysis reveals that PRMT1 expression in human melanoma is inversely correlated with expression of human leukocyte antigen molecules, infiltration of CD8+ T cells, and overall survival. Taken together, we identify PRMT1 as a negative regulator of anti-tumor immunity, unveiling clinical type I PRMT inhibitors as immunotherapeutic agents or as adjuncts to existing immunotherapies.
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Affiliation(s)
- Tirta M Djajawi
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Melbourne, VIC 3086, Australia
| | - Lizzy Pijpers
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Akash Srivaths
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Melbourne, VIC 3086, Australia
| | - David Chisanga
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Melbourne, VIC 3086, Australia
| | - Kok Fei Chan
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Melbourne, VIC 3086, Australia
| | - Simon J Hogg
- Oncology Discovery, AbbVie, South San Francisco, CA 94080, USA
| | - Liam Neil
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Melbourne, VIC 3086, Australia
| | - Sarahi Mendoza Rivera
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Nenad Bartonicek
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Sarah L Ellis
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Melbourne, VIC 3086, Australia
| | - Terry C C Lim Kam Sian
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; Monash Proteomics and Metabolomics Platform, Department of Medicine, School of Clinical Sciences, Monash University, Clayton, VIC 3800, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Science, Monash University, Clayton, VIC 3168, Australia
| | - Pouya Faridi
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Monash Proteomics and Metabolomics Platform, Department of Medicine, School of Clinical Sciences, Monash University, Clayton, VIC 3800, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Science, Monash University, Clayton, VIC 3168, Australia
| | - Yang Liao
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Melbourne, VIC 3086, Australia
| | - Bhupinder Pal
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Melbourne, VIC 3086, Australia
| | - Andreas Behren
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Melbourne, VIC 3086, Australia
| | - Wei Shi
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Melbourne, VIC 3086, Australia
| | - Stephin J Vervoort
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Ricky W Johnstone
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Conor J Kearney
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Melbourne, VIC 3086, Australia.
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Baldwin LA, Bartonicek N, Yang J, Wu SZ, Deng N, Roden D, Chan CL, Al-Eryani G, Zanker DJ, Parker BS, Swarbrick A, Junankar S. Abstract P1-04-04: Dna barcoding reveals ongoing immunoediting of clonal cancer populations during metastatic progression and in response to immunotherapy. Cancer Res 2022. [DOI: 10.1158/1538-7445.sabcs21-p1-04-04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
As cancers develop and spread they must continually evade immune destruction. Understanding mechanisms of immune evasion in cancer is clinically significant as demonstrated with the successes of immune checkpoint inhibitors. Breast cancer is known to be highly immune evasive and responds poorly to the current immunotherapies, indicating alternative immune pathways must be targeted. We hypothesise that there are unidentified genetic mechanisms that enable immune evasion in breast cancer. We aim to uncover and target these mechanisms to sensitise immune evasive breast cancer cells to immune destruction in the context of immunotherapy treatment. DNA barcoding technology offers a new approach to understanding immune evasion. By stably integrating a unique DNA barcode sequence into each cell, we can study clonal immune evasion in vivo. Using this technology, we identified cancer cell clones from the 4T1 murine mammary carcinoma cell line that are highly enriched in lung metastases following treatment with combination immunotherapy (anti-CTLA-4 plus anti-PD-1). We isolated these specific immune evasive clones and established them as clonal cell lines. We have identified stark clonal differences in both PD-L1 and MHC I expression at both the RNA and protein level, and shown that MHC I expression is only partially controlled by epigenetic mechanisms. In addition, immune evasive subclones co-cultured with stimulated T cells resulted in less activated T cells than their less evasive counterparts. Furthermore, RNA sequencing of these clones has identified a gene signature that is strongly associated with decreased survival in both the METABRIC and TCGA cohorts. We have demonstrated ongoing immunoediting in the 4T1 model in vivo, both during metastasis and immunotherapy treatment. We have also identified subclonal populations of cells within a single tumour utilising different mechanisms of immune evasion. RNA sequencing has revealed a gene signature strongly associated with poor survival of basal-like breast cancer in two cohorts. Further pathway-level analysis of the resulting gene signature is required to elucidate the drivers of this aggressive and immune evasive phenotype. By targeting newly identified mechanisms of immune evasion in combination with current immunotherapies, we hope to improve the long-term survival of breast cancer patients.
Citation Format: Louise A Baldwin, Nenad Bartonicek, Jessica Yang, Sunny Z Wu, Niantao Deng, Daniel Roden, Chia-Ling Chan, Ghamdan Al-Eryani, Damien J Zanker, Belinda S Parker, Alexander Swarbrick, Simon Junankar. Dna barcoding reveals ongoing immunoediting of clonal cancer populations during metastatic progression and in response to immunotherapy [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P1-04-04.
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Affiliation(s)
| | | | - Jessica Yang
- Garvan Institute of Medical Research, Sydney, Australia
| | - Sunny Z Wu
- Garvan Institute of Medical Research, Sydney, Australia
| | - Niantao Deng
- Garvan Institute of Medical Research, Sydney, Australia
| | - Daniel Roden
- Garvan Institute of Medical Research, Sydney, Australia
| | | | | | - Damien J Zanker
- Sir Peter MacCallum Department of Oncology, Melbourne, Australia
| | - Belinda S Parker
- Sir Peter MacCallum Department of Oncology, Melbourne, Australia
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Quek C, Silva IP, Al-Eryani G, Mayer A, Bartonicek N, Harvey K, Buckley C, Braubach O, Thompson JF, Stretch JR, Saw RPM, Shannon KF, Menzies AM, Scolyer RA, Long GV, Swarbrick A, Wilmott JS. Abstract 2761: CODEX highly multiplex image mapping to CITEseq datasets reveal the spatial dynamics of the TME during the development of acquired resistant in immunotherapy treated melanoma. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-2761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Primary and acquired resistance to anti-PD-1 and CTLA-4 immunotherapies remains a major obstacle to improving the outcomes of cancer patients. This study utilized a combination of scRNAseq, CITE-seq, a method for CODEX, 40+ protein marker tissue imaging to characterize the molecular and spatial features of cells within melanoma biopsies of patients receiving anti-PD-1 and CTLA-4 immunotherapies. Analysis was conducted on melanoma biopsies taken pre-treatment, early during treatment (7-14 days) and after disease progression. Five patients underwent all analyses; three were responding, two had primary resistance and one had acquired resistance. Tissue dissociates underwent ssRNAseq along with CITE-seq, which incorporated 153+ antibodies to extensively define tumor and immune cell phenotypes. A separate portion of the same lesion underwent formalin fixation and paraffin embedding and was then analyzed using the CODEX high-multiplex imaging system to spatially localize 40+ markers in the tumor. The CODEX imaging system and processor (Akoya Biosciences) were used to generate multiplex images. HALO AI (Indica Labs) was used to perform cell segmentation and quantify single-cell marker expression of the 40+ markers. Tumor areas were classified into vasculature (CD34+/CD31+), melanoma (SOX10+) and stroma regions using the DenseNet deep learning classifier within HALO AI. The subsequent output contained single-cell expression, tissue classification and x and y location data, which were used to map to the CITE-seq data using the CamaraLab STvEA (Govek et al, biorix 2019) to identify CITE-seq defined populations within tissue sections. CODEX analysis of 2.2M cells revealed distinct immune phenotypes of tumor infiltrated cells compared to their peritumor counterparts, with a gradient in the upregulation of immunosuppressive and exhaustive signaling upon entering the tumor region. Changes in cellular populations during treatment were significantly related to the spatial location of the cells within the tumor. Treatment with immunotherapies causes a dynamic change in these profiles which relates to the development of tumor resistance.
Citation Format: Camelia Quek, Ines P. Silva, Ghamdan Al-Eryani, Aaron Mayer, Nenad Bartonicek, Kate Harvey, Chi Buckley, Oliver Braubach, John F. Thompson, Jonathan R. Stretch, Robyn P M Saw, Kerwin F. Shannon, Alexander M. Menzies, Richard A. Scolyer, Georgina V. Long, Alexander Swarbrick, James S. Wilmott. CODEX highly multiplex image mapping to CITEseq datasets reveal the spatial dynamics of the TME during the development of acquired resistant in immunotherapy treated melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2761.
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Affiliation(s)
- Camelia Quek
- 1Melanoma Institute Australia, Sydney, Australia
| | | | | | | | | | - Kate Harvey
- 2Garvan Institute of Medical Research, Sydney, Australia
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4
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Wu SZ, Roden DL, Al-Eryani G, Bartonicek N, Harvey K, Cazet AS, Chan CL, Junankar S, Hui MN, Millar EA, Beretov J, Horvath L, Joshua AM, Stricker P, Wilmott JS, Quek C, Long GV, Scolyer RA, Yeung BZ, Segara D, Mak C, Warrier S, Powell JE, O’Toole S, Lim E, Swarbrick A. Cryopreservation of human cancers conserves tumour heterogeneity for single-cell multi-omics analysis. Genome Med 2021; 13:81. [PMID: 33971952 PMCID: PMC8111910 DOI: 10.1186/s13073-021-00885-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 04/07/2021] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND High throughput single-cell RNA sequencing (scRNA-Seq) has emerged as a powerful tool for exploring cellular heterogeneity among complex human cancers. scRNA-Seq studies using fresh human surgical tissue are logistically difficult, preclude histopathological triage of samples, and limit the ability to perform batch processing. This hindrance can often introduce technical biases when integrating patient datasets and increase experimental costs. Although tissue preservation methods have been previously explored to address such issues, it is yet to be examined on complex human tissues, such as solid cancers and on high throughput scRNA-Seq platforms. METHODS Using the Chromium 10X platform, we sequenced a total of ~ 120,000 cells from fresh and cryopreserved replicates across three primary breast cancers, two primary prostate cancers and a cutaneous melanoma. We performed detailed analyses between cells from each condition to assess the effects of cryopreservation on cellular heterogeneity, cell quality, clustering and the identification of gene ontologies. In addition, we performed single-cell immunophenotyping using CITE-Seq on a single breast cancer sample cryopreserved as solid tissue fragments. RESULTS Tumour heterogeneity identified from fresh tissues was largely conserved in cryopreserved replicates. We show that sequencing of single cells prepared from cryopreserved tissue fragments or from cryopreserved cell suspensions is comparable to sequenced cells prepared from fresh tissue, with cryopreserved cell suspensions displaying higher correlations with fresh tissue in gene expression. We showed that cryopreservation had minimal impacts on the results of downstream analyses such as biological pathway enrichment. For some tumours, cryopreservation modestly increased cell stress signatures compared to freshly analysed tissue. Further, we demonstrate the advantage of cryopreserving whole-cells for detecting cell-surface proteins using CITE-Seq, which is impossible using other preservation methods such as single nuclei-sequencing. CONCLUSIONS We show that the viable cryopreservation of human cancers provides high-quality single-cells for multi-omics analysis. Our study guides new experimental designs for tissue biobanking for future clinical single-cell RNA sequencing studies.
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Affiliation(s)
- Sunny Z. Wu
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW Australia
- St Vincent’s Clinical School, Faculty of Medicine UNSW, Sydney, NSW Australia
| | - Daniel L. Roden
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW Australia
- St Vincent’s Clinical School, Faculty of Medicine UNSW, Sydney, NSW Australia
| | - Ghamdan Al-Eryani
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW Australia
- St Vincent’s Clinical School, Faculty of Medicine UNSW, Sydney, NSW Australia
| | - Nenad Bartonicek
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW Australia
- St Vincent’s Clinical School, Faculty of Medicine UNSW, Sydney, NSW Australia
| | - Kate Harvey
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW Australia
| | - Aurélie S. Cazet
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW Australia
- St Vincent’s Clinical School, Faculty of Medicine UNSW, Sydney, NSW Australia
| | - Chia-Ling Chan
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW Australia
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, Australia
| | - Simon Junankar
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW Australia
- St Vincent’s Clinical School, Faculty of Medicine UNSW, Sydney, NSW Australia
| | - Mun N. Hui
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW Australia
- Chris O’Brien Lifehouse, Camperdown, NSW Australia
| | - Ewan A. Millar
- NSW Health Pathology, Department of Anatomical Pathology, St George Hospital, Kogarah, NSW Australia
- School of Medical Sciences, UNSW Sydney, Kensington, Australia
- Faculty of Medicine & Health Sciences, Sydney Western University, Campbelltown, NSW Australia
| | - Julia Beretov
- NSW Health Pathology, Department of Anatomical Pathology, St George Hospital, Kogarah, NSW Australia
- St George & Sutherland Clinical School, UNSW Sydney, Kensington, Australia
| | - Lisa Horvath
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW Australia
- Chris O’Brien Lifehouse, Camperdown, NSW Australia
- University of Sydney, Camperdown, NSW Australia
| | - Anthony M. Joshua
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW Australia
- St Vincent’s Hospital, Darlinghurst, NSW Australia
| | | | - James S. Wilmott
- Melanoma Institute Australia, The University of Sydney, Sydney, Australia
- The University of Sydney, Sydney, Australia
| | - Camelia Quek
- Melanoma Institute Australia, The University of Sydney, Sydney, Australia
- The University of Sydney, Sydney, Australia
| | - Georgina V. Long
- Melanoma Institute Australia, The University of Sydney, Sydney, Australia
- The University of Sydney, Sydney, Australia
- Royal North Shore Hospital, St Leonards, NSW Australia
| | - Richard A. Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, Australia
- The University of Sydney, Sydney, Australia
- Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Sydney, Australia
| | | | | | - Cindy Mak
- Chris O’Brien Lifehouse, Camperdown, NSW Australia
| | - Sanjay Warrier
- Department of Breast Surgery, Chris O’Brien Lifehouse, Camperdown, NSW 2050 Australia
- Royal Prince Alfred Institute of Academic Surgery, Sydney University, Sydney, Australia
| | - Joseph E. Powell
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, Australia
- UNSW Cellular Genomics Futures Institute, University of New South Wales, Sydney, Australia
| | - Sandra O’Toole
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW Australia
- St Vincent’s Clinical School, Faculty of Medicine UNSW, Sydney, NSW Australia
| | - Elgene Lim
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW Australia
- St Vincent’s Clinical School, Faculty of Medicine UNSW, Sydney, NSW Australia
- St Vincent’s Hospital, Darlinghurst, NSW Australia
| | - Alexander Swarbrick
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW Australia
- St Vincent’s Clinical School, Faculty of Medicine UNSW, Sydney, NSW Australia
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5
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Youlten SE, Kemp JP, Logan JG, Ghirardello EJ, Sergio CM, Dack MRG, Guilfoyle SE, Leitch VD, Butterfield NC, Komla-Ebri D, Chai RC, Corr AP, Smith JT, Mohanty ST, Morris JA, McDonald MM, Quinn JMW, McGlade AR, Bartonicek N, Jansson M, Hatzikotoulas K, Irving MD, Beleza-Meireles A, Rivadeneira F, Duncan E, Richards JB, Adams DJ, Lelliott CJ, Brink R, Phan TG, Eisman JA, Evans DM, Zeggini E, Baldock PA, Bassett JHD, Williams GR, Croucher PI. Osteocyte transcriptome mapping identifies a molecular landscape controlling skeletal homeostasis and susceptibility to skeletal disease. Nat Commun 2021; 12:2444. [PMID: 33953184 PMCID: PMC8100170 DOI: 10.1038/s41467-021-22517-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 03/11/2021] [Indexed: 12/17/2022] Open
Abstract
Osteocytes are master regulators of the skeleton. We mapped the transcriptome of osteocytes from different skeletal sites, across age and sexes in mice to reveal genes and molecular programs that control this complex cellular-network. We define an osteocyte transcriptome signature of 1239 genes that distinguishes osteocytes from other cells. 77% have no previously known role in the skeleton and are enriched for genes regulating neuronal network formation, suggesting this programme is important in osteocyte communication. We evaluated 19 skeletal parameters in 733 knockout mouse lines and reveal 26 osteocyte transcriptome signature genes that control bone structure and function. We showed osteocyte transcriptome signature genes are enriched for human orthologs that cause monogenic skeletal disorders (P = 2.4 × 10-22) and are associated with the polygenic diseases osteoporosis (P = 1.8 × 10-13) and osteoarthritis (P = 1.6 × 10-7). Thus, we reveal the molecular landscape that regulates osteocyte network formation and function and establish the importance of osteocytes in human skeletal disease.
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Affiliation(s)
- Scott E Youlten
- Bone Biology, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - John P Kemp
- University of Queensland Diamantina Institute, UQ, Brisbane, QLD, Australia
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - John G Logan
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Elena J Ghirardello
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Claudio M Sergio
- Bone Biology, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia
| | - Michael R G Dack
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Siobhan E Guilfoyle
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Victoria D Leitch
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- RMIT Centre for Additive Manufacturing, School of Engineering, RMIT University, Melbourne, VIC, UK
| | - Natalie C Butterfield
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Davide Komla-Ebri
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Ryan C Chai
- Bone Biology, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia
| | - Alexander P Corr
- Bone Biology, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
- Faculty of Science, University of Bath, Bath, UK
| | - James T Smith
- Bone Biology, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
- Faculty of Science, University of Bath, Bath, UK
| | - Sindhu T Mohanty
- Bone Biology, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia
| | - John A Morris
- New York Genome Center, New York, NY, USA
- Faculty of Arts and Science, Department of Biology, New York University, New York, NY, USA
| | - Michelle M McDonald
- Bone Biology, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Julian M W Quinn
- Bone Biology, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia
| | - Amelia R McGlade
- Bone Biology, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia
| | - Nenad Bartonicek
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, Sydney, NSW, Australia
| | - Matt Jansson
- Viapath Genetics Laboratory, Viapath Analytics LLP, Guy's Hospital, London, UK
- Department of Clinical Genetics, Guy's Hospital, London, UK
| | - Konstantinos Hatzikotoulas
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Phoenix, AZ, USA
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Melita D Irving
- Department of Clinical Genetics, Guy's and St Thomas' NHS Trust, London, UK
| | | | | | - Emma Duncan
- Faculty of Life Sciences and Medicine, Department of Twin Research & Genetic Epidemiology, School of Life Course Sciences, King's College London, London, UK
- Australian Translational Genomics Centre, Institute of Health and Biomedical Innovation, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, St Lucia, QLD, Australia
| | - J Brent Richards
- Faculty of Life Sciences and Medicine, Department of Twin Research & Genetic Epidemiology, School of Life Course Sciences, King's College London, London, UK
- Faculty of Medicine, McGill University, Quebec, Canada
| | | | | | - Robert Brink
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
- Division of Immunology, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia
| | - Tri Giang Phan
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
- Division of Immunology, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia
| | - John A Eisman
- Bone Biology, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
- School of Medicine Sydney, University of Notre Dame Australia, Fremantle, Australia
| | - David M Evans
- University of Queensland Diamantina Institute, UQ, Brisbane, QLD, Australia
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Phoenix, AZ, USA
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Paul A Baldock
- Bone Biology, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia
| | - J H Duncan Bassett
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
| | - Graham R Williams
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
| | - Peter I Croucher
- Bone Biology, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia.
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia.
- School of Biotechnology and Biomolecular Sciences, UNSW Australia, Sydney, Australia.
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6
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Philp LK, Rockstroh A, Sadowski MC, Taherian Fard A, Lehman M, Tevz G, Libério MS, Bidgood CL, Gunter JH, McPherson S, Bartonicek N, Wade JD, Otvos L, Nelson CC. Leptin antagonism inhibits prostate cancer xenograft growth and progression. Endocr Relat Cancer 2021; 28:353-375. [PMID: 33794502 DOI: 10.1530/erc-20-0405] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 03/31/2021] [Indexed: 11/08/2022]
Abstract
Hyperleptinaemia is a well-established therapeutic side effect of drugs inhibiting the androgen axis in prostate cancer (PCa), including main stay androgen deprivation therapy (ADT) and androgen targeted therapies (ATT). Given significant crossover between the adipokine hormone signalling of leptin and multiple cancer-promoting hallmark pathways, including growth, proliferation, migration, angiogenesis, metabolism and inflammation, targeting the leptin axis is therapeutically appealing, especially in advanced PCa where current therapies fail to be curative. In this study, we uncover leptin as a novel universal target in PCa and are the first to highlight increased intratumoural leptin and leptin receptor (LEPR) expression in PCa cells and patients' tumours exposed to androgen deprivation, as is observed in patients' tumours of metastatic and castrate resistant (CRPC) PCa. We also reveal the world-first preclinical evidence that demonstrates marked efficacy of targeted leptin-signalling blockade, using Allo-aca, a potent, specific, and safe LEPR peptide antagonist. Allo-aca-suppressed tumour growth and delayed progression to CRPC in mice bearing LNCaP xenografts, with reduced tumour vascularity and altered pathways of apoptosis, transcription/translation, and energetics in tumours determined as potential mechanisms underpinning anti-tumour efficacy. We highlight LEPR blockade in combination with androgen axis inhibition represents a promising new therapeutic strategy vital in advanced PCa treatment.
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Affiliation(s)
- Lisa K Philp
- Australian Prostate Cancer Research Centre - Queensland, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Princess Alexandra Hospital, Translational Research Institute, Brisbane, Queensland, Australia
| | - Anja Rockstroh
- Australian Prostate Cancer Research Centre - Queensland, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Princess Alexandra Hospital, Translational Research Institute, Brisbane, Queensland, Australia
| | - Martin C Sadowski
- Australian Prostate Cancer Research Centre - Queensland, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Princess Alexandra Hospital, Translational Research Institute, Brisbane, Queensland, Australia
| | - Atefeh Taherian Fard
- Australian Prostate Cancer Research Centre - Queensland, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Princess Alexandra Hospital, Translational Research Institute, Brisbane, Queensland, Australia
| | - Melanie Lehman
- Australian Prostate Cancer Research Centre - Queensland, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Princess Alexandra Hospital, Translational Research Institute, Brisbane, Queensland, Australia
| | - Gregor Tevz
- Australian Prostate Cancer Research Centre - Queensland, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Princess Alexandra Hospital, Translational Research Institute, Brisbane, Queensland, Australia
| | - Michelle S Libério
- Australian Prostate Cancer Research Centre - Queensland, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Princess Alexandra Hospital, Translational Research Institute, Brisbane, Queensland, Australia
| | - Charles L Bidgood
- Australian Prostate Cancer Research Centre - Queensland, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Princess Alexandra Hospital, Translational Research Institute, Brisbane, Queensland, Australia
| | - Jennifer H Gunter
- Australian Prostate Cancer Research Centre - Queensland, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Princess Alexandra Hospital, Translational Research Institute, Brisbane, Queensland, Australia
| | - Stephen McPherson
- Australian Prostate Cancer Research Centre - Queensland, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Princess Alexandra Hospital, Translational Research Institute, Brisbane, Queensland, Australia
| | - Nenad Bartonicek
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - John D Wade
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria, Australia
- School of Chemistry, University of Melbourne, Melbourne, Victoria, Australia
| | - Laszlo Otvos
- OLPE, LLC, Audubon, Pennsylvania, USA
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
| | - Colleen C Nelson
- Australian Prostate Cancer Research Centre - Queensland, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Princess Alexandra Hospital, Translational Research Institute, Brisbane, Queensland, Australia
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7
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Philp LK, Rockstroh A, Lehman M, Sadowski MC, Bartonicek N, Wade JD, Otvos L, Nelson CC. Adiponectin receptor activation inhibits prostate cancer xenograft growth. Endocr Relat Cancer 2020; 27:711-729. [PMID: 33112829 DOI: 10.1530/erc-20-0297] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 10/01/2020] [Indexed: 11/08/2022]
Abstract
Adiponectin is an adipokine originally identified as dysregulated in obesity, with a key role in insulin sensitisation and in maintaining systemic energy balance. However, adiponectin is progressively emerging as having aberrant signalling in multiple disease states, including prostate cancer (PCa). Circulating adiponectin is lower in patients with PCa than in non-malignant disease, and inversely correlates with cancer severity. More severe hypoadiponectinemia is observed in advanced PCa than in organ-confined disease. Given the crossover between adiponectin signalling and several cancer hallmark pathways that influence PCa growth and progression, we hypothesised that targeting dysregulated adiponectin signalling may inhibit tumour growth and progression. We, therefore, aimed to test the efficacy of correcting the hypoadiponectinemia and dysregulated adiponectin signalling observed in PCa, a world-first PCa therapeutic approach, using peptide adiponectin receptor (ADIPOR) agonist ADP355 in mice bearing subcutaneous LNCaP xenografts. We demonstrate significant evidence for PCa growth inhibition by ADP355, which slowed tumour growth and delayed progression of serum PCa biomarker, prostate-specific antigen (PSA), compared to vehicle. ADP355 conferred a significant advantage by increasing time on treatment with a delayed ethical endpoint. mRNA sequencing and protein expression analyses of tumours revealed ADP355 PCa growth inhibition may be through altered cellular energetics, cellular stress and protein synthesis, which may culminate in apoptosis, as evidenced by the increased apoptotic marker in ADP355-treated tumours. Our findings highlight the efficacy of ADP355 in targeting classical adiponectin-associated signalling pathways in vivo and provide insights into the promising future for modulating adiponectin signalling through ADIPOR agonism as a novel anti-tumour treatment modality.
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Affiliation(s)
- Lisa K Philp
- Australian Prostate Cancer Research Centre - Queensland, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Princess Alexandra Hospital, Translational Research Institute, Brisbane, Queensland, Australia
| | - Anja Rockstroh
- Australian Prostate Cancer Research Centre - Queensland, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Princess Alexandra Hospital, Translational Research Institute, Brisbane, Queensland, Australia
| | - Melanie Lehman
- Australian Prostate Cancer Research Centre - Queensland, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Princess Alexandra Hospital, Translational Research Institute, Brisbane, Queensland, Australia
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, Canada
| | - Martin C Sadowski
- Australian Prostate Cancer Research Centre - Queensland, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Princess Alexandra Hospital, Translational Research Institute, Brisbane, Queensland, Australia
| | - Nenad Bartonicek
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - John D Wade
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria, Australia
- School of Chemistry, University of Melbourne, Melbourne, Victoria, Australia
| | - Laszlo Otvos
- OLPE, LLC, Audubon, Pennsylvania, USA
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
| | - Colleen C Nelson
- Australian Prostate Cancer Research Centre - Queensland, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Princess Alexandra Hospital, Translational Research Institute, Brisbane, Queensland, Australia
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8
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Wu SZ, Roden DL, Wang C, Holliday H, Harvey K, Cazet AS, Murphy KJ, Pereira B, Al-Eryani G, Bartonicek N, Hou R, Torpy JR, Junankar S, Chan CL, Lam CE, Hui MN, Gluch L, Beith J, Parker A, Robbins E, Segara D, Mak C, Cooper C, Warrier S, Forrest A, Powell J, O'Toole S, Cox TR, Timpson P, Lim E, Liu XS, Swarbrick A. Stromal cell diversity associated with immune evasion in human triple-negative breast cancer. EMBO J 2020; 39:e104063. [PMID: 32790115 DOI: 10.15252/embj.2019104063] [Citation(s) in RCA: 191] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 06/22/2020] [Accepted: 06/30/2020] [Indexed: 12/30/2022] Open
Abstract
The tumour stroma regulates nearly all stages of carcinogenesis. Stromal heterogeneity in human triple-negative breast cancers (TNBCs) remains poorly understood, limiting the development of stromal-targeted therapies. Single-cell RNA sequencing of five TNBCs revealed two cancer-associated fibroblast (CAF) and two perivascular-like (PVL) subpopulations. CAFs clustered into two states: the first with features of myofibroblasts and the second characterised by high expression of growth factors and immunomodulatory molecules. PVL cells clustered into two states consistent with a differentiated and immature phenotype. We showed that these stromal states have distinct morphologies, spatial relationships and functional properties in regulating the extracellular matrix. Using cell signalling predictions, we provide evidence that stromal-immune crosstalk acts via a diverse array of immunoregulatory molecules. Importantly, the investigation of gene signatures from inflammatory-CAFs and differentiated-PVL cells in independent TNBC patient cohorts revealed strong associations with cytotoxic T-cell dysfunction and exclusion, respectively. Such insights present promising candidates to further investigate for new therapeutic strategies in the treatment of TNBCs.
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Affiliation(s)
- Sunny Z Wu
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Daniel L Roden
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Chenfei Wang
- Department of Data Sciences, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Holly Holliday
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Kate Harvey
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Aurélie S Cazet
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Kendelle J Murphy
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Brooke Pereira
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Ghamdan Al-Eryani
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Nenad Bartonicek
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Rui Hou
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, WA, Australia
| | - James R Torpy
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Simon Junankar
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Chia-Ling Chan
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Chuan En Lam
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Mun N Hui
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,Chris O'Brien Lifehouse, Camperdown, NSW, Australia
| | - Laurence Gluch
- The Strathfield Breast Centre, Strathfield, NSW, Australia
| | - Jane Beith
- Chris O'Brien Lifehouse, Camperdown, NSW, Australia
| | | | | | | | - Cindy Mak
- Chris O'Brien Lifehouse, Camperdown, NSW, Australia
| | - Caroline Cooper
- Pathology Queensland, Princess Alexandra Hospital, Brisbane, Qld, Australia.,Southside Clinical Unit, Faculty of Medicine, University of Queensland, Brisbane, Qld, Australia
| | - Sanjay Warrier
- Department of Breast Surgery, Chris O'Brien Lifehouse, Camperdown, NSW, Australia.,Royal Prince Alfred Institute of Academic Surgery, Sydney University, Sydney, NSW, Australia
| | - Alistair Forrest
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, WA, Australia.,RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Joseph Powell
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia.,UNSW Cellular Genomics Futures Institute, University of New South Wales, Sydney, NSW, Australia
| | - Sandra O'Toole
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia.,Australian Clinical Laboratories, Northern Beaches Hospital, Frenchs Forest, NSW, Australia
| | - Thomas R Cox
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Paul Timpson
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Elgene Lim
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia.,St Vincent's Hospital, Darlinghurst, NSW, Australia
| | - X Shirley Liu
- Department of Data Sciences, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Alexander Swarbrick
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
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9
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Moradi Marjaneh M, Beesley J, O'Mara TA, Mukhopadhyay P, Koufariotis LT, Kazakoff S, Hussein N, Fachal L, Bartonicek N, Hillman KM, Kaufmann S, Sivakumaran H, Smart CE, McCart Reed AE, Ferguson K, Saunus JM, Lakhani SR, Barnes DR, Antoniou AC, Dinger ME, Waddell N, Easton DF, Dunning AM, Chenevix-Trench G, Edwards SL, French JD. Non-coding RNAs underlie genetic predisposition to breast cancer. Genome Biol 2020; 21:7. [PMID: 31910864 PMCID: PMC6947989 DOI: 10.1186/s13059-019-1876-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 11/01/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Genetic variants identified through genome-wide association studies (GWAS) are predominantly non-coding and typically attributed to altered regulatory elements such as enhancers and promoters. However, the contribution of non-coding RNAs to complex traits is not clear. RESULTS Using targeted RNA sequencing, we systematically annotated multi-exonic non-coding RNA (mencRNA) genes transcribed from 1.5-Mb intervals surrounding 139 breast cancer GWAS signals and assessed their contribution to breast cancer risk. We identify more than 4000 mencRNA genes and show their expression distinguishes normal breast tissue from tumors and different breast cancer subtypes. Importantly, breast cancer risk variants, identified through genetic fine-mapping, are significantly enriched in mencRNA exons, but not the promoters or introns. eQTL analyses identify mencRNAs whose expression is associated with risk variants. Furthermore, chromatin interaction data identify hundreds of mencRNA promoters that loop to regions that contain breast cancer risk variants. CONCLUSIONS We have compiled the largest catalog of breast cancer-associated mencRNAs to date and provide evidence that modulation of mencRNAs by GWAS variants may provide an alternative mechanism underlying complex traits.
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Affiliation(s)
- Mahdi Moradi Marjaneh
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Current address: UK Dementia Research Institute, Imperial College London, London, UK
| | - Jonathan Beesley
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Tracy A O'Mara
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Pamela Mukhopadhyay
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | | | - Stephen Kazakoff
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Nehal Hussein
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Laura Fachal
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | | | - Kristine M Hillman
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Susanne Kaufmann
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Haran Sivakumaran
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Chanel E Smart
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Amy E McCart Reed
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Kaltin Ferguson
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Jodi M Saunus
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Sunil R Lakhani
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia
- Pathology Queensland, The Royal Brisbane & Women's Hospital, Herston, Brisbane, Australia
| | - Daniel R Barnes
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Marcel E Dinger
- Garvan Institute of Medical Research, Sydney, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, Australia
| | - Nicola Waddell
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | | | - Stacey L Edwards
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, Australia.
| | - Juliet D French
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, Australia.
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10
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Piggin CL, Roden DL, Law AMK, Molloy MP, Krisp C, Swarbrick A, Naylor MJ, Kalyuga M, Kaplan W, Oakes SR, Gallego-Ortega D, Clark SJ, Carroll JS, Bartonicek N, Ormandy CJ. ELF5 modulates the estrogen receptor cistrome in breast cancer. PLoS Genet 2020; 16:e1008531. [PMID: 31895944 PMCID: PMC6959601 DOI: 10.1371/journal.pgen.1008531] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 01/14/2020] [Accepted: 11/20/2019] [Indexed: 11/28/2022] Open
Abstract
Acquired resistance to endocrine therapy is responsible for half of the therapeutic failures in the treatment of breast cancer. Recent findings have implicated increased expression of the ETS transcription factor ELF5 as a potential modulator of estrogen action and driver of endocrine resistance, and here we provide the first insight into the mechanisms by which ELF5 modulates estrogen sensitivity. Using chromatin immunoprecipitation sequencing we found that ELF5 binding overlapped with FOXA1 and ER at super enhancers, enhancers and promoters, and when elevated, caused FOXA1 and ER to bind to new regions of the genome, in a pattern that replicated the alterations to the ER/FOXA1 cistrome caused by the acquisition of resistance to endocrine therapy. RNA sequencing demonstrated that these changes altered estrogen-driven patterns of gene expression, the expression of ER transcription-complex members, and 6 genes known to be involved in driving the acquisition of endocrine resistance. Using rapid immunoprecipitation mass spectrometry of endogenous proteins, and proximity ligation assays, we found that ELF5 interacted physically with members of the ER transcription complex, such as DNA-PKcs. We found 2 cases of endocrine-resistant brain metastases where ELF5 levels were greatly increased and ELF5 patterns of gene expression were enriched, compared to the matched primary tumour. Thus ELF5 alters ER-driven gene expression by modulating the ER/FOXA1 cistrome, by interacting with it, and by modulating the expression of members of the ER transcriptional complex, providing multiple mechanisms by which ELF5 can drive endocrine resistance.
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Affiliation(s)
- Catherine L. Piggin
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Victoria Street Darlinghurst Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Australia
| | - Daniel L. Roden
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Victoria Street Darlinghurst Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Australia
| | - Andrew M. K. Law
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Victoria Street Darlinghurst Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Australia
| | - Mark P. Molloy
- Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
| | - Christoph Krisp
- Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
| | - Alexander Swarbrick
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Victoria Street Darlinghurst Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Australia
| | - Matthew J. Naylor
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Victoria Street Darlinghurst Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Maria Kalyuga
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Victoria Street Darlinghurst Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Australia
| | - Warren Kaplan
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Victoria Street Darlinghurst Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Australia
| | - Samantha R. Oakes
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Victoria Street Darlinghurst Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Australia
| | - David Gallego-Ortega
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Victoria Street Darlinghurst Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Australia
| | - Susan J. Clark
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Victoria Street Darlinghurst Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Australia
| | - Jason S. Carroll
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre Robinson Way, Cambridge, United Kingdom
| | - Nenad Bartonicek
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Victoria Street Darlinghurst Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Australia
| | - Christopher J. Ormandy
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Victoria Street Darlinghurst Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Australia
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11
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Liu PY, Tee AE, Milazzo G, Hannan KM, Maag J, Mondal S, Atmadibrata B, Bartonicek N, Peng H, Ho N, Mayoh C, Ciaccio R, Sun Y, Henderson MJ, Gao J, Everaert C, Hulme AJ, Wong M, Lan Q, Cheung BB, Shi L, Wang JY, Simon T, Fischer M, Zhang XD, Marshall GM, Norris MD, Haber M, Vandesompele J, Li J, Mestdagh P, Hannan RD, Dinger ME, Perini G, Liu T. The long noncoding RNA lncNB1 promotes tumorigenesis by interacting with ribosomal protein RPL35. Nat Commun 2019; 10:5026. [PMID: 31690716 PMCID: PMC6831662 DOI: 10.1038/s41467-019-12971-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 10/09/2019] [Indexed: 12/22/2022] Open
Abstract
The majority of patients with neuroblastoma due to MYCN oncogene amplification and consequent N-Myc oncoprotein over-expression die of the disease. Here our analyses of RNA sequencing data identify the long noncoding RNA lncNB1 as one of the transcripts most over-expressed in MYCN-amplified, compared with MYCN-non-amplified, human neuroblastoma cells and also the most over-expressed in neuroblastoma compared with all other cancers. lncNB1 binds to the ribosomal protein RPL35 to enhance E2F1 protein synthesis, leading to DEPDC1B gene transcription. The GTPase-activating protein DEPDC1B induces ERK protein phosphorylation and N-Myc protein stabilization. Importantly, lncNB1 knockdown abolishes neuroblastoma cell clonogenic capacity in vitro and leads to neuroblastoma tumor regression in mice, while high levels of lncNB1 and RPL35 in human neuroblastoma tissues predict poor patient prognosis. This study therefore identifies lncNB1 and its binding protein RPL35 as key factors for promoting E2F1 protein synthesis, N-Myc protein stability and N-Myc-driven oncogenesis, and as therapeutic targets. MYCN amplification is common in neuroblastomas. Here, the authors identify a long noncoding RNA, lncNB1 in these cancers and show that it promotes tumorigenesis by binding to ribosomal protein, RPL35 to enhance E2F1 and DEPDC1B protein synthesis, which phosphorylates ERK to stabilise N-Myc.
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Affiliation(s)
- Pei Y Liu
- Children's Cancer Institute Australia for Medical Research, Randwick, NSW, 2031, Australia
| | - Andrew E Tee
- Children's Cancer Institute Australia for Medical Research, Randwick, NSW, 2031, Australia
| | - Giorgio Milazzo
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Katherine M Hannan
- Australian Cancer Research Foundation Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia.,Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Jesper Maag
- Garvan Institute of Medical Research, Sydney, Darlinghurst, NSW, 2010, Australia.,Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Sujanna Mondal
- Children's Cancer Institute Australia for Medical Research, Randwick, NSW, 2031, Australia
| | - Bernard Atmadibrata
- Children's Cancer Institute Australia for Medical Research, Randwick, NSW, 2031, Australia
| | - Nenad Bartonicek
- Garvan Institute of Medical Research, Sydney, Darlinghurst, NSW, 2010, Australia.,Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Hui Peng
- Advanced Analytics Institute, University of Technology Sydney, Broadway, NSW, 2007, Australia
| | - Nicholas Ho
- Children's Cancer Institute Australia for Medical Research, Randwick, NSW, 2031, Australia
| | - Chelsea Mayoh
- Children's Cancer Institute Australia for Medical Research, Randwick, NSW, 2031, Australia
| | - Roberto Ciaccio
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Yuting Sun
- Children's Cancer Institute Australia for Medical Research, Randwick, NSW, 2031, Australia
| | - Michelle J Henderson
- Children's Cancer Institute Australia for Medical Research, Randwick, NSW, 2031, Australia
| | - Jixuan Gao
- Children's Cancer Institute Australia for Medical Research, Randwick, NSW, 2031, Australia
| | - Celine Everaert
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - Amy J Hulme
- Children's Cancer Institute Australia for Medical Research, Randwick, NSW, 2031, Australia
| | - Matthew Wong
- Children's Cancer Institute Australia for Medical Research, Randwick, NSW, 2031, Australia
| | - Qing Lan
- Department of Neurosurgery, the Second Affiliated Hospital of Soochow University, 215004, Suzhou, Jiangsu, P.R. China
| | - Belamy B Cheung
- Children's Cancer Institute Australia for Medical Research, Randwick, NSW, 2031, Australia
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, 201203, Shanghai, China
| | - Jenny Y Wang
- Children's Cancer Institute Australia for Medical Research, Randwick, NSW, 2031, Australia
| | - Thorsten Simon
- Department of Pediatric Oncology and Hematology, University Hospital, University of Cologne, Cologne, Germany
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University Hospital, University of Cologne, Cologne, Germany
| | - Xu D Zhang
- School of Medicine and Public Health, Priority Research Centre for Cancer Research, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Glenn M Marshall
- Children's Cancer Institute Australia for Medical Research, Randwick, NSW, 2031, Australia.,Kids Cancer Centre, Sydney Children's Hospital, High Street, Randwick, NSW, 2031, Australia
| | - Murray D Norris
- Children's Cancer Institute Australia for Medical Research, Randwick, NSW, 2031, Australia
| | - Michelle Haber
- Children's Cancer Institute Australia for Medical Research, Randwick, NSW, 2031, Australia
| | - Jo Vandesompele
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - Jinyan Li
- Advanced Analytics Institute, University of Technology Sydney, Broadway, NSW, 2007, Australia
| | - Pieter Mestdagh
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - Ross D Hannan
- Australian Cancer Research Foundation Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia.,Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, 3010, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia.,School of Biomedical Sciences, University of Queensland, St Lucia, QLD, 4067, Australia
| | - Marcel E Dinger
- Garvan Institute of Medical Research, Sydney, Darlinghurst, NSW, 2010, Australia.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Giovanni Perini
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy.
| | - Tao Liu
- Children's Cancer Institute Australia for Medical Research, Randwick, NSW, 2031, Australia.
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12
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Salomon R, Kaczorowski D, Valdes-Mora F, Nordon RE, Neild A, Farbehi N, Bartonicek N, Gallego-Ortega D. Droplet-based single cell RNAseq tools: a practical guide. Lab Chip 2019; 19:1706-1727. [PMID: 30997473 DOI: 10.1039/c8lc01239c] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Droplet based scRNA-seq systems such as Drop-seq, inDrop and Chromium 10X have been the catalyst for the wide adoption of high-throughput scRNA-seq technologies in the research laboratory. In order to understand the capabilities of these systems to deeply interrogate biology; here we provide a practical guide through all the steps involved in a typical scRNA-seq experiment. Through comparing and contrasting these three main droplet based systems (and their derivatives), we provide an overview of all critical considerations in obtaining high quality and biologically relevant data. We also discuss the limitations of these systems and how they fit into the emerging field of Genomic Cytometry.
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Affiliation(s)
- Robert Salomon
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia.
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13
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Hardwick SA, Bassett SD, Kaczorowski D, Blackburn J, Barton K, Bartonicek N, Carswell SL, Tilgner HU, Loy C, Halliday G, Mercer TR, Smith MA, Mattick JS. Targeted, High-Resolution RNA Sequencing of Non-coding Genomic Regions Associated With Neuropsychiatric Functions. Front Genet 2019; 10:309. [PMID: 31031799 PMCID: PMC6473190 DOI: 10.3389/fgene.2019.00309] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 03/21/2019] [Indexed: 12/18/2022] Open
Abstract
The human brain is one of the last frontiers of biomedical research. Genome-wide association studies (GWAS) have succeeded in identifying thousands of haplotype blocks associated with a range of neuropsychiatric traits, including disorders such as schizophrenia, Alzheimer's and Parkinson's disease. However, the majority of single nucleotide polymorphisms (SNPs) that mark these haplotype blocks fall within non-coding regions of the genome, hindering their functional validation. While some of these GWAS loci may contain cis-acting regulatory DNA elements such as enhancers, we hypothesized that many are also transcribed into non-coding RNAs that are missing from publicly available transcriptome annotations. Here, we use targeted RNA capture ('RNA CaptureSeq') in combination with nanopore long-read cDNA sequencing to transcriptionally profile 1,023 haplotype blocks across the genome containing non-coding GWAS SNPs associated with neuropsychiatric traits, using post-mortem human brain tissue from three neurologically healthy donors. We find that the majority (62%) of targeted haplotype blocks, including 13% of intergenic blocks, are transcribed into novel, multi-exonic RNAs, most of which are not yet recorded in GENCODE annotations. We validated our findings with short-read RNA-seq, providing orthogonal confirmation of novel splice junctions and enabling a quantitative assessment of the long-read assemblies. Many novel transcripts are supported by independent evidence of transcription including cap analysis of gene expression (CAGE) data and epigenetic marks, and some show signs of potential functional roles. We present these transcriptomes as a preliminary atlas of non-coding transcription in human brain that can be used to connect neurological phenotypes with gene expression.
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Affiliation(s)
- Simon A. Hardwick
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Faculty of Medicine, University of New South Wales Sydney, Kensington, NSW, Australia
- Brain and Mind Research Institute and Center for Neurogenetics, Weill Cornell Medicine, New York, NY, United States
| | - Samuel D. Bassett
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Faculty of Medicine, University of New South Wales Sydney, Kensington, NSW, Australia
| | - Dominik Kaczorowski
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - James Blackburn
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Faculty of Medicine, University of New South Wales Sydney, Kensington, NSW, Australia
| | - Kirston Barton
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Nenad Bartonicek
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Faculty of Medicine, University of New South Wales Sydney, Kensington, NSW, Australia
| | - Shaun L. Carswell
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Hagen U. Tilgner
- Brain and Mind Research Institute and Center for Neurogenetics, Weill Cornell Medicine, New York, NY, United States
| | - Clement Loy
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Brain and Mind Centre, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia
| | - Glenda Halliday
- Brain and Mind Centre, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia
| | - Tim R. Mercer
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Faculty of Medicine, University of New South Wales Sydney, Kensington, NSW, Australia
- Altius Institute for Biomedical Sciences, Seattle, WA, United States
| | - Martin A. Smith
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Faculty of Medicine, University of New South Wales Sydney, Kensington, NSW, Australia
| | - John S. Mattick
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Faculty of Medicine, University of New South Wales Sydney, Kensington, NSW, Australia
- Green Templeton College, Oxford, United Kingdom
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14
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Tousignant KD, Rockstroh A, Taherian Fard A, Lehman ML, Wang C, McPherson SJ, Philp LK, Bartonicek N, Dinger ME, Nelson CC, Sadowski MC. Lipid Uptake Is an Androgen-Enhanced Lipid Supply Pathway Associated with Prostate Cancer Disease Progression and Bone Metastasis. Mol Cancer Res 2019; 17:1166-1179. [PMID: 30808729 DOI: 10.1158/1541-7786.mcr-18-1147] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/03/2019] [Accepted: 02/21/2019] [Indexed: 11/16/2022]
Abstract
De novo lipogenesis is a well-described androgen receptor (AR)-regulated metabolic pathway that supports prostate cancer tumor growth by providing fuel, membrane material, and steroid hormone precursor. In contrast, our current understanding of lipid supply from uptake of exogenous lipids and its regulation by AR is limited, and exogenous lipids may play a much more significant role in prostate cancer and disease progression than previously thought. By applying advanced automated quantitative fluorescence microscopy, we provide the most comprehensive functional analysis of lipid uptake in cancer cells to date and demonstrate that treatment of AR-positive prostate cancer cell lines with androgens results in significantly increased cellular uptake of fatty acids, cholesterol, and low-density lipoprotein particles. Consistent with a direct, regulatory role of AR in this process, androgen-enhanced lipid uptake can be blocked by the AR-antagonist enzalutamide, but is independent of proliferation and cell-cycle progression. This work for the first time comprehensively delineates the lipid transporter landscape in prostate cancer cell lines and patient samples by analysis of transcriptomics and proteomics data, including the plasma membrane proteome. We show that androgen exposure or deprivation regulates the expression of multiple lipid transporters in prostate cancer cell lines and tumor xenografts and that mRNA and protein expression of lipid transporters is enhanced in bone metastatic disease when compared with primary, localized prostate cancer. Our findings provide a strong rationale to investigate lipid uptake as a therapeutic cotarget in the fight against advanced prostate cancer in combination with inhibitors of lipogenesis to delay disease progression and metastasis. IMPLICATIONS: Prostate cancer exhibits metabolic plasticity in acquiring lipids from uptake and lipogenesis at different disease stages, indicating potential therapeutic benefit by cotargeting lipid supply.
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Affiliation(s)
- Kaylyn D Tousignant
- Australian Prostate Cancer Research Centre, Queensland, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Princess Alexandra Hospital, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Anja Rockstroh
- Australian Prostate Cancer Research Centre, Queensland, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Princess Alexandra Hospital, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Atefeh Taherian Fard
- Australian Prostate Cancer Research Centre, Queensland, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Princess Alexandra Hospital, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Melanie L Lehman
- Australian Prostate Cancer Research Centre, Queensland, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Princess Alexandra Hospital, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Chenwei Wang
- Australian Prostate Cancer Research Centre, Queensland, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Princess Alexandra Hospital, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Stephen J McPherson
- Australian Prostate Cancer Research Centre, Queensland, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Princess Alexandra Hospital, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Lisa K Philp
- Australian Prostate Cancer Research Centre, Queensland, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Princess Alexandra Hospital, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Nenad Bartonicek
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, Australia
- St Vincent's Clinical School, UNSW Sydney, Sydney, Australia
| | - Marcel E Dinger
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, Australia
- St Vincent's Clinical School, UNSW Sydney, Sydney, Australia
| | - Colleen C Nelson
- Australian Prostate Cancer Research Centre, Queensland, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Princess Alexandra Hospital, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Martin C Sadowski
- Australian Prostate Cancer Research Centre, Queensland, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Princess Alexandra Hospital, Translational Research Institute, Woolloongabba, Queensland, Australia.
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15
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Tee AE, Liu PY, Milazzo G, Hannan KM, Maag J, Bartonicek N, Song R, Jiang CC, Zhang XD, Norris MD, Haber M, Marshall GM, Li J, Vandesompele J, Mattick JS, Mestdagh P, Perini G, Hannan RD, Dinger ME, Liu T. Abstract 2453: Eradication of neuroblastoma by suppressing the expression of a single noncoding RNA. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-2453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
N-Myc gene amplification occurs in one quarter of human neuroblastoma tissues, and is a marker for poor patient prognosis. We performed RNA sequencing experiments, and identified 5 transcripts, including RP1NB1, which were most considerably differentially expressed between N-Myc gene amplified and nonamplified human neuroblastoma cell lines. Affymetrix microarray studies revealed that DEPD was one of the few genes considerably downregulated in neuroblastoma cells after RP1NB1 depletion. Chromatin immunoprecipitation assays showed that knocking down RP1NB1 expression reduced histone H3 lysine 4 trimethylation, a marker for active gene transcription, at the DEPD gene promoter. Luciferase assays demonstrated that knocking down RP1NB1 decreased DEPD gene promoter activity. Depletion of RP1NB1 or DEPD with two independent siRNAs or shRNAs significantly reduced ERK protein phosphorylation, N-Myc protein phosphorylation at Serine 62, N-Myc protein stabilization, neuroblastoma cell proliferation and survival. Clonogenic assays showed that knocking down RP1NB1 with doxycycline completely abolished colony formation capacity of neuroblastoma cells stably transfected with doxycycline-inducible RP1NB1 shRNAs. Importantly, treatment with doxycycline in mice xenografted with neuroblastoma cells stably transfected with doxycycline-inducible RP1NB1 shRNA led to tumor eradication. In human neuroblastoma tissues from 600 neuroblastoma patients, high levels of RP1NB1 gene expression correlated with DEPD gene expression and poor patient prognosis. In conclusion, this study identifies the novel long noncoding RNA RP1NB1 as an important regulator of N-Myc protein stability and neuroblastoma tumorigenesis.
Citation Format: Andrew E. Tee, Pei Y. Liu, Giorgio Milazzo, Kate M. Hannan, Jesper Maag, Nenad Bartonicek, Renhua Song, Chen C. Jiang, Xu D. Zhang, Murray D. Norris, Michelle Haber, Glenn M. Marshall, Jinyan Li, Jo Vandesompele, John S. Mattick, Pieter Mestdagh, Giovanni Perini, Ross D. Hannan, Marcel E. Dinger, Tao Liu. Eradication of neuroblastoma by suppressing the expression of a single noncoding RNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2453.
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Affiliation(s)
- Andrew E. Tee
- 1Children's Cancer Institute Australia, Sydney, Australia
| | - Pei Y. Liu
- 1Children's Cancer Institute Australia, Sydney, Australia
| | | | - Kate M. Hannan
- 3Australian Cancer Research Foundation Department of Cancer Biology and Therapeutics, The Australian National University, Canberra, Australia
| | - Jesper Maag
- 4Garvan Institute of Medical Research, Sydney, Australia
| | | | - Renhua Song
- 5Advanced Analytics Institute, Sydney, Australia
| | - Chen C. Jiang
- 6School of Medicine and Public Health, University of Newcastle, Australia
| | - Xu D. Zhang
- 6School of Medicine and Public Health, University of Newcastle, Australia
| | | | - Michelle Haber
- 1Children's Cancer Institute Australia, Sydney, Australia
| | | | - Jinyan Li
- 5Advanced Analytics Institute, Sydney, Australia
| | | | | | | | | | - Ross D. Hannan
- 3Australian Cancer Research Foundation Department of Cancer Biology and Therapeutics, The Australian National University, Canberra, Australia
| | | | - Tao Liu
- 1Children's Cancer Institute Australia, Sydney, Australia
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16
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Lancaster GI, Langley KG, Berglund NA, Kammoun HL, Reibe S, Estevez E, Weir J, Mellett NA, Pernes G, Conway JRW, Lee MKS, Timpson P, Murphy AJ, Masters SL, Gerondakis S, Bartonicek N, Kaczorowski DC, Dinger ME, Meikle PJ, Bond PJ, Febbraio MA. Evidence that TLR4 Is Not a Receptor for Saturated Fatty Acids but Mediates Lipid-Induced Inflammation by Reprogramming Macrophage Metabolism. Cell Metab 2018; 27:1096-1110.e5. [PMID: 29681442 DOI: 10.1016/j.cmet.2018.03.014] [Citation(s) in RCA: 280] [Impact Index Per Article: 46.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 12/22/2017] [Accepted: 03/25/2018] [Indexed: 02/06/2023]
Abstract
Chronic inflammation is a hallmark of obesity and is linked to the development of numerous diseases. The activation of toll-like receptor 4 (TLR4) by long-chain saturated fatty acids (lcSFAs) is an important process in understanding how obesity initiates inflammation. While experimental evidence supports an important role for TLR4 in obesity-induced inflammation in vivo, via a mechanism thought to involve direct binding to and activation of TLR4 by lcSFAs, several lines of evidence argue against lcSFAs being direct TLR4 agonists. Using multiple orthogonal approaches, we herein provide evidence that while loss-of-function models confirm that TLR4 does, indeed, regulate lcSFA-induced inflammation, TLR4 is not a receptor for lcSFAs. Rather, we show that TLR4-dependent priming alters cellular metabolism, gene expression, lipid metabolic pathways, and membrane lipid composition, changes that are necessary for lcSFA-induced inflammation. These results reconcile previous discordant observations and challenge the prevailing view of TLR4's role in initiating obesity-induced inflammation.
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Affiliation(s)
- Graeme I Lancaster
- Baker Heart and Diabetes Institute, 75 Commercial Road, Melbourne, VIC 3004, Australia; Department of Immunology, Monash University, Melbourne, VIC 3004, Australia.
| | - Katherine G Langley
- Baker Heart and Diabetes Institute, 75 Commercial Road, Melbourne, VIC 3004, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Nils Anton Berglund
- Bioinformatics Institute (A(∗)STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Helene L Kammoun
- Baker Heart and Diabetes Institute, 75 Commercial Road, Melbourne, VIC 3004, Australia
| | - Saskia Reibe
- Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia
| | - Emma Estevez
- Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia
| | - Jacquelyn Weir
- Baker Heart and Diabetes Institute, 75 Commercial Road, Melbourne, VIC 3004, Australia
| | - Natalie A Mellett
- Baker Heart and Diabetes Institute, 75 Commercial Road, Melbourne, VIC 3004, Australia
| | - Gerard Pernes
- Baker Heart and Diabetes Institute, 75 Commercial Road, Melbourne, VIC 3004, Australia
| | - James R W Conway
- Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia; Faculty of Medicine, St Vincent's Clinical School, Faculty of Medicine, University of NSW, Sydney, NSW 2010, Australia
| | - Man K S Lee
- Baker Heart and Diabetes Institute, 75 Commercial Road, Melbourne, VIC 3004, Australia
| | - Paul Timpson
- Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia; Faculty of Medicine, St Vincent's Clinical School, Faculty of Medicine, University of NSW, Sydney, NSW 2010, Australia
| | - Andrew J Murphy
- Baker Heart and Diabetes Institute, 75 Commercial Road, Melbourne, VIC 3004, Australia; Department of Immunology, Monash University, Melbourne, VIC 3004, Australia
| | - Seth L Masters
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Steve Gerondakis
- Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Nenad Bartonicek
- Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia
| | | | - Marcel E Dinger
- Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia; Faculty of Medicine, St Vincent's Clinical School, Faculty of Medicine, University of NSW, Sydney, NSW 2010, Australia
| | - Peter J Meikle
- Baker Heart and Diabetes Institute, 75 Commercial Road, Melbourne, VIC 3004, Australia
| | - Peter J Bond
- Bioinformatics Institute (A(∗)STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Mark A Febbraio
- Baker Heart and Diabetes Institute, 75 Commercial Road, Melbourne, VIC 3004, Australia; Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia; Faculty of Medicine, St Vincent's Clinical School, Faculty of Medicine, University of NSW, Sydney, NSW 2010, Australia.
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17
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Bartonicek N, Clark MB, Quek XC, Torpy JR, Pritchard AL, Maag JLV, Gloss BS, Crawford J, Taft RJ, Hayward NK, Montgomery GW, Mattick JS, Mercer TR, Dinger ME. Intergenic disease-associated regions are abundant in novel transcripts. Genome Biol 2017; 18:241. [PMID: 29284497 PMCID: PMC5747244 DOI: 10.1186/s13059-017-1363-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 11/21/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Genotyping of large populations through genome-wide association studies (GWAS) has successfully identified many genomic variants associated with traits or disease risk. Unexpectedly, a large proportion of GWAS single nucleotide polymorphisms (SNPs) and associated haplotype blocks are in intronic and intergenic regions, hindering their functional evaluation. While some of these risk-susceptibility regions encompass cis-regulatory sites, their transcriptional potential has never been systematically explored. RESULTS To detect rare tissue-specific expression, we employed the transcript-enrichment method CaptureSeq on 21 human tissues to identify 1775 multi-exonic transcripts from 561 intronic and intergenic haploblocks associated with 392 traits and diseases, covering 73.9 Mb (2.2%) of the human genome. We show that a large proportion (85%) of disease-associated haploblocks express novel multi-exonic non-coding transcripts that are tissue-specific and enriched for GWAS SNPs as well as epigenetic markers of active transcription and enhancer activity. Similarly, we captured transcriptomes from 13 melanomas, targeting nine melanoma-associated haploblocks, and characterized 31 novel melanoma-specific transcripts that include fusion proteins, novel exons and non-coding RNAs, one-third of which showed allelically imbalanced expression. CONCLUSIONS This resource of previously unreported transcripts in disease-associated regions ( http://gwas-captureseq.dingerlab.org ) should provide an important starting point for the translational community in search of novel biomarkers, disease mechanisms, and drug targets.
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Affiliation(s)
- N Bartonicek
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- Faculty of Medicine, St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - M B Clark
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, UK
| | - X C Quek
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- Faculty of Medicine, St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - J R Torpy
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- Faculty of Medicine, St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - A L Pritchard
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - J L V Maag
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- Faculty of Medicine, St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - B S Gloss
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- Faculty of Medicine, St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - J Crawford
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - R J Taft
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- Illumina, Inc., San Diego, CA, USA
| | - N K Hayward
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - G W Montgomery
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - J S Mattick
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- Faculty of Medicine, St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - T R Mercer
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- Faculty of Medicine, St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
- Altius Institute for Biomedical Sciences, Seattle, USA
| | - M E Dinger
- Garvan Institute of Medical Research, Sydney, NSW, Australia.
- Faculty of Medicine, St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia.
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18
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Betts JA, Moradi Marjaneh M, Al-Ejeh F, Lim YC, Shi W, Sivakumaran H, Tropée R, Patch AM, Clark MB, Bartonicek N, Wiegmans AP, Hillman KM, Kaufmann S, Bain AL, Gloss BS, Crawford J, Kazakoff S, Wani S, Wen SW, Day B, Möller A, Cloonan N, Pearson J, Brown MA, Mercer TR, Waddell N, Khanna KK, Dray E, Dinger ME, Edwards SL, French JD. Long Noncoding RNAs CUPID1 and CUPID2 Mediate Breast Cancer Risk at 11q13 by Modulating the Response to DNA Damage. Am J Hum Genet 2017; 101:255-266. [PMID: 28777932 PMCID: PMC5544418 DOI: 10.1016/j.ajhg.2017.07.007] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 07/10/2017] [Indexed: 02/06/2023] Open
Abstract
Breast cancer risk is strongly associated with an intergenic region on 11q13. We have previously shown that the strongest risk-associated SNPs fall within a distal enhancer that regulates CCND1. Here, we report that, in addition to regulating CCND1, this enhancer regulates two estrogen-regulated long noncoding RNAs, CUPID1 and CUPID2. We provide evidence that the risk-associated SNPs are associated with reduced chromatin looping between the enhancer and the CUPID1 and CUPID2 bidirectional promoter. We further show that CUPID1 and CUPID2 are predominantly expressed in hormone-receptor-positive breast tumors and play a role in modulating pathway choice for the repair of double-strand breaks. These data reveal a mechanism for the involvement of this region in breast cancer.
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MESH Headings
- Breast Neoplasms/genetics
- Cell Line, Tumor
- Chromatin/metabolism
- Chromosomes, Human, Pair 11/genetics
- Cyclin D1/genetics
- DNA Breaks, Double-Stranded
- DNA Damage/genetics
- DNA Repair/genetics
- Enhancer Elements, Genetic/genetics
- Estrogens/metabolism
- Female
- Gene Expression Regulation, Neoplastic
- Genetic Predisposition to Disease/genetics
- Humans
- MCF-7 Cells
- Polymorphism, Single Nucleotide/genetics
- Promoter Regions, Genetic/genetics
- RNA Interference
- RNA, Long Noncoding/genetics
- RNA, Small Interfering/genetics
- RNA, Guide, CRISPR-Cas Systems
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Affiliation(s)
- Joshua A Betts
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia
| | - Mahdi Moradi Marjaneh
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Fares Al-Ejeh
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Yi Chieh Lim
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Wei Shi
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Haran Sivakumaran
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Romain Tropée
- Queensland University of Technology at the Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Ann-Marie Patch
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Michael B Clark
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford OX1 2JD, UK; Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Nenad Bartonicek
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia
| | - Adrian P Wiegmans
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Kristine M Hillman
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Susanne Kaufmann
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Amanda L Bain
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Brian S Gloss
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia
| | - Joanna Crawford
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Stephen Kazakoff
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Shivangi Wani
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Shu W Wen
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Bryan Day
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Andreas Möller
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Nicole Cloonan
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - John Pearson
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Melissa A Brown
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia
| | - Timothy R Mercer
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia
| | - Nicola Waddell
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Kum Kum Khanna
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Eloise Dray
- Queensland University of Technology at the Translational Research Institute, Brisbane, QLD 4102, Australia; Queensland University of Technology, Institute of Health and Biomedical Innovation, Brisbane, QLD 4059, Australia
| | - Marcel E Dinger
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia
| | - Stacey L Edwards
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia.
| | - Juliet D French
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia.
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19
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Tevz G, McGrath S, Demeter R, Magrini V, Jeet V, Rockstroh A, McPherson S, Lai J, Bartonicek N, An J, Batra J, Dinger ME, Lehman ML, Williams ED, Nelson CC. Identification of a novel fusion transcript between human relaxin-1 (RLN1) and human relaxin-2 (RLN2) in prostate cancer. Mol Cell Endocrinol 2016; 420:159-68. [PMID: 26499396 DOI: 10.1016/j.mce.2015.10.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 10/13/2015] [Accepted: 10/16/2015] [Indexed: 11/23/2022]
Abstract
Simultaneous expression of highly homologous RLN1 and RLN2 genes in prostate impairs their accurate delineation. We used PacBio SMRT sequencing and RNA-Seq in LNCaP cells in order to dissect the expression of RLN1 and RLN2 variants. We identified a novel fusion transcript comprising the RLN1 and RLN2 genes and found evidence of its expression in the normal and prostate cancer tissues. The RLN1-RLN2 fusion putatively encodes RLN2 isoform with the deleted secretory signal peptide. The identification of the fusion transcript provided information to determine unique RLN1-RLN2 fusion and RLN1 regions. The RLN1-RLN2 fusion was co-expressed with RLN1 in LNCaP cells, but the two gene products were inversely regulated by androgens. We showed that RLN1 is underrepresented in common PCa cell lines in comparison to normal and PCa tissue. The current study brings a highly relevant update to the relaxin field, and will encourage further studies of RLN1 and RLN2 in PCa and broader.
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Affiliation(s)
- Gregor Tevz
- Institute of Health and Biomedical Innovation, Australian Prostate Cancer Research Centre-Queensland, Queensland University of Technology/Translational Research Institute, Brisbane, QLD, Australia
| | - Sean McGrath
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Ryan Demeter
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Vincent Magrini
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Varinder Jeet
- Institute of Health and Biomedical Innovation, Australian Prostate Cancer Research Centre-Queensland, Queensland University of Technology/Translational Research Institute, Brisbane, QLD, Australia
| | - Anja Rockstroh
- Institute of Health and Biomedical Innovation, Australian Prostate Cancer Research Centre-Queensland, Queensland University of Technology/Translational Research Institute, Brisbane, QLD, Australia
| | - Stephen McPherson
- Institute of Health and Biomedical Innovation, Australian Prostate Cancer Research Centre-Queensland, Queensland University of Technology/Translational Research Institute, Brisbane, QLD, Australia
| | - John Lai
- Institute of Health and Biomedical Innovation, Australian Prostate Cancer Research Centre-Queensland, Queensland University of Technology/Translational Research Institute, Brisbane, QLD, Australia
| | - Nenad Bartonicek
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, Australia
| | - Jiyuan An
- Institute of Health and Biomedical Innovation, Australian Prostate Cancer Research Centre-Queensland, Queensland University of Technology/Translational Research Institute, Brisbane, QLD, Australia
| | - Jyotsna Batra
- Institute of Health and Biomedical Innovation, Australian Prostate Cancer Research Centre-Queensland, Queensland University of Technology/Translational Research Institute, Brisbane, QLD, Australia
| | - Marcel E Dinger
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, Australia
| | - Melanie L Lehman
- Institute of Health and Biomedical Innovation, Australian Prostate Cancer Research Centre-Queensland, Queensland University of Technology/Translational Research Institute, Brisbane, QLD, Australia; Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Elizabeth D Williams
- Institute of Health and Biomedical Innovation, Australian Prostate Cancer Research Centre-Queensland, Queensland University of Technology/Translational Research Institute, Brisbane, QLD, Australia
| | - Colleen C Nelson
- Institute of Health and Biomedical Innovation, Australian Prostate Cancer Research Centre-Queensland, Queensland University of Technology/Translational Research Institute, Brisbane, QLD, Australia; Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada.
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20
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Quek XC, Thomson DW, Maag JLV, Bartonicek N, Signal B, Clark MB, Gloss BS, Dinger ME. lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs. Nucleic Acids Res 2014; 43:D168-73. [PMID: 25332394 PMCID: PMC4384040 DOI: 10.1093/nar/gku988] [Citation(s) in RCA: 388] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Despite the prevalence of long noncoding RNA (lncRNA) genes in eukaryotic genomes, only a small proportion have been examined for biological function. lncRNAdb, available at http://lncrnadb.org, provides users with a comprehensive, manually curated reference database of 287 eukaryotic lncRNAs that have been described independently in the scientific literature. In addition to capturing a great proportion of the recent literature describing functions for individual lncRNAs, lncRNAdb now offers an improved user interface enabling greater accessibility to sequence information, expression data and the literature. The new features in lncRNAdb include the integration of Illumina Body Atlas expression profiles, nucleotide sequence information, a BLAST search tool and easy export of content via direct download or a REST API. lncRNAdb is now endorsed by RNAcentral and is in compliance with the International Nucleotide Sequence Database Collaboration.
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Affiliation(s)
- Xiu Cheng Quek
- Garvan Institute of Medical Research, 384 Victoria Street, Sydney, NSW 2010, Australia St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2052, Australia
| | - Daniel W Thomson
- Garvan Institute of Medical Research, 384 Victoria Street, Sydney, NSW 2010, Australia
| | - Jesper L V Maag
- Garvan Institute of Medical Research, 384 Victoria Street, Sydney, NSW 2010, Australia St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2052, Australia
| | - Nenad Bartonicek
- Garvan Institute of Medical Research, 384 Victoria Street, Sydney, NSW 2010, Australia
| | - Bethany Signal
- Garvan Institute of Medical Research, 384 Victoria Street, Sydney, NSW 2010, Australia
| | - Michael B Clark
- Garvan Institute of Medical Research, 384 Victoria Street, Sydney, NSW 2010, Australia MRC Functional Genomics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3PT, UK
| | - Brian S Gloss
- Garvan Institute of Medical Research, 384 Victoria Street, Sydney, NSW 2010, Australia St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2052, Australia
| | - Marcel E Dinger
- Garvan Institute of Medical Research, 384 Victoria Street, Sydney, NSW 2010, Australia St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2052, Australia
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Davis MPA, van Dongen S, Abreu-Goodger C, Bartonicek N, Enright AJ. Kraken: a set of tools for quality control and analysis of high-throughput sequence data. Methods 2013; 63:41-9. [PMID: 23816787 PMCID: PMC3991327 DOI: 10.1016/j.ymeth.2013.06.027] [Citation(s) in RCA: 270] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 06/21/2013] [Accepted: 06/22/2013] [Indexed: 12/18/2022] Open
Abstract
New sequencing technologies pose significant challenges in terms of data complexity and magnitude. It is essential that efficient software is developed with performance that scales with this growth in sequence information. Here we present a comprehensive and integrated set of tools for the analysis of data from large scale sequencing experiments. It supports adapter detection and removal, demultiplexing of barcodes, paired-end data, a range of read architectures and the efficient removal of sequence redundancy. Sequences can be trimmed and filtered based on length, quality and complexity. Quality control plots track sequence length, composition and summary statistics with respect to genomic annotation. Several use cases have been integrated into a single streamlined pipeline, including both mRNA and small RNA sequencing experiments. This pipeline interfaces with existing tools for genomic mapping and differential expression analysis.
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Affiliation(s)
- Matthew P A Davis
- EMBL - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
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22
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Lupini L, Bassi C, Ferracin M, Bartonicek N, D'Abundo L, Zagatti B, Callegari E, Musa G, Moshiri F, Gramantieri L, Corrales FJ, Enright AJ, Sabbioni S, Negrini M. miR-221 affects multiple cancer pathways by modulating the level of hundreds messenger RNAs. Front Genet 2013; 4:64. [PMID: 23630541 PMCID: PMC3635019 DOI: 10.3389/fgene.2013.00064] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 04/08/2013] [Indexed: 12/19/2022] Open
Abstract
microRNA miR-221 is frequently over-expressed in a variety of human neoplasms. Aim of this study was to identify new miR-221 gene targets to improve our understanding on the molecular tumor-promoting mechanisms affected by miR-221. Gene expression profiling of miR-221-transfected-SNU-398 cells was analyzed by the Sylamer algorithm to verify the enrichment of miR-221 targets among down-modulated genes. This analysis revealed that enforced expression of miR-221 in SNU-398 cells caused the down-regulation of 602 mRNAs carrying sequences homologous to miR-221 seed sequence within their 3'UTRs. Pathways analysis performed on these genes revealed their prominent involvement in cell proliferation and apoptosis. Activation of E2F, MYC, NFkB, and β-catenin pathways was experimentally proven. Some of the new miR-221 target genes, including RB1, WEE1 (cell cycle inhibitors), APAF1 (pro-apoptotic), ANXA1, CTCF (transcriptional repressor), were individually validated as miR-221 targets in SNU-398, HepG2, and HEK293 cell lines. By identifying a large set of miR-221 gene targets, this study improves our knowledge about miR-221 molecular mechanisms involved in tumorigenesis. The modulation of mRNA level of 602 genes confirms the ability of miR-221 to promote cancer by affecting multiple oncogenic pathways.
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Affiliation(s)
- Laura Lupini
- Dipartimento di Morfologia, Chirurgia e Medicina Sperimentale, Università di Ferrara Ferrara, Italy
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23
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Parts L, Hedman ÅK, Keildson S, Knights AJ, Abreu-Goodger C, van de Bunt M, Guerra-Assunção JA, Bartonicek N, van Dongen S, Mägi R, Nisbet J, Barrett A, Rantalainen M, Nica AC, Quail MA, Small KS, Glass D, Enright AJ, Winn J, Deloukas P, Dermitzakis ET, McCarthy MI, Spector TD, Durbin R, Lindgren CM. Extent, causes, and consequences of small RNA expression variation in human adipose tissue. PLoS Genet 2012; 8:e1002704. [PMID: 22589741 PMCID: PMC3349731 DOI: 10.1371/journal.pgen.1002704] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 03/27/2012] [Indexed: 12/12/2022] Open
Abstract
Small RNAs are functional molecules that modulate mRNA transcripts and have been implicated in the aetiology of several common diseases. However, little is known about the extent of their variability within the human population. Here, we characterise the extent, causes, and effects of naturally occurring variation in expression and sequence of small RNAs from adipose tissue in relation to genotype, gene expression, and metabolic traits in the MuTHER reference cohort. We profiled the expression of 15 to 30 base pair RNA molecules in subcutaneous adipose tissue from 131 individuals using high-throughput sequencing, and quantified levels of 591 microRNAs and small nucleolar RNAs. We identified three genetic variants and three RNA editing events. Highly expressed small RNAs are more conserved within mammals than average, as are those with highly variable expression. We identified 14 genetic loci significantly associated with nearby small RNA expression levels, seven of which also regulate an mRNA transcript level in the same region. In addition, these loci are enriched for variants significant in genome-wide association studies for body mass index. Contrary to expectation, we found no evidence for negative correlation between expression level of a microRNA and its target mRNAs. Trunk fat mass, body mass index, and fasting insulin were associated with more than twenty small RNA expression levels each, while fasting glucose had no significant associations. This study highlights the similar genetic complexity and shared genetic control of small RNA and mRNA transcripts, and gives a quantitative picture of small RNA expression variation in the human population. Genetic information is transmitted to the cell only through RNA molecules. A special class of RNAs is comprised of the small (up to 30 nucleotide) ones, known to be potent regulators of various cellular processes. At the same time, they have not been as widely studied as messenger RNAs—we do not know how much variation in their sequence and expression level occurs naturally in human populations or how this variability influences other traits. We measured small RNA levels and genetic variability in fat tissue from 131 individuals by high-throughput sequencing. We could associate the expression levels with genetic background of the individuals, as well as changes in metabolic traits. Surprisingly, we found no large scale influence of small RNA variation on mRNA levels, their main regulatory target. Overall, our study is the first to give a quantitative picture of the naturally occurring variation in these important regulatory molecules in human fat tissue.
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Affiliation(s)
- Leopold Parts
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Åsa K. Hedman
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Sarah Keildson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | | | - Cei Abreu-Goodger
- European Bioinformatics Institute, Hinxton, United Kingdom
- National Laboratory of Genomics for Biodiversity (Langebio), Cinvestav, Irapuato, Mexico
| | - Martijn van de Bunt
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Diabetes, Endocrinology, and Metabolism, University of Oxford, Oxford, United Kingdom
| | - José Afonso Guerra-Assunção
- European Bioinformatics Institute, Hinxton, United Kingdom
- PDBC, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | | | - Reedik Mägi
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - James Nisbet
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Amy Barrett
- Oxford Centre for Diabetes, Endocrinology, and Metabolism, University of Oxford, Oxford, United Kingdom
| | - Mattias Rantalainen
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Alexandra C. Nica
- Department of Genetic Medicine and Development and Institute of Genetics and Genomics in Geneva, University of Geneva Medical School, Geneva, Switzerland
| | | | - Kerrin S. Small
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Daniel Glass
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | | | - John Winn
- Microsoft Research, Cambridge, United Kingdom
| | | | - Panos Deloukas
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Emmanouil T. Dermitzakis
- Department of Genetic Medicine and Development and Institute of Genetics and Genomics in Geneva, University of Geneva Medical School, Geneva, Switzerland
| | - Mark I. McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Diabetes, Endocrinology, and Metabolism, University of Oxford, Oxford, United Kingdom
| | - Timothy D. Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Richard Durbin
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- * E-mail: (RD); (CML)
| | - Cecilia M. Lindgren
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- * E-mail: (RD); (CML)
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Gurha P, Abreu-Goodger C, Wang T, Ramirez MO, Drumond AL, van Dongen S, Chen Y, Bartonicek N, Enright AJ, Lee B, Kelm RJ, Reddy AK, Taffet GE, Bradley A, Wehrens XH, Entman ML, Rodriguez A. Targeted deletion of microRNA-22 promotes stress-induced cardiac dilation and contractile dysfunction. Circulation 2012; 125:2751-61. [PMID: 22570371 DOI: 10.1161/circulationaha.111.044354] [Citation(s) in RCA: 141] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
BACKGROUND Delineating the role of microRNAs (miRNAs) in the posttranscriptional gene regulation offers new insights into how the heart adapts to pathological stress. We developed a knockout of miR-22 in mice and investigated its function in the heart. METHODS AND RESULTS Here, we show that miR-22-deficient mice are impaired in inotropic and lusitropic response to acute stress by dobutamine. Furthermore, the absence of miR-22 sensitized mice to cardiac decompensation and left ventricular dilation after long-term stimulation by pressure overload. Calcium transient analysis revealed reduced sarcoplasmic reticulum Ca(2+) load in association with repressed sarcoplasmic reticulum Ca(2+) ATPase activity in mutant myocytes. Genetic ablation of miR-22 also led to a decrease in cardiac expression levels for Serca2a and muscle-restricted genes encoding proteins in the vicinity of the cardiac Z disk/titin cytoskeleton. These phenotypes were attributed in part to inappropriate repression of serum response factor activity in stressed hearts. Global analysis revealed increased expression of the transcriptional/translational repressor purine-rich element binding protein B, a highly conserved miR-22 target implicated in the negative control of muscle expression. CONCLUSION These data indicate that miR-22 functions as an integrator of Ca(2+) homeostasis and myofibrillar protein content during stress in the heart and shed light on the mechanisms that enhance propensity toward heart failure.
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Affiliation(s)
- Priyatansh Gurha
- Baylor College of Medicine, Department of Molecular and Human Genetics, One Baylor Plaza, Houston, TX, 77030, USA
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25
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Mayoral RJ, Deho L, Rusca N, Bartonicek N, Saini HK, Enright AJ, Monticelli S. MiR-221 influences effector functions and actin cytoskeleton in mast cells. PLoS One 2011; 6:e26133. [PMID: 22022537 PMCID: PMC3192147 DOI: 10.1371/journal.pone.0026133] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Accepted: 09/20/2011] [Indexed: 02/01/2023] Open
Abstract
Mast cells have essential effector and immunoregulatory functions in IgE-associated allergic disorders and certain innate and adaptive immune responses, but the role of miRNAs in regulating mast cell functions is almost completely unexplored. To examine the role of the activation-induced miRNA miR-221 in mouse mast cells, we developed robust lentiviral systems for miRNA overexpression and depletion. While miR-221 favored mast cell adhesion and migration towards SCF or antigen in trans-well migration assays, as well as cytokine production and degranulation in response to IgE-antigen complexes, neither miR-221 overexpression, nor its ablation, interfered with mast cell differentiation. Transcriptional profiling of miR-221-overexpressing mast cells revealed modulation of many transcripts, including several associated with the cytoskeleton; indeed, miR-221 overexpression was associated with reproducible increases in cortical actin in mast cells, and with altered cellular shape and cell cycle in murine fibroblasts. Our bioinformatics analysis showed that this effect was likely mediated by the composite effect of miR-221 on many primary and secondary targets in resting cells. Indeed, miR-221-induced cellular alterations could not be recapitulated by knockdown of one of the major targets of miR-221. We propose a model in which miR-221 has two different roles in mast cells: in resting cells, basal levels of miR-221 contribute to the regulation of the cell cycle and cytoskeleton, a general mechanism probably common to other miR-221-expressing cell types, such as fibroblasts. Vice versa, upon induction in response to mast cell stimulation, miR-221 effects are mast cell-specific and activation-dependent, contributing to the regulation of degranulation, cytokine production and cell adherence. Our studies provide new insights into the roles of miR-221 in mast cell biology, and identify novel mechanisms that may contribute to mast cell-related pathological conditions, such as asthma, allergy and mastocytosis.
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Affiliation(s)
| | - Lorenzo Deho
- Institute for Research in Biomedicine, Bellinzona, Switzerland
| | - Nicole Rusca
- Institute for Research in Biomedicine, Bellinzona, Switzerland
| | - Nenad Bartonicek
- EMBL - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Harpreet Kaur Saini
- EMBL - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Anton J. Enright
- EMBL - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Silvia Monticelli
- Institute for Research in Biomedicine, Bellinzona, Switzerland
- * E-mail:
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27
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Rasmussen KD, Simmini S, Abreu-Goodger C, Bartonicek N, Di Giacomo M, Bilbao-Cortes D, Horos R, Von Lindern M, Enright AJ, O'Carroll D. The miR-144/451 locus is required for erythroid homeostasis. ACTA ACUST UNITED AC 2010; 207:1351-8. [PMID: 20513743 PMCID: PMC2901075 DOI: 10.1084/jem.20100458] [Citation(s) in RCA: 242] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The process of erythropoiesis must be efficient and robust to supply the organism with red bloods cells both under condition of homeostasis and stress. The microRNA (miRNA) pathway was recently shown to regulate erythroid development. Here, we show that expression of the locus encoding miR-144 and miR-451 is strictly dependent on Argonaute 2 and is required for erythroid homeostasis. Mice deficient for the miR-144/451 cluster display a cell autonomous impairment of late erythroblast maturation, resulting in erythroid hyperplasia, splenomegaly, and a mild anemia. Analysis of gene expression profiles from wild-type and miR-144/451–deficient erythroblasts revealed that the miR-144/451 cluster acts as a “tuner” of gene expression, influencing the expression of many genes. MiR-451 imparts a greater impact on target gene expression than miR-144. Accordingly, mice deficient in miR-451 alone exhibited a phenotype indistinguishable from miR-144/451–deficient mice. Thus, the miR-144/451 cluster tunes gene expression to impart a robustness to erythropoiesis that is critical under conditions of stress.
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Affiliation(s)
- Kasper D Rasmussen
- European Molecular Biology Laboratory, Mouse Biology Unit, Monterotondo Scalo, 00015, Italy
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Abstract
MADNet is a user-friendly data mining and visualization tool for rapid analysis of diverse high-throughput biological data such as microarray, phage display or even metagenome experiments. It presents biological information in the context of metabolic and signalling pathways, transcription factors and drug targets through minimal user input, consisting only of the file with the experimental data. These data are integrated with information stored in various biological databases such as NCBI nucleotide and protein databases, metabolic and signalling pathway databases (KEGG), transcription regulation (TRANSFAC©) and drug target database (DrugBank). MADNet is freely available for academic use at http://www.bioinfo.hr/madnet.
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Affiliation(s)
- Igor Segota
- Bioinformatics Group, Division of Biology, Faculty of Science, Zagreb University, Horvatovac 102a, 10000 Zagreb, Croatia
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