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Ozturk K, Panwala R, Sheen J, Ford K, Jayne N, Portell A, Zhang DE, Hutter S, Haferlach T, Ideker T, Mali P, Carter H. Interface-guided phenotyping of coding variants in the transcription factor RUNX1. Cell Rep 2024; 43:114436. [PMID: 38968069 DOI: 10.1016/j.celrep.2024.114436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 05/15/2024] [Accepted: 06/19/2024] [Indexed: 07/07/2024] Open
Abstract
Single-gene missense mutations remain challenging to interpret. Here, we deploy scalable functional screening by sequencing (SEUSS), a Perturb-seq method, to generate mutations at protein interfaces of RUNX1 and quantify their effect on activities of downstream cellular programs. We evaluate single-cell RNA profiles of 115 mutations in myelogenous leukemia cells and categorize them into three functionally distinct groups, wild-type (WT)-like, loss-of-function (LoF)-like, and hypomorphic, that we validate in orthogonal assays. LoF-like variants dominate the DNA-binding site and are recurrent in cancer; however, recurrence alone does not predict functional impact. Hypomorphic variants share characteristics with LoF-like but favor protein interactions, promoting gene expression indicative of nerve growth factor (NGF) response and cytokine recruitment of neutrophils. Accessible DNA near differentially expressed genes frequently contains RUNX1-binding motifs. Finally, we reclassify 16 variants of uncertain significance and train a classifier to predict 103 more. Our work demonstrates the potential of targeting protein interactions to better define the landscape of phenotypes reachable by missense mutations.
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Affiliation(s)
- Kivilcim Ozturk
- Division of Medical Genetics, Department of Medicine, University of California, San Diego, La Jolla, CA, USA; Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
| | - Rebecca Panwala
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Jeanna Sheen
- School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Kyle Ford
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Nathan Jayne
- School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Andrew Portell
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Dong-Er Zhang
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Stephan Hutter
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 Munich, Germany
| | - Torsten Haferlach
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 Munich, Germany
| | - Trey Ideker
- Division of Medical Genetics, Department of Medicine, University of California, San Diego, La Jolla, CA, USA; Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Prashant Mali
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
| | - Hannah Carter
- Division of Medical Genetics, Department of Medicine, University of California, San Diego, La Jolla, CA, USA; Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.
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2
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Çıldır ÖŞ, Özmen Ö, Kul S, Rişvanlı A, Özalp G, Sabuncu A, Kul O. Genetic analysis of PALB2 gene WD40 domain in canine mammary tumour patients. Vet Med Sci 2024; 10:e1366. [PMID: 38527110 PMCID: PMC10962921 DOI: 10.1002/vms3.1366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 11/30/2023] [Accepted: 01/07/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND DNA repair mechanisms are essential for tumorigenesis and disruption of HR mechanism is an important predisposing factor of human breast cancers (BC). PALB2 is an important part of the HR. There are similarities between canine mammary tumours (CMT) and BCs. As its human counterpart, PALB2 mutations could be a predisposing factor of CMT. OBJECTIVES In this study, we aimed to investigate the impacts of PALB2 variants on tumorigenesis and canine mammary tumor (CMT) malignancy. METHODS We performed Sanger sequencing to detect germline mutations in the WD40 domain of the canine PALB2 gene in CMT patients. We conducted in silico analysis to investigate the variants, and compared the germline PALB2 mutations in humans that cause breast cancer (BC) with the variants detected in dogs with CMT. RESULTS We identified an intronic (c.3096+8C>G) variant, two exonic (p.A1050V and p.R1354R) variants, and a 3' UTR variant (c.4071T>C). Of these, p.R1354R and c.4071T>C novel variants were identified for the first time in this study. We found that the p.A1050V mutation had a significant effect. However, we could not determine sufficient similarity due to the differences in nucleotide/amino acid sequences between two species. Nonetheless, possible variants of human sequences in the exact location as their dog counterparts are associated with several cancer types, implying that the variants could be crucial for tumorigenesis in dogs. Our results did not show any effect of the variants on tumor malignancy. CONCLUSIONS The current project is the first study investigating the relationship between the PALB2 gene WD40 domain and CMTs. Our findings will contribute to a better understanding of the pathogenic mechanism of the PALB2 gene in CMTs. In humans, variant positions in canines have been linked to cancer-related phenotypes such as familial BC, endometrial tumor, and hereditary cancer predisposition syndrome. The results of bioinformatics analyses should be investigated through functional tests or case-control studies.
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Affiliation(s)
- Özge Şebnem Çıldır
- Department of GeneticsFaculty of Veterinary MedicineKafkas UniversityKarsTürkiye
- Department of GeneticsFaculty of Veterinary MedicineAnkara UniversityAnkaraTürkiye
| | - Özge Özmen
- Department of GeneticsFaculty of Veterinary MedicineAnkara UniversityAnkaraTürkiye
| | - Selim Kul
- Department of Animal BreedingFaculty of Veterinary MedicineYozgat Bozok UniversityYozgatTürkiye
| | - Ali Rişvanlı
- Department of Obstetrics and GynecologyFaculty of Veterinary MedicineFırat UniversityElazığTürkiye
- Department of Obstetrics and GynecologyFaculty of Veterinary MedicineKyrgyz‐Turkish Manas UniversityBishkekKyrgyzstan
| | - Gözde Özalp
- Department of Obstetrics and GynecologyFaculty of Veterinary MedicineBursa Uludağ UniversityBursaTürkiye
| | - Ahmet Sabuncu
- Department of Obstetrics and GynecologyFaculty of Veterinary Medicineİstanbul UniversityİstanbulTürkiye
| | - Oğuz Kul
- Department of PathologyFaculty of Veterinary MedicineKırıkkale UniversityKırıkkaleTürkiye
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Ozturk K, Panwala R, Sheen J, Ford K, Payne N, Zhang DE, Hutter S, Haferlach T, Ideker T, Mali P, Carter H. Interface-guided phenotyping of coding variants in the transcription factor RUNX1 with SEUSS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.03.551876. [PMID: 37577681 PMCID: PMC10418284 DOI: 10.1101/2023.08.03.551876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Understanding the consequences of single amino acid substitutions in cancer driver genes remains an unmet need. Perturb-seq provides a tool to investigate the effects of individual mutations on cellular programs. Here we deploy SEUSS, a Perturb-seq like approach, to generate and assay mutations at physical interfaces of the RUNX1 Runt domain. We measured the impact of 115 mutations on RNA profiles in single myelogenous leukemia cells and used the profiles to categorize mutations into three functionally distinct groups: wild-type (WT)-like, loss-of-function (LOF)-like and hypomorphic. Notably, the largest concentration of functional mutations (non-WT-like) clustered at the DNA binding site and contained many of the more frequently observed mutations in human cancers. Hypomorphic variants shared characteristics with loss of function variants but had gene expression profiles indicative of response to neural growth factor and cytokine recruitment of neutrophils. Additionally, DNA accessibility changes upon perturbations were enriched for RUNX1 binding motifs, particularly near differentially expressed genes. Overall, our work demonstrates the potential of targeting protein interaction interfaces to better define the landscape of prospective phenotypes reachable by amino acid substitutions.
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4
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Roy A, Chauhan S, Bhattacharya S, Jakhmola V, Tyagi K, Sachdeva A, Wasai A, Mandal S. Runt-related transcription factors in human carcinogenesis: a friend or foe? J Cancer Res Clin Oncol 2023:10.1007/s00432-023-04769-0. [PMID: 37081242 DOI: 10.1007/s00432-023-04769-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 04/08/2023] [Indexed: 04/22/2023]
Abstract
PURPOSE Cancer is one of the deadliest pathologies with more than 19 million new cases and 10 million cancer-related deaths across the globe. Despite development of advanced therapeutic interventions, cancer remains as a fatal pathology due to lack of early prognostic biomarkers, therapy resistance and requires identification of novel drug targets. METHODS Runt-related transcription factors (Runx) family controls several cellular and physiological functions including osteogenesis. Recent literatures from PubMed was mined and the review was written in comprehensive manner RESULTS: Recent literature suggests that aberrant expression of Runx contributes to tumorigenesis of many organs. Conversely, cell- and tissue-specific tumor suppressor roles of Runx are also reported. In this review, we have provided the structural/functional properties of Runx isoforms and its regulation in context of human cancer. Moreover, in an urgent need to discover novel therapeutic interventions against cancer, we comprehensively discussed the reported oncogenic and tumor suppressive roles of Runx isoforms in several tumor types and discussed the discrepancies that may have risen on Runx as a driver of malignant transformation. CONCLUSION Runx may be a novel therapeutic target against a battery of deadly human cancers.
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Affiliation(s)
- Adhiraj Roy
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Sector 125, Noida, Uttar Pradesh, 201303, India.
| | - Shivi Chauhan
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Sector 125, Noida, Uttar Pradesh, 201303, India
| | - Sujata Bhattacharya
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Sector 125, Noida, Uttar Pradesh, 201303, India
| | - Vibhuti Jakhmola
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Sector 125, Noida, Uttar Pradesh, 201303, India
| | - Komal Tyagi
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Sector 125, Noida, Uttar Pradesh, 201303, India
| | - Abha Sachdeva
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Sector 125, Noida, Uttar Pradesh, 201303, India
| | - Abdul Wasai
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Sector 125, Noida, Uttar Pradesh, 201303, India
| | - Supratim Mandal
- Department of Microbiology, University of Kalyani, Kalyani, Nadia, West Bengal, 741235, India
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5
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Qiu W, Xiao Z, Yang Y, Jiang L, Song S, Qi X, Chen Y, Yang H, Liu J, Chu L. USP10 deubiquitinates RUNX1 and promotes proneural-to-mesenchymal transition in glioblastoma. Cell Death Dis 2023; 14:207. [PMID: 36949071 PMCID: PMC10033651 DOI: 10.1038/s41419-023-05734-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 03/03/2023] [Accepted: 03/13/2023] [Indexed: 03/24/2023]
Abstract
The mesenchymal (MES) subtype of glioblastoma (GBM) is a highly aggressive, malignant and proliferative cancer that is resistant to chemotherapy. Runt-related transcription factor 1 (RUNX1) was shown to support MES GBM, however, its underlying mechanisms are unclear. Here, we identified USP10 as a deubiquitinating enzyme that regulates RUNX1 stabilization and is mainly expressed in MES GBM. Overexpression of USP10 upregulated RUNX1 and induced proneural-to-mesenchymal transition (PMT), thus maintaining MES properties in GBM. Conversely, USP10 knockdown inhibited RUNX1 and resulted in the loss of MES properties. USP10 was shown to interact with RUNX1, with RUNX1 being stabilized upon deubiquitylation. Moreover, we found that USP10 inhibitor Spautin-1 induced RUNX1 degradation and inhibited MES properties in vitro and in vivo. Furthermore, USP10 was strongly correlated with RUNX1 expression in samples of different subtypes of human GBM and had prognostic value for GBM patients. We identified USP10 as a key deubiquitinase for RUNX1 protein stabilization. USP10 maintains MES properties of GBM, and promotes PMT of GBM cells. Our study indicates that the USP10/RUNX1 axis may be a potential target for novel GBM treatments.
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Affiliation(s)
- Wenjin Qiu
- Department of Neurosurgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550001, Guizhou, China
| | - Zumu Xiao
- Department of Neurosurgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550001, Guizhou, China
| | - Yushi Yang
- Department of Pathology, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | - Lishi Jiang
- Department of Neurosurgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550001, Guizhou, China
| | - Shibin Song
- Department of Neurosurgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550001, Guizhou, China
| | - Xiaolan Qi
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education & Key Laboratory of Medical Molecular Biology of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou, China
| | - Yimin Chen
- Department of Neurosurgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550001, Guizhou, China
| | - Hua Yang
- Department of Neurosurgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550001, Guizhou, China
| | - Jian Liu
- Department of Neurosurgery, Guizhou Provincial People's Hospital, Guiyang, 550001, Guizhou, China.
| | - Liangzhao Chu
- Department of Neurosurgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550001, Guizhou, China.
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Khan AS, Campbell KJ, Cameron ER, Blyth K. The RUNX/CBFβ Complex in Breast Cancer: A Conundrum of Context. Cells 2023; 12:641. [PMID: 36831308 PMCID: PMC9953914 DOI: 10.3390/cells12040641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/07/2023] [Accepted: 02/10/2023] [Indexed: 02/19/2023] Open
Abstract
Dissecting and identifying the major actors and pathways in the genesis, progression and aggressive advancement of breast cancer is challenging, in part because neoplasms arising in this tissue represent distinct diseases and in part because the tumors themselves evolve. This review attempts to illustrate the complexity of this mutational landscape as it pertains to the RUNX genes and their transcription co-factor CBFβ. Large-scale genomic studies that characterize genetic alterations across a disease subtype are a useful starting point and as such have identified recurring alterations in CBFB and in the RUNX genes (particularly RUNX1). Intriguingly, the functional output of these mutations is often context dependent with regards to the estrogen receptor (ER) status of the breast cancer. Therefore, such studies need to be integrated with an in-depth understanding of both the normal and corrupted function in mammary cells to begin to tease out how loss or gain of function can alter the cell phenotype and contribute to disease progression. We review how alterations to RUNX/CBFβ function contextually ascribe to breast cancer subtypes and discuss how the in vitro analyses and mouse model systems have contributed to our current understanding of these proteins in the pathogenesis of this complex set of diseases.
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Affiliation(s)
- Adiba S. Khan
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Rd, Glasgow G61 1BD, UK; (A.S.K.); (K.J.C.)
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - Kirsteen J. Campbell
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Rd, Glasgow G61 1BD, UK; (A.S.K.); (K.J.C.)
| | - Ewan R. Cameron
- School of Biodiversity One Health & Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK;
| | - Karen Blyth
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Rd, Glasgow G61 1BD, UK; (A.S.K.); (K.J.C.)
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
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7
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Zhang F, Cho WC. Therapeutic potential of RUNX1 and RUNX2 in bone metastasis of breast cancer. Expert Opin Ther Targets 2023; 27:413-417. [PMID: 37243490 DOI: 10.1080/14728222.2023.2219395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/15/2023] [Accepted: 05/25/2023] [Indexed: 05/28/2023]
Affiliation(s)
- Fei Zhang
- Department of Health Technology and Informatics, Hong Kong Polytechnic University, Hong Kong SAR, China
| | - William C Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong SAR, China
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8
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Mikami M, Masuda T, Kanatani T, Noura M, Umeda K, Hiramatsu H, Kubota H, Daifu T, Iwai A, Hattori EY, Furuichi K, Takasaki S, Tanaka S, Matsui Y, Matsuo H, Hirata M, Kataoka TR, Nakahata T, Kuwahara Y, Iehara T, Hosoi H, Imai Y, Takita J, Sugiyama H, Adachi S, Kamikubo Y. RUNX1-Survivin Axis Is a Novel Therapeutic Target for Malignant Rhabdoid Tumors. Mol Cells 2022; 45:886-895. [PMID: 36572559 PMCID: PMC9794559 DOI: 10.14348/molcells.2022.2031] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 07/18/2022] [Accepted: 08/06/2022] [Indexed: 12/28/2022] Open
Abstract
Malignant rhabdoid tumor (MRT) is a highly aggressive pediatric malignancy with no effective therapy. Therefore, it is necessary to identify a target for the development of novel molecule-targeting therapeutic agents. In this study, we report the importance of the runt-related transcription factor 1 (RUNX1) and RUNX1-Baculoviral IAP (inhibitor of apoptosis) Repeat-Containing 5 (BIRC5/survivin) axis in the proliferation of MRT cells, as it can be used as an ideal target for anti-tumor strategies. The mechanism of this reaction can be explained by the interaction of RUNX1 with the RUNX1-binding DNA sequence located in the survivin promoter and its positive regulation. Specific knockdown of RUNX1 led to decreased expression of survivin, which subsequently suppressed the proliferation of MRT cells in vitro and in vivo. We also found that our novel RUNX inhibitor, Chb-M, which switches off RUNX1 using alkylating agent-conjugated pyrrole-imidazole polyamides designed to specifically bind to consensus RUNX-binding sequences (5'-TGTGGT-3'), inhibited survivin expression in vivo. Taken together, we identified a novel interaction between RUNX1 and survivin in MRT. Therefore the negative regulation of RUNX1 activity may be a novel strategy for MRT treatment.
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Affiliation(s)
- Masamitsu Mikami
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto 606-8303, Japan
| | - Tatsuya Masuda
- Department of Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto 606-8303, Japan
| | - Takuya Kanatani
- Department of Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto 606-8303, Japan
| | - Mina Noura
- Department of Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto 606-8303, Japan
| | - Katsutsugu Umeda
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto 606-8303, Japan
| | - Hidefumi Hiramatsu
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto 606-8303, Japan
| | - Hirohito Kubota
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto 606-8303, Japan
| | - Tomoo Daifu
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto 606-8303, Japan
| | - Atsushi Iwai
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto 606-8303, Japan
| | - Etsuko Yamamoto Hattori
- Department of Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto 606-8303, Japan
| | - Kana Furuichi
- Department of Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto 606-8303, Japan
| | - Saho Takasaki
- Department of Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto 606-8303, Japan
| | - Sunao Tanaka
- Department of Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto 606-8303, Japan
| | - Yasuzumi Matsui
- Department of Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto 606-8303, Japan
| | - Hidemasa Matsuo
- Department of Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto 606-8303, Japan
| | - Masahiro Hirata
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto 606-8507, Japan
| | - Tatsuki R. Kataoka
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto 606-8507, Japan
| | - Tatsutoshi Nakahata
- Drug Discovery Technology Development Office, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Yasumichi Kuwahara
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Tomoko Iehara
- Department of Pediatrics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Hajime Hosoi
- Department of Pediatrics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Yoichi Imai
- Department of Hematology/Oncology, IMSUT Hospital, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto 606-8303, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8303, Japan
| | - Souichi Adachi
- Department of Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto 606-8303, Japan
| | - Yasuhiko Kamikubo
- Department of Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto 606-8303, Japan
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Abstract
Identifying differences in networks has become a canonical problem in many biological applications. Existing methods try to accomplish this goal by either directly comparing the estimated structures of two networks, or testing the null hypothesis that the covariance or inverse covariance matrices in two populations are identical. However, estimation approaches do not provide measures of uncertainty, e.g., p-values, whereas existing testing approaches could lead to misleading results, as we illustrate in this paper. To address these shortcomings, we propose a qualitative hypothesis testing framework, which tests whether the connectivity structures in the two networks are the same. our framework is especially appropriate if the goal is to identify nodes or edges that are differentially connected. No existing approach could test such hypotheses and provide corresponding measures of uncertainty. Theoretically, we show that under appropriate conditions, our proposal correctly controls the type-I error rate in testing the qualitative hypothesis. Empirically, we demonstrate the performance of our proposal using simulation studies and applications in cancer genomics.
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Affiliation(s)
| | - Ali Shojaie
- Department of Biostatistics, University of Washington
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10
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Cromer MK, Barsan VV, Jaeger E, Wang M, Hampton JP, Chen F, Kennedy D, Xiao J, Khrebtukova I, Granat A, Truong T, Porteus MH. Ultra-deep sequencing validates safety of CRISPR/Cas9 genome editing in human hematopoietic stem and progenitor cells. Nat Commun 2022; 13:4724. [PMID: 35953477 PMCID: PMC9372057 DOI: 10.1038/s41467-022-32233-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 07/22/2022] [Indexed: 12/25/2022] Open
Abstract
As CRISPR-based therapies enter the clinic, evaluation of safety remains a critical and active area of study. Here, we employ a clinical next generation sequencing (NGS) workflow to achieve high sequencing depth and detect ultra-low frequency variants across exons of genes associated with cancer, all exons, and genome wide. In three separate primary human hematopoietic stem and progenitor cell (HSPC) donors assessed in technical triplicates, we electroporated high-fidelity Cas9 protein targeted to three loci (AAVS1, HBB, and ZFPM2) and harvested genomic DNA at days 4 and 10. Our results demonstrate that clinically relevant delivery of high-fidelity Cas9 to primary HSPCs and ex vivo culture up to 10 days does not introduce or enrich for tumorigenic variants and that even a single SNP in a gRNA spacer sequence is sufficient to eliminate Cas9 off-target activity in primary, repair-competent human HSPCs.
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Affiliation(s)
- M Kyle Cromer
- Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
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11
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Wanowska E, Samorowska K, Szcześniak MW. Emerging Roles of Long Noncoding RNAs in Breast Cancer Epigenetics and Epitranscriptomics. Front Cell Dev Biol 2022; 10:922351. [PMID: 35865634 PMCID: PMC9294602 DOI: 10.3389/fcell.2022.922351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Breast carcinogenesis is a multistep process that involves both genetic and epigenetic changes. Epigenetics refers to reversible changes in gene expression that are not accompanied by changes in gene sequence. In breast cancer (BC), dysregulated epigenetic changes, such as DNA methylation and histone modifications, are accompanied by epitranscriptomic changes, in particular adenine to inosine modifications within RNA molecules. Factors that trigger these phenomena are largely unknown, but there is evidence for widespread participation of long noncoding RNAs (lncRNAs) that already have been linked to virtually any aspect of BC biology, making them promising biomarkers and therapeutic targets in BC patients. Here, we provide a systematic review of known and possible roles of lncRNAs in epigenetic and epitranscriptomic processes, along with methods and tools to study them, followed by a brief overview of current challenges regarding the use of lncRNAs in medical applications.
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Affiliation(s)
- Elżbieta Wanowska
- Department of Biological Sciences, Auburn University, Auburn, AL, United States
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland
- *Correspondence: Elżbieta Wanowska, ; Michał Wojciech Szcześniak,
| | - Klaudia Samorowska
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland
| | - Michał Wojciech Szcześniak
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland
- *Correspondence: Elżbieta Wanowska, ; Michał Wojciech Szcześniak,
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12
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Daifu T, Mikami M, Hiramatsu H, Iwai A, Umeda K, Noura M, Kubota H, Masuda T, Furuichi K, Takasaki S, Noguchi Y, Morita K, Bando T, Hirata M, Kataoka TR, Nakahata T, Kuwahara Y, Iehara T, Hosoi H, Takita J, Sugiyama H, Adachi S, Kamikubo Y. Suppression of malignant rhabdoid tumors through Chb-M'-mediated RUNX1 inhibition. Pediatr Blood Cancer 2021; 68:e28789. [PMID: 33180377 DOI: 10.1002/pbc.28789] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 10/16/2020] [Accepted: 10/19/2020] [Indexed: 02/03/2023]
Abstract
Malignant rhabdoid tumor (MRT) is a rare and highly aggressive pediatric malignancy primarily affecting infants and young children. Intensive multimodal therapies currently given to MRT patients are not sufficiently potent to control this highly malignant tumor. Therefore, additive or alternative therapy for these patients with a poor prognosis is necessary. We herein demonstrated that the inhibition of runt-related transcription factor 1 (RUNX1) by novel alkylating conjugated pyrrole-imidazole (PI) polyamides, which specifically recognize and bind to RUNX-binding DNA sequences, was highly effective in the treatment of rhabdoid tumor cell lines in vitro as well as in an in vivo mouse model. Therefore, suppression of RUNX1 activity may be a novel strategy for MRT therapy.
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Affiliation(s)
- Tomoo Daifu
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Masamitsu Mikami
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Hidefumi Hiramatsu
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Atsushi Iwai
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Katsutsugu Umeda
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Mina Noura
- Department of Human Health Sciences, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Hirohito Kubota
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Tatsuya Masuda
- Department of Human Health Sciences, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Kana Furuichi
- Department of Human Health Sciences, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Saho Takasaki
- Department of Human Health Sciences, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Yuki Noguchi
- Department of Human Health Sciences, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Ken Morita
- Department of Human Health Sciences, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Masahiro Hirata
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
| | - Tatsuki R Kataoka
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
| | - Tatsutoshi Nakahata
- Drug Discovery Technology Development Office, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Yasumichi Kuwahara
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto, Japan
| | - Tomoko Iehara
- Department of Pediatrics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto, Japan
| | - Hajime Hosoi
- Department of Pediatrics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto, Japan
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Souichi Adachi
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan.,Department of Human Health Sciences, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Yasuhiko Kamikubo
- Department of Human Health Sciences, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan
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13
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Weidle UH, Birzele F, Nopora A. microRNAs Promoting Growth of Gastric Cancer Xenografts and Correlation to Clinical Prognosis. Cancer Genomics Proteomics 2021; 18:1-15. [PMID: 33419892 DOI: 10.21873/cgp.20237] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/02/2020] [Accepted: 10/05/2020] [Indexed: 02/06/2023] Open
Abstract
The annual death toll for gastric cancer is in the range of 700,000 worldwide. Even in patients with early-stage gastric cancer recurrence within five years has been observed after surgical resection and following chemotherapy with therapy-resistant features. Therefore, the identification of new targets and treatment modalities for gastric cancer is of paramount importance. In this review we focus on the role of microRNAs with documented efficacy in preclinical xenograft models with respect to growth of human gastric cancer cells. We have identified 31 miRs (-10b, -19a, -19b, -20a, -23a/b, -25, -27a-3p, -92a, -93, -100, -106a, -130a, -135a, -135b-5p, -151-5p, -187, -199-3p, -215, -221-3p, -224, -340a, -382, -421, -425, -487a, -493, -532-3p, -575, -589, -664a-3p) covering 26 different targets which promote growth of gastric cancer cells in vitro and in vivo as xenografts. Five miRs (miRs -10b, 151-5p, -187, 532-3p and -589) additionally have an impact on metastasis. Thirteen of the identified miRs (-19b, -20a/b, -25, -92a, -106a, -135a, -187, -221-3p, -340a, -421, -493, -575 and -589) have clinical impact on worse prognosis in patients.
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Affiliation(s)
- Ulrich H Weidle
- Roche Pharma Research and Early Development, Roche Innovation Center Munich, Penzberg, Germany;
| | - Fabian Birzele
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland
| | - Adam Nopora
- Roche Pharma Research and Early Development, Roche Innovation Center Munich, Penzberg, Germany;
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14
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Thakuri BKC, Zhang J, Zhao J, Nguyen LN, Nguyen LNT, Schank M, Khanal S, Dang X, Cao D, Lu Z, Wu XY, Jiang Y, El Gazzar M, Ning S, Wang L, Moorman JP, Yao ZQ. HCV-Associated Exosomes Upregulate RUNXOR and RUNX1 Expressions to Promote MDSC Expansion and Suppressive Functions through STAT3-miR124 Axis. Cells 2020; 9:cells9122715. [PMID: 33353065 PMCID: PMC7766103 DOI: 10.3390/cells9122715] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/09/2020] [Accepted: 12/17/2020] [Indexed: 12/17/2022] Open
Abstract
RUNX1 overlapping RNA (RUNXOR) is a long non-coding RNA and plays a pivotal role in the differentiation of myeloid cells via targeting runt-related transcription factor 1 (RUNX1). We and others have previously reported that myeloid-derived suppressor cells (MDSCs) expand and inhibit host immune responses during chronic viral infections; however, the mechanisms responsible for MDSC differentiation and suppressive functions, in particular the role of RUNXOR–RUNX1, remain unclear. Here, we demonstrated that RUNXOR and RUNX1 expressions are significantly upregulated and associated with elevated levels of immunosuppressive molecules, such as arginase 1 (Arg1), inducible nitric oxide synthase (iNOS), signal transducer and activator of transcription 3 (STAT3), and reactive oxygen species (ROS) in MDSCs during chronic hepatitis C virus (HCV) infection. Mechanistically, we discovered that HCV-associated exosomes (HCV-Exo) can induce the expressions of RUNXOR and RUNX1, which in turn regulates miR-124 expression via STAT3 signaling, thereby promoting MDSC differentiation and suppressive functions. Importantly, overexpression of RUNXOR in healthy CD33+ myeloid cells promoted differentiation and suppressive functions of MDSCs. Conversely, silencing RUNXOR or RUNX1 expression in HCV-derived CD33+ myeloid cells significantly inhibited their differentiation and expressions of suppressive molecules and improved the function of co-cultured autologous CD4 T cells. Taken together, these results indicate that the RUNXOR–RUNX1–STAT3–miR124 axis enhances the differentiation and suppressive functions of MDSCs and could be a potential target for immunomodulation in conjunction with antiviral therapy during chronic HCV infection.
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Affiliation(s)
- Bal Krishna Chand Thakuri
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Jinyu Zhang
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Juan Zhao
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Lam N. Nguyen
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Lam N. T. Nguyen
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Madison Schank
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Sushant Khanal
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Xindi Dang
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Dechao Cao
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Zeyuan Lu
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Xiao Y. Wu
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Yong Jiang
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
| | - Mohamed El Gazzar
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
| | - Shunbin Ning
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Ling Wang
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Jonathan P. Moorman
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
- Hepatitis (HCV/HBV/HIV) Program, James H. Quillen VA Medical Center, Department of Veterans Affairs, Johnson City, TN 37614, USA
| | - Zhi Q. Yao
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
- Hepatitis (HCV/HBV/HIV) Program, James H. Quillen VA Medical Center, Department of Veterans Affairs, Johnson City, TN 37614, USA
- Correspondence: ; Tel.: +1-423-439-8029; Fax: +1-423-439-7010
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15
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Wang W, Chen Y, Xu A, Cai M, Cao J, Zhu H, Yang B, Shao X, Ying M, He Q. Protein phase separation: A novel therapy for cancer? Br J Pharmacol 2020; 177:5008-5030. [PMID: 32851637 DOI: 10.1111/bph.15242] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 07/18/2020] [Accepted: 08/17/2020] [Indexed: 12/14/2022] Open
Abstract
In recent years, phase separation has been increasingly reported to play a pivotal role in a wide range of biological processes. Due to the close relationships between cancer and disorders in intracellular physiological function, the identification of new mechanisms involved in intracellular regulation has been regarded as a new direction for cancer therapy. Introducing the concept of phase separation into complex descriptions of disease mechanisms may provide many different insights. Here, we review the recent findings on the phase separation of cancer-related proteins, describing the possible relationships between phase separation and key proteins associated with cancer and indicate possible regulatory modalities, especially drug candidates for phase separation, which may provide more effective strategies for cancer therapy.
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Affiliation(s)
- Wei Wang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Yingqian Chen
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Aixiao Xu
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Minyi Cai
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Ji Cao
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Hong Zhu
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Bo Yang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Xuejing Shao
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Meidan Ying
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Qiaojun He
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
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16
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Rose JT, Moskovitz E, Boyd JR, Gordon JA, Bouffard NA, Fritz AJ, Illendula A, Bushweller JH, Lian JB, Stein JL, Zaidi SK, Stein GS. Inhibition of the RUNX1-CBFβ transcription factor complex compromises mammary epithelial cell identity: a phenotype potentially stabilized by mitotic gene bookmarking. Oncotarget 2020; 11:2512-2530. [PMID: 32655837 PMCID: PMC7335667 DOI: 10.18632/oncotarget.27637] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 05/20/2020] [Indexed: 12/12/2022] Open
Abstract
RUNX1 has recently been shown to play an important role in determination of mammary epithelial cell identity. However, mechanisms by which loss of the RUNX1 transcription factor in mammary epithelial cells leads to epithelial-to-mesenchymal transition (EMT) are not known. Here, we report that interaction between RUNX1 and its heterodimeric partner CBFβ is essential for sustaining mammary epithelial cell identity. Disruption of RUNX1-CBFβ interaction, DNA binding, and association with mitotic chromosomes alters cell morphology, global protein synthesis, and phenotype-related gene expression. During interphase, RUNX1 is organized as punctate, predominantly nuclear, foci that are dynamically redistributed during mitosis, with a subset localized to mitotic chromosomes. Genome-wide RUNX1 occupancy profiles for asynchronous, mitotically enriched, and early G1 breast epithelial cells reveal RUNX1 associates with RNA Pol II-transcribed protein coding and long non-coding RNA genes and RNA Pol I-transcribed ribosomal genes critical for mammary epithelial proliferation, growth, and phenotype maintenance. A subset of these genes remains occupied by the protein during the mitosis to G1 transition. Together, these findings establish that the RUNX1-CBFβ complex is required for maintenance of the normal mammary epithelial phenotype and its disruption leads to EMT. Importantly, our results suggest, for the first time, that RUNX1 mitotic bookmarking of a subset of epithelial-related genes may be an important epigenetic mechanism that contributes to stabilization of the mammary epithelial cell identity.
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Affiliation(s)
- Joshua T. Rose
- Department of Biochemistry and University of Vermont Cancer Center, Robert Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
- These authors contributed equally to this work
| | - Eliana Moskovitz
- Department of Biochemistry and University of Vermont Cancer Center, Robert Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
- These authors contributed equally to this work
| | - Joseph R. Boyd
- Department of Biochemistry and University of Vermont Cancer Center, Robert Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Jonathan A. Gordon
- Department of Biochemistry and University of Vermont Cancer Center, Robert Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Nicole A. Bouffard
- Microscopy Imaging Center at the Robert Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Andrew J. Fritz
- Department of Biochemistry and University of Vermont Cancer Center, Robert Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Anuradha Illendula
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - John H. Bushweller
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Jane B. Lian
- Department of Biochemistry and University of Vermont Cancer Center, Robert Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Janet L. Stein
- Department of Biochemistry and University of Vermont Cancer Center, Robert Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Sayyed K. Zaidi
- Department of Biochemistry and University of Vermont Cancer Center, Robert Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Gary S. Stein
- Department of Biochemistry and University of Vermont Cancer Center, Robert Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
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Nie Y, Zhou L, Wang H, Chen N, Jia L, Wang C, Wang Y, Chen J, Wen X, Niu C, Li H, Guo R, Zhang S, Cui J, Hoffman AR, Hu JF, Li W. Profiling the epigenetic interplay of lncRNA RUNXOR and oncogenic RUNX1 in breast cancer cells by gene in situ cis-activation. Am J Cancer Res 2019; 9:1635-1649. [PMID: 31497347 PMCID: PMC6726995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 07/19/2019] [Indexed: 06/10/2023] Open
Abstract
RUNX1 is frequently mutated as chromosomal translocations in a variety of hematological malignancies. Recent studies show that RUNX1 is also mutated somatically in many solid tumors. We have recently identified a 260 kb un-spliced intragenic overlapping long noncoding RNA RUNXOR in the RUNX1 locus, yet its role as an epigenetic regulator in tumors remains to be characterized. To delineate this RUNXOR-RUNX1 regulatory interplay in breast cancer cells, we devised a novel "gene in situ cis-activation" approach to activate the endogenous RUNXOR gene. We found that the in situ activation of RUNXOR lncRNA upregulated RUNX1 in cis from the P1 promoter. The preferred activation of the P1 promoter caused a shift to the RUNX1c isoform expression. Using a chromatin conformation capture (3C) approach, we showed that RUNXOR lncRNA epigenetically activated the RUNX1 P1 promoter in cis by altering the local chromatin structure. The binding of RUNXOR lncRNA triggered DNA demethylation and induced active histone modification markers in the P1 CpG island. Changes in RUNX1 isoform composition correlated with a trend to cell cycle arrest at G0/G1, although cell proliferation rate, apoptosis, and migration ability were not significantly changed. Our results reveal an underlying epigenetic mechanism by which the lncRNA regulates in cis the RUNX1 promoter usage in breast cancer cells, thereby shedding light on potential genetic therapies in malignancies in which RUNX1 loss-of-function mutations frequently occur.
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Affiliation(s)
- Yuanyuan Nie
- Stem Cell and Cancer Center, First Hospital, Jilin UniversityChangchun 130061, Jilin, China
- Stanford University Medical School, VA Palo Alto Health Care SystemPalo Alto, CA 94304, USA
| | - Lei Zhou
- Stem Cell and Cancer Center, First Hospital, Jilin UniversityChangchun 130061, Jilin, China
| | - Hong Wang
- Stem Cell and Cancer Center, First Hospital, Jilin UniversityChangchun 130061, Jilin, China
| | - Naifei Chen
- Stem Cell and Cancer Center, First Hospital, Jilin UniversityChangchun 130061, Jilin, China
| | - Lin Jia
- Stem Cell and Cancer Center, First Hospital, Jilin UniversityChangchun 130061, Jilin, China
- Stanford University Medical School, VA Palo Alto Health Care SystemPalo Alto, CA 94304, USA
| | - Cong Wang
- Stem Cell and Cancer Center, First Hospital, Jilin UniversityChangchun 130061, Jilin, China
- Stanford University Medical School, VA Palo Alto Health Care SystemPalo Alto, CA 94304, USA
| | - Yichen Wang
- Stem Cell and Cancer Center, First Hospital, Jilin UniversityChangchun 130061, Jilin, China
- Stanford University Medical School, VA Palo Alto Health Care SystemPalo Alto, CA 94304, USA
| | - Jingcheng Chen
- Stem Cell and Cancer Center, First Hospital, Jilin UniversityChangchun 130061, Jilin, China
- Stanford University Medical School, VA Palo Alto Health Care SystemPalo Alto, CA 94304, USA
| | - Xue Wen
- Stem Cell and Cancer Center, First Hospital, Jilin UniversityChangchun 130061, Jilin, China
| | - Chao Niu
- Stem Cell and Cancer Center, First Hospital, Jilin UniversityChangchun 130061, Jilin, China
| | - Hui Li
- Stem Cell and Cancer Center, First Hospital, Jilin UniversityChangchun 130061, Jilin, China
| | - Rui Guo
- Stem Cell and Cancer Center, First Hospital, Jilin UniversityChangchun 130061, Jilin, China
| | - Songling Zhang
- Stem Cell and Cancer Center, First Hospital, Jilin UniversityChangchun 130061, Jilin, China
| | - Jiuwei Cui
- Stem Cell and Cancer Center, First Hospital, Jilin UniversityChangchun 130061, Jilin, China
| | - Andrew R Hoffman
- Stanford University Medical School, VA Palo Alto Health Care SystemPalo Alto, CA 94304, USA
| | - Ji-Fan Hu
- Stem Cell and Cancer Center, First Hospital, Jilin UniversityChangchun 130061, Jilin, China
- Stanford University Medical School, VA Palo Alto Health Care SystemPalo Alto, CA 94304, USA
| | - Wei Li
- Stem Cell and Cancer Center, First Hospital, Jilin UniversityChangchun 130061, Jilin, China
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Hasan MS, Wu X, Zhang L. Uncovering missed indels by leveraging unmapped reads. Sci Rep 2019; 9:11093. [PMID: 31366961 PMCID: PMC6668410 DOI: 10.1038/s41598-019-47405-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 07/12/2019] [Indexed: 02/08/2023] Open
Abstract
In current practice, Next Generation Sequencing (NGS) applications start with mapping/aligning short reads to the reference genome, with the aim of identifying genetic variants. Although existing alignment tools have shown great accuracy in mapping short reads to the reference genome, a significant number of short reads still remain unmapped and are often excluded from downstream analyses thereby causing nonnegligible information loss in the subsequent variant calling procedure. This paper describes Genesis-indel, a computational pipeline that explores the unmapped reads to identify novel indels that are initially missed in the original procedure. Genesis-indel is applied to the unmapped reads of 30 breast cancer patients from TCGA. Results show that the unmapped reads are conserved between the two subtypes of breast cancer investigated in this study and might contribute to the divergence between the subtypes. Genesis-indel identifies 72,997 novel high-quality indels previously not found, among which 16,141 have not been annotated in the widely used mutation database. Statistical analysis of these indels shows significant enrichment of indels residing in oncogenes and tumour suppressor genes. Functional annotation further reveals that these indels are strongly correlated with pathways of cancer and can have high to moderate impact on protein functions. Additionally, some of the indels overlap with the genes that do not have any indel mutations called from the originally mapped reads but have been shown to contribute to the tumorigenesis in multiple carcinomas, further emphasizing the importance of rescuing indels hidden in the unmapped reads in cancer and disease studies.
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Affiliation(s)
| | - Xiaowei Wu
- Department of Statistics, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Liqing Zhang
- Department of Computer Science, Virginia Tech, Blacksburg, VA, 24061, USA.
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19
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Down-regulation of lncRNA-NEF indicates poor prognosis in intrahepatic cholangiocarcinoma. Biosci Rep 2019; 39:BSR20181573. [PMID: 31015363 PMCID: PMC6527927 DOI: 10.1042/bsr20181573] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 01/26/2019] [Accepted: 03/18/2019] [Indexed: 11/17/2022] Open
Abstract
LncRNA-NEF is a tumor suppressor lncRNA in liver cancer. The present study aimed to investigate the role of lncRNA-NEF in intrahepatic cholangiocarcinoma (IHCC), which is second most common type of primary cancer of the hepatobiliary system that causes high mortality rate. In the present study we found that lncRNA-NEF was down-regulated, while Runt-related transcription factor 1 (RUNX1) was up-regulated in tumor tissues than in adjacent healthy tissues of IHCC patients. Expression levels of lncRNA-NEF and RUNX1 were significantly and reversely correlated in tumor tissues but not in adjacent healthy tissues. Plasma levels of lncRNA-NEF were significantly lower in IHCC patients than in healthy controls. Down-regulation of lncRNA-NEF effectively distinguished stage I and II IHCC patients from healthy controls. Patients were followed up for 5 years, patients with high plasma levels of lncRNA-NEF showed significantly better survival conditions compared with patients with low expression levels of lncRNA-NEF. LncRNA-NEF overexpression led to inhibited expression of RUNX1 in cells of IHCC cell lines and inhibited cancer cell migration and invasion. In contrast, RUNX1 overexpression showed no significant effects on lncRNA-NEF expression, but attenuated the effects of lncRNA-NEF overexpression on cancer cell migration and invasion. We therefore concluded that lncRNA-NEF participated in IHCC possibly by interacting with RUNX1.
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Zhu SY, Wu QY, Zhang CX, Wang Q, Ling J, Huang XT, Sun X, Yuan M, Wu D, Yin HF. miR-20a inhibits the killing effect of natural killer cells to cervical cancer cells by downregulating RUNX1. Biochem Biophys Res Commun 2018; 505:309-316. [PMID: 30249397 DOI: 10.1016/j.bbrc.2018.09.102] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 09/16/2018] [Indexed: 12/28/2022]
Abstract
BACKGROUND NK cells are presented in tumor microenvironments and acts as an essential defense line against multiple malignancies. Recently, miRNAs are reported to involve in the development of natural killer (NK) cells via negatively regulating gene expression. Here, we aim to explore the function and mechanism underlying how miR-20a modulated the killing effect of NK cells to cervical cancer cells. METHODS Abundances of miR-20a and runt-related transcription factor 1 (RUNX1) in NK cells from cervical cancer patients and healthy donors were detected by qRT-PCR and western blot. The releases of IFN-γ and TNF-α were determined by ELISA. The cytotoxicity of NK cells against cervical cancer cells was measured by CytoTox 96 non-radioactive cytotoxicity assay. Luciferase reporter, western blot, and RNA immunoprecipitation (RIP) assays were performed to assess the interaction between miR-20a and RUNX1. RESULT miR-20a was upregulated while RUNX1 was downregulated in NK cells from cervical cancer patients compared to healthy donors. IL-2 stimulated the releases of IFN-γ and TNF-α, and the killing effect of NK cells to cervical cancer cells, which was overturned by miR-20a introduction. RUNX1 was identified to be a target of miR-20a. Restoration of RUNX1 abolished the inhibitory effects of miR-20a on the secretions of IFN-γ and TNF-α, as well as the killing effect of NK cells to colorectal cancer cells. CONCLUSION miR-20a attenuated the killing effect of NK cells to cervical cancer cells by directly targeting RUNX1.
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Affiliation(s)
- Suo-Yu Zhu
- Department of Obstetrics and Gynecology, Affiliated Jiangyin Hospital of South-East University, Jiangyin, 214400, China
| | - Qun-Ying Wu
- Department of Obstetrics and Gynecology, Affiliated Jiangyin Hospital of South-East University, Jiangyin, 214400, China
| | - Chen-Xia Zhang
- Department of Obstetrics and Gynecology, Affiliated Jiangyin Hospital of South-East University, Jiangyin, 214400, China
| | - Qiong Wang
- Department of Oncology, Affiliated Jiangyin Hospital of South-East University, Jiangyin, 214400, China
| | - Jing Ling
- Department of Obstetrics and Gynecology, Affiliated Jiangyin Hospital of South-East University, Jiangyin, 214400, China
| | - Xian-Ting Huang
- Department of Oncology, Affiliated Jiangyin Hospital of South-East University, Jiangyin, 214400, China
| | - Xia Sun
- Department of Oncology, Affiliated Jiangyin Hospital of South-East University, Jiangyin, 214400, China
| | - Ming Yuan
- Department of Oncology, Affiliated Jiangyin Hospital of South-East University, Jiangyin, 214400, China
| | - Dan Wu
- Department of Oncology, Affiliated Jiangyin Hospital of South-East University, Jiangyin, 214400, China
| | - Hua-Fang Yin
- Department of Oncology, Affiliated Jiangyin Hospital of South-East University, Jiangyin, 214400, China.
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21
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Penkert J, Schmidt G, Hofmann W, Schubert S, Schieck M, Auber B, Ripperger T, Hackmann K, Sturm M, Prokisch H, Hille-Betz U, Mark D, Illig T, Schlegelberger B, Steinemann D. Breast cancer patients suggestive of Li-Fraumeni syndrome: mutational spectrum, candidate genes, and unexplained heredity. Breast Cancer Res 2018; 20:87. [PMID: 30086788 PMCID: PMC6081832 DOI: 10.1186/s13058-018-1011-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 06/27/2018] [Indexed: 01/07/2023] Open
Abstract
Background Breast cancer is the most prevalent tumor entity in Li-Fraumeni syndrome. Up to 80% of individuals with a Li-Fraumeni-like phenotype do not harbor detectable causative germline TP53 variants. Yet, no systematic panel analyses for a wide range of cancer predisposition genes have been conducted on cohorts of women with breast cancer fulfilling Li-Fraumeni(-like) clinical diagnostic criteria. Methods To specifically help explain the diagnostic gap of TP53 wild-type Li-Fraumeni(-like) breast cancer cases, we performed array-based CGH (comparative genomic hybridization) and panel-based sequencing of 94 cancer predisposition genes on 83 breast cancer patients suggestive of Li-Fraumeni syndrome who had previously had negative test results for causative BRCA1, BRCA2, and TP53 germline variants. Results We identified 13 pathogenic or likely pathogenic germline variants in ten patients and in nine genes, including four copy number aberrations and nine single-nucleotide variants or small indels. Three patients presented as double-mutation carriers involving two different genes each. In five patients (5 of 83; 6% of cohort), we detected causative pathogenic variants in established hereditary breast cancer susceptibility genes (i.e., PALB2, CHEK2, ATM). Five further patients (5 of 83; 6% of cohort) were found to harbor pathogenic variants in genes lacking a firm association with breast cancer susceptibility to date (i.e., Fanconi pathway genes, RECQ family genes, CDKN2A/p14ARF, and RUNX1). Conclusions Our study details the mutational spectrum in breast cancer patients suggestive of Li-Fraumeni syndrome and indicates the need for intensified research on monoallelic variants in Fanconi pathway and RECQ family genes. Notably, this study further reveals a large portion of still unexplained Li-Fraumeni(-like) cases, warranting comprehensive investigation of recently described candidate genes as well as noncoding regions of the TP53 gene in patients with Li-Fraumeni(-like) syndrome lacking TP53 variants in coding regions. Electronic supplementary material The online version of this article (10.1186/s13058-018-1011-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Judith Penkert
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany.
| | - Gunnar Schmidt
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
| | - Winfried Hofmann
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
| | - Stephanie Schubert
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
| | - Maximilian Schieck
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
| | - Bernd Auber
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
| | - Tim Ripperger
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
| | - Karl Hackmann
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Partner Site Dresden, Dresden, Germany
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Holger Prokisch
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Ursula Hille-Betz
- Department of Gynecology and Obstetrics, Hannover Medical School, Hannover, Germany
| | - Dorothea Mark
- Department of Internal Medicine, Hematology/Oncology, University Hospital Frankfurt, Frankfurt, Germany
| | - Thomas Illig
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
| | - Brigitte Schlegelberger
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
| | - Doris Steinemann
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
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22
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Zaidi SK, Fritz AJ, Tracy KM, Gordon JA, Tye CE, Boyd J, Van Wijnen AJ, Nickerson JA, Imbalzano AN, Lian JB, Stein JL, Stein GS. Nuclear organization mediates cancer-compromised genetic and epigenetic control. Adv Biol Regul 2018; 69:1-10. [PMID: 29759441 PMCID: PMC6102062 DOI: 10.1016/j.jbior.2018.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 04/13/2018] [Accepted: 05/02/2018] [Indexed: 12/19/2022]
Abstract
Nuclear organization is functionally linked to genetic and epigenetic regulation of gene expression for biological control and is modified in cancer. Nuclear organization supports cell growth and phenotypic properties of normal and cancer cells by facilitating physiologically responsive interactions of chromosomes, genes and regulatory complexes at dynamic three-dimensional microenvironments. We will review nuclear structure/function relationships that include: 1. Epigenetic bookmarking of genes by phenotypic transcription factors to control fidelity and plasticity of gene expression as cells enter and exit mitosis; 2. Contributions of chromatin remodeling to breast cancer nuclear morphology, metabolism and effectiveness of chemotherapy; 3. Relationships between fidelity of nuclear organization and metastasis of breast cancer to bone; 4. Dynamic modifications of higher-order inter- and intra-chromosomal interactions in breast cancer cells; 5. Coordinate control of cell growth and phenotype by tissue-specific transcription factors; 6. Oncofetal epigenetic control by bivalent histone modifications that are functionally related to sustaining the stem cell phenotype; and 7. Noncoding RNA-mediated regulation in the onset and progression of breast cancer. The discovery of components to nuclear organization that are functionally related to cancer and compromise gene expression have the potential for translation to innovative cancer diagnosis and targeted therapy.
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Affiliation(s)
- Sayyed K Zaidi
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, VT, United States
| | - Andrew J Fritz
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, VT, United States
| | - Kirsten M Tracy
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, VT, United States
| | - Jonathan A Gordon
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, VT, United States
| | - Coralee E Tye
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, VT, United States
| | - Joseph Boyd
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, VT, United States
| | - Andre J Van Wijnen
- Departments of Orthopedic Surgery, Biochemistry & Molecular Biology, Mayo Clinic, Rochester, MN, United States
| | - Jeffrey A Nickerson
- Department of Pediatrics, UMass Medical School, Worcester, MA, United States
| | - Antony N Imbalzano
- Graduate Program in Cell Biology and Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, MA, United States
| | - Jane B Lian
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, VT, United States
| | - Janet L Stein
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, VT, United States.
| | - Gary S Stein
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, VT, United States.
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23
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Meng G. Applying Expression Profile Similarity for Discovery of Patient-Specific Functional Mutations. High Throughput 2018; 7:E6. [PMID: 29485617 PMCID: PMC5876532 DOI: 10.3390/ht7010006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 02/04/2018] [Accepted: 02/14/2018] [Indexed: 02/07/2023] Open
Abstract
The progress of cancer genome sequencing projects yields unprecedented information of mutations for numerous patients. However, the complexity of mutation profiles of cancer patients hinders the further understanding to mechanisms of oncogenesis. One basic question is how to find mutations with functional impacts. In this work, we introduce a computational method to predict functional somatic mutations of each patient by integrating mutation recurrence with expression profile similarity. With this method, the functional mutations are determined by checking the mutation enrichment among a group of patients with similar expression profiles. We applied this method to three cancer types and identified the functional mutations. Comparison of the predictions for three cancer types suggested that most of the functional mutations were cancer-type-specific with one exception to p53. By checking predicted results, we found that our method effectively filtered non-functional mutations resulting from large protein sizes. In addition, this method can also perform functional annotation to each patient to describe their association with signalling pathways or biological processes. In breast cancer, we predicted "cell adhesion" and other terms to be significantly associated with oncogenesis.
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Affiliation(s)
- Guofeng Meng
- BT science Inc., No. 24, Tang'an Road, Shanghai, China.
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24
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Ramsey J, Butnor K, Peng Z, Leclair T, van der Velden J, Stein G, Lian J, Kinsey CM. Loss of RUNX1 is associated with aggressive lung adenocarcinomas. J Cell Physiol 2017; 233:3487-3497. [PMID: 28926105 DOI: 10.1002/jcp.26201] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 09/08/2017] [Indexed: 12/25/2022]
Abstract
The mammalian runt-related factor 1 (RUNX1) is a master transcription factor that regulates lineage specification of hematopoietic stem cells. RUNX1 translocations result in the development of myeloid leukemias. Recently, RUNX1 has been implicated as a tumor suppressor in other cancers. We postulated RUNX1 expression may be associated with lung adenocarcinoma etiology and/or progression. We evaluated the association of RUNX1 mRNA expression with overall survival data from The Cancer Genome Atlas (TCGA), a publically available database. Compared to high expression levels, Low RUNX1 levels from lung adenocarcinomas were associated with a worse overall survival (Hazard Ratio = 2.014 (1.042-3.730 95% confidence interval), log-rank p = 0.035) compared to those that expressed high RUNX1 levels. Further immunohistochemical examination of 85 surgical specimens resected at the University of Vermont Medical Center identified that low RUNX1 protein expression was associated with larger tumors (p = 0.038). Gene expression network analysis was performed on the same subset of TCGA cases that demonstrated differential survival by RUNX1 expression. This analysis, which reveals regulatory relationships, showed that reduced RUNX1 levels were closely linked to upregulation of the transcription factor E2F1. To interrogate this relationship, RUNX1 was depleted in a lung cancer cell line that expresses high levels of RUNX1. Loss of RUNX1 resulted in enhanced proliferation, migration, and invasion. RUNX1 depletion also resulted in increased mRNA expression of E2F1 and multiple E2F1 target genes. Our data implicate loss of RUNX1 as driver of lung adenocarcinoma aggression, potentially through deregulation of the E2F1 pathway.
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Affiliation(s)
- Jon Ramsey
- Department of Biochemistry, University of Vermont, Burlington, Vermont
| | - Kelly Butnor
- Department of Pathology, University of Vermont Medical Center, Burlington, Vermont
| | - Zhihua Peng
- Department of Pathology, University of Vermont Medical Center, Burlington, Vermont
| | - Tim Leclair
- Department of Thoracic Surgery and Interventional Pulmonology, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Jos van der Velden
- Department of Pathology, University of Vermont Medical Center, Burlington, Vermont
| | - Gary Stein
- Department of Biochemistry, University of Vermont, Burlington, Vermont
| | - Jane Lian
- Department of Biochemistry, University of Vermont, Burlington, Vermont
| | - C Matthew Kinsey
- Pulmonary and Critical Care, University of Vermont Medical Center, Burlington, Vermont
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Wang W, Xu ZZ, Costanzo M, Boone C, Lange CA, Myers CL. Pathway-based discovery of genetic interactions in breast cancer. PLoS Genet 2017; 13:e1006973. [PMID: 28957314 PMCID: PMC5619706 DOI: 10.1371/journal.pgen.1006973] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 08/10/2017] [Indexed: 01/22/2023] Open
Abstract
Breast cancer is the second largest cause of cancer death among U.S. women and the leading cause of cancer death among women worldwide. Genome-wide association studies (GWAS) have identified several genetic variants associated with susceptibility to breast cancer, but these still explain less than half of the estimated genetic contribution to the disease. Combinations of variants (i.e. genetic interactions) may play an important role in breast cancer susceptibility. However, due to a lack of statistical power, the current tests for genetic interactions from GWAS data mainly leverage prior knowledge to focus on small sets of genes or SNPs that are known to have an association with breast cancer. Thus, many genetic interactions, particularly among novel variants, remain understudied. Reverse-genetic interaction screens in model organisms have shown that genetic interactions frequently cluster into highly structured motifs, where members of the same pathway share similar patterns of genetic interactions. Based on this key observation, we recently developed a method called BridGE to search for such structured motifs in genetic networks derived from GWAS studies and identify pathway-level genetic interactions in human populations. We applied BridGE to six independent breast cancer cohorts and identified significant pathway-level interactions in five cohorts. Joint analysis across all five cohorts revealed a high confidence consensus set of genetic interactions with support in multiple cohorts. The discovered interactions implicated the glutathione conjugation, vitamin D receptor, purine metabolism, mitotic prometaphase, and steroid hormone biosynthesis pathways as major modifiers of breast cancer risk. Notably, while many of the pathways identified by BridGE show clear relevance to breast cancer, variants in these pathways had not been previously discovered by traditional single variant association tests, or single pathway enrichment analysis that does not consider SNP-SNP interactions.
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Affiliation(s)
- Wen Wang
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, United States of America
| | - Zack Z. Xu
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, United States of America
- HealthPartners Institute, Minneapolis, MN, United States of America
| | | | - Charles Boone
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Carol A. Lange
- Departments of Medicine and Pharmacology, Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States of America
| | - Chad L. Myers
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, United States of America
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26
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Breast ductal carcinoma in situ carry mutational driver events representative of invasive breast cancer. Mod Pathol 2017; 30:952-963. [PMID: 28338653 DOI: 10.1038/modpathol.2017.21] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 02/11/2017] [Accepted: 02/19/2017] [Indexed: 12/31/2022]
Abstract
The spectrum of genomic alterations in ductal carcinoma in situ (DCIS) is relatively unexplored, but is likely to provide useful insights into its biology, its progression to invasive carcinoma and the risk of recurrence. DCIS (n=20) with a range of phenotypes was assessed by massively parallel sequencing for mutations and copy number alterations and variants validated by Sanger sequencing. PIK3CA mutations were identified in 11/20 (55%), TP53 mutations in 6/20 (30%), and GATA3 mutations in 9/20 (45%). Screening an additional 91 cases for GATA3 mutations identified a final frequency of 27% (30/111), with a high proportion of missense variants (8/30). TP53 mutations were exclusive to high grade DCIS and more frequent in PR-negative tumors compared with PR-positive tumors (P=0.037). TP53 mutant tumors also had a significantly higher fraction of the genome altered by copy number than wild-type tumors (P=0.005), including a significant positive association with amplification or gain of ERBB2 (P<0.05). The association between TP53 mutation and ERBB2 amplification was confirmed in a wider DCIS cohort using p53 immunohistochemistry as a surrogate marker for TP53 mutations (P=0.03). RUNX1 mutations and MAP2K4 copy number loss were novel findings in DCIS. Frequent copy number alterations included gains on 1q, 8q, 17q, and 20q and losses on 8p, 11q, 16q, and 17p. Patterns of genomic alterations observed in DCIS were similar to those previously reported for invasive breast cancers, with all DCIS having at least one bona fide breast cancer driver event. However, an increase in GATA3 mutations and fewer copy number changes were noted in DCIS compared with invasive carcinomas. The role of such alterations as prognostic and predictive biomarkers in DCIS is an avenue for further investigation.
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27
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Dey N, Krie A, Klein J, Williams K, McMillan A, Elsey R, Sun Y, Williams C, De P, Leyland-Jones B. Down's Syndrome and Triple Negative Breast Cancer: A Rare Occurrence of Distinctive Clinical Relationship. Int J Mol Sci 2017; 18:ijms18061218. [PMID: 28590426 PMCID: PMC5486041 DOI: 10.3390/ijms18061218] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 05/31/2017] [Accepted: 06/05/2017] [Indexed: 02/05/2023] Open
Abstract
Down’s syndrome (DS), the most common genetic cause of significant intellectual disability in children and adults is caused by the trisomy of either all or a part of human chromosome 21 (HSA21). Patients with DS mostly suffer from characteristic tumor types. Although individual patients of DS are at a higher risk for acute leukemia and testicular cancers, other types of solid tumors including breast cancers are mostly uncommon and have significantly lower-than-expected age-adjusted incidence rates. Except for an increased risk of retinoblastomas, and lymphomas, the risk of developing solid tumors has been found to be lower in both children and adults, and breast cancer was found to be almost absent (Hasle H., The Lancet Oncology, 2001). A study conducted in the United States found only one death when 11.65 were expected (Scholl T et al., Dev Med Child Neurol. 1982). A recent study examined mammogram reports of women with DS treated in the largest medical facility specifically serving adults with DS in the United States. It was found that only 0.7% women with DS had been diagnosed with breast cancers (Chicoine B et al., Intellect Dev Disabil. 2015). Here we describe a case of breast cancer in a 25-year-old patient with DS. The disease was presented as lymph node positive carcinoma with alterations of tumor suppressor genes characteristic to the triple negative breast cancer subtype. Comprehensive Genomic Profiling (CGP) revealed a wild-type status for BRCA1. The CGP report showed a frameshift mutation, A359fs*10 of the tumor suppressor gene INPP4B and another frameshift mutation, R282fs*63 of tumor suppressor gene TP53 in the tumor biopsy as characteristically found in triple-negative breast cancers. The VUS (Variance of Unknown Significance) alteration(s) were identified in ASXL1 (L1395V), NTRK1 (G18E), DDR2 (I159T), RUNX1 (amplification), ERG (amplification), SOX2 (T26A), FAM123B (G1031D), and HNF1A (A301T). Bonafide cancer-related genes of chromosome 21 amplified in the patient’s tumor are RUNX1 and ERG genes. After the completion of the radiation, the patient was placed on everolimus which was based on the result of her CGP report. Thus, post-mastectomy radiation therapy was completed with a recommendation for everolimus for one year. During the time of writing of this report, no metastatic lesions were identified. The patient currently has no evidence of disease.
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Affiliation(s)
- Nandini Dey
- Center for Precision Oncology, Department of Molecular and Experimental Medicine, Avera Cancer Institute, Sioux Falls, SD 57105, USA.
- Departmental of Internal Medicine, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD 57105, USA.
| | - Amy Krie
- Center for Precision Oncology, Department of Molecular and Experimental Medicine, Avera Cancer Institute, Sioux Falls, SD 57105, USA.
| | - Jessica Klein
- Center for Precision Oncology, Department of Molecular and Experimental Medicine, Avera Cancer Institute, Sioux Falls, SD 57105, USA.
| | - Kirstin Williams
- Center for Precision Oncology, Department of Molecular and Experimental Medicine, Avera Cancer Institute, Sioux Falls, SD 57105, USA.
| | - Amanda McMillan
- Center for Precision Oncology, Department of Molecular and Experimental Medicine, Avera Cancer Institute, Sioux Falls, SD 57105, USA.
| | - Rachel Elsey
- Center for Precision Oncology, Department of Molecular and Experimental Medicine, Avera Cancer Institute, Sioux Falls, SD 57105, USA.
| | - Yuliang Sun
- Center for Precision Oncology, Department of Molecular and Experimental Medicine, Avera Cancer Institute, Sioux Falls, SD 57105, USA.
| | - Casey Williams
- Center for Precision Oncology, Department of Molecular and Experimental Medicine, Avera Cancer Institute, Sioux Falls, SD 57105, USA.
- Departmental of Internal Medicine, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD 57105, USA.
| | - Pradip De
- Center for Precision Oncology, Department of Molecular and Experimental Medicine, Avera Cancer Institute, Sioux Falls, SD 57105, USA.
- Departmental of Internal Medicine, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD 57105, USA.
| | - Brian Leyland-Jones
- Center for Precision Oncology, Department of Molecular and Experimental Medicine, Avera Cancer Institute, Sioux Falls, SD 57105, USA.
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28
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Jeselsohn R, Cornwell M, Pun M, Buchwalter G, Nguyen M, Bango C, Huang Y, Kuang Y, Paweletz C, Fu X, Nardone A, De Angelis C, Detre S, Dodson A, Mohammed H, Carroll JS, Bowden M, Rao P, Long HW, Li F, Dowsett M, Schiff R, Brown M. Embryonic transcription factor SOX9 drives breast cancer endocrine resistance. Proc Natl Acad Sci U S A 2017; 114:E4482-E4491. [PMID: 28507152 PMCID: PMC5465894 DOI: 10.1073/pnas.1620993114] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The estrogen receptor (ER) drives the growth of most luminal breast cancers and is the primary target of endocrine therapy. Although ER blockade with drugs such as tamoxifen is very effective, a major clinical limitation is the development of endocrine resistance especially in the setting of metastatic disease. Preclinical and clinical observations suggest that even following the development of endocrine resistance, ER signaling continues to exert a pivotal role in tumor progression in the majority of cases. Through the analysis of the ER cistrome in tamoxifen-resistant breast cancer cells, we have uncovered a role for an RUNX2-ER complex that stimulates the transcription of a set of genes, including most notably the stem cell factor SOX9, that promote proliferation and a metastatic phenotype. We show that up-regulation of SOX9 is sufficient to cause relative endocrine resistance. The gain of SOX9 as an ER-regulated gene associated with tamoxifen resistance was validated in a unique set of clinical samples supporting the need for the development of improved ER antagonists.
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Affiliation(s)
- Rinath Jeselsohn
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02215;
- Center for Functional Cancer Epigenetics, Dana Farber Cancer Institute, Boston, MA 02215
- Breast Oncology Center, Dana Farber Cancer Institute, Boston, MA 02215
| | - MacIntosh Cornwell
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02215
| | - Matthew Pun
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02215
| | - Gilles Buchwalter
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02215
- Center for Functional Cancer Epigenetics, Dana Farber Cancer Institute, Boston, MA 02215
| | - Mai Nguyen
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02215
| | - Clyde Bango
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02215
| | - Ying Huang
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02215
| | - Yanan Kuang
- Belfer Center for Applied Cancer Science, Dana Farber Cancer Institute, Boston, MA 02215
| | - Cloud Paweletz
- Belfer Center for Applied Cancer Science, Dana Farber Cancer Institute, Boston, MA 02215
| | - Xiaoyong Fu
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030
| | - Agostina Nardone
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030
| | - Carmine De Angelis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030
| | - Simone Detre
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, London, SW3 6JB, United Kingdom
| | - Andrew Dodson
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, London, SW3 6JB, United Kingdom
| | - Hisham Mohammed
- Nuclear Transcription Factor Laboratory, Cancer Research UK, Cambridge Institute, Cambridge University, Li Ka Shing Centre, Cambridge, CB2 0RE, United Kingdom
| | - Jason S Carroll
- Nuclear Transcription Factor Laboratory, Cancer Research UK, Cambridge Institute, Cambridge University, Li Ka Shing Centre, Cambridge, CB2 0RE, United Kingdom
| | - Michaela Bowden
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02215
| | - Prakash Rao
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02215
| | - Henry W Long
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02215
| | - Fugen Li
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02215
| | - Mitchell Dowsett
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, London, SW3 6JB, United Kingdom
- The Breast Cancer Now Toby Robin's Research Centre, Institute of Cancer Research, London, SW7 3RP, United Kingdom
| | - Rachel Schiff
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030
| | - Myles Brown
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02215;
- Center for Functional Cancer Epigenetics, Dana Farber Cancer Institute, Boston, MA 02215
- Breast Oncology Center, Dana Farber Cancer Institute, Boston, MA 02215
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29
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Adamaki M, Vlahopoulos S, Lambrou GI, Papavassiliou AG, Moschovi M. Aberrant AML1 gene expression in the diagnosis of childhood leukemias not characterized by AML1-involved cytogenetic abnormalities. Tumour Biol 2017; 39:1010428317694308. [PMID: 28349830 DOI: 10.1177/1010428317694308] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The AML1 ( acute myeloid leukemia 1) gene, a necessary prerequisite of embryonic hematopoiesis and a critical regulator of normal hematopoietic development, is one of the most frequently mutated genes in human leukemia, involving over 50 chromosome translocations and over 20 partner genes. In the few existing studies investigating AML1 gene expression in childhood leukemias, aberrant upregulation seems to specifically associate with AML1 translocations and amplifications. The aim of this study was to determine whether overexpression also extends to other leukemic subtypes than the ones karyotypically involving AML1. We use quantitative real-time polymerase chain reaction methodology to investigate gene expression in 100 children with acute leukemias and compare them to those of healthy controls. We show that in childhood acute lymphoblastic leukemia, AML1 gene overexpression is associated with a variety of leukemic subtypes, both immunophenotypically and cytogenetically. Statistically significantly higher transcripts of the gene were detected in the acute lymphoblastic leukemia group as compared to the acute myeloid leukemia group, where AML1 overexpression appeared to associate with cytogenetic abnormalities additional to those that engage the AML1 gene, or that are reported as showing a "normal" karyotype. Collectively, our study shows that AML1 gene overexpression characterizes a broader range of leukemic subtypes than previously thought, including various maturation stages of B-cell acute lymphoblastic leukemia and cytogenetic types additional to those involving the AML1 gene.
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Affiliation(s)
- Maria Adamaki
- 1 Pediatric Hematology/Oncology Unit, First Department of Pediatrics, Medical School, National and Kapodistrian University of Athens and "Aghia Sofia" Children's Hospital, Athens, Greece
| | - Spiros Vlahopoulos
- 1 Pediatric Hematology/Oncology Unit, First Department of Pediatrics, Medical School, National and Kapodistrian University of Athens and "Aghia Sofia" Children's Hospital, Athens, Greece
| | - George I Lambrou
- 1 Pediatric Hematology/Oncology Unit, First Department of Pediatrics, Medical School, National and Kapodistrian University of Athens and "Aghia Sofia" Children's Hospital, Athens, Greece
| | - Athanasios G Papavassiliou
- 2 Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria Moschovi
- 1 Pediatric Hematology/Oncology Unit, First Department of Pediatrics, Medical School, National and Kapodistrian University of Athens and "Aghia Sofia" Children's Hospital, Athens, Greece
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30
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Khawaled S, Aqeilan RI. RUNX1, a new regulator of EMT in breast cancer. Oncotarget 2017; 8:17407-17408. [PMID: 28407696 PMCID: PMC5392256 DOI: 10.18632/oncotarget.15623] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 02/18/2017] [Indexed: 11/25/2022] Open
Affiliation(s)
- Saleh Khawaled
- Lautenberg Center for Immunology and Cancer Research, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem
| | - Rami I Aqeilan
- Lautenberg Center for Immunology and Cancer Research, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem
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31
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Rooney N, Riggio AI, Mendoza-Villanueva D, Shore P, Cameron ER, Blyth K. Runx Genes in Breast Cancer and the Mammary Lineage. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 962:353-368. [PMID: 28299668 DOI: 10.1007/978-981-10-3233-2_22] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A full understanding of RUNX gene function in different epithelial lineages has been thwarted by the lethal phenotypes observed when constitutively knocking out these mammalian genes. However temporal expression of the Runx genes throughout the different phases of mammary gland development is indicative of a functional role in this tissue. A few studies have emerged describing how these genes impact on the fate of mammary epithelial cells by regulating lineage differentiation and stem/progenitor cell potential, with implications for the transformed state. The importance of the RUNX/CBFβ core factor binding complex in breast cancer has very recently been highlighted with both RUNX1 and CBFβ appearing in a comprehensive gene list of predicted breast cancer driver mutations. Nonetheless, the evidence to date shows that the RUNX genes can have dualistic outputs with respect to promoting or constraining breast cancer phenotypes, and that this may be aligned to individual subtypes of the clinical disease. We take this opportunity to review the current literature on RUNX and CBFβ in the normal and neoplastic mammary lineage while appreciating that this is likely to be the tip of the iceberg in our knowledge.
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Affiliation(s)
- Nicholas Rooney
- Beatson Institute for Cancer Research, Bearsden, Glasgow, G61 1BD, UK
| | | | | | - Paul Shore
- Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
| | - Ewan R Cameron
- School of Veterinary Medicine, University of Glasgow, Bearsden, Glasgow, G61 1QH, UK
| | - Karen Blyth
- Beatson Institute for Cancer Research, Bearsden, Glasgow, G61 1BD, UK.
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32
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Recouvreux MS, Grasso EN, Echeverria PC, Rocha-Viegas L, Castilla LH, Schere-Levy C, Tocci JM, Kordon EC, Rubinstein N. RUNX1 and FOXP3 interplay regulates expression of breast cancer related genes. Oncotarget 2016; 7:6552-65. [PMID: 26735887 PMCID: PMC4872732 DOI: 10.18632/oncotarget.6771] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 11/28/2015] [Indexed: 12/21/2022] Open
Abstract
Runx1 participation in epithelial mammary cells is still under review. Emerging data indicates that Runx1 could be relevant for breast tumor promotion. However, to date no studies have specifically evaluated the functional contribution of Runx1 to control gene expression in mammary epithelial tumor cells. It has been described that Runx1 activity is defined by protein context interaction. Interestingly, Foxp3 is a breast tumor suppressor gene. Here we show that endogenous Runx1 and Foxp3 physically interact in normal mammary cells and this interaction blocks Runx1 transcriptional activity. Furthermore we demonstrate that Runx1 is able to bind to R-spondin 3 (RSPO3) and Gap Junction protein Alpha 1 (GJA1) promoters. This binding upregulates Rspo3 oncogene expression and downregulates GJA1 tumor suppressor gene expression in a Foxp3-dependent manner. Moreover, reduced Runx1 transcriptional activity decreases tumor cell migration properties. Collectively, these data provide evidence of a new mechanism for breast tumor gene expression regulation, in which Runx1 and Foxp3 physically interact to control mammary epithelial cell gene expression fate. Our work suggests for the first time that Runx1 could be involved in breast tumor progression depending on Foxp3 availability.
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Affiliation(s)
- María Sol Recouvreux
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Buenos Aires, Argentina.,Present Address: Oncology Institute "Angel H Roffo", Buenos Aires, Argentina
| | - Esteban Nicolás Grasso
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Buenos Aires, Argentina.,Present Address: Immunopharmacology Laboratory, IQUIBICEN-CONICET, FCEN-UBA, Buenos Aires, Argentina
| | | | - Luciana Rocha-Viegas
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Buenos Aires, Argentina.,Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, UBA, Buenos Aires, Argentina
| | - Lucio Hernán Castilla
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Carolina Schere-Levy
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Buenos Aires, Argentina
| | - Johanna Melisa Tocci
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Buenos Aires, Argentina
| | - Edith Claudia Kordon
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Buenos Aires, Argentina.,Departamento de Química Biológica, UBA, Buenos Aires, Argentina
| | - Natalia Rubinstein
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Buenos Aires, Argentina.,Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, UBA, Buenos Aires, Argentina
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33
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Wang X, Li L, Wu Y, Zhang R, Zhang M, Liao D, Wang G, Qin G, Xu RH, Kang T. CBX4 Suppresses Metastasis via Recruitment of HDAC3 to the Runx2 Promoter in Colorectal Carcinoma. Cancer Res 2016; 76:7277-7289. [PMID: 27864346 DOI: 10.1158/0008-5472.can-16-2100] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/14/2016] [Accepted: 10/31/2016] [Indexed: 11/16/2022]
Abstract
Polycomb chromobox (CBX) proteins participate in the polycomb repressive complex (PRC1) that mediates epigenetic gene silencing and endows PRC1 with distinct oncogenic or tumor suppressor functions in a cell-type-dependent manner. In this study, we report that inhibition of cell migration, invasion, and metastasis in colorectal carcinoma requires CBX4-mediated repression of Runx2, a key transcription factor that promotes colorectal carcinoma metastasis. CBX4 inversely correlated with Runx2 expression in colorectal carcinoma tissues, and the combination of high CBX4 expression and low Runx2 expression significantly correlated with overall survival, more so than either CBX4 or Runx2 expression alone. Mechanistically, CBX4 maintained recruited histone deacetylase 3 (HDAC3) to the Runx2 promoter, which maintained a deacetylated histone H3K27 state to suppress Runx2 expression. This function of CBX4 was dependent on its interaction with HDAC3, but not on its SUMO E3 ligase, its chromodomain, or the PRC1 complex. Disrupting the CBX4-HDAC3 interaction abolished Runx2 inhibition as well as the inhibition of cell migration and invasion. Collectively, our data show that CBX4 may act as a tumor suppressor in colorectal carcinoma, and strategies that stabilize the interaction of CBX4 with HDAC3 may benefit the colorectal carcinoma patients with metastases. Cancer Res; 76(24); 7277-89. ©2016 AACR.
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Affiliation(s)
- Xin Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Liping Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yuanzhong Wu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ruhua Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Meifang Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Dan Liao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Gang Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ge Qin
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Rui-Hua Xu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Tiebang Kang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.
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34
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Li N, Zhang QY, Zou JL, Li ZW, Tian TT, Dong B, Liu XJ, Ge S, Zhu Y, Gao J, Shen L. miR-215 promotes malignant progression of gastric cancer by targeting RUNX1. Oncotarget 2016; 7:4817-28. [PMID: 26716895 PMCID: PMC4826245 DOI: 10.18632/oncotarget.6736] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 11/29/2015] [Indexed: 12/19/2022] Open
Abstract
Objective miR-215 was reported to be downregulated and functioned as a tumor suppressor in several cancers. In contrast, miR-215 was preferentially upregulated in gastric cancer (GC) according to our data. Thus, we studied the potential biological function of miR-215 in GC. Methods miR-215 expression was measured in 77 paired GC tissues and adjacent non-tumor tissues. Biological functions of miR-215 were analyzed using cell viability, colony formation, migration, invasion, cell cycle, apoptosis and luciferase assays as well as via tumorigenicity and metastasis analysis. Results miR-215 was significantly upregulated in 7 GC cell lines and 77 GC tissues compared to adjacent non-tumor tissues (P < 0.05), and miR-215 expression was greater in advanced GC (stage III/IV; P < 0.05). Ectopic expression of miR-215 in GES-1 and HGC-27 cells (low miR-215 expression) promoted cell growth, migration, invasion, and metastasis, and these were reversed in NCI-N87 cells (high miR-215 expression) after miR-215 downregulation. Potential target genes of miR-215 were predicted and RUNX1, a transcription factor and a tumor suppressor, was confirmed to be potential target according to luciferase studies. RUNX1 was downregulated in GC tissues compared to adjacent non-tumor tissues (P < 0.05), and RUNX1 reversed partial function of miR-215 in vitro. Conclusion miR-215 promotes malignant progression of GC by targeting RUNX1, and RUNX1 can partially reverse miR-215 effects.
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Affiliation(s)
- Na Li
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, China
| | - Qi-Yue Zhang
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, China
| | - Jian-Ling Zou
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, China
| | - Zhong-Wu Li
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, China
| | - Tian-Tian Tian
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, China
| | - Bin Dong
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, China
| | - Xi-Juan Liu
- Central Laboratory, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, China
| | - Sai Ge
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, China
| | - Yan Zhu
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, China
| | - Jing Gao
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, China
| | - Lin Shen
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, China
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35
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Estrogenic gper signaling regulates mir144 expression in cancer cells and cancer-associated fibroblasts (cafs). Oncotarget 2016; 6:16573-87. [PMID: 26030000 PMCID: PMC4599290 DOI: 10.18632/oncotarget.4117] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 04/20/2015] [Indexed: 12/20/2022] Open
Abstract
MicroRNAs (miRNAs) are small non coding RNA molecules that play a crucial role in several pathophysiological conditions, including cancer. The stimulation of hormone-sensitive tumors by estrogens are mediated by estrogen receptor (ER)α and G protein estrogen receptor (GPER). Previous studies have reported that ERα regulates miRNA expression, while this ability of GPER remains to be elucidated. Here, we demonstrate that in SkBr3 breast cancer and HepG2 hepatocarcinoma cells, 17β-estradiol (E2) and the selective GPER ligand G-1 induce miR144 expression through GPER and the involvement of the PI3K/ERK1/2/Elk1 transduction pathway. Moreover, we show that E2 and G-1 down-regulate through miR144 the onco-suppressor Runx1 and increase cell cycle progression. The capability of E2 and G-1 in triggering the induction of miR144 and the down-regulation of Runx1 was also confirmed in cancer-associated fibroblasts (CAFs) that are main components of the tumor microenvironment driving cancer progression. Further confirming these results, Runx1 protein levels were found decreased in tumor xenografts upon G-1 treatment. On the basis of our findings miR144 and Runx1 may be included among the oncotargets of GPER action. Moreover, the present data provide new insights regarding the ability of estrogens to trigger the GPER/miR144/Runx1 transduction pathway toward the stimulation of cancer progression.
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36
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Illendula A, Gilmour J, Grembecka J, Tirumala VSS, Boulton A, Kuntimaddi A, Schmidt C, Wang L, Pulikkan JA, Zong H, Parlak M, Kuscu C, Pickin A, Zhou Y, Gao Y, Mishra L, Adli M, Castilla LH, Rajewski RA, Janes KA, Guzman ML, Bonifer C, Bushweller JH. Small Molecule Inhibitor of CBFβ-RUNX Binding for RUNX Transcription Factor Driven Cancers. EBioMedicine 2016; 8:117-131. [PMID: 27428424 PMCID: PMC4919611 DOI: 10.1016/j.ebiom.2016.04.032] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 04/12/2016] [Accepted: 04/25/2016] [Indexed: 10/29/2022] Open
Abstract
Transcription factors have traditionally been viewed with skepticism as viable drug targets, but they offer the potential for completely novel mechanisms of action that could more effectively address the stem cell like properties, such as self-renewal and chemo-resistance, that lead to the failure of traditional chemotherapy approaches. Core binding factor is a heterodimeric transcription factor comprised of one of 3 RUNX proteins (RUNX1-3) and a CBFβ binding partner. CBFβ enhances DNA binding of RUNX subunits by relieving auto-inhibition. Both RUNX1 and CBFβ are frequently mutated in human leukemia. More recently, RUNX proteins have been shown to be key players in epithelial cancers, suggesting the targeting of this pathway could have broad utility. In order to test this, we developed small molecules which bind to CBFβ and inhibit its binding to RUNX. Treatment with these inhibitors reduces binding of RUNX1 to target genes, alters the expression of RUNX1 target genes, and impacts cell survival and differentiation. These inhibitors show efficacy against leukemia cells as well as basal-like (triple-negative) breast cancer cells. These inhibitors provide effective tools to probe the utility of targeting RUNX transcription factor function in other cancers.
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Affiliation(s)
- Anuradha Illendula
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Jane Gilmour
- School of Cancer Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, UK
| | | | | | - Adam Boulton
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Aravinda Kuntimaddi
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Charles Schmidt
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Lixin Wang
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - John A Pulikkan
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Hongliang Zong
- Division of Hematology/Oncology, Department of Medicine, Weill Medical College of Cornell University, New York, NY, USA
| | - Mahmut Parlak
- Department of Biochemistry, University of Virginia, Charlottesville, VA, USA
| | - Cem Kuscu
- Department of Biochemistry, University of Virginia, Charlottesville, VA, USA
| | - Anna Pickin
- School of Cancer Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, UK
| | - Yunpeng Zhou
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Yan Gao
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Lauren Mishra
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | - Mazhar Adli
- Department of Biochemistry, University of Virginia, Charlottesville, VA, USA
| | - Lucio H Castilla
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Roger A Rajewski
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, USA
| | - Kevin A Janes
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Monica L Guzman
- Division of Hematology/Oncology, Department of Medicine, Weill Medical College of Cornell University, New York, NY, USA
| | - Constanze Bonifer
- School of Cancer Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, UK
| | - John H Bushweller
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
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Lin TC, Su CY, Wu PY, Lai TC, Pan WA, Jan YH, Chang YC, Yeh CT, Chen CL, Ger LP, Chang HT, Yang CJ, Huang MS, Liu YP, Lin YF, Shyy JYJ, Tsai MD, Hsiao M. The nucleolar protein NIFK promotes cancer progression via CK1α/β-catenin in metastasis and Ki-67-dependent cell proliferation. eLife 2016; 5. [PMID: 26984280 PMCID: PMC4811767 DOI: 10.7554/elife.11288] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 02/11/2016] [Indexed: 12/22/2022] Open
Abstract
Nucleolar protein interacting with the FHA domain of pKi-67 (NIFK) is a Ki-67-interacting protein. However, its precise function in cancer remains largely uninvestigated. Here we show the clinical significance and metastatic mechanism of NIFK in lung cancer. NIFK expression is clinically associated with poor prognosis and metastasis. Furthermore, NIFK enhances Ki-67-dependent proliferation, and promotes migration, invasion in vitro and metastasis in vivo via downregulation of casein kinase 1α (CK1α), a suppressor of pro-metastatic TCF4/β-catenin signaling. Inversely, CK1α is upregulated upon NIFK knockdown. The silencing of CK1α expression in NIFK-silenced cells restores TCF4/β-catenin transcriptional activity, cell migration, and metastasis. Furthermore, RUNX1 is identified as a transcription factor of CSNK1A1 (CK1α) that is negatively regulated by NIFK. Our results demonstrate the prognostic value of NIFK, and suggest that NIFK is required for lung cancer progression via the RUNX1-dependent CK1α repression, which activates TCF4/β-catenin signaling in metastasis and the Ki-67-dependent regulation in cell proliferation. DOI:http://dx.doi.org/10.7554/eLife.11288.001 Cancer cells can rapidly divide to form a tumor. Small groups of cells can leave the tumor to migrate to other sites in the body, and it is these “secondary” tumors that are often responsible for the death of cancer patients. Many proteins influence how and when cells divide and migrate. One such protein called Ki67 is only produced when cells are dividing and it is often used in the clinic as a marker to indicate whether cells have become cancerous. However, it is not clear how Ki67 regulates the progression of cancer. Ki67 interacts with another protein called NIFK, and Lin, Su et al. have now investigated the role of NIFK in cancer. First, publicly available data on the levels of proteins in tumor samples from cancer patients were analyzed. This revealed that, in several different types of cancer, tumors that produced more NIFK were more likely to spread to other parts of the body than tumors that produced smaller amounts of NIFK. Next, Lin, Su et al carried out experiments using human lung cancer cells. This revealed that cells that produced larger amounts of NIFK were more likely to migrate, while cells with lower levels of NIFK divided and migrated less often. Further experiments showed that NIFK increases the activity of genes that are involved in cell migration. NIFK achieves this by reducing the production of a protein that inhibits the activity of another protein called β-catenin. Lin, Su et al.’s findings reveal a new role for NIFK in promoting the development of cancer. A future challenge is to find out whether chemicals that inhibit NIFK could be used in the treatment of lung cancer. DOI:http://dx.doi.org/10.7554/eLife.11288.002
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Affiliation(s)
| | - Chia-Yi Su
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Pei-Yu Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | | | - Wen-An Pan
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Yi-Hua Jan
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Yu-Chang Chang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Chi-Tai Yeh
- Department of Medical Research and Education, Taipei Medical University-Shuang Ho Hospital, New Taipei City, Taiwan
| | - Chi-Long Chen
- Department of Pathology, Taipei Medical University Hospital, Taipei Medical University, Taipei, Taiwan.,Department of Pathology, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Luo-Ping Ger
- Department of Medical Education and Research, Kaohsiung Veterans General, Kaohsiung, Taiwan
| | - Hong-Tai Chang
- Department of Surgery, Kaohsiung Veterans General, Kaohsiung, Taiwan.,Department of Emergency Medicine, Kaohsiung Veterans General, Kaohsiung, Taiwan
| | - Chih-Jen Yang
- Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Ming-Shyan Huang
- Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Yu-Peng Liu
- Graduate Institute of Clinical Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yuan-Feng Lin
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - John Y-J Shyy
- Department of Medicine, University of California, San Diego, San Diego, United States
| | - Ming-Daw Tsai
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.,Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Michael Hsiao
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
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Role of Long Noncoding RNAs in Neoplasia: Special Emphasis on Prostate Cancer. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 324:229-54. [PMID: 27017010 DOI: 10.1016/bs.ircmb.2016.01.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Recent advances in sequencing technology have dramatically improved the ability of investigators to study nucleic acid biology. Bolstered by these new and powerful techniques, the field of noncoding RNA (ncRNA) research, in particular, has witnessed a period of significant progress, wherein multiple new and unique species of ncRNA elements have been discovered and characterized. The current categories of ncRNAs include tRNA, rRNA, snoRNA, snRNA, piRNA, miRNA, and lncRNA, among others. The largest of these RNAs are the long noncoding RNAs (lncRNAs) that perform a diverse set of functions within the cell. Importantly, lncRNAs have recently been implicated in the pathogenesis of multiple types of cancer, including breast, lung, gastric, liver, and prostate. This reviews the major lncRNAs currently believed to play a role in human malignancies with a special emphasis on lncRNAs germane to cancer of the prostate gland. Continued investigation of lncRNA will likely prove to be exceedingly valuable, as they may provide novel therapeutic targets for the treatment of cancer. In addition, lncRNAs offer the potential to serve as diagnostic and prognostic biomarkers for cancer. The present state of lncRNA-based strategies for use in the management of cancer will also be highlighted.
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Marouf C, Göhler S, Filho MIDS, Hajji O, Hemminki K, Nadifi S, Försti A. Analysis of functional germline variants in APOBEC3 and driver genes on breast cancer risk in Moroccan study population. BMC Cancer 2016; 16:165. [PMID: 26920143 PMCID: PMC4768349 DOI: 10.1186/s12885-016-2210-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 02/21/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Breast cancer (BC) is the most prevalent cancer in women and a major public health problem in Morocco. Several Moroccan studies have focused on studying this disease, but more are needed, especially at the genetic and molecular levels. Therefore, we investigated the potential association of several functional germline variants in the genes commonly mutated in sporadic breast cancer. METHODS In this case-control study, we examined 36 single nucleotide polymorphisms (SNPs) in 13 genes (APOBEC3A, APOBEC3B, ARID1B, ATR, MAP3K1, MLL2, MLL3, NCOR1, RUNX1, SF3B1, SMAD4, TBX3, TTN), which were located in the core promoter, 5'-and 3'UTR or which were nonsynonymous SNPs to assess their potential association with inherited predisposition to breast cancer development. Additionally, we identified a ~29.5-kb deletion polymorphism between APOBEC3A and APOBEC3B and explored possible associations with BC. A total of 226 Moroccan breast cancer cases and 200 matched healthy controls were included in this study. RESULTS The analysis showed that12 SNPs in 8 driver genes, 4 SNPs in APOBEC3B gene and 1 SNP in APOBEC3A gene were associated with BC risk and/or clinical outcome at P ≤ 0.05 level. RUNX1_rs8130963 (odds ratio (OR) = 2.25; 95 % CI 1.42-3.56; P = 0.0005; dominant model), TBX3_rs8853 (OR = 2.04; 95 % CI 1.38-3.01; P = 0.0003; dominant model), TBX3_rs1061651 (OR= 2.14; 95 % CI1.43-3.18; P = 0.0002; dominant model), TTN_rs12465459 (OR = 2.02; 95 % confidence interval 1.33-3.07; P = 0.0009; dominant model), were the most significantly associated SNPs with BC risk. A strong association with clinical outcome were detected for the genes SMAD4 _rs3819122 with tumor size (OR = 0.45; 95 % CI 0.25-0.82; P = 0.009) and TTN_rs2244492 with estrogen receptor (OR = 0.45; 95 % CI 0.25-0.82; P = 0.009). CONCLUSION Our results suggest that genetic variations in driver and APOBEC3 genes were associated with the risk of BC and may have impact on clinical outcome. However, the reported association between the deletion polymorphism and BC risk was not confirmed in the Moroccan population. These preliminary findings require replication in larger studies.
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Affiliation(s)
- Chaymaa Marouf
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Laboratory of Genetics and Molecular Pathology-Medical School of Casablanca, Casablanca, Morocco. .,University Hassan II Ain Chock, Center Of Doctoral Sciences "In Health Sciences", Casablanca, Morocco.
| | - Stella Göhler
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | | | - Omar Hajji
- Department of Oncology, Littoral Clinic, Casablanca, Morocco.
| | - Kari Hemminki
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Center for Primary Health Care Research, Clinical Research Center, Lund University, Malmö, Sweden.
| | - Sellama Nadifi
- Laboratory of Genetics and Molecular Pathology-Medical School of Casablanca, Casablanca, Morocco. .,University Hassan II Ain Chock, Center Of Doctoral Sciences "In Health Sciences", Casablanca, Morocco.
| | - Asta Försti
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Center for Primary Health Care Research, Clinical Research Center, Lund University, Malmö, Sweden.
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40
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Chimge NO, Little GH, Baniwal SK, Adisetiyo H, Xie Y, Zhang T, O'Laughlin A, Liu ZY, Ulrich P, Martin A, Mhawech-Fauceglia P, Ellis MJ, Tripathy D, Groshen S, Liang C, Li Z, Schones DE, Frenkel B. RUNX1 prevents oestrogen-mediated AXIN1 suppression and β-catenin activation in ER-positive breast cancer. Nat Commun 2016; 7:10751. [PMID: 26916619 PMCID: PMC4773428 DOI: 10.1038/ncomms10751] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Accepted: 01/11/2016] [Indexed: 12/21/2022] Open
Abstract
Recent high-throughput studies revealed recurrent RUNX1 mutations in breast cancer, specifically in oestrogen receptor-positive (ER+) tumours. However, mechanisms underlying the implied RUNX1-mediated tumour suppression remain elusive. Here, by depleting mammary epithelial cells of RUNX1 in vivo and in vitro, we demonstrate combinatorial regulation of AXIN1 by RUNX1 and oestrogen. RUNX1 and ER occupy adjacent elements in AXIN1's second intron, and RUNX1 antagonizes oestrogen-mediated AXIN1 suppression. Accordingly, RNA-seq and immunohistochemical analyses demonstrate an ER-dependent correlation between RUNX1 and AXIN1 in tumour biopsies. RUNX1 loss in ER+ mammary epithelial cells increases β-catenin, deregulates mitosis and stimulates cell proliferation and expression of stem cell markers. However, it does not stimulate LEF/TCF, c-Myc or CCND1, and it does not accelerate G1/S cell cycle phase transition. Finally, RUNX1 loss-mediated deregulation of β-catenin and mitosis is ameliorated by AXIN1 stabilization in vitro, highlighting AXIN1 as a potential target for the management of ER+ breast cancer. The tumour suppressor RUNX1 is often lost or mutated in oestrogen receptor-positive breast cancers. In this study, the authors demonstrate that the loss of RUNX1 unleashes oestrogen-mediated inhibition of AXIN1, a negative regulator of β-catenin, resulting in β-catenin signalling-mediated cancer cell proliferation and mitosis deregulation.
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Affiliation(s)
- Nyam-Osor Chimge
- Department of Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California 90033, USA.,Institute for Genetic Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California 90033, USA
| | - Gillian H Little
- Institute for Genetic Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California 90033, USA
| | - Sanjeev K Baniwal
- Institute for Genetic Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California 90033, USA
| | - Helty Adisetiyo
- Institute for Genetic Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California 90033, USA
| | - Ying Xie
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Tian Zhang
- Department of Molecular Microbiology and Immunology, Keck School of Medicine of the University of Southern California, Los Angeles, California 90033, USA
| | - Andie O'Laughlin
- Institute for Genetic Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California 90033, USA
| | - Zhi Y Liu
- Institute for Genetic Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California 90033, USA
| | - Peaches Ulrich
- Institute for Genetic Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California 90033, USA
| | - Anthony Martin
- Institute for Genetic Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California 90033, USA
| | - Paulette Mhawech-Fauceglia
- Department of Pathology, Keck School of Medicine of the University of Southern California, Los Angeles, California 90033, USA
| | - Matthew J Ellis
- Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Debu Tripathy
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Susan Groshen
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California 90033, USA.,USC/Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, California 90033, USA
| | - Chengyu Liang
- Department of Molecular Microbiology and Immunology, Keck School of Medicine of the University of Southern California, Los Angeles, California 90033, USA
| | - Zhe Li
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Dustin E Schones
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, California 91010, USA
| | - Baruch Frenkel
- Institute for Genetic Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California 90033, USA.,USC/Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, California 90033, USA.,Department of Orthopedic Surgery, Keck School of Medicine of the University of Southern California, Los Angeles, California 90033, USA.,Department of Biochemistry and Molecular Biology, Keck School of Medicine of the University of Southern California, Los Angeles, California 90033, USA
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41
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Qadi AA, Taberlay PC, Phillips JL, Young A, West AC, Brettingham-Moore KH, Dickinson JL, Holloway AF. The Leukemia Inhibitory Factor Receptor Gene Is a Direct Target of RUNX1. J Cell Biochem 2015; 117:49-58. [DOI: 10.1002/jcb.25246] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 05/29/2015] [Indexed: 12/15/2022]
Affiliation(s)
- Abeer A. Qadi
- Menzies Institute for Medical Research; University of Tasmania; Hobart Tasmania 7000 Australia
| | - Phillippa C. Taberlay
- Genomics and Epigenetics Division; The Garvan Institute of Medical Research; Darlinghurst New South Wales 2010 Australia
| | - Jessica L. Phillips
- Menzies Institute for Medical Research; University of Tasmania; Hobart Tasmania 7000 Australia
| | - Arabella Young
- Menzies Institute for Medical Research; University of Tasmania; Hobart Tasmania 7000 Australia
| | - Alison C. West
- Menzies Institute for Medical Research; University of Tasmania; Hobart Tasmania 7000 Australia
| | | | - Joanne L. Dickinson
- Menzies Institute for Medical Research; University of Tasmania; Hobart Tasmania 7000 Australia
| | - Adele F. Holloway
- School of Medicine; University of Tasmania; Hobart Tasmania 7000 Australia
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Browne G, Taipaleenmäki H, Bishop NM, Madasu SC, Shaw LM, van Wijnen AJ, Stein JL, Stein GS, Lian JB. Runx1 is associated with breast cancer progression in MMTV-PyMT transgenic mice and its depletion in vitro inhibits migration and invasion. J Cell Physiol 2015; 230:2522-32. [PMID: 25802202 DOI: 10.1002/jcp.24989] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 03/16/2015] [Indexed: 01/12/2023]
Abstract
Runx1 is a transcription factor essential for definitive hematopoiesis, and genetic abnormalities in Runx1 cause leukemia. Runx1 is functionally promiscuous and acts as either an oncogene or tumor suppressor gene in certain epithelial cancers. Recent evidence suggests that Runx1 is an important factor in breast cancer, however, its role remains ambiguous. Here, we addressed whether Runx1 has a specific pathological role during breast cancer progression and show that Runx1 has an oncogenic function. We observed elevated Runx1 expression in a subset of human breast cancers. Furthermore, throughout the course of disease progression in a classical mouse model of breast cancer (i.e., the MMTV-PyMT transgenic model), Runx1 expression increases in the primary site (mammary gland) and is further upregulated in tumors and distal lung metastatic lesions. Ex vivo studies using tumor epithelial cells derived from these mice express significantly higher levels of Runx1 than normal mammary epithelial cells. The tumor cells exhibit increased rates of migration and invasion, indicative of an aggressive cancer phenotype. Inhibition of Runx1 expression using RNA interference significantly abrogates these cancer-relevant phenotypic characteristics. Importantly, our data establish that Runx1 contributes to murine mammary tumor development and malignancy and potentially represents a key disease-promoting and prognostic factor in human breast cancer progression and metastasis.
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Affiliation(s)
- Gillian Browne
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, Vermont.,Department of Cell Biology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Hanna Taipaleenmäki
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, Massachusetts.,Heisenberg-Group for Molecular Skeletal Biology, Department of Trauma, Hand & Reconstructive Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nicole M Bishop
- Microscopy Imaging Center, University of Vermont College of Medicine, Burlington, Vermont
| | - Sharath C Madasu
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, Vermont
| | - Leslie M Shaw
- Department of Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Andre J van Wijnen
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, Massachusetts.,Department of Orthopedic Surgery, Mayo Clinic, Rochester, Minnesota
| | - Janet L Stein
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, Vermont.,Department of Cell Biology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Gary S Stein
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, Vermont.,Department of Cell Biology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Jane B Lian
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, Vermont.,Department of Cell Biology, University of Massachusetts Medical School, Worcester, Massachusetts
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PVT1: a rising star among oncogenic long noncoding RNAs. BIOMED RESEARCH INTERNATIONAL 2015; 2015:304208. [PMID: 25883951 PMCID: PMC4391155 DOI: 10.1155/2015/304208] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 03/12/2015] [Indexed: 12/13/2022]
Abstract
It is becoming increasingly clear that short and long noncoding RNAs critically participate in the regulation of cell growth, differentiation, and (mis)function. However, while the functional characterization of short non-coding RNAs has been reaching maturity, there is still a paucity of well characterized long noncoding RNAs, even though large studies in recent years are rapidly increasing the number of annotated ones. The long noncoding RNA PVT1 is encoded by a gene that has been long known since it resides in the well-known cancer risk region 8q24. However, a couple of accidental concurrent conditions have slowed down the study of this gene, that is, a preconception on the primacy of the protein-coding over noncoding RNAs and the prevalent interest in its neighbor MYC oncogene. Recent studies have brought PVT1 under the spotlight suggesting interesting models of functioning, such as competing endogenous RNA activity and regulation of protein stability of important oncogenes, primarily of the MYC oncogene. Despite some advancements in modelling the PVT1 role in cancer, there are many questions that remain unanswered concerning the precise molecular mechanisms underlying its functioning.
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44
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Paci P, Colombo T, Farina L. Computational analysis identifies a sponge interaction network between long non-coding RNAs and messenger RNAs in human breast cancer. BMC SYSTEMS BIOLOGY 2014; 8:83. [PMID: 25033876 PMCID: PMC4113672 DOI: 10.1186/1752-0509-8-83] [Citation(s) in RCA: 199] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Accepted: 06/24/2014] [Indexed: 12/14/2022]
Abstract
Background Non-coding RNAs (ncRNAs) are emerging as key regulators of many cellular processes in both physiological and pathological states. Moreover, the constant discovery of new non-coding RNA species suggests that the study of their complex functions is still in its very early stages. This variegated class of RNA species encompasses the well-known microRNAs (miRNAs) and the most recently acknowledged long non-coding RNAs (lncRNAs). Interestingly, in the last couple of years, a few studies have shown that some lncRNAs can act as miRNA sponges, i.e. as competing endogenous RNAs (ceRNAs), able to reduce the amount of miRNAs available to target messenger RNAs (mRNAs). Results We propose a computational approach to explore the ability of lncRNAs to act as ceRNAs by protecting mRNAs from miRNA repression. A seed match analysis was performed to validate the underlying regression model. We built normal and cancer networks of miRNA-mediated sponge interactions (MMI-networks) using breast cancer expression data provided by The Cancer Genome Atlas. Conclusions Our study highlights a marked rewiring in the ceRNA program between normal and pathological breast tissue, documented by its “on/off” switch from normal to cancer, and vice-versa. This mutually exclusive activation confers an interesting character to ceRNAs as potential oncosuppressive, or oncogenic, protagonists in cancer. At the heart of this phenomenon is the lncRNA PVT1, as illustrated by both the width of its antagonist mRNAs in normal-MMI-network, and the relevance of the latter in breast cancer. Interestingly, PVT1 revealed a net binding preference towards the mir-200 family as the bone of contention with its rival mRNAs.
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Affiliation(s)
- Paola Paci
- Institute for System Analysis and Computer Science "Antonio Ruberti", National Research Council, Viale Manzoni 30, 00185 Rome, Italy.
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Ferrari N, Mohammed ZMA, Nixon C, Mason SM, Mallon E, McMillan DC, Morris JS, Cameron ER, Edwards J, Blyth K. Expression of RUNX1 correlates with poor patient prognosis in triple negative breast cancer. PLoS One 2014; 9:e100759. [PMID: 24967588 PMCID: PMC4072705 DOI: 10.1371/journal.pone.0100759] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 05/28/2014] [Indexed: 12/21/2022] Open
Abstract
The RUNX1 transcription factor is widely recognised for its tumour suppressor effects in leukaemia. Recently a putative link to breast cancer has started to emerge, however the function of RUNX1 in breast cancer is still unknown. To investigate if RUNX1 expression was important to clinical outcome in primary breast tumours a tissue microarray (TMA) containing biopsies from 483 patients with primary operable invasive ductal breast cancer was stained by immunohistochemistry. RUNX1 was associated with progesterone receptor (PR)-positive tumours (P<0.05), more tumour CD4+(P<0.05) and CD8+(P<0.01) T-lymphocytic infiltrate, increased tumour CD138+plasma cell (P<0.01) and more CD68+macrophage infiltrate (P<0.001). RUNX1 expression did not influence outcome of oestrogen receptor (ER)-positive or HER2-positive disease, however on univariate analysis a high RUNX1 protein was significantly associated with poorer cancer-specific survival in patients with ER-negative (P<0.05) and with triple negative (TN) invasive breast cancer (P<0.05). Furthermore, multivariate Cox regression analysis of cancer-specific survival showed a trend towards significance in ER-negative patients (P<0.1) and was significant in triple negative patients (P<0.05). Of relevance, triple negative breast cancer currently lacks good biomarkers and patients with this subtype do not benefit from the option of targeted therapy unlike patients with ER-positive or HER2-positive disease. Using multivariate analysis RUNX1 was identified as an independent prognostic marker in the triple negative subgroup. Overall, our study identifies RUNX1 as a new prognostic indicator correlating with poor prognosis specifically in the triple negative subtype of human breast cancer.
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Affiliation(s)
- Nicola Ferrari
- Transgenic Models Lab, Cancer Research UK Beatson Institute, Glasgow, Scotland, United Kingdom
| | - Zahra M. A. Mohammed
- Academic Unit of Surgery, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Colin Nixon
- Transgenic Models Lab, Cancer Research UK Beatson Institute, Glasgow, Scotland, United Kingdom
| | - Susan M. Mason
- Transgenic Models Lab, Cancer Research UK Beatson Institute, Glasgow, Scotland, United Kingdom
| | - Elizabeth Mallon
- University Pathology Unit, Southern General Hospital, Glasgow, Scotland, United Kingdom
| | - Donald C. McMillan
- Academic Unit of Surgery, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Joanna S. Morris
- School of Veterinary Medicine, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Ewan R. Cameron
- School of Veterinary Medicine, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Joanne Edwards
- Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Karen Blyth
- Transgenic Models Lab, Cancer Research UK Beatson Institute, Glasgow, Scotland, United Kingdom
- * E-mail:
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46
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Affiliation(s)
- Chun-Chao Wang
- Department of Biomedical Engineering; University of Virginia; Charlottesville, VA USA
| | - Kevin A Janes
- Department of Biomedical Engineering; University of Virginia; Charlottesville, VA USA
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47
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Candelaria NR, Liu K, Lin CY. Estrogen receptor alpha: molecular mechanisms and emerging insights. J Cell Biochem 2014; 114:2203-8. [PMID: 23649536 DOI: 10.1002/jcb.24584] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 04/29/2013] [Indexed: 11/11/2022]
Abstract
Estrogen receptor alpha (ERα) is a cellular receptor for the female sex hormone estrogen and other natural and synthetic ligands and play critical roles in normal development and physiology and in the etiology and treatment of endocrine-related diseases. ERα is a member of the nuclear receptor superfamily of transcription factors and regulates target gene expression in a ligand-dependent manner. It has also been shown to interact with G-protein coupled receptors and associated signaling molecules in the cytoplasm. Transcriptionally, ERα either binds DNA directly through conserved estrogen response element sequence motifs or indirectly by tethering to other interacting transcription factors and nucleate transcriptional regulatory complexes which include an array of co-regulator proteins. Genome-scale studies of ERα transcriptional activity and localization have revealed mechanistic complexity and insights including novel interactions with several transcription factors, including FOXA1, AP-2g, GATA3, and RUNX1, which function as pioneering, collaborative, or tethering factors. The major challenge and exciting prospect moving forward is the comprehensive definition and integration of ERα complexes and mechanisms and their tissue-specific roles in normal physiology and in human diseases.
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Affiliation(s)
- Nicholes R Candelaria
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204‐5506, USA
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48
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Janes KA, Lauffenburger DA. Models of signalling networks - what cell biologists can gain from them and give to them. J Cell Sci 2013; 126:1913-21. [PMID: 23720376 DOI: 10.1242/jcs.112045] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Computational models of cell signalling are perceived by many biologists to be prohibitively complicated. Why do math when you can simply do another experiment? Here, we explain how conceptual models, which have been formulated mathematically, have provided insights that directly advance experimental cell biology. In the past several years, models have influenced the way we talk about signalling networks, how we monitor them, and what we conclude when we perturb them. These insights required wet-lab experiments but would not have arisen without explicit computational modelling and quantitative analysis. Today, the best modellers are cross-trained investigators in experimental biology who work closely with collaborators but also undertake experimental work in their own laboratories. Biologists would benefit by becoming conversant in core principles of modelling in order to identify when a computational model could be a useful complement to their experiments. Although the mathematical foundations of a model are useful to appreciate its strengths and weaknesses, they are not required to test or generate a worthwhile biological hypothesis computationally.
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Affiliation(s)
- Kevin A Janes
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
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49
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Kang BH, Jensen KJ, Hatch JA, Janes KA. Simultaneous profiling of 194 distinct receptor transcripts in human cells. Sci Signal 2013; 6:rs13. [PMID: 23921087 DOI: 10.1126/scisignal.2003624] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Many signal transduction cascades are initiated by transmembrane receptors with the presence or absence and abundance of receptors dictating cellular responsiveness. We provide a validated array of quantitative reverse transcription polymerase chain reaction (qRT-PCR) reagents for high-throughput profiling of the presence and relative abundance of transcripts for 194 transmembrane receptors in the human genome. We found that the qRT-PCR array had greater sensitivity and specificity for the detected receptor transcript profiles compared to conventional oligonucleotide microarrays or exon microarrays. The qRT-PCR array also distinguished functional receptor presence versus absence more accurately than deep sequencing of adenylated RNA species by RNA sequencing (RNA-seq). By applying qRT-PCR-based receptor transcript profiling to 40 human cell lines representing four main tissues (pancreas, skin, breast, and colon), we identified clusters of cell lines with enhanced signaling capabilities and revealed a role for receptor silencing in defining tissue lineage. Ectopic expression of the interleukin-10 (IL-10) receptor-encoding gene IL10RA in melanoma cells engaged an IL-10 autocrine loop not otherwise present in this cell type, which altered signaling, gene expression, and cellular responses to proinflammatory stimuli. Our array provides a rapid, inexpensive, and convenient means for assigning a receptor signature to any human cell or tissue type.
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Affiliation(s)
- Byong H Kang
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
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50
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Chimge NO, Frenkel B. The RUNX family in breast cancer: relationships with estrogen signaling. Oncogene 2013; 32:2121-30. [PMID: 23045283 PMCID: PMC5770236 DOI: 10.1038/onc.2012.328] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 06/20/2012] [Accepted: 06/20/2012] [Indexed: 12/22/2022]
Abstract
The three RUNX family members are lineage specific master regulators, which also have important, context-dependent roles in carcinogenesis as either tumor suppressors or oncogenes. Here we review evidence for such roles in breast cancer (BCa). RUNX1, the predominant RUNX family member in breast epithelial cells, has a tumor suppressor role reflected by many somatic mutations found in primary tumor biopsies. The classical tumor suppressor gene RUNX3 does not consist of such a mutation hot spot, but it too seems to inhibit BCa; it is often inactivated in human BCa tumors and its haploinsufficiency in mice leads to spontaneous BCa development. The tumor suppressor activities of RUNX1 and RUNX3 are mediated in part by antagonism of estrogen signaling, a feature recently attributed to RUNX2 as well. Paradoxically, however RUNX2, a master osteoblast regulator, has been implicated in various aspects of metastasis in general and bone metastasis in particular. Reciprocating the anti-estrogenic tumor suppressor activity of RUNX proteins, inhibition of RUNX2 by estrogens may help explain their context-dependent anti-metastatic roles. Such roles are reserved to non-osseous metastasis, because ERα is associated with increased, not decreased skeletal dissemination of BCa cells. Finally, based on diverse expression patterns in BCa subtypes, the successful use of future RUNX-based therapies will most likely require careful patient selection.
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Affiliation(s)
- N-O Chimge
- Department of Biochemistry and Molecular Biology, Institute for Genetic Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - B Frenkel
- Departments of Orthopaedic Surgery and Biochemistry and Molecular Biology, Institute for Genetic Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
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