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Perlman BS, Burget N, Zhou Y, Schwartz GW, Petrovic J, Modrusan Z, Faryabi RB. Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.02.601745. [PMID: 39005446 PMCID: PMC11244972 DOI: 10.1101/2024.07.02.601745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Recent advances in high-resolution mapping of spatial interactions among regulatory elements support the existence of complex topological assemblies of enhancers and promoters known as enhancer-promoter hubs or cliques. Yet, organization principles of these multi-interacting enhancer-promoter hubs and their potential role in regulating gene expression in cancer remains unclear. Here, we systematically identified enhancer-promoter hubs in breast cancer, lymphoma, and leukemia. We found that highly interacting enhancer-promoter hubs form at key oncogenes and lineage-associated transcription factors potentially promoting oncogenesis of these diverse cancer types. Genomic and optical mapping of interactions among enhancer and promoter elements further showed that topological alterations in hubs coincide with transcriptional changes underlying acquired resistance to targeted therapy in T cell leukemia and B cell lymphoma. Together, our findings suggest that enhancer-promoter hubs are dynamic and heterogeneous topological assemblies with the potential to control gene expression circuits promoting oncogenesis and drug resistance.
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2
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Pancsa T, Pósfai B, Schubert A, Almási S, Papp E, Chien YCC, Kálmán E, Kovács KA, Kulka J, Varga L, Cserni G, Kuthi L. TRPS1 expression in breast angiosarcoma. Virchows Arch 2024:10.1007/s00428-024-03852-2. [PMID: 38902365 DOI: 10.1007/s00428-024-03852-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 05/14/2024] [Accepted: 06/13/2024] [Indexed: 06/22/2024]
Abstract
Angiosarcoma (AS) of the breast, a rare mesenchymal neoplasm, exhibits distinct forms based on etiological and genetic features. While cases with typical clinical presentation and morphology allow for a straightforward diagnosis, challenges arise when clinical data are scarce, diagnostic material is limited, or morphological characteristics overlap with other tumors, including undifferentiated carcinomas. The trichorhinophalangeal syndrome protein 1 (TRPS1), once regarded as highly specific for breast carcinomas, now faces doubts regarding its reliability. This study explores TRPS1 expression in breast AS. Our investigation revealed that 60% of AS cases displayed TRPS1 labeling, contrasting with the 40% lacking expression. Scoring by four independent readers established a consensus, designating 12/35 ASs as unequivocally TRPS1-positive. However, uncertainty surrounded nine further cases due to a lack of reader agreement (being substantial as reflected by a kappa value of 0.76). These findings challenge the perceived specificity of TRPS1, shedding light on its presence in a noteworthy proportion of breast ASs. Consequently, the study underscores the importance of a comprehensive approach in evaluating breast ASs and expands the range of entities within the differential diagnosis associated with TRPS1 labeling.
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Affiliation(s)
- Tamás Pancsa
- Department of Pathology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Boglárka Pósfai
- Department of Pathology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Anna Schubert
- Department of Pathology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Szintia Almási
- Department of Pathology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Eszter Papp
- Department of Surgical and Molecular Pathology, Tumor Pathology Center, National Institute of Oncology, Budapest, Hungary
| | - Yi-Che Chang Chien
- Department of Pathology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Endre Kálmán
- Department of Pathology, Faculty of Medicine and Clinical Center, University of Pécs, Pécs, Hungary
| | - Kristóf Attila Kovács
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Budapest, Hungary
| | - Janina Kulka
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Budapest, Hungary
| | - Linda Varga
- Department of Oncotherapy, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Gábor Cserni
- Department of Pathology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
- Department of Pathology, Bács-Kiskun County Teaching Hospital, Kecskemét, Hungary
| | - Levente Kuthi
- Department of Surgical and Molecular Pathology, Tumor Pathology Center, National Institute of Oncology, Budapest, Hungary.
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary.
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Tollot-Wegner M, Jessen M, Kim K, Sanz-Moreno A, Spielmann N, Gailus-Durner V, Fuchs H, Hrabe de Angelis M, von Eyss B. TRPS1 maintains luminal progenitors in the mammary gland by repressing SRF/MRTF activity. Breast Cancer Res 2024; 26:74. [PMID: 38702730 PMCID: PMC11067134 DOI: 10.1186/s13058-024-01824-7] [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: 12/22/2023] [Accepted: 04/12/2024] [Indexed: 05/06/2024] Open
Abstract
The transcription factor TRPS1 is a context-dependent oncogene in breast cancer. In the mammary gland, TRPS1 activity is restricted to the luminal population and is critical during puberty and pregnancy. Its function in the resting state remains however unclear. To evaluate whether it could be a target for cancer therapy, we investigated TRPS1 function in the healthy adult mammary gland using a conditional ubiquitous depletion mouse model where long-term depletion does not affect fitness. Using transcriptomic approaches, flow cytometry and functional assays, we show that TRPS1 activity is essential to maintain a functional luminal progenitor compartment. This requires the repression of both YAP/TAZ and SRF/MRTF activities. TRPS1 represses SRF/MRTF activity indirectly by modulating RhoA activity. Our work uncovers a hitherto undisclosed function of TRPS1 in luminal progenitors intrinsically linked to mechanotransduction in the mammary gland. It may also provide new insights into the oncogenic functions of TRPS1 as luminal progenitors are likely the cells of origin of many breast cancers.
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Affiliation(s)
- Marie Tollot-Wegner
- Transcriptional Control of Tissue Homeostasis Lab, Leibniz Institute on Aging, Fritz Lipmann Institute E.V., Beutenbergstr. 11, 07745, Jena, Germany
| | - Marco Jessen
- Transcriptional Control of Tissue Homeostasis Lab, Leibniz Institute on Aging, Fritz Lipmann Institute E.V., Beutenbergstr. 11, 07745, Jena, Germany
| | - KyungMok Kim
- Transcriptional Control of Tissue Homeostasis Lab, Leibniz Institute on Aging, Fritz Lipmann Institute E.V., Beutenbergstr. 11, 07745, Jena, Germany
| | - Adrián Sanz-Moreno
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, Ingolstaedter Landstr.1, Neuherberg, Germany
| | - Nadine Spielmann
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, Ingolstaedter Landstr.1, Neuherberg, Germany
| | - Valerie Gailus-Durner
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, Ingolstaedter Landstr.1, Neuherberg, Germany
| | - Helmut Fuchs
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, Ingolstaedter Landstr.1, Neuherberg, Germany
| | - Martin Hrabe de Angelis
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, Ingolstaedter Landstr.1, Neuherberg, Germany
- Chair of Experimental Genetics, TUM School of Life Sciences, Technische Universität München, Alte Akademie 8, 85354, Freising, Germany
- German Center for Diabetes Research (DZD), Ingolstaedter Landstraße. 1, 85764, Neuherberg, Germany
| | - Björn von Eyss
- Transcriptional Control of Tissue Homeostasis Lab, Leibniz Institute on Aging, Fritz Lipmann Institute E.V., Beutenbergstr. 11, 07745, Jena, Germany.
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4
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Lui JW, Tsang JY, Li J, Ko CW, Tam F, Loong TCW, Tse GM. TRPS1 is a promising marker for all subtypes of breast cancer. Histopathology 2024; 84:822-836. [PMID: 38173281 DOI: 10.1111/his.15126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/09/2023] [Accepted: 12/12/2023] [Indexed: 01/05/2024]
Abstract
AIMS Trichorhinophalangeal syndrome-1 (TRPS1) has been proposed as a novel breast marker with equally high expression in breast cancer (BC) subtypes, making it a useful diagnostic tool. Here, its expression was evaluated alongside other commonly used markers [GATA3, GCDFP15, mammaglobin (MGB) and SOX10] in a large cohort of BCs (n = 1852) and their corresponding nodal metastases. Its usefulness as a diagnostic tool and its correlation with clinicopathological features were assessed. METHODS AND RESULTS TRPS1 was expressed at 75.8% overall in the BC cohort, with at least 58% expression among BC subtypes. It was less sensitive than GATA3 for luminal and HER2-overexpressing (HER2-OE) cancers (luminal A: 82 versus 97%; luminal B: 80 versus 95%; HER2-OE: 62 versus 76%), but it was the most sensitive for TNBC (60 versus ≤ 41%). It showed a stable expression in nodal metastases (primary tumour 76 versus nodal metastasis 78%), unlike a reduced nodal expression for GATA3 (86 versus 77%). TRPS1 outperformed GATA3 in detecting non-luminal cancers when paired with other breast markers. TRPS1 and GCDFP15 was the most sensitive combination in TNBC detection, with a 76% detection rate. For TRPS1-negative and GCDFP15-negative TNBCs, SOX10 was more sensitive than GATA3 (29 versus 24%). CONCLUSIONS TRPS1 is a highly sensitive marker for all breast cancer subtypes, outperforming GATA3 in non-luminal cancers and displaying the highest sensitivity for TNBC detection when combined with GCDFP15. It is a valuable addition to the breast marker panel for accurate identification of BC.
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Affiliation(s)
- Joshua W Lui
- Department of Anatomical and Cellular Pathology and State Key Laboratory of Translational Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Julia Y Tsang
- Department of Anatomical and Cellular Pathology and State Key Laboratory of Translational Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Joshua Li
- Department of Anatomical and Cellular Pathology and State Key Laboratory of Translational Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Chun-Wai Ko
- Department of Anatomical and Cellular Pathology and State Key Laboratory of Translational Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Fiona Tam
- Department of Pathology, Kwong Wah Hospital, Hong Kong, China
| | | | - Gary M Tse
- Department of Anatomical and Cellular Pathology and State Key Laboratory of Translational Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
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Abrar M, Ali S, Hussain I, Khatoon H, Batool F, Ghazanfar S, Corcoran D, Kawakami Y, Abbasi AA. Cis-regulatory control of mammalian Trps1 gene expression. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2024. [PMID: 38369890 DOI: 10.1002/jez.b.23246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 12/22/2023] [Accepted: 01/31/2024] [Indexed: 02/20/2024]
Abstract
TRPS1 serves as the causative gene for tricho-rhino phalangeal syndrome, known for its craniofacial and skeletal abnormalities. The Trps1 gene encodes a protein that represses Wnt signaling through strong interactions with Wnt signaling inhibitors. The identification of genomic cis-acting regulatory sequences governing Trps1 expression is crucial for understanding its role in embryogenesis. Nevertheless, to date, no investigations have been conducted concerning these aspects of Trps1. To identify deeply conserved noncoding elements (CNEs) within the Trps1 locus, we employed a comparative genomics approach, utilizing slowly evolving fish such as coelacanth and spotted gar. These analyses resulted in the identification of eight CNEs in the intronic region of the Trps1 gene. Functional characterization of these CNEs in zebrafish revealed their regulatory potential in various tissues, including pectoral fins, heart, and pharyngeal arches. RNA in-situ hybridization experiments revealed concordance between the reporter expression pattern induced by the identified set of CNEs and the spatial expression pattern of the trps1 gene in zebrafish. Comparative in vivo data from zebrafish and mice for CNE7/hs919 revealed conserved functions of these enhancers. Each of these eight CNEs was further investigated in cell line-based reporter assays, revealing their repressive potential. Taken together, in vivo and in vitro assays suggest a context-dependent dual functionality for the identified set of Trps1-associated CNE enhancers. This functionally characterized set of CNE-enhancers will contribute to a more comprehensive understanding of the developmental roles of Trps1 and can aid in the identification of noncoding DNA variants associated with human diseases.
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Affiliation(s)
- Muhammad Abrar
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Shahid Ali
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, Illinois, USA
| | - Irfan Hussain
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
- Center of Regenerative Medicine and Stem Cells Research, Aga Khan University Hospital, Karachi, Pakistan
| | - Hizran Khatoon
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Fatima Batool
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Shakira Ghazanfar
- National Institute for Genomics Advanced Biotechnology, National Agriculture Research Centre (NARC), Islamabad, Pakistan
| | - Dylan Corcoran
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Yasuhiko Kawakami
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Amir Ali Abbasi
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
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6
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Lynn TJ, Shi J, Liu H, Monaco SE, Prichard JW, Lin F. Trichorhinophalangeal Syndrome Type 1 Is a Highly Sensitive and Specific Marker for Diagnosing Triple-Negative Breast Carcinomas on Cytologic Samples. Arch Pathol Lab Med 2024; 148:e1-e8. [PMID: 37406296 DOI: 10.5858/arpa.2022-0411-oa] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2023] [Indexed: 07/07/2023]
Abstract
CONTEXT.— Definitive diagnosis of metastatic triple-negative breast carcinoma (TNBC) is challenging on cytologic samples. Recent studies demonstrated that trichorhinophalangeal syndrome type 1 (TRPS1) is a highly sensitive and specific marker for diagnosing breast carcinomas, including TNBC, on surgical specimens. OBJECTIVE.— To evaluate TRPS1 expression in TNBCs on cytologic samples and a large series of nonbreast tumors on tissue microarray sections. DESIGN.— Immunohistochemical (IHC) analysis of TRPS1 and GATA-binding protein 3 (GATA3) was performed on 35 TNBC cases on surgical specimens, and 29 consecutive TNBC cases on cytologic specimens. IHC analysis of TRPS1 expression was also performed on 1079 nonbreast tumors on tissue microarray sections. RESULTS.— Of the surgical specimens, 35 of 35 TNBC cases (100%) were positive for TRPS1, all with diffuse positivity, whereas 27 of 35 (77%) were positive for GATA3, with diffuse positivity in 7 cases (26%). Of the cytologic samples, 27 of 29 TNBC cases (93%) were positive for TRPS1, with diffuse positivity in 20 cases (74%), whereas 12 of 29 (41%) were positive for GATA3, with diffuse positivity in 2 cases (17%). Of the nonbreast malignant tumors, TRPS1 expression was seen in 9.4% (3 of 32) of melanomas, 10.7% (3 of 28) of small cell carcinomas of the bladder, and 9.7% (4 of 41) of ovarian serous carcinomas. CONCLUSIONS.— Our data confirm that TRPS1 is a highly sensitive and specific marker for diagnosing TNBC cases on surgical specimens as reported in the literature. In addition, these data demonstrate that TRPS1 is a much more sensitive marker than GATA3 in detecting metastatic TNBC cases on cytologic samples. Therefore, inclusion of TRPS1 in the diagnostic IHC panel is recommended when a metastatic TNBC is suspected.
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Affiliation(s)
- Terrance J Lynn
- From the Department of Laboratory Medicine, Geisinger Medical Center, Danville, Pennsylvania
| | - Jianhui Shi
- From the Department of Laboratory Medicine, Geisinger Medical Center, Danville, Pennsylvania
| | - Haiyan Liu
- From the Department of Laboratory Medicine, Geisinger Medical Center, Danville, Pennsylvania
| | - Sara E Monaco
- From the Department of Laboratory Medicine, Geisinger Medical Center, Danville, Pennsylvania
| | - Jeffrey W Prichard
- From the Department of Laboratory Medicine, Geisinger Medical Center, Danville, Pennsylvania
| | - Fan Lin
- From the Department of Laboratory Medicine, Geisinger Medical Center, Danville, Pennsylvania
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7
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Torres HM, Fang F, May DG, Bosshardt P, Hinojosa L, Roux KJ, Tao J. Comprehensive analysis of the proximity-dependent nuclear interactome for the oncoprotein NOTCH1 in live cells. J Biol Chem 2024; 300:105522. [PMID: 38043798 PMCID: PMC10788534 DOI: 10.1016/j.jbc.2023.105522] [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: 05/31/2023] [Revised: 10/25/2023] [Accepted: 11/21/2023] [Indexed: 12/05/2023] Open
Abstract
Notch signaling plays a critical role in cell fate decisions in all cell types. Furthermore, gain-of-function mutations in NOTCH1 have been uncovered in many human cancers. Disruption of Notch signaling has recently emerged as an attractive disease treatment strategy. However, the nuclear interaction landscape of the oncoprotein NOTCH1 remains largely unexplored. We therefore employed here a proximity-dependent biotin identification approach to identify in vivo protein associations with the nuclear Notch1 intracellular domain in live cells. We identified a large set of previously reported and unreported proteins that associate with NOTCH1, including general transcription and elongation factors, DNA repair and replication factors, coactivators, corepressors, and components of the NuRD and SWI/SNF chromatin remodeling complexes. We also found that Notch1 intracellular domain associates with protein modifiers and components of other signaling pathways that may influence Notch signal transduction and protein stability such as USP7. We further validated the interaction of NOTCH1 with histone deacetylase 1 or GATAD2B using protein network analysis, proximity-based ligation, in vivo cross-linking and coimmunoprecipitation assays in several Notch-addicted cancer cell lines. Through data mining, we also revealed potential drug targets for the inhibition of Notch signaling. Collectively, these results provide a valuable resource to uncover the mechanisms that fine-tune Notch signaling in tumorigenesis and inform therapeutic targets for Notch-addicted tumors.
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Affiliation(s)
- Haydee M Torres
- Cancer Biology & Immunotherapies Group, Sanford Research, Sioux Falls, South Dakota, USA; Department of Chemistry and Biochemistry, South Dakota State University, Brookings, South Dakota, USA
| | - Fang Fang
- Cancer Biology & Immunotherapies Group, Sanford Research, Sioux Falls, South Dakota, USA
| | - Danielle G May
- Enabling Technologies Group, Sanford Research, Sioux Falls, South Dakota, USA
| | - Paige Bosshardt
- Cancer Biology & Immunotherapies Group, Sanford Research, Sioux Falls, South Dakota, USA
| | - Leetoria Hinojosa
- Cancer Biology & Immunotherapies Group, Sanford Research, Sioux Falls, South Dakota, USA
| | - Kyle J Roux
- Enabling Technologies Group, Sanford Research, Sioux Falls, South Dakota, USA; Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, South Dakota, USA
| | - Jianning Tao
- Cancer Biology & Immunotherapies Group, Sanford Research, Sioux Falls, South Dakota, USA; Department of Chemistry and Biochemistry, South Dakota State University, Brookings, South Dakota, USA; Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, South Dakota, USA.
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8
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Jovanović B, Temko D, Stevens LE, Seehawer M, Fassl A, Murphy K, Anand J, Garza K, Gulvady A, Qiu X, Harper NW, Daniels VW, Xiao-Yun H, Ge JY, Alečković M, Pyrdol J, Hinohara K, Egri SB, Papanastasiou M, Vadhi R, Font-Tello A, Witwicki R, Peluffo G, Trinh A, Shu S, Diciaccio B, Ekram MB, Subedee A, Herbert ZT, Wucherpfennig KW, Letai AG, Jaffe JD, Sicinski P, Brown M, Dillon D, Long HW, Michor F, Polyak K. Heterogeneity and transcriptional drivers of triple-negative breast cancer. Cell Rep 2023; 42:113564. [PMID: 38100350 PMCID: PMC10842760 DOI: 10.1016/j.celrep.2023.113564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 10/05/2023] [Accepted: 11/22/2023] [Indexed: 12/17/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is a heterogeneous disease with limited treatment options. To characterize TNBC heterogeneity, we defined transcriptional, epigenetic, and metabolic subtypes and subtype-driving super-enhancers and transcription factors by combining functional and molecular profiling with computational analyses. Single-cell RNA sequencing revealed relative homogeneity of the major transcriptional subtypes (luminal, basal, and mesenchymal) within samples. We found that mesenchymal TNBCs share features with mesenchymal neuroblastoma and rhabdoid tumors and that the PRRX1 transcription factor is a key driver of these tumors. PRRX1 is sufficient for inducing mesenchymal features in basal but not in luminal TNBC cells via reprogramming super-enhancer landscapes, but it is not required for mesenchymal state maintenance or for cellular viability. Our comprehensive, large-scale, multiplatform, multiomics study of both experimental and clinical TNBC is an important resource for the scientific and clinical research communities and opens venues for future investigation.
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Affiliation(s)
- Bojana Jovanović
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel Temko
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Laura E Stevens
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Marco Seehawer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Anne Fassl
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Katherine Murphy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jayati Anand
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kodie Garza
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Anushree Gulvady
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Xintao Qiu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Nicholas W Harper
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Veerle W Daniels
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Huang Xiao-Yun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jennifer Y Ge
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA
| | - Maša Alečković
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Jason Pyrdol
- Departments of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Departments of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Kunihiko Hinohara
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Shawn B Egri
- The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA
| | | | - Raga Vadhi
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Alba Font-Tello
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Robert Witwicki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Guillermo Peluffo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Anne Trinh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Shaokun Shu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Benedetto Diciaccio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Muhammad B Ekram
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Ashim Subedee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Zachary T Herbert
- Department of Molecular Biology Core Facility, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kai W Wucherpfennig
- Departments of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Departments of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Anthony G Letai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Jacob D Jaffe
- The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA
| | - Deborah Dillon
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Franziska Michor
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA; Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA; Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA; Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA; Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
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9
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Sun J, Lian X, Lv C, Li H, Lin Z, Luo S, Liu Y, Xu Y, Jiang X, Xu W, Liao S, Chen Z, Wang S. Trps1 acts as a regulator of Sf-1 transcription and testosterone synthesis in mouse Leydig cells. Cell Biol Toxicol 2023; 39:3141-3157. [PMID: 37531013 DOI: 10.1007/s10565-023-09823-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 07/26/2023] [Indexed: 08/03/2023]
Abstract
Infertility has attracted global concern, and disruption of testosterone is a common cause of male infertility. Exploring the critical factors in testosterone biosynthesis may provide new insights for disease research and clinical therapy. Research on trichorhinophalangeal syndrome-1 (Trps1) gene has recently been focus on cancers; it is yet unknown whether Trps1 produces a marked effect in the male reproductive system. In the current study, single-cell RNA sequencing analysis of trichorhinophalangeal syndrome-1 gene (Trps1) expression in mouse testes and cleavage under targets and tagmentation and RNA sequencing were utilized to investigate the functionality of Trps1 in mouse Leydig cells. Knockdown of Trps1 increased testosterone synthesis in vitro and vivo using adeno-associated viral delivery and conditional knockout models. The results showed that Trps1 was abundantly expressed in Leydig cells. The expression levels of both steroidogenic factor-1 (Sf-1) and steroidogenic enzymes (Cyp11a1, Hsd3b, Cyp17a1, and Hsd17b3) as well as testosterone secretion were increased after Trps1 deficiency in vivo and vitro. Furthermore, disruption of Trps1 reduced histone deacetylase 1/2 activity and increased histone H3 acetylation in the Sf-1 promoter, thereby promoting testosterone secretion. Interestingly, Sf-1 also regulated the transcription of Trps1 through activating transcription factor 2. These results indicate that Trps1 targets Sf-1 to affect steroidogenesis through histone acetylation and shed light on the critical role of Trps1 functioning in the mouse Leydig cells.
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Affiliation(s)
- Jiandong Sun
- Key Laboratory of Stem Cell Engineering and Regenerative Medicine of Fujian Province University, Fujian Medical University, Fuzhou, 350122, People's Republic of China
| | - Xiuli Lian
- Key Laboratory of Stem Cell Engineering and Regenerative Medicine of Fujian Province University, Fujian Medical University, Fuzhou, 350122, People's Republic of China
- Department of Histology and Embryology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, People's Republic of China
| | - Chengyu Lv
- Department of Obstetrics and Gynecology, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, 350001, People's Republic of China
| | - Hua Li
- Key Laboratory of Stem Cell Engineering and Regenerative Medicine of Fujian Province University, Fujian Medical University, Fuzhou, 350122, People's Republic of China
- Department of Histology and Embryology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, People's Republic of China
| | - Zihang Lin
- Key Laboratory of Stem Cell Engineering and Regenerative Medicine of Fujian Province University, Fujian Medical University, Fuzhou, 350122, People's Republic of China
| | - Shanshan Luo
- Key Laboratory of Stem Cell Engineering and Regenerative Medicine of Fujian Province University, Fujian Medical University, Fuzhou, 350122, People's Republic of China
| | - Yue Liu
- Key Laboratory of Stem Cell Engineering and Regenerative Medicine of Fujian Province University, Fujian Medical University, Fuzhou, 350122, People's Republic of China
- Department of Histology and Embryology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, People's Republic of China
| | - Yinglin Xu
- Department of Histology and Embryology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, People's Republic of China
| | - Xia Jiang
- Key Laboratory of Stem Cell Engineering and Regenerative Medicine of Fujian Province University, Fujian Medical University, Fuzhou, 350122, People's Republic of China
| | - Weiwei Xu
- Key Laboratory of Stem Cell Engineering and Regenerative Medicine of Fujian Province University, Fujian Medical University, Fuzhou, 350122, People's Republic of China
| | - Shumin Liao
- Key Laboratory of Stem Cell Engineering and Regenerative Medicine of Fujian Province University, Fujian Medical University, Fuzhou, 350122, People's Republic of China
| | - Zhangting Chen
- Key Laboratory of Stem Cell Engineering and Regenerative Medicine of Fujian Province University, Fujian Medical University, Fuzhou, 350122, People's Republic of China
| | - Shie Wang
- Key Laboratory of Stem Cell Engineering and Regenerative Medicine of Fujian Province University, Fujian Medical University, Fuzhou, 350122, People's Republic of China.
- Department of Histology and Embryology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, People's Republic of China.
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10
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Sun H, Ding Q, Sahin AA. Immunohistochemistry in the Diagnosis and Classification of Breast Tumors. Arch Pathol Lab Med 2023; 147:1119-1132. [PMID: 37490413 DOI: 10.5858/arpa.2022-0464-ra] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/10/2023] [Indexed: 07/27/2023]
Abstract
CONTEXT.— In the clinical practice of breast pathology, immunohistochemistry (IHC) of different markers is widely used for the diagnosis and classification of breast lesions. OBJECTIVE.— To provide an overview of currently used and recently identified IHC stains that have been implemented in the field of diagnostic breast pathology. DATA SOURCES.— Data were obtained from literature review and clinical experience of the authors as breast pathologists. CONCLUSIONS.— In the current review, we summarize the common uses of IHC stains for diagnosing different types of breast lesions, especially invasive and noninvasive breast lesions, and benign and malignant spindle cell lesions. In addition, the cutting-edge knowledge of diagnostic carcinoma markers will lead us to further understand the different types of breast carcinoma and differentiate breast carcinomas from other carcinomas of similar morphology. Knowing the strengths and limitations of these markers is essential to the clinical practice of breast pathology.
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Affiliation(s)
- Hongxia Sun
- From the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston
| | - Qingqing Ding
- From the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston
| | - Aysegul A Sahin
- From the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston
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11
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Ma T, Guo L, Yan H, Wang L. Cobind: quantitative analysis of the genomic overlaps. BIOINFORMATICS ADVANCES 2023; 3:vbad104. [PMID: 37600846 PMCID: PMC10438957 DOI: 10.1093/bioadv/vbad104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/17/2023] [Accepted: 08/04/2023] [Indexed: 08/22/2023]
Abstract
Motivation Analyzing the overlap between two sets of genomic intervals is a frequent task in the field of bioinformatics. Typically, this is accomplished by counting the number (or proportion) of overlapped regions, which applies an arbitrary threshold to determine if two genomic intervals are overlapped. By making binary calls but disregarding the magnitude of the overlap, such an approach often leads to biased, non-reproducible, and incomparable results. Results We developed the cobind package, which incorporates six statistical measures: the Jaccard coefficient, Sørensen-Dice coefficient, Szymkiewicz-Simpson coefficient, collocation coefficient, pointwise mutual information (PMI), and normalized PMI. These measures allow for a quantitative assessment of the collocation strength between two sets of genomic intervals. To demonstrate the effectiveness of these methods, we applied them to analyze CTCF's binding sites identified from ChIP-seq, cancer-specific open-chromatin regions (OCRs) identified from ATAC-seq of 17 cancer types, and oligodendrocytes-specific OCRs identified from scATAC-seq. Our results indicated that these new approaches effectively re-discover CTCF's cofactors, as well as cancer-specific and oligodendrocytes-specific master regulators implicated in disease and cell type development. Availability and implementation The cobind package is implemented in Python and freely available at https://cobind.readthedocs.io/en/latest/.
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Affiliation(s)
- Tao Ma
- Division of Computational Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, United States
| | - Lingyun Guo
- Department of Computer Science and Engineering, University of Minnesota Twin Cities, Minneapolis, MN 55455, United States
| | - Huihuang Yan
- Division of Computational Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, United States
| | - Liguo Wang
- Division of Computational Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, United States
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota Rochester, Rochester, MN 55904, United States
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12
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Kathman SG, Koo SJ, Lindsey GL, Her HL, Blue SM, Li H, Jaensch S, Remsberg JR, Ahn K, Yeo GW, Ghosh B, Cravatt BF. Remodeling oncogenic transcriptomes by small molecules targeting NONO. Nat Chem Biol 2023; 19:825-836. [PMID: 36864190 PMCID: PMC10337234 DOI: 10.1038/s41589-023-01270-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 01/20/2023] [Indexed: 03/04/2023]
Abstract
Much of the human proteome is involved in mRNA homeostasis, but most RNA-binding proteins lack chemical probes. Here we identify electrophilic small molecules that rapidly and stereoselectively decrease the expression of transcripts encoding the androgen receptor and its splice variants in prostate cancer cells. We show by chemical proteomics that the compounds engage C145 of the RNA-binding protein NONO. Broader profiling revealed that covalent NONO ligands suppress an array of cancer-relevant genes and impair cancer cell proliferation. Surprisingly, these effects were not observed in cells genetically disrupted for NONO, which were instead resistant to NONO ligands. Reintroduction of wild-type NONO, but not a C145S mutant, restored ligand sensitivity in NONO-disrupted cells. The ligands promoted NONO accumulation in nuclear foci and stabilized NONO-RNA interactions, supporting a trapping mechanism that may prevent compensatory action of paralog proteins PSPC1 and SFPQ. These findings show that NONO can be co-opted by covalent small molecules to suppress protumorigenic transcriptional networks.
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Affiliation(s)
- Stefan G Kathman
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA.
| | - Seong Joo Koo
- Molecular and Cellular Pharmacology, Discovery Technologies and Molecular Pharmacology, Janssen Research and Development, Beerse, Belgium
| | - Garrett L Lindsey
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Hsuan-Lin Her
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | - Steven M Blue
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Haoxin Li
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Steffen Jaensch
- High Dimensional and Computational Biology, Discovery Technologies and Molecular Pharmacology, Janssen Research and Development, Beerse, Belgium
| | - Jarrett R Remsberg
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Kay Ahn
- Molecular and Cellular Pharmacology, Discovery Technologies and Molecular Pharmacology, Janssen Research and Development, Spring House, PA, USA.
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Brahma Ghosh
- Discovery Chemistry, Janssen Research and Development, Spring House, PA, USA.
| | - Benjamin F Cravatt
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA.
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13
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Yang L, Fan Q, Wang J, Yang X, Yuan J, Li Y, Sun X, Wang Y. TRPS1 regulates the opposite effect of progesterone via RANKL in endometrial carcinoma and breast carcinoma. Cell Death Discov 2023; 9:185. [PMID: 37344459 DOI: 10.1038/s41420-023-01484-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 06/05/2023] [Accepted: 06/14/2023] [Indexed: 06/23/2023] Open
Abstract
Medroxyprogesterone (MPA) has therapeutic effect on endometrial carcinoma (EC), while it could promote the carcinogenesis of breast cancer (BC) by activating receptor activator of NF-kB ligand (RANKL). However, the selective mechanism of MPA in endometrium and breast tissue remains obscure. Multiomics analysis of chromatin immunoprecipitation sequencing (ChIP-seq) and RNA sequencing (RNA-seq) were performed in cell lines derived from endometrial cancer and mammary tumor to screen the differential co-regulatory factors of progesterone receptor (PR). Dual-luciferase assays and ChIP-PCR assays were used to validate the transcriptional regulation. Co-immunoprecipitation (Co-IP) and immunofluorescence assays were carried out to explore molecular interactions between PR, the cofactor transcriptional repressor GATA binding 1 (TRPS1), and histone deacetylase 2 (HDAC2). Subsequently, human endometrial cancer/breast cancer xenograft models were established to investigate the regulation effect of cofactor TRPS1 in vivo. In the current study, we found that MPA downregulated RANKL expression in a time- and dose-dependent manner in EC, while had the opposite effect on BC. Then PR could recruit cofactor TRPS1 to the promoter of RANKL, leading to histone deacetylation of RANKL to repress its transcription in EC, whereas MPA disassociated the PR/TRPS1/HDAC2 complex to enhance RANKL histone acetylation in BC. Therefore, TRPS1, the coregulator recruited by PR played a critical role in the selective mechanism of progesterone in EC and BC and could become a potential candidate for targeted therapy to improve the anticancer effect of MPA on EC and avoid its carcinogenic effect on BC.
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Affiliation(s)
- Linlin Yang
- Department of Gynecological Oncology, The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Municipal Key Clinical Specialty, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China
| | - Qiong Fan
- Department of Gynecological Oncology, The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Municipal Key Clinical Specialty, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China
| | - Jing Wang
- Department of Gynecological Oncology, The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Municipal Key Clinical Specialty, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China
| | - Xiaoming Yang
- Department of Gynecological Oncology, The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Municipal Key Clinical Specialty, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China
| | - Jiangjing Yuan
- Department of Gynecological Oncology, The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Municipal Key Clinical Specialty, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China
| | - Yuhong Li
- Department of Gynecological Oncology, The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Municipal Key Clinical Specialty, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China
| | - Xiao Sun
- Department of Gynecological Oncology, The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Shanghai Municipal Key Clinical Specialty, Shanghai, China.
- Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China.
| | - Yudong Wang
- Department of Gynecological Oncology, The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Shanghai Municipal Key Clinical Specialty, Shanghai, China.
- Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China.
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14
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Baban F, Koepplin JW, Ahmad M, Clarke-Brodber AL, Bois MC, Hartley CP, Sturgis CD. TRPS1 outperforms GATA3 in pleural effusions with metastatic breast carcinoma versus mesothelioma. Diagn Cytopathol 2023. [PMID: 37096814 DOI: 10.1002/dc.25148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 03/28/2023] [Accepted: 04/17/2023] [Indexed: 04/26/2023]
Abstract
INTRODUCTION In evaluating malignant pleural fluid cytology, metastatic adenocarcinomas and mesotheliomas are often differential diagnoses. GATA binding protein 3 (GATA3) has historically been used to confirm metastatic breast carcinomas; however, GATA3 has low specificity if mesothelioma is included in differential diagnoses. Trichorhinophalangeal syndrome type 1 (TRPS1) protein is expressed in all types of breast carcinomas, with reported high specificity and sensitivity. We investigated the performance of TRPS1 immunohistochemistry (IHC) and compared it to GATA3 in pleural fluids diagnosed with metastatic breast carcinoma and mesothelioma. METHODS Thirty-six consecutive ThinPrep pleural fluids and 4 pleural fine needle aspirations (FNAs) with diagnoses of metastatic breast carcinoma (21) and mesothelioma (19) were retrieved, and IHC with TRPS1 and GATA3 was performed on all. Immunoreactivity scores for TRPS1 were calculated by multiplying percentage of immunoreactive cells by staining intensity. Immunoreactivity scores were negative if 0 or 1, low positive if 2, intermediate positive if 3 or 4, or high positive if 6 or 9. Nuclear immunoreactivity of ≥10% with at least moderate intensity was judged GATA3 positive. RESULTS GATA3 showed immunoreactivity in all metastatic breast carcinomas and 84% of mesotheliomas. TRPS1 was immunoreactive in all breast carcinoma cases (18 with a score of 9 and 3 with a score of 6). TRPS1 showed low positivity in 5% of mesothelioma cases with all other cases being negative. CONCLUSION When cytomorphologic differential diagnoses of mesothelioma exist, TRPS1 is a more specific marker than GATA3 for confirmation of metastatic breast carcinoma in pleural fluid cytology.
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Affiliation(s)
- Farah Baban
- Department of Laboratory Medicine and Pathology, Division of Anatomic Pathology-Mayo Clinic, Rochester, Minnesota, USA
| | - Justin W Koepplin
- Department of Laboratory Medicine and Pathology, Division of Anatomic Pathology-Mayo Clinic, Rochester, Minnesota, USA
| | - Muhammad Ahmad
- Department of Laboratory Medicine and Pathology, Division of Anatomic Pathology-Mayo Clinic, Rochester, Minnesota, USA
| | - Anna-Lee Clarke-Brodber
- Department of Laboratory Medicine and Pathology, Division of Anatomic Pathology-Mayo Clinic, Rochester, Minnesota, USA
| | - Melanie C Bois
- Department of Laboratory Medicine and Pathology, Division of Anatomic Pathology-Mayo Clinic, Rochester, Minnesota, USA
| | - Christopher P Hartley
- Department of Laboratory Medicine and Pathology, Division of Anatomic Pathology-Mayo Clinic, Rochester, Minnesota, USA
| | - Charles D Sturgis
- Department of Laboratory Medicine and Pathology, Division of Anatomic Pathology-Mayo Clinic, Rochester, Minnesota, USA
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15
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Du X, Wang H, Xu J, Zhang Y, Chen T, Li G. Profiling and integrated analysis of transcriptional addiction gene expression and prognostic value in hepatocellular carcinoma. Aging (Albany NY) 2023; 15:204676. [PMID: 37171044 PMCID: PMC10188332 DOI: 10.18632/aging.204676] [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: 01/06/2023] [Accepted: 04/15/2023] [Indexed: 05/13/2023]
Abstract
Transcriptional dysregulation caused by genomic and epigenetic alterations in cancer is called "transcriptional addiction". Transcriptional addiction is an important pathogenic factor of tumor malignancy. Hepatocellular carcinoma (HCC) genomes are highly heterogeneous, with many dysregulated genes. Our study analyzed the possibility that transcriptional addiction-related genes play a significant role in HCC. All data sources for conducting this study were public cancer databases and tissue microarrays. We identified 38 transcriptional addiction genes, and most were differentially expressed genes. Among patients of different groups, there were significant differences in overall survival rates. Both nomogram and risk score were independent predictors of HCC outcomes. Transcriptional addiction gene expression characteristics determine the sensitivity of patients to immunotherapy, cisplatin, and sorafenib. Besides, HDAC2 was identified as an oncogene, and its expression was correlated with patient survival time. Our study conclusively demonstrated that transcriptional addiction is crucial in HCC. We provided biomarkers for predicting the prognosis of HCC patients, which can more precisely guide the patient's treatment.
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Affiliation(s)
- Xiaowei Du
- First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Hao Wang
- Second Department of Oncology, Seventh People’s Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jing Xu
- Second Department of Oncology, Seventh People’s Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yufei Zhang
- Second Department of Oncology, Seventh People’s Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Tingsong Chen
- Second Department of Oncology, Seventh People’s Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Gao Li
- Second Department of Oncology, Seventh People’s Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai, China
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16
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Nameki RA, Chang H, Yu P, Abbasi F, Lin X, Reddy J, Haro M, Fonseca MAS, Freedman ML, Drapkin R, Corona RI, Lawrenson K. Rewiring of master transcription factor cistromes during high-grade serous ovarian cancer development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.11.536378. [PMID: 37090516 PMCID: PMC10120620 DOI: 10.1101/2023.04.11.536378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
The transcription factors MECOM, PAX8, SOX17 and WT1 are candidate master regulators of high-grade serous 'ovarian' cancer (HGSC), yet their cooperative role in the hypothesized tissue of origin, the fallopian tube secretory epithelium (FTSEC) is unknown. We generated 26 epigenome (CUT&TAG, CUT&RUN, ATAC-seq and HiC) data sets and 24 profiles of RNA-seq transcription factor knock-down followed by RNA sequencing in FTSEC and HGSC models to define binding sites and gene sets regulated by these factors in cis and trans. This revealed that MECOM, PAX8, SOX17 and WT1 are lineage-enriched, super-enhancer associated master regulators whose cooperative DNA-binding patterns and target genes are re-wired during tumor development. All four TFs were indispensable for HGSC clonogenicity and survival but only depletion of PAX8 and WT1 impaired FTSEC cell survival. These four TFs were pharmacologically inhibited by transcriptional inhibitors only in HGSCs but not in FTSECs. Collectively, our data highlights that tumor-specific epigenetic remodeling is tightly related to MECOM, PAX8, SOX17 and WT1 activity and these transcription factors are targetable in a tumor-specific manner through transcriptional inhibitors.
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Affiliation(s)
- Robbin A. Nameki
- Women’s Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Heidi Chang
- Women’s Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Pak Yu
- Women’s Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Forough Abbasi
- Women’s Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Xianzhi Lin
- Women’s Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jessica Reddy
- Women’s Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Marcela Haro
- Women’s Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Marcos AS Fonseca
- Women’s Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Matthew L. Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Ronny Drapkin
- Ovarian Cancer Research Center, Department of Obstetrics and Gynecology, University of Pennsylvania Perelman School of Medicine, PA, USA
| | - Rosario I. Corona
- Women’s Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kate Lawrenson
- Women’s Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Cancer Prevention and Control Program, Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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17
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A Genome-Wide Association Study Identified Novel Genetic Susceptibility Loci for Oral Cancer in Taiwan. Int J Mol Sci 2023; 24:ijms24032789. [PMID: 36769103 PMCID: PMC9917812 DOI: 10.3390/ijms24032789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/26/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Taiwan has the highest incidence rate of oral cancer in the world. Although oral cancer is mostly an environmentally induced cancer, genetic factors also play an important role in its etiology. Genome-wide association studies (GWAS) have identified nine susceptibility regions for oral cancers in populations of European descent. In this study, we performed the first GWAS of oral cancer in Taiwan with 1529 cases and 44,572 controls. We confirmed two previously reported loci on the 6p21.33 (HLA-B) and 6p21.32 (HLA-DQ gene cluster) loci, highlighting the importance of the human leukocyte antigen and, hence, the immunologic mechanisms in oral carcinogenesis. The TERT-CLMPT1L locus on 5p15.33, the 4q23 ADH1B locus, and the LAMC3 locus on 9q34.12 were also consistent in the Taiwanese. We found two new independent loci on 6p21.32, rs401775 in SKIV2L gene and rs9267798 in TNXB gene. We also found two suggestive novel Taiwanese-specific loci near the TPRS1 gene on 8q23.3 and in the TMED3 gene on 15q25.1. This study identified both common and unique oral cancer susceptibility loci in the Taiwanese as compared to populations of European descent and shed significant light on the etiology of oral cancer in Taiwan.
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18
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Cho WC, Nagarajan P, Ding Q, Prieto VG, Torres-Cabala CA. Trichorhinophalangeal Syndrome Type 1-Positive Cells in Breast Dermal Granulation Tissues and Scars: A Potential Diagnostic Pitfall. Am J Dermatopathol 2022; 44:964-967. [PMID: 35925150 DOI: 10.1097/dad.0000000000002268] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
ABSTRACT Trichorhinophalangeal syndrome type 1 (TRPS1) immunohistochemistry has been gaining popularity in recent years in the field of surgical pathology for its utility as a highly sensitive and specific marker for breast carcinomas, including those with triple-negative phenotype. More recent data suggest TRPS1 may also prove its utility in the diagnosis of mesenchymal tumors arising in the breast parenchyma, including malignant phyllodes tumors and primary chondrosarcomas and osteosarcomas of the breast. However, little is known about TRPS1 expression in nontumor cells, such as stromal fibroblasts/myofibroblasts of dermal granulation tissues and scars. Here, we describe our unique experience with TRPS1-positive cells, morphologically consistent with reactive fibroblasts/myofibroblasts, seen in dermal granulation tissues and scars from breast skin specimens of a 51-year-old woman with a history of bilateral invasive ductal carcinomas of the breast, status after bilateral total mastectomy and chemoradiation, who presented with nonhealing wounds on the chests. To the best of our knowledge, this is the first reported case of strong TRPS1 expression in dermal granulation tissue/scar. As the usage of TRPS1 immunohistochemistry in routine clinical practice, including in the field of dermatopathology, will likely increase over time, awareness of this potential diagnostic pitfall is important to avoid overinterpretation of the findings.
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Affiliation(s)
- Woo Cheal Cho
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
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Cloutier JM, Ingram DR, Wani K, Lazar AJ, Wang WL. Frequent TRPS1 expression in synovial sarcoma is associated with SS18-SSX fusion oncoprotein activity. Hum Pathol 2022; 130:88-94. [PMID: 36162599 DOI: 10.1016/j.humpath.2022.09.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 09/21/2022] [Indexed: 12/14/2022]
Abstract
Synovial sarcoma is an aggressive translocation-associated soft tissue tumor driven by an SS18-SSX fusion oncoprotein. TRPS1 is a recently identified marker for breast carcinoma, but less is known about its expression in other tumor types. We encountered a case of synovial sarcoma showing strong and diffuse expression of TRPS1. To better characterize this observation, we examined the immunohistochemical expression of TRPS1 in 165 cases of synovial sarcoma, including 70 primary, 21 recurrent, and 74 metastatic tumors, using tissue microarrays. TRPS1 expression was observed in 86% of cases. Among the positive cases, TRPS1 labeled >50% of tumor cells in 57% of cases, and staining intensity was strong or moderate in 68%. Metastatic tumors more frequently demonstrated strong and diffuse TRPS1 expression compared to primary tumors. To understand the mechanism of TRPS1 expression, we interrogated publicly available gene expression and ChIP-seq datasets and found that TRPS1 transcript levels are increased in synovial sarcoma compared to other soft tissue sarcomas. Data from ChIP-seq experiments showed enrichment of SS18-SSX protein at the TRPS1 locus and co-localization with RNA pol II. The TRPS1 locus is also enriched in several histone modifications associated with active transcription. In functional knockdown data, repression of SS18::SSX in synovial sarcoma cell lines is associated with reduced TRPS1 transcript levels, further supporting a model whereby TRPS1 expression is mediated, at least in part, by the SS18-SSX fusion oncoprotein. Knowledge of TRPS1 expression in synovial sarcoma may help avoid potential diagnostic pitfalls in the immunohistochemical workup of tumors.
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Affiliation(s)
- Jeffrey M Cloutier
- Department of Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA.
| | - Davis R Ingram
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Khalida Wani
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Alexander J Lazar
- Department of Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA; Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Wei-Lien Wang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA; Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
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Chen C, Hang J, Chen Y, Lin S, Chiu H, Hsu C, Lai C, Yang C. The diagnostic utility of trichorhinophalangeal syndrome type 1 immunohistochemistry for metastatic breast carcinoma in effusion cytology specimens. Cancer Cytopathol 2022; 131:226-233. [PMID: 36399408 DOI: 10.1002/cncy.22663] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/11/2022] [Accepted: 10/04/2022] [Indexed: 11/19/2022]
Abstract
BACKGROUND Trichorhinophalangeal syndrome type 1 (TRPS1) is a novel immunohistochemical marker with excellent performance in distinguishing breast carcinoma from other cancers in surgical specimens. The aim of this study was to evaluate the diagnostic utility of TRPS1 compared with GATA3 for metastatic breast carcinoma in effusion cytology specimens. METHODS In total, 91 cell blocks of malignant effusion specimens, including 47 metastatic breast carcinomas (nine triple-negative breast carcinomas [TNBCs] and 38 non-TNBCs) and 44 nonmammary malignancies, were selected for TRPS1 and GATA3 immunohistochemistry. Modified H scores ≥ 200 were considered positive staining. RESULTS The positive rate of TRPS1 was similar between TNBC and non-TNBC (77.8% vs 73.3%, p = .802), whereas the positive rate of GATA3 was lower in TNBC than in non-TNBC (66.7% vs 89.5%, p = .087). The positive rate of TRPS1 was significantly higher in breast carcinoma than in urothelial carcinoma (74.5% vs 0%, p < .001), whereas the positive rate of GATA3 showed no difference between these two (85.1% vs 85.7%, p = .956). Notably, diffuse and strong aberrant expression of TRPS1 was observed in one lung adenocarcinoma and one serous adenocarcinoma in this series. The overall sensitivity, specificity, positive predictive value, and negative predictive value of TRPS1 immunohistochemistry for breast carcinoma were 74.5%, 95.5%, 94.6%, and 77.8%, respectively. CONCLUSION TRPS1 is a sensitive and specific marker for metastatic breast cancer in serous effusion cell-block specimens. It shows superior sensitivity and specificity compared with GATA3, especially in the TNBC setting and for excluding urothelial carcinoma.
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Affiliation(s)
- Chih‐Jung Chen
- Department of Pathology and Laboratory Medicine Taichung Veterans General Hospital Taichung Taiwan
- School of Medicine Chung Shan Medical University Taichung Taiwan
- Department of Post‐Baccalaureate Medicine College of Medicine National Chung Hsing University Taichung Taiwan
| | - Jen‐Fan Hang
- Department of Pathology and Laboratory Medicine Taipei Veterans General Hospital Taipei Taiwan
- School of Medicine National Yang Ming Chiao Tung University Taipei Taiwan
- Institute of Clinical Medicine National Yang Ming Chiao Tung University Taipei Taiwan
| | - Yun‐An Chen
- Department of Pathology and Laboratory Medicine Taichung Veterans General Hospital Taichung Taiwan
| | - Shu‐Jiuan Lin
- Department of Pathology and Laboratory Medicine Taichung Veterans General Hospital Taichung Taiwan
| | - Hung‐Ming Chiu
- Department of Pathology and Laboratory Medicine Taichung Veterans General Hospital Taichung Taiwan
| | - Chih‐Yi Hsu
- Department of Pathology and Laboratory Medicine Taipei Veterans General Hospital Taipei Taiwan
- School of Medicine National Yang Ming Chiao Tung University Taipei Taiwan
| | - Chiung‐Ru Lai
- Department of Pathology and Laboratory Medicine Taipei Veterans General Hospital Taipei Taiwan
- School of Medicine National Yang Ming Chiao Tung University Taipei Taiwan
| | - Chi‐Shun Yang
- Department of Pathology and Laboratory Medicine Taichung Veterans General Hospital Taichung Taiwan
- Department of Medical Laboratory Science and Biotechnology Central Taiwan University of Science and Technology Taichung Taiwan
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Identification of Candidate MicroRNA-mRNA Subnetwork for Predicting the Osteosarcoma Progression by Bioinformatics Analysis. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:1821233. [PMID: 36238488 PMCID: PMC9553349 DOI: 10.1155/2022/1821233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 08/24/2022] [Indexed: 12/04/2022]
Abstract
Osteosarcoma (OS) is the pretty common primary cancer of the bone among the malignancies in adolescents. A single molecular component or a limited number of molecules is insufficient as a predictive biomarker of OS progression. Hence, it is necessary to find novel network biomarkers to improve the prediction and therapeutic effect for OS. Here, we identified 230 DE-miRNAs and 821 DE-mRNAs through two miRNA expression-profiling datasets and three mRNA expression-profiling datasets. We found that hsa-miR-494 is closely linked with the survival of OS patients. In addition, we analyzed GO and KEGG enrichment for targets of hsa-miR-494-5p and hsa-miR-494-3p through R programming. And five mRNAs were predicted as common targets of hsa-miR-494-5p and hsa-miR-494-3p. We further revealed that upregulated TRPS1 was strongly correlated with poor outcomes in OS patients through the survival analysis based on the TARGET database. The qRT-PCR study verified that the expression of hsa-miR-494-5p and hsa-miR-494-3p was declined considerably, while TRPS1 was notably raised in OS cells when compared to the osteoblasts. Thus, we generated a new regulatory subnetwork of key miRNAs and target mRNAs using Cytoscape software. These results indicate that the novel miRNA-mRNA subnetwork composed of hsa-miR-494-5p, hsa-miR-494-3p, and TRPS1 might be a characteristic molecule for assessing the prognostic value of OS patients.
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22
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Functional mechanisms of TRPS1 in disease progression and its potential role in personalized medicine. Pathol Res Pract 2022; 237:154022. [PMID: 35863130 DOI: 10.1016/j.prp.2022.154022] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/04/2022] [Accepted: 07/12/2022] [Indexed: 11/22/2022]
Abstract
The gene of transcriptional repressor GATA binding 1 (TRPS1), as an atypical GATA transcription factor, has received considerable attention in a plethora of physiological and pathological processes, and may become a promising biomarker for targeted therapies in diseases and tumors. However, there still lacks a comprehensive exploration of its functions and promising clinical applications. Herein, relevant researches published in English from 2000 to 2022 were retrieved from PubMed, Google Scholar and MEDLINE, concerning the roles of TRPS1 in organ differentiation and tumorigenesis. This systematic review predominantly focused on summarizing the structural characteristics and biological mechanisms of TRPS1, its involvement in tricho-rhino-phalangeal syndrome (TRPS), its participation in the development of multiple tissues, the recent advances of its vital features in metabolic disorders as well as malignant tumors, in order to prospect its potential applications in disease detection and cancer targeted therapy. From the clinical perspective, the deeply and thoroughly understanding of the complicated context-dependent and cell-lineage-specific mechanisms of TRPS1 would not only gain novel insights into the complex etiology of diseases, but also provide the fundamental basis for the development of therapeutic drugs targeting both TRPS1 and its critical cofactors, which would facilitate individualized treatment.
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23
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Baranovsky A, Ivanov T, Granovskaya M, Papatsenko D, Pervouchine DD. Transcriptome analysis reveals high tumor heterogeneity with respect to re-activation of stemness and proliferation programs. PLoS One 2022; 17:e0268626. [PMID: 35587924 PMCID: PMC9119523 DOI: 10.1371/journal.pone.0268626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 05/03/2022] [Indexed: 12/01/2022] Open
Abstract
Significant alterations in signaling pathways and transcriptional regulatory programs together represent major hallmarks of many cancers. These, among all, include the reactivation of stemness, which is registered by the expression of pathways that are active in the embryonic stem cells (ESCs). Here, we assembled gene sets that reflect the stemness and proliferation signatures and used them to analyze a large panel of RNA-seq data from The Cancer Genome Atlas (TCGA) Consortium in order to specifically assess the expression of stemness-related and proliferation-related genes across a collection of different tumor types. We introduced a metric that captures the collective similarity of the expression profile of a tumor to that of ESCs, which showed that stemness and proliferation signatures vary greatly between different tumor types. We also observed a high degree of intertumoral heterogeneity in the expression of stemness- and proliferation-related genes, which was associated with increased hazard ratios in a fraction of tumors and mirrored by high intratumoral heterogeneity and a remarkable stemness capacity in metastatic lesions across cancer cells in single cell RNA-seq datasets. Taken together, these results indicate that the expression of stemness signatures is highly heterogeneous and cannot be used as a universal determinant of cancer. This calls into question the universal validity of diagnostic tests that are based on stem cell markers.
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Affiliation(s)
- Artem Baranovsky
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Timofei Ivanov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | | | - Dmitri Papatsenko
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Dmitri D. Pervouchine
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- * E-mail:
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Ding Q, Huo L, Peng Y, Yoon EC, Li Z, Sahin AA. Immunohistochemical Markers for Distinguishing Metastatic Breast Carcinoma from Other Common Malignancies: Update and Revisit. Semin Diagn Pathol 2022; 39:313-321. [DOI: 10.1053/j.semdp.2022.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/02/2022] [Accepted: 04/11/2022] [Indexed: 11/11/2022]
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Liu D, Hu Z, Jiang J, Zhang J, Hu C, Huang J, Wei Q. Five hypoxia and immunity related genes as potential biomarkers for the prognosis of osteosarcoma. Sci Rep 2022; 12:1617. [PMID: 35102149 PMCID: PMC8804019 DOI: 10.1038/s41598-022-05103-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 01/06/2022] [Indexed: 12/14/2022] Open
Abstract
Osteosarcoma accounts for a frequently occurring cancer of the primary skeletal system. In osteosarcoma cells, a hypoxic microenvironment is commonly observed that drives tumor growth, progression, and heterogeneity. Hypoxia and tumor-infiltrating immune cells might be closely related to the prognosis of osteosarcoma. In this study, we aimed to determine the biomarkers and therapeutic targets related to hypoxia and immunity through bioinformatics methods to improve the clinical prognosis of patients. We downloaded the gene expression data of osteosarcoma samples and normal samples in the UCSC Xena database and GTEx database, respectively, and downloaded the validation dataset (GSE21257) in the GEO database. Subsequently, we performed GO enrichment analysis and KEGG pathway enrichment analysis on the data of the extracted osteosarcoma hypoxia-related genes. Through univariate COX regression analysis, lasso regression analysis, multivariate COX regression analysis, etc., we established a predictive model for the prognosis of osteosarcoma. Five genes, including ST3GAL4, TRIM8, STC2, TRPS1, and FAM207A, were found by screening. In particular, we analyzed the immune cell composition of each gene based on the five genes through the CIBERSORT algorithm and verified each gene at the cell and tissue level. Our findings are valuable for the clinical diagnosis and treatment of this disease.
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Affiliation(s)
- Dachang Liu
- Department of Orthopedics Trauma and Hand Surgery, Guangxi Medical University First Affiliated Hospital, Guangxi Medical University, Nanning, 530021, China
| | - Ziwei Hu
- Guangxi Medical University, Nanning, 530021, China
| | - Jie Jiang
- Department of Spine and Osteopathic Surgery, Guangxi Medical University First Affiliated Hospital, Guangxi Medical University, Nanning, 530021, China
| | - Junlei Zhang
- Department of Orthopedics Trauma and Hand Surgery, Guangxi Medical University First Affiliated Hospital, Guangxi Medical University, Nanning, 530021, China
| | - Chunlong Hu
- Department of Orthopedics Trauma and Hand Surgery, Guangxi Medical University First Affiliated Hospital, Guangxi Medical University, Nanning, 530021, China
| | - Jian Huang
- Guangxi Medical University, Nanning, 530021, China
| | - Qingjun Wei
- Department of Orthopedics Trauma and Hand Surgery, Guangxi Medical University First Affiliated Hospital, Guangxi Medical University, Nanning, 530021, China.
- Guangxi Medical University, Nanning, 530021, China.
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Baur B, Lee DI, Haag J, Chasman D, Gould M, Roy S. Deciphering the Role of 3D Genome Organization in Breast Cancer Susceptibility. Front Genet 2022; 12:788318. [PMID: 35087569 PMCID: PMC8787344 DOI: 10.3389/fgene.2021.788318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 12/21/2021] [Indexed: 11/25/2022] Open
Abstract
Cancer risk by environmental exposure is modulated by an individual's genetics and age at exposure. This age-specific period of susceptibility is referred to as the "Window of Susceptibility" (WOS). Rats have a similar WOS for developing breast cancer. A previous study in rat identified an age-specific long-range regulatory interaction for the cancer gene, Pappa, that is associated with breast cancer susceptibility. However, the global role of three-dimensional genome organization and downstream gene expression programs in the WOS is not known. Therefore, we generated Hi-C and RNA-seq data in rat mammary epithelial cells within and outside the WOS. To systematically identify higher-order changes in 3D genome organization, we developed NE-MVNMF that combines network enhancement followed by multitask non-negative matrix factorization. We examined three-dimensional genome organization dynamics at the level of individual loops as well as higher-order domains. Differential chromatin interactions tend to be associated with differentially up-regulated genes with the WOS and recapitulate several human SNP-gene interactions associated with breast cancer susceptibility. Our approach identified genomic blocks of regions with greater overall differences in contact count between the two time points when the cluster assignments change and identified genes and pathways implicated in early carcinogenesis and cancer treatment. Our results suggest that WOS-specific changes in 3D genome organization are linked to transcriptional changes that may influence susceptibility to breast cancer.
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Affiliation(s)
- Brittany Baur
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, United States
| | - Da-Inn Lee
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, United States
| | - Jill Haag
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, United States
| | - Deborah Chasman
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, United States
| | - Michael Gould
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, United States
| | - Sushmita Roy
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, United States
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, United States
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Wang J, Wang WL, Sun H, Huo L, Wu Y, Chen H, Gan Q, Meis JM, Maloney N, Lazar AJ, Yoon EC, Albarracin CT, Krishnamurthy S, Middleton LP, Resetkova E, Yu W, Tan D, Lu W, Solis Soto LM, Wang S, Wistuba II, Parwani AV, Prieto VG, Sahin AA, Li Z, Ding Q. Expression of TRPS1 in phyllodes tumor and sarcoma of the breast. Hum Pathol 2022; 121:73-80. [DOI: 10.1016/j.humpath.2022.01.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 12/31/2022]
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Du T, Pan L, Zheng C, Chen K, Yang Y, Chen J, Chao X, Li M, Lu J, Luo R, Zhang J, Wu Y, He J, Jiang D, Sun P. Matrix Gla protein (MGP), GATA3, and TRPS1: a novel diagnostic panel to determine breast origin. Breast Cancer Res 2022; 24:70. [PMID: 36284362 PMCID: PMC9598034 DOI: 10.1186/s13058-022-01569-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 10/18/2022] [Indexed: 11/30/2022] Open
Abstract
Background Metastatic breast carcinoma is commonly considered during differential diagnosis when metastatic disease is detected in females. In addition to the tumor morphology and documented clinical history, sensitive and specific immunohistochemical (IHC) markers such as GCDFP-15, mammaglobin, and GATA3 are helpful for determining breast origin. However, these markers are reported to show lower sensitivity in certain subtypes, such as triple-negative breast cancer (TNBC). Materials and methods Using bioinformatics analyses, we identified a potential diagnostic panel to determine breast origin: matrix Gla protein (MGP), transcriptional repressor GATA binding 1 (TRPS1), and GATA-binding protein 3 (GATA3). We compared MGP, TRPS1, and GATA3 expression in different subtypes of breast carcinoma of (n = 1201) using IHC. As a newly identified marker, MGP expression was also evaluated in solid tumors (n = 2384) and normal tissues (n = 1351) from different organs. Results MGP and TRPS1 had comparable positive expression in HER2-positive (91.2% vs. 92.0%, p = 0.79) and TNBC subtypes (87.3% vs. 91.2%, p = 0.18). GATA3 expression was lower than MGP (p < 0.001) or TRPS1 (p < 0.001), especially in HER2-positive (77.0%, p < 0.001) and TNBC (43.3%, p < 0.001) subtypes. TRPS1 had the highest positivity rate (97.9%) in metaplastic TNBCs, followed by MGP (88.6%), while only 47.1% of metaplastic TNBCs were positive for GATA3. When using MGP, GATA3, and TRPS1 as a novel IHC panel, 93.0% of breast carcinomas were positive for at least two markers, and only 9 cases were negative for all three markers. MGP was detected in 36 cases (3.0%) that were negative for both GATA3 and TRPS1. MGP showed mild-to-moderate positive expression in normal hepatocytes, renal tubules, as well as 31.1% (99/318) of hepatocellular carcinomas. Rare cases (0.6–5%) had focal MGP expression in renal, ovarian, lung, urothelial, and cholangiocarcinomas. Conclusions Our findings suggest that MGP is a newly identified sensitive IHC marker to support breast origin. MGP, TRPS1, and GATA3 could be applied as a reliable diagnostic panel to determine breast origin in clinical practice. Supplementary Information The online version contains supplementary material available at 10.1186/s13058-022-01569-1.
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Affiliation(s)
- Tian Du
- grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060 People’s Republic of China ,grid.488530.20000 0004 1803 6191Department of Breast Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, 510060 People’s Republic of China
| | - Lu Pan
- grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060 People’s Republic of China ,grid.488530.20000 0004 1803 6191Department of Pathology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060 People’s Republic of China
| | - Chengyou Zheng
- grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060 People’s Republic of China ,grid.488530.20000 0004 1803 6191Department of Pathology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060 People’s Republic of China
| | - Keming Chen
- grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060 People’s Republic of China ,grid.488530.20000 0004 1803 6191Department of Pathology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060 People’s Republic of China
| | - Yuanzhong Yang
- grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060 People’s Republic of China ,grid.488530.20000 0004 1803 6191Department of Pathology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060 People’s Republic of China
| | - Jiewei Chen
- grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060 People’s Republic of China ,grid.488530.20000 0004 1803 6191Department of Pathology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060 People’s Republic of China
| | - Xue Chao
- grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060 People’s Republic of China ,grid.488530.20000 0004 1803 6191Department of Pathology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060 People’s Republic of China
| | - Mei Li
- grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060 People’s Republic of China ,grid.488530.20000 0004 1803 6191Department of Pathology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060 People’s Republic of China
| | - Jiabin Lu
- grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060 People’s Republic of China ,grid.488530.20000 0004 1803 6191Department of Pathology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060 People’s Republic of China
| | - Rongzhen Luo
- grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060 People’s Republic of China ,grid.488530.20000 0004 1803 6191Department of Pathology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060 People’s Republic of China
| | - Jinhui Zhang
- grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060 People’s Republic of China ,grid.488530.20000 0004 1803 6191Department of Pathology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060 People’s Republic of China
| | - Yu Wu
- grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060 People’s Republic of China ,grid.488530.20000 0004 1803 6191Department of Pathology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060 People’s Republic of China
| | - Jiehua He
- grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060 People’s Republic of China ,grid.488530.20000 0004 1803 6191Department of Pathology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060 People’s Republic of China
| | - Dongping Jiang
- grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060 People’s Republic of China ,grid.488530.20000 0004 1803 6191Department of Medical Imaging, Sun Yat-Sen University Cancer Center, Guangzhou, 510060 People’s Republic of China
| | - Peng Sun
- grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060 People’s Republic of China ,grid.488530.20000 0004 1803 6191Department of Pathology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060 People’s Republic of China
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Reddy J, Fonseca MAS, Corona RI, Nameki R, Segato Dezem F, Klein IA, Chang H, Chaves-Moreira D, Afeyan LK, Malta TM, Lin X, Abbasi F, Font-Tello A, Sabedot T, Cejas P, Rodríguez-Malavé N, Seo JH, Lin DC, Matulonis U, Karlan BY, Gayther SA, Pasaniuc B, Gusev A, Noushmehr H, Long H, Freedman ML, Drapkin R, Young RA, Abraham BJ, Lawrenson K. Predicting master transcription factors from pan-cancer expression data. SCIENCE ADVANCES 2021; 7:eabf6123. [PMID: 34818047 PMCID: PMC8612691 DOI: 10.1126/sciadv.abf6123] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Critical developmental “master transcription factors” (MTFs) can be subverted during tumorigenesis to control oncogenic transcriptional programs. Current approaches to identifying MTFs rely on ChIP-seq data, which is unavailable for many cancers. We developed the CaCTS (Cancer Core Transcription factor Specificity) algorithm to prioritize candidate MTFs using pan-cancer RNA sequencing data. CaCTS identified candidate MTFs across 34 tumor types and 140 subtypes including predictions for cancer types/subtypes for which MTFs are unknown, including e.g. PAX8, SOX17, and MECOM as candidates in ovarian cancer (OvCa). In OvCa cells, consistent with known MTF properties, these factors are required for viability, lie proximal to superenhancers, co-occupy regulatory elements globally, co-bind loci encoding OvCa biomarkers, and are sensitive to pharmacologic inhibition of transcription. Our predictions of MTFs, especially for tumor types with limited understanding of transcriptional drivers, pave the way to therapeutic targeting of MTFs in a broad spectrum of cancers.
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Affiliation(s)
- Jessica Reddy
- Women’s Cancer Research Program at the Samuel
Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles,
CA, USA
- Division of Gynecologic Oncology, Department of
Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA,
USA
| | - Marcos A. S. Fonseca
- Women’s Cancer Research Program at the Samuel
Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles,
CA, USA
- Division of Gynecologic Oncology, Department of
Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA,
USA
| | - Rosario I. Corona
- Women’s Cancer Research Program at the Samuel
Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles,
CA, USA
- Division of Gynecologic Oncology, Department of
Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA,
USA
- Center for Bioinformatics and Functional Genomics,
Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Robbin Nameki
- Women’s Cancer Research Program at the Samuel
Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles,
CA, USA
- Division of Gynecologic Oncology, Department of
Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA,
USA
| | - Felipe Segato Dezem
- Women’s Cancer Research Program at the Samuel
Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles,
CA, USA
- Division of Gynecologic Oncology, Department of
Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA,
USA
- Center for Bioinformatics and Functional Genomics,
Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Isaac A. Klein
- Whitehead Institute for Biomedical Research,
Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer
Institute, Boston, MA, USA
| | - Heidi Chang
- Women’s Cancer Research Program at the Samuel
Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles,
CA, USA
- Division of Gynecologic Oncology, Department of
Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA,
USA
| | | | - Lena K. Afeyan
- Whitehead Institute for Biomedical Research,
Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of
Technology, Cambridge, MA, USA
| | | | - Xianzhi Lin
- Women’s Cancer Research Program at the Samuel
Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles,
CA, USA
- Division of Gynecologic Oncology, Department of
Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA,
USA
| | - Forough Abbasi
- Women’s Cancer Research Program at the Samuel
Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles,
CA, USA
- Division of Gynecologic Oncology, Department of
Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA,
USA
- Center for Bioinformatics and Functional Genomics,
Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Alba Font-Tello
- Center for Functional Cancer Epigenetics, Dana-Farber
Cancer Institute, Boston, MA, USA
| | | | - Paloma Cejas
- Center for Functional Cancer Epigenetics, Dana-Farber
Cancer Institute, Boston, MA, USA
| | - Norma Rodríguez-Malavé
- Center for Bioinformatics and Functional Genomics,
Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer
Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber
Cancer Institute, Boston, MA, USA
| | - De-Chen Lin
- Department of Medicine, Cedars-Sinai Medical
Center, Los Angeles, CA, USA
| | - Ursula Matulonis
- Division of Gynecologic Oncology, Dana Farber
Cancer Institute, Boston, MA, USA
| | - Beth Y. Karlan
- Women’s Cancer Research Program at the Samuel
Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles,
CA, USA
- Division of Gynecologic Oncology, Department of
Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA,
USA
- Cancer Population Genetics, Jonsson Comprehensive
Cancer Center, David Geffen School of Medicine, University of California, Los
Angeles, Los Angeles, CA, USA
| | - Simon A. Gayther
- Center for Bioinformatics and Functional Genomics,
Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Bogdan Pasaniuc
- Bioinformatics Interdepartmental Program,
University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School
of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Pathology and Laboratory Medicine,
David Geffen School of Medicine, University of California, Los Angeles, Los
Angeles, CA, USA
- Department of Computational Medicine, David Geffen
School of Medicine, University of California, Los Angeles, Los Angeles, CA,
USA
| | - Alexander Gusev
- Center for Functional Cancer Epigenetics, Dana-Farber
Cancer Institute, Boston, MA, USA
- McGraw/Patterson Center for Population Sciences,
Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Henry Long
- Center for Functional Cancer Epigenetics, Dana-Farber
Cancer Institute, Boston, MA, USA
| | - Matthew L. Freedman
- Department of Medical Oncology, Dana-Farber Cancer
Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber
Cancer Institute, Boston, MA, USA
- The Eli and Edythe L. Broad Institute, Cambridge,
MA, USA
| | - Ronny Drapkin
- Penn Ovarian Cancer Research Center, University of
Pennsylvania, Philadelphia, PA, USA
| | - Richard A. Young
- Whitehead Institute for Biomedical Research,
Cambridge, MA, USA
- Department of Biology, M.I.T., Cambridge, MA,
USA
| | - Brian J. Abraham
- Department of Computational Biology, St. Jude
Children’s Research Hospital, Memphis, TN, USA
- Corresponding author.
(B.J.A.);
(K.L.)
| | - Kate Lawrenson
- Women’s Cancer Research Program at the Samuel
Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles,
CA, USA
- Division of Gynecologic Oncology, Department of
Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA,
USA
- Center for Bioinformatics and Functional Genomics,
Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Corresponding author.
(B.J.A.);
(K.L.)
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30
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Ai D, Yao J, Yang F, Huo L, Chen H, Lu W, Soto LMS, Jiang M, Raso MG, Wang S, Bell D, Liu J, Wang H, Tan D, Torres-Cabala C, Gan Q, Wu Y, Albarracin C, Hung MC, Meric-Bernstam F, Wistuba II, Prieto VG, Sahin AA, Ding Q. TRPS1: a highly sensitive and specific marker for breast carcinoma, especially for triple-negative breast cancer. Mod Pathol 2021; 34:710-719. [PMID: 33011748 DOI: 10.1038/s41379-020-00692-8] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/15/2020] [Accepted: 09/22/2020] [Indexed: 02/05/2023]
Abstract
Currently there is no highly specific and sensitive marker to identify breast cancer-the most common malignancy in women. Breast cancer can be categorized as estrogen receptor (ER)/progesterone receptor (PR)-positive luminal, human epidermal growth factor receptor 2 (HER2)-positive, or triple-negative breast cancer (TNBC) types based on the expression of ER, PR, and HER2. Although GATA3 is the most widely used tumor marker at present to determine the breast origin, which has been shown to be an excellent marker for ER-positive and low-grade breast cancer, but it does not work well for TNBC with sensitivity as low as <20% in metaplastic breast carcinoma. In the current study, through TCGA data mining we identified trichorhinophalangeal syndrome type 1 (TRPS1) as a specific gene for breast carcinoma across 31 solid tumor types. Moreover, high mRNA level of TRPS1 was found in all four subtypes of breast carcinoma including ER/PR-positive luminal A and B types, HER2-positive type, and basal-type/TNBC. We then analyzed TRPS1 expression in 479 cases of various types of breast cancer using immunochemistry staining, and found that TRPS1 and GATA3 had comparable positive expression in ER-positive (98% vs. 95%) and HER2-positive (87% vs. 88%) breast carcinomas. However, TRPS1 which was highly expressed in TNBC, was significantly higher than GATA3 expression in metaplastic (86% vs. 21%) and nonmetaplastic (86% vs. 51%) TNBC. In addition, TRPS1 expression was evaluated in 1234 cases of solid tumor from different organs. In contrast to the high expression of GATA3 in urothelial carcinoma, TRPS1 showed no or little expression in urothelial carcinomas or in other tumor types including lung adenocarcinoma, pancreatic adenocarcinoma, colon and gastric adenocarcinoma, renal cell carcinoma, melanoma, and ovarian carcinoma. These findings suggest that TRPS1 is a highly sensitive and specific marker for breast carcinoma and can be used as a great diagnostic tool, especially for TNBC.
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Affiliation(s)
- Di Ai
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jun Yao
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Fei Yang
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Lei Huo
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Hui Chen
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Wei Lu
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Luisa Maren Solis Soto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Mei Jiang
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Maria Gabriela Raso
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Shufang Wang
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Diana Bell
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jinsong Liu
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Huamin Wang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Dongfeng Tan
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Carlos Torres-Cabala
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Qiong Gan
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yun Wu
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Constance Albarracin
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Mien-Chie Hung
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,Graduate Institute of Biomedical Sciences, Research Center for Cancer Biology, and Center for Molecular Medicine, China Medical University, Taichung, 404, Taiwan
| | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutic, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Victor G Prieto
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Aysegul A Sahin
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
| | - Qingqing Ding
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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31
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Yang J, Liu X, Huang Y, He L, Zhang W, Ren J, Wang Y, Wu J, Wu X, Shan L, Yang X, Sun L, Liang J, Zhang Y, Shang Y. TRPS1 drives heterochromatic origin refiring and cancer genome evolution. Cell Rep 2021; 34:108814. [PMID: 33691114 DOI: 10.1016/j.celrep.2021.108814] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 12/18/2020] [Accepted: 02/10/2021] [Indexed: 02/06/2023] Open
Abstract
Exploitation of naturally occurring genetic mutations could empower the discovery of novel aspects of established cancer genes. We report here that TRPS1, a gene linked to the tricho-rhino-phalangeal syndrome (TRPS) and recently identified as a potential breast cancer driver, promotes breast carcinogenesis through regulating replication. Epigenomic decomposition of TRPS1 landscape reveals nearly half of H3K9me3-marked heterochromatic origins are occupied by TRPS1, where it encourages the chromatin loading of APC/C, resulting in uncontrolled origin refiring. TRPS1 binds to the genome through its atypical H3K9me3 reading via GATA and IKAROS domains, while TRPS-related mutations affect its chromatin binding, replication boosting, and tumorigenicity. Concordantly, overexpression of wild-type but not TRPS-associated mutants of TRPS1 is sufficient to drive cancer genome amplifications, which experience an extrachromosomal route and dynamically evolve to confer therapeutic resistance. Together, these results uncover a critical function of TRPS1 in driving heterochromatin origin firing and breast cancer genome evolution.
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Affiliation(s)
- Jianguo Yang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Xiaoping Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Yunchao Huang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Lin He
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Wenting Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Jie Ren
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Yue Wang
- Department of Biochemistry and Molecular Biology, School of Medicine, Hangzhou Normal University, Hangzhou 311121, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Jiajing Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Xiaodi Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Lin Shan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Xiaohan Yang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Luyang Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Jing Liang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Yu Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China.
| | - Yongfeng Shang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China; Department of Biochemistry and Molecular Biology, School of Medicine, Hangzhou Normal University, Hangzhou 311121, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China.
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32
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Kang TZE, Zhu L, Yang D, Ding D, Zhu X, Wan YCE, Liu J, Ramakrishnan S, Chan LL, Chan SY, Wang X, Gan H, Han J, Ishibashi T, Li Q, Chan KM. The elevated transcription of ADAM19 by the oncohistone H2BE76K contributes to oncogenic properties in breast cancer. J Biol Chem 2021; 296:100374. [PMID: 33548228 PMCID: PMC7949156 DOI: 10.1016/j.jbc.2021.100374] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 01/26/2021] [Accepted: 02/02/2021] [Indexed: 02/05/2023] Open
Abstract
The recent discovery of the cancer-associated E76K mutation in histone H2B (H2BE76-to-K) in several types of cancers revealed a new class of oncohistone. H2BE76K weakens the stability of histone octamers, alters gene expression, and promotes colony formation. However, the mechanism linking the H2BE76K mutation to cancer development remains largely unknown. In this study, we knock in the H2BE76K mutation in MDA-MB-231 breast cancer cells using CRISPR/Cas9 and show that the E76K mutant histone H2B preferentially localizes to genic regions. Interestingly, genes upregulated in the H2BE76K mutant cells are enriched for the E76K mutant H2B and are involved in cell adhesion and proliferation pathways. We focused on one H2BE76K target gene, ADAM19 (a disintegrin and metalloproteinase-domain-containing protein 19), a gene highly expressed in various human cancers including breast invasive carcinoma, and demonstrate that H2BE76K directly promotes ADAM19 transcription by facilitating efficient transcription along the gene body. ADAM19 depletion reduced the colony formation ability of the H2BE76K mutant cells, whereas wild-type MDA-MB-231 cells overexpressing ADAM19 mimics the colony formation phenotype of the H2BE76K mutant cells. Collectively, our data demonstrate the mechanism by which H2BE76K deregulates the expression of genes that control oncogenic properties through a combined effect of its specific genomic localization and nucleosome destabilization effect.
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Affiliation(s)
- Tze Zhen Evangeline Kang
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China; Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
| | - Lina Zhu
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China; Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
| | - Du Yang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Peking, China
| | - Dongbo Ding
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Xiaoxuan Zhu
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China; Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
| | - Yi Ching Esther Wan
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China; Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
| | - Jiaxian Liu
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China; Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
| | - Saravanan Ramakrishnan
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China; Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
| | - Landon Long Chan
- Department of Oncology, Princess Margaret Hospital, Hong Kong, China
| | - Siu Yuen Chan
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Xin Wang
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China; Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
| | - Haiyun Gan
- Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Junhong Han
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Sichuan, China
| | - Toyotaka Ishibashi
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Qing Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Peking, China
| | - Kui Ming Chan
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China; Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China.
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Farcas AM, Nagarajan S, Cosulich S, Carroll JS. Genome-Wide Estrogen Receptor Activity in Breast Cancer. Endocrinology 2021; 162:bqaa224. [PMID: 33284960 PMCID: PMC7787425 DOI: 10.1210/endocr/bqaa224] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Indexed: 12/13/2022]
Abstract
The largest subtype of breast cancer is characterized by the expression and activity of the estrogen receptor alpha (ERalpha/ER). Although several effective therapies have significantly improved survival, the adaptability of cancer cells means that patients frequently stop responding or develop resistance to endocrine treatment. ER does not function in isolation and multiple associating factors have been reported to play a role in regulating the estrogen-driven transcriptional program. This review focuses on the dynamic interplay between some of these factors which co-occupy ER-bound regulatory elements, their contribution to estrogen signaling, and their possible therapeutic applications. Furthermore, the review illustrates how some ER association partners can influence and reprogram the genomic distribution of the estrogen receptor. As this dynamic ER activity enables cancer cell adaptability and impacts the clinical outcome, defining how this plasticity is determined is fundamental to our understanding of the mechanisms of disease progression.
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Affiliation(s)
- Anca M Farcas
- Bioscience, Oncology R&D, AstraZeneca, Cambridge, UK
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Sankari Nagarajan
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | | | - Jason S Carroll
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
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34
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Zhang J, Ma X, Zhou R, Zhou Y. TRPS1 and YAP1 Regulate Cell Proliferation and Drug Resistance of Osteosarcoma via Competitively Binding to the Target of circTADA2A - miR-129-5p. Onco Targets Ther 2020; 13:12397-12407. [PMID: 33293831 PMCID: PMC7719346 DOI: 10.2147/ott.s276953] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 11/09/2020] [Indexed: 12/15/2022] Open
Abstract
Introduction The yes-associated protein (YAP) and trichorhinophalangeal syndrome 1 (TRPS1) have been reported to account for the pathogenesis of cancers and may play an important role in osteosarcoma (OS). This study intended to investigate the modulatory effect and relationship of TRPS1 and YAP1 in OS cells. Methods The expression difference of YAP1 and TRPS1 in OS cells was measured. Then, the effect of circTADA2A silence on YAP1 and TRPS1 expression as well as OS proliferation and drug resistance was estimated. Results TRPS1 and YAP1 were upregulated in OS cell lines, and TRPS1 and YAP1 were highly expressed in MG63 and U2OS cells, respectively. The cell proliferation of MG63 was lower than that of U2OS, but the opposite result was observed in the presence of cisplatin (DDP). CircTADA2A was upregulated while miR-129-5p was downregulated in MG63 and U2OS cells compared. Besides, circTADA2A knockdown inhibited cell proliferation and reduced DDP resistance in both MG63 and U2OS. MiR-129-5p was increased but TRPS1 and YAP1 were decreased by circTADA2A knockdown. Meanwhile, circTADA2A knockdown reduced TRPS1 protein expression but enhanced phosphorylated (p)-YAP1. In xenograft OS tumor mice, circTADA2A knockdown inhibited tumor growth in the absence or presence of DDP. Finally, miR-129-5p could bind to circTADA2A, TRPS1 and YAPS. Discussion CircRNA TADA2A could target miR-129-5p, which was competitively bound by TRPS1 and YAP1, thereby regulating OS cell proliferation and drug resistance.
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Affiliation(s)
- Jinyu Zhang
- Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming 650118, People's Republic of China
| | - Xiang Ma
- Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming 650118, People's Republic of China
| | - Ruiqi Zhou
- Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming 650118, People's Republic of China
| | - Yichi Zhou
- Department of Orthopaedics, CR & WISCO General Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, Hubei 430000, People's Republic of China
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35
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Nameki R, Chang H, Reddy J, Corona RI, Lawrenson K. Transcription factors in epithelial ovarian cancer: histotype-specific drivers and novel therapeutic targets. Pharmacol Ther 2020; 220:107722. [PMID: 33137377 DOI: 10.1016/j.pharmthera.2020.107722] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 10/26/2020] [Indexed: 02/06/2023]
Abstract
Transcription factors (TFs) are major contributors to cancer risk and somatic development. In preclinical and clinical studies, direct or indirect inhibition of TF-mediated oncogenic gene expression profiles have proven to be effective in many tumor types, highlighting this group of proteins as valuable therapeutic targets. In spite of this, our understanding of TFs in epithelial ovarian cancer (EOC) is relatively limited. EOC is a heterogeneous disease composed of five major histologic subtypes; high-grade serous, low-grade serous, endometrioid, clear cell and mucinous. Each histology is associated with unique clinical etiologies, sensitivity to therapies, and molecular signatures - including diverse transcriptional regulatory programs. While some TFs are shared across EOC subtypes, a set of TFs are expressed in a histotype-specific manner and likely explain part of the histologic diversity of EOC subtypes. Targeting TFs present with unique opportunities for development of novel precision medicine strategies for ovarian cancer. This article reviews the critical TFs in EOC subtypes and highlights the potential of exploiting TFs as biomarkers and therapeutic targets.
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Affiliation(s)
- Robbin Nameki
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Heidi Chang
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jessica Reddy
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Rosario I Corona
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kate Lawrenson
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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36
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Wu H, Huang Z, Huang M, Dang Y, Lu H, Qin X, Liang L, Yang L, Ma J, Chen G, Lv Z. Clinical significance and biological function of transcriptional repressor GATA binding 1 in gastric cancer: a study based on data mining, RT-qPCR, immunochemistry, and vitro experiment. Cell Cycle 2020; 19:2866-2885. [PMID: 33044891 DOI: 10.1080/15384101.2020.1827499] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Transcriptional repressor GATA binding 1 (TRPS1) is a newly discovered transcription factor, which has been reported in many tumors, except for gastric cancer (GC). In this study, we aimed to grope for clinical significance and biological function of TRPS1 in GC. TRPS1 expression in GC and its relationship with clinicopathological features were analyzed based on public databases, and verified by immunohistochemistry and RT-qPCR. Kaplan-Meier survival curve and Cox regression model were used to estimate the influence of TRPS1 on the univariate prognosis and multivariate survival risk factors of GC. The effects of TRPS1 on malignant biological behaviors of GC cells were studied by CCK8 cell proliferation, scratch test, and Transwell assay. The function of TRPS1 was further analyzed by signaling pathway analysis. TRPS1 mRNA expression in GC tissues was up-regulated and was of great significance in some prognostic factors. Protein expression of TRPS1 in tumor tissues was significantly higher than that in paracancerous tissues. Over-expression of TRPS1 was a poor prognostic indicator for GC patients. TRPS1 knockdown could inhibit the proliferation, migration, and invasion of GC cells. The important role of TRPS1 was in the extracellular matrix, and it was involved in actin binding and proteoglycan in cancer. The hub genes of TRPS1 (FN1, ITGB1) were defined. TRPS1 may be a tumor promoter and promote the development of GC by influencing the malignant biological behaviors of GC. TRPS1 is expected to be a key diagnostic and prognostic indicator for GC patients.
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Affiliation(s)
- Hong Wu
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University , Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Zhiguang Huang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University , Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Menglan Huang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University , Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Yiwu Dang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University , Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Huiping Lu
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University , Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Xingan Qin
- Gastrointestinal Surgery, First Affiliated Hospital of Guangxi Medical University , Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Liang Liang
- Gastrointestinal Surgery, First Affiliated Hospital of Guangxi Medical University , Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Lihua Yang
- Medical Oncology, First Affiliated Hospital of Guangxi Medical University , Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Jie Ma
- Medical Oncology, First Affiliated Hospital of Guangxi Medical University , Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Gang Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University , Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Zili Lv
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University , Nanning, Guangxi Zhuang Autonomous Region, P.R. China
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Hu J, Zhang H, Liu L, Han B, Zhou G, Su P. TRPS1 Confers Multidrug Resistance of Breast Cancer Cells by Regulating BCRP Expression. Front Oncol 2020; 10:934. [PMID: 32695669 PMCID: PMC7338551 DOI: 10.3389/fonc.2020.00934] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 05/12/2020] [Indexed: 11/13/2022] Open
Abstract
Multidrug resistance (MDR) is the major obstruction in the successful treatment of breast cancer (BCa). The elucidation of molecular events that confer chemoresistance of BCa is of major therapeutic importance. Several studies have elucidated the correlation of TRPS1 and BCa. Here we focused on the role of TRPS1 in acquisition of chemoresistance, and reported a unique role of TRPS1 renders BCa cells resistant to chemotherapeutic drugs via the regulation of BCRP expression. Bioinformation analysis based on publicly available BCa data suggested that TRPS1 overexpression linked to chemoresistance. Mechanistically, TRPS1 regulated BCRP expression and efflux transportation. Overexpression of TRPS1 led to upregulation of BCRP while its inhibition resulted in repression of BCRP. The correlation of TRPS1 and BCRP was further confirmed by immunohistochemistry in 180 BCa samples. MTT assay demonstrated that manipulation of TRPS1 expression affects the chemosensitivity of BCa cells. In total, high expression of TRPS1 confers MDR of BCa which is mediated by BCRP. Our data demonstrated a new insight into mechanisms and strategies to overcome chemoresistance in BCa.
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Affiliation(s)
- Jing Hu
- Department of Pathology, Qilu Hospital of Shandong University, Jinan, China
| | - Hui Zhang
- Department of Pathology, Qilu Hospital of Shandong University, Jinan, China
| | - Long Liu
- Department of Pathology, Qilu Hospital of Shandong University, Jinan, China
| | - Bo Han
- Department of Pathology, Qilu Hospital of Shandong University, Jinan, China
| | - Gengyin Zhou
- Department of Pathology, Qilu Hospital of Shandong University, Jinan, China
| | - Peng Su
- Department of Pathology, Qilu Hospital of Shandong University, Jinan, China
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38
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Cornelissen LM, Drenth AP, van der Burg E, de Bruijn R, Pritchard CEJ, Huijbers IJ, Zwart W, Jonkers J. TRPS1 acts as a context-dependent regulator of mammary epithelial cell growth/differentiation and breast cancer development. Genes Dev 2019; 34:179-193. [PMID: 31879358 PMCID: PMC7000918 DOI: 10.1101/gad.331371.119] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 12/04/2019] [Indexed: 12/31/2022]
Abstract
In this study, Cornelissen et al. set out to elucidate the role of the GATA-type zinc finger transcription factor TRPS1 in breast cancer. Using in vitro and in vivo loss-of-function approaches, the authors demonstrate that TRPS1 can function as a context-dependent tumor suppressor in breast cancer, while being essential for growth and differentiation of normal mammary epithelial cells. The GATA-type zinc finger transcription factor TRPS1 has been implicated in breast cancer. However, its precise role remains unclear, as both amplifications and inactivating mutations in TRPS1 have been reported. Here, we used in vitro and in vivo loss-of-function approaches to dissect the role of TRPS1 in mammary gland development and invasive lobular breast carcinoma, which is hallmarked by functional loss of E-cadherin. We show that TRPS1 is essential in mammary epithelial cells, since TRPS1-mediated suppression of interferon signaling promotes in vitro proliferation and lactogenic differentiation. Similarly, TRPS1 expression is indispensable for proliferation of mammary organoids and in vivo survival of luminal epithelial cells during mammary gland development. However, the consequences of TRPS1 loss are dependent on E-cadherin status, as combined inactivation of E-cadherin and TRPS1 causes persistent proliferation of mammary organoids and accelerated mammary tumor formation in mice. Together, our results demonstrate that TRPS1 can function as a context-dependent tumor suppressor in breast cancer, while being essential for growth and differentiation of normal mammary epithelial cells.
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Affiliation(s)
- Lisette M Cornelissen
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands.,Oncode Institute, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Anne Paulien Drenth
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands.,Oncode Institute, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Eline van der Burg
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands.,Oncode Institute, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Roebi de Bruijn
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands.,Oncode Institute, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands.,Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Colin E J Pritchard
- Transgenic Core Facility, Mouse Clinic for Cancer and Aging (MCCA), The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Ivo J Huijbers
- Transgenic Core Facility, Mouse Clinic for Cancer and Aging (MCCA), The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Wilbert Zwart
- Oncode Institute, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands.,Division of Oncogenomics, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands.,Laboratory of Chemical Biology, Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, the Netherlands
| | - Jos Jonkers
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands.,Oncode Institute, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
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Waterhouse MP, Ugur R, Khaled WT. Therapeutic and Mechanistic Perspectives of Protein Complexes in Breast Cancer. Front Cell Dev Biol 2019; 7:335. [PMID: 31921847 PMCID: PMC6932950 DOI: 10.3389/fcell.2019.00335] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/27/2019] [Indexed: 12/24/2022] Open
Abstract
Breast cancer affects one in eight women making it the most common cancer in the United Kingdom, accounting for 15% of all new cancer cases. One of the main challenges in treating breast cancer is the heterogeneous nature of the disease. At present, targeted therapies are available for hormone receptor- and HER2-positive tumors. However, no targeted therapies are currently available for patients with triple negative breast cancer (TNBC). This likely contributes to the poor prognostic outcome for TNBC patients. Consequently, there is a clear clinical need for the development of novel drugs that efficiently target TNBC. Extensive genomic and transcriptomic characterization of TNBC has in recent years identified a plethora of putative oncogenes. However, these driver oncogenes are often critical in other cell types and/or transcription factors making them very difficult to target directly. Therefore, other approaches may be required for developing novel therapeutics that fully exploit the specific functions of TNBC oncogenes in tumor cells. Here, we will argue that more research is needed to identify the protein-protein interactions of TNBC oncogenes as a means for (a) mechanistically understanding the biological function of these oncogenes in TNBC and (b) providing novel therapeutic targets that can be exploited for selectively inhibiting the oncogenic roles of TNBC oncogenes in cancer cells, whilst sparing normal healthy cells.
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Affiliation(s)
| | | | - Walid T. Khaled
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
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40
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Penolazzi L, Lambertini E, Scussel Bergamin L, Gandini C, Musio A, De Bonis P, Cavallo M, Piva R. Reciprocal Regulation of TRPS1 and miR-221 in Intervertebral Disc Cells. Cells 2019; 8:cells8101170. [PMID: 31569377 PMCID: PMC6829335 DOI: 10.3390/cells8101170] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/25/2019] [Accepted: 09/27/2019] [Indexed: 12/13/2022] Open
Abstract
Intervertebral disc (IVD), a moderately moving joint located between the vertebrae, has a limited capacity for self-repair, and treating injured intervertebral discs remains a major challenge. The development of innovative therapies to reverse IVD degeneration relies primarily on the discovery of key molecules that, occupying critical points of regulatory mechanisms, can be proposed as potential intradiscal injectable biological agents. This study aimed to elucidate the underlying mechanism of the reciprocal regulation of two genes differently involved in IVD homeostasis, the miR-221 microRNA and the TRPS1 transcription factor. Human lumbar IVD tissue samples and IVD primary cells were used to specifically evaluate gene expression and perform functional analysis including the luciferase gene reporter assay, chromatin immunoprecipitation, cell transfection with hTRPS1 overexpression vector and antagomiR-221. A high-level expression of TRPS1 was significantly associated with a lower pathological stage, and TRPS1 overexpression strongly decreased miR-221 expression, while increasing the chondrogenic phenotype and markers of antioxidant defense and stemness. Additionally, TRPS1 was able to repress miR-221 expression by associating with its promoter and miR-221 negatively control TRPS1 expression by targeting the TRPS1-3'UTR gene. As a whole, these results suggest that, in IVD cells, a double-negative feedback loop between a potent chondrogenic differentiation suppressor (miR-221) and a regulator of axial skeleton development (TRPS1) exists. Our hypothesis is that the hostile degenerated IVD microenvironment may be counteracted by regenerative/reparative strategies aimed at maintaining or stimulating high levels of TRPS1 expression through inhibition of one of its negative regulators such as miR-221.
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Affiliation(s)
- Letizia Penolazzi
- Department of Biomedical and Specialty Surgical Sciences, University of Ferrara, 44121 Ferrara, Italy.
| | - Elisabetta Lambertini
- Department of Biomedical and Specialty Surgical Sciences, University of Ferrara, 44121 Ferrara, Italy.
| | - Leticia Scussel Bergamin
- Department of Biomedical and Specialty Surgical Sciences, University of Ferrara, 44121 Ferrara, Italy.
| | - Carlotta Gandini
- Department of Biomedical and Specialty Surgical Sciences, University of Ferrara, 44121 Ferrara, Italy.
| | - Antonio Musio
- Department of Neurosurgery, S. Anna University Hospital, 44124 Ferrara, Italy.
| | - Pasquale De Bonis
- Department of Neurosurgery, S. Anna University Hospital, 44124 Ferrara, Italy.
| | - Michele Cavallo
- Department of Neurosurgery, S. Anna University Hospital, 44124 Ferrara, Italy.
| | - Roberta Piva
- Department of Biomedical and Specialty Surgical Sciences, University of Ferrara, 44121 Ferrara, Italy.
- Center for Studies on Gender Medicine, University of Ferrara, 44121 Ferrara, Italy.
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41
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Garrido-Castro AC, Lin NU, Polyak K. Insights into Molecular Classifications of Triple-Negative Breast Cancer: Improving Patient Selection for Treatment. Cancer Discov 2019; 9:176-198. [PMID: 30679171 PMCID: PMC6387871 DOI: 10.1158/2159-8290.cd-18-1177] [Citation(s) in RCA: 712] [Impact Index Per Article: 142.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 12/19/2018] [Accepted: 12/20/2018] [Indexed: 12/15/2022]
Abstract
Triple-negative breast cancer (TNBC) remains the most challenging breast cancer subtype to treat. To date, therapies directed to specific molecular targets have rarely achieved clinically meaningful improvements in outcomes of patients with TNBC, and chemotherapy remains the standard of care. Here, we seek to review the most recent efforts to classify TNBC based on the comprehensive profiling of tumors for cellular composition and molecular features. Technologic advances allow for tumor characterization at ever-increasing depth, generating data that, if integrated with clinical-pathologic features, may help improve risk stratification of patients, guide treatment decisions and surveillance, and help identify new targets for drug development. SIGNIFICANCE: TNBC is characterized by higher rates of relapse, greater metastatic potential, and shorter overall survival compared with other major breast cancer subtypes. The identification of biomarkers that can help guide treatment decisions in TNBC remains a clinically unmet need. Understanding the mechanisms that drive resistance is key to the design of novel therapeutic strategies to help prevent the development of metastatic disease and, ultimately, to improve survival in this patient population.
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Affiliation(s)
- Ana C Garrido-Castro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Nancy U Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
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