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Shah OS, Nasrazadani A, Foldi J, Atkinson JM, Kleer CG, McAuliffe PF, Johnston TJ, Stallaert W, da Silva EM, Selenica P, Dopeso H, Pareja F, Mandelker D, Weigelt B, Reis-Filho JS, Bhargava R, Lucas PC, Lee AV, Oesterreich S. Spatial molecular profiling of mixed invasive ductal-lobular breast cancers reveals heterogeneity in intrinsic molecular subtypes, oncogenic signatures, and mutations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.09.557013. [PMID: 38915645 PMCID: PMC11195088 DOI: 10.1101/2023.09.09.557013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Mixed invasive ductal and lobular carcinoma (MDLC) is a rare histologic subtype of breast cancer displaying both E-cadherin positive ductal and E-cadherin negative lobular morphologies within the same tumor, posing challenges with regard to anticipated clinical management. It remains unclear whether these distinct morphologies also have distinct biology and risk of recurrence. Our spatially-resolved transcriptomic, genomic, and single-cell profiling revealed clinically significant differences between ductal and lobular tumor regions including distinct intrinsic subtype heterogeneity (e.g., MDLC with TNBC/basal ductal and ER+/luminal lobular regions), distinct enrichment of senescence/dormancy and oncogenic (ER and MYC) signatures, genetic and epigenetic CDH1 inactivation in lobular, but not ductal regions, and single-cell ductal and lobular sub-populations with unique oncogenic signatures further highlighting intra-regional heterogeneity. Altogether, we demonstrated that the intra-tumoral morphological/histological heterogeneity within MDLC is underpinned by intrinsic subtype and oncogenic heterogeneity which may result in prognostic uncertainty and therapeutic dilemma. Significance MDLC displays both ductal and lobular tumor regions. Our multi-omic profiling approach revealed that these morphologically distinct tumor regions harbor distinct intrinsic subtypes and oncogenic features that may cause prognostic uncertainty and therapeutic dilemma. Thus histopathological/molecular profiling of individual tumor regions may guide clinical decision making and benefit patients with MDLC, particularly in the advanced setting where there is increased reliance on next generation sequencing.
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Zou J, Li Z, Carleton N, Oesterreich S, Lee AV, Tseng GC. Mutual information for detecting multi-class biomarkers when integrating multiple bulk or single-cell transcriptomic studies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.11.598484. [PMID: 38915481 PMCID: PMC11195192 DOI: 10.1101/2024.06.11.598484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Motivation Biomarker detection plays a pivotal role in biomedical research. Integrating omics studies from multiple cohorts can enhance statistical power, accuracy and robustness of the detection results. However, existing methods for horizontally combining omics studies are mostly designed for two-class scenarios (e.g., cases versus controls) and are not directly applicable for studies with multi-class design (e.g., samples from multiple disease subtypes, treatments, tissues, or cell types). Results We propose a statistical framework, namely Mutual Information Concordance Analysis (MICA), to detect biomarkers with concordant multi-class expression pattern across multiple omics studies from an information theoretic perspective. Our approach first detects biomarkers with concordant multi-class patterns across partial or all of the omics studies using a global test by mutual information. A post hoc analysis is then performed for each detected biomarkers and identify studies with concordant pattern. Extensive simulations demonstrate improved accuracy and successful false discovery rate control of MICA compared to an existing MCC method. The method is then applied to two practical scenarios: four tissues of mouse metabolism-related transcriptomic studies, and three sources of estrogen treatment expression profiles. Detected biomarkers by MICA show intriguing biological insights and functional annotations. Additionally, we implemented MICA for single-cell RNA-Seq data for tumor progression biomarkers, highlighting critical roles of ribosomal function in the tumor microenvironment of triple-negative breast cancer and underscoring the potential of MICA for detecting novel therapeutic targets. Availability https://github.com/jianzou75/MICA.
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Affiliation(s)
- Jian Zou
- Department of Statistics, School of Public Health, Chongqing Medical University, Chongqing, 400016, Chongqing, China
| | - Zheqi Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 02215, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, 02215, Massachusetts, USA
| | - Neil Carleton
- Women’s Cancer Research Center, UPMC Hillman Cancer Center (HCC), Pittsburgh, 15232, Pennsylvania, USA
- Magee-Womens Research Institute, Pittsburgh, 15213, Pennsylvania, USA
- Medical Scientist Training Program, School of Medicine, University of Pittsburgh, Pittsburgh, 15213, Pennsylvania, USA
| | - Steffi Oesterreich
- Women’s Cancer Research Center, UPMC Hillman Cancer Center (HCC), Pittsburgh, 15232, Pennsylvania, USA
- Magee-Womens Research Institute, Pittsburgh, 15213, Pennsylvania, USA
- Department of Pharmacology & Chemical Biology, University of Pittsburgh, Pittsburgh, 15213, Pennsylvania, USA
| | - Adrian V. Lee
- Women’s Cancer Research Center, UPMC Hillman Cancer Center (HCC), Pittsburgh, 15232, Pennsylvania, USA
- Magee-Womens Research Institute, Pittsburgh, 15213, Pennsylvania, USA
- Department of Pharmacology & Chemical Biology, University of Pittsburgh, Pittsburgh, 15213, Pennsylvania, USA
| | - George C. Tseng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, 15213, Pennsylvania, USA
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Boyer JA, Sharma M, Dorso MA, Mai N, Amor C, Reiter JM, Kannan R, Gadal S, Xu J, Miele M, Li Z, Chen X, Chang Q, Pareja F, Worland S, Warner D, Sperry S, Chiang GG, Thompson PA, Yang G, Ouerfelli O, de Stanchina E, Wendel HG, Rosen EY, Chandarlapaty S, Rosen N. eIF4A controls translation of estrogen receptor alpha and is a therapeutic target in advanced breast cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.08.593195. [PMID: 38766126 PMCID: PMC11100762 DOI: 10.1101/2024.05.08.593195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
The majority of human breast cancers are dependent on hormone-stimulated estrogen receptor alpha (ER) and are sensitive to its inhibition. Treatment resistance arises in most advanced cancers due to genetic alterations that promote ligand independent activation of ER itself or ER target genes. Whereas re-targeting of the ER ligand binding domain (LBD) with newer ER antagonists can work in some cases, these drugs are largely ineffective in many genetic backgrounds including ER fusions that lose the LBD or in cancers that hyperactivate ER targets. By identifying the mechanism of ER translation, we herein present an alternative strategy to target ER and difficult to treat ER variants. We find that ER translation is cap-independent and mTOR inhibitor insensitive, but dependent on 5' UTR elements and sensitive to pharmacologic inhibition of the translation initiation factor eIF4A, an mRNA helicase. EIF4A inhibition rapidly reduces expression of ER and short-lived targets of ER such as cyclin D1 and other components of the cyclin D-CDK complex in breast cancer cells. These effects translate into suppression of growth of a variety of ligand-independent breast cancer models including those driven by ER fusion proteins that lack the ligand binding site. The efficacy of eIF4A inhibition is enhanced when it is combined with fulvestrant-an ER degrader. Concomitant inhibition of ER synthesis and induction of its degradation causes synergistic and durable inhibition of ER expression and tumor growth. The clinical importance of these findings is confirmed by results of an early clinical trial (NCT04092673) of the selective eIF4A inhibitor zotatifin in patients with estrogen receptor positive metastatic breast cancer. Multiple clinical responses have been observed on combination therapy including durable regressions. These data suggest that eIF4A inhibition could be a useful new strategy for treating advanced ER+ breast cancer.
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Affiliation(s)
- Jacob A. Boyer
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Program in Molecular Pharmacology, Department of Medicine, Memorial Sloan-Kettering Cancer Center (MSKCC), New York, NY, USA
- Ludwig Institute for Cancer Research, Princeton University, Princeton, NJ, USA
| | - Malvika Sharma
- Program in Molecular Pharmacology, Department of Medicine, Memorial Sloan-Kettering Cancer Center (MSKCC), New York, NY, USA
| | - Madeline A. Dorso
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nicholas Mai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Corina Amor
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Department of Cancer Biology and Genetics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jason M. Reiter
- Program in Molecular Pharmacology, Department of Medicine, Memorial Sloan-Kettering Cancer Center (MSKCC), New York, NY, USA
| | - Ram Kannan
- Department of Cancer Biology and Genetics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sunyana Gadal
- Program in Molecular Pharmacology, Department of Medicine, Memorial Sloan-Kettering Cancer Center (MSKCC), New York, NY, USA
| | - Jianing Xu
- Program in Molecular Pharmacology, Department of Medicine, Memorial Sloan-Kettering Cancer Center (MSKCC), New York, NY, USA
| | - Matthew Miele
- Microchemistry and Proteomics Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zhuoning Li
- Microchemistry and Proteomics Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Xiaoping Chen
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY 11065, USA
| | - Qing Chang
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY 11065, USA
| | - Fresia Pareja
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Stephan Worland
- Department of Cancer Biology, eFFECTOR Therapeutics, Inc., San Diego, CA, United States
| | - Douglas Warner
- Department of Cancer Biology, eFFECTOR Therapeutics, Inc., San Diego, CA, United States
| | - Sam Sperry
- Department of Cancer Biology, eFFECTOR Therapeutics, Inc., San Diego, CA, United States
| | - Gary G. Chiang
- Department of Cancer Biology, eFFECTOR Therapeutics, Inc., San Diego, CA, United States
| | - Peggy A. Thompson
- Department of Cancer Biology, eFFECTOR Therapeutics, Inc., San Diego, CA, United States
| | - Guangli Yang
- The Organic Synthesis Core Facility, MSK, New York, NY, USA
| | | | - Elisa de Stanchina
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY 11065, USA
| | - Hans-Guido Wendel
- Department of Cancer Biology and Genetics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ezra Y. Rosen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sarat Chandarlapaty
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Neal Rosen
- Program in Molecular Pharmacology, Department of Medicine, Memorial Sloan-Kettering Cancer Center (MSKCC), New York, NY, USA
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Wang Y, Wang Y, He H, Xiong Y. Absence of GATA3/FOXA1 co-expression predicts poor prognosis in upper tract urothelial carcinoma. Front Oncol 2024; 14:1302864. [PMID: 38425344 PMCID: PMC10902436 DOI: 10.3389/fonc.2024.1302864] [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: 09/27/2023] [Accepted: 01/30/2024] [Indexed: 03/02/2024] Open
Abstract
Objective GATA binding protein 3 (GATA3) and forkhead box A1 (FOXA1) have been individually implicated in the progression of upper tract urothelial carcinoma (UTUC). This study aims to evaluate the prognostic value of GATA3/FOXA1 co-expression in UTUC patients. Methods We collected 108 UTUC pathological tissue samples with complete follow-up data and 24 normal control urothelial tissues. We created a 132-site microarray and performed immunohistochemistry (IHC) to measure GATA3 and FOXA1 expression levels. Kaplan-Meier survival and Cox regression analyses were conducted to assess UTUC prognosis. Results GATA3 expression was positively correlated with FOXA1 (P=0.031). Absence of GATA3/FOXA1 co-expression (GATA3-/FOXA1-) was associated with tumor extensive necrosis (P=0.001) after Bonferroni correction for multiple comparisons. GATA3-/FOXA1- was associated with shorter Disease-Free Survival (DFS) (P=0.001) and Cancer-Specific Survival (CSS) (P<0.001) than other combination groups. Multivariate analyses identified extensive necrosis as an independent prognostic factor for CSS (P=0.030). Conclusions Our study revealed a positive correlation between GATA3 and FOXA1 expression in UTUC. GATA3-/FOXA1- is linked to tumor extensive necrosis and poor prognosis in UTUC and may serve as a potential biomarker for UTUC patients.
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Affiliation(s)
- Yue Wang
- Department of Pathology, Peking University First Hospital, Beijing, China
| | - Yunfan Wang
- Department of Pathology, Peking University Shougang Hospital, Beijing, China
| | - Huiying He
- Department of Pathology, School of Basic Medical Sciences, Peking University Third Hospital, Peking University Health Science Center, Beijing, China
| | - Yan Xiong
- Department of Pathology, Peking University First Hospital, Beijing, China
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Hosseinzadeh L, Kikhtyak Z, Laven-Law G, Pederson SM, Puiu CG, D'Santos CS, Lim E, Carroll JS, Tilley WD, Dwyer AR, Hickey TE. The androgen receptor interacts with GATA3 to transcriptionally regulate a luminal epithelial cell phenotype in breast cancer. Genome Biol 2024; 25:44. [PMID: 38317241 PMCID: PMC10840202 DOI: 10.1186/s13059-023-03161-y] [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: 12/27/2023] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND The androgen receptor (AR) is a tumor suppressor in estrogen receptor (ER) positive breast cancer, a role sustained in some ER negative breast cancers. Key factors dictating AR genomic activity in a breast context are largely unknown. Herein, we employ an unbiased chromatin immunoprecipitation-based proteomic technique to identify endogenous AR interacting co-regulatory proteins in ER positive and negative models of breast cancer to gain new insight into mechanisms of AR signaling in this disease. RESULTS The DNA-binding factor GATA3 is identified and validated as a novel AR interacting protein in breast cancer cells irrespective of ER status. AR activation by the natural ligand 5α-dihydrotestosterone (DHT) increases nuclear AR-GATA3 interactions, resulting in AR-dependent enrichment of GATA3 chromatin binding at a sub-set of genomic loci. Silencing GATA3 reduces but does not prevent AR DNA binding and transactivation of genes associated with AR/GATA3 co-occupied loci, indicating a co-regulatory role for GATA3 in AR signaling. DHT-induced AR/GATA3 binding coincides with upregulation of luminal differentiation genes, including EHF and KDM4B, established master regulators of a breast epithelial cell lineage. These findings are validated in a patient-derived xenograft model of breast cancer. Interaction between AR and GATA3 is also associated with AR-mediated growth inhibition in ER positive and ER negative breast cancer. CONCLUSIONS AR and GATA3 interact to transcriptionally regulate luminal epithelial cell differentiation in breast cancer regardless of ER status. This interaction facilitates the tumor suppressor function of AR and mechanistically explains why AR expression is associated with less proliferative, more differentiated breast tumors and better overall survival in breast cancer.
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Affiliation(s)
- Leila Hosseinzadeh
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, Australia
| | - Zoya Kikhtyak
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, Australia
| | - Geraldine Laven-Law
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, Australia
| | - Stephen M Pederson
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, Australia
| | - Caroline G Puiu
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, Australia
| | - Clive S D'Santos
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Elgene Lim
- Garvan Institute of Medical Research, University of New South Wales, Sydney, Australia
| | - Jason S Carroll
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Wayne D Tilley
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, Australia
| | - Amy R Dwyer
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, Australia
| | - Theresa E Hickey
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, Australia.
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Kocanova S, Raynal F, Goiffon I, Oksuz BA, Baú D, Kamgoué A, Cantaloube S, Zhan Y, Lajoie B, Marti-Renom MA, Dekker J, Bystricky K. Enhancer-driven 3D chromatin domain folding modulates transcription in human mammary tumor cells. Life Sci Alliance 2024; 7:e202302154. [PMID: 37989525 PMCID: PMC10663337 DOI: 10.26508/lsa.202302154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 11/03/2023] [Accepted: 11/06/2023] [Indexed: 11/23/2023] Open
Abstract
The genome is organized in functional compartments and structural domains at the sub-megabase scale. How within these domains interactions between numerous cis-acting enhancers and promoters regulate transcription remains an open question. Here, we determined chromatin folding and composition over several hundred kb around estrogen-responsive genes in human breast cancer cell lines after hormone stimulation. Modeling of 5C data at 1.8 kb resolution was combined with quantitative 3D analysis of multicolor FISH measurements at 100 nm resolution and integrated with ChIP-seq data on transcription factor binding and histone modifications. We found that rapid estradiol induction of the progesterone gene expression occurs in the context of preexisting, cell type-specific chromosomal architectures encompassing the 90 kb progesterone gene coding region and an enhancer-spiked 5' 300 kb upstream genomic region. In response to estradiol, interactions between estrogen receptor α (ERα) bound regulatory elements are reinforced. Whereas initial enhancer-gene contacts coincide with RNA Pol 2 binding and transcription initiation, sustained hormone stimulation promotes ERα accumulation creating a regulatory hub stimulating transcript synthesis. In addition to implications for estrogen receptor signaling, we uncover that preestablished chromatin architectures efficiently regulate gene expression upon stimulation without the need for de novo extensive rewiring of long-range chromatin interactions.
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Affiliation(s)
- Silvia Kocanova
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France
| | - Flavien Raynal
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France
| | - Isabelle Goiffon
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France
| | - Betul Akgol Oksuz
- https://ror.org/0464eyp60 Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Davide Baú
- Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain
| | - Alain Kamgoué
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France
| | - Sylvain Cantaloube
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France
| | - Ye Zhan
- https://ror.org/0464eyp60 Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Bryan Lajoie
- https://ror.org/0464eyp60 Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Marc A Marti-Renom
- Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain
- Genome Biology Program, Centre de Regulació Genòmica (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Job Dekker
- https://ror.org/0464eyp60 Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Kerstin Bystricky
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France
- Institut Universitaire de France (IUF), Paris, France
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7
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Beddows I, Fan H, Heinze K, Johnson BK, Leonova A, Senz J, Djirackor S, Cho KR, Pearce CL, Huntsman DG, Anglesio MS, Shen H. Cell State of Origin Impacts Development of Distinct Endometriosis-Related Ovarian Carcinoma Histotypes. Cancer Res 2024; 84:26-38. [PMID: 37874327 PMCID: PMC10758692 DOI: 10.1158/0008-5472.can-23-1362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 09/01/2023] [Accepted: 10/20/2023] [Indexed: 10/25/2023]
Abstract
Clear cell ovarian carcinoma (CCOC) and endometrioid ovarian carcinoma (ENOC) are ovarian carcinoma histotypes, which are both thought to arise from ectopic endometrial (or endometrial-like) cells through an endometriosis intermediate. How the same cell type of origin gives rise to two morphologically and biologically different histotypes has been perplexing, particularly given that recurrent genetic mutations are common to both and present in nonmalignant precursors. We used RNA transcription analysis to show that the expression profiles of CCOC and ENOC resemble those of normal endometrium at secretory and proliferative phases of the menstrual cycle, respectively. DNA methylation at the promoter of the estrogen receptor (ER) gene (ESR1) was enriched in CCOC, which could potentially lock the cells in the secretory state. Compared with normal secretory-type endometrium, CCOC was further defined by increased expression of cysteine and glutathione synthesis pathway genes and downregulation of the iron antiporter, suggesting iron addiction and highlighting ferroptosis as a potential therapeutic target. Overall, these findings suggest that while CCOC and ENOC arise from the same cell type, these histotypes likely originate from different cell states. This "cell state of origin" model may help to explain the presence of histologic and molecular cancer subtypes arising in other organs. SIGNIFICANCE Two cancer histotypes diverge from a common cell of origin epigenetically locked in different cell states, highlighting the importance of considering cell state to better understand the cell of origin of cancer.
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Affiliation(s)
- Ian Beddows
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan
| | - Huihui Fan
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan
| | - Karolin Heinze
- Department of Obstetrics and Gynaecology, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Anna Leonova
- Department of Obstetrics and Gynaecology, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Janine Senz
- Department of Obstetrics and Gynaecology, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Kathleen R. Cho
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Celeste Leigh Pearce
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - David G. Huntsman
- Department of Obstetrics and Gynaecology, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Pathology & Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael S. Anglesio
- Department of Obstetrics and Gynaecology, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hui Shen
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan
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Qiang Z, Jubber I, Lloyd K, Cumberbatch M, Griffin J. Gene of the month: GATA3. J Clin Pathol 2023; 76:793-797. [PMID: 37726118 DOI: 10.1136/jcp-2023-209017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2023] [Indexed: 09/21/2023]
Abstract
GATA binding protein 3 (GATA3) is a zinc-finger pioneer transcription factor involved in diverse processes. GATA3 regulates gene expression through binding nucleosomal DNA and facilitating chromatin remodelling. Post-translational modifications modulate its activity. During development, GATA3 plays a key role in cell differentiation. Mutations in GATA3 are linked to breast and bladder cancer. GATA3 expression is a feature of the luminal subtype of bladder cancer and has implications for immune status and therapeutic response. It also has clinical relevance in squamous cell carcinomas and soft tissue sarcomas. This paper reviews the structure and function of GATA3, its role in cancer and its use and pitfalls as an immunohistochemical marker.
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Affiliation(s)
- Zekai Qiang
- Academic Urology Unit, The University of Sheffield, Sheffield, UK
| | - Ibrahim Jubber
- Academic Urology Unit, The University of Sheffield, Sheffield, UK
| | - Kirsty Lloyd
- Department of Histopathology, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | | | - Jon Griffin
- Academic Urology Unit, The University of Sheffield, Sheffield, UK
- Department of Histopathology, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
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Shi W, Zhong B, Dong J, Hu X, Li L. Super enhancer-driven core transcriptional regulatory circuitry crosstalk with cancer plasticity and patient mortality in triple-negative breast cancer. Front Genet 2023; 14:1258862. [PMID: 37900187 PMCID: PMC10602724 DOI: 10.3389/fgene.2023.1258862] [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: 07/14/2023] [Accepted: 10/02/2023] [Indexed: 10/31/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is a clinically aggressive subtype of breast cancer. Core transcriptional regulatory circuitry (CRC) consists of autoregulated transcription factors (TFs) and their enhancers, which dominate gene expression programs and control cell fate. However, there is limited knowledge of CRC in TNBC. Herein, we systemically characterized the activated super-enhancers (SEs) and interrogated 14 CRCs in breast cancer. We found that CRCs could be broadly involved in DNA conformation change, metabolism process, and signaling response affecting the gene expression reprogramming. Furthermore, these CRC TFs are capable of coordinating with partner TFs bridging the enhancer-promoter loops. Notably, the CRC TF and partner pairs show remarkable specificity for molecular subtypes of breast cancer, especially in TNBC. USF1, SOX4, and MYBL2 were identified as the TNBC-specific CRC TFs. We further demonstrated that USF1 was a TNBC immunophenotype-related TF. Our findings that the rewiring of enhancer-driven CRCs was related to cancer immune and mortality, will facilitate the development of epigenetic anti-cancer treatment strategies.
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Affiliation(s)
- Wensheng Shi
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Central South University, Changsha, Hunan, China
- Furong Laboratory, Changsha, Hunan, China
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Bowen Zhong
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Central South University, Changsha, Hunan, China
- Furong Laboratory, Changsha, Hunan, China
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jiaming Dong
- Department of Radiation, Cangzhou Central Hospital, Changsha, China
| | - Xiheng Hu
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Central South University, Changsha, Hunan, China
- Furong Laboratory, Changsha, Hunan, China
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lingfang Li
- Department of Cardiovascular Medicine, Xiangya Hospital, Central South University, Changsha, China
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Huang J, Zhang JL, Ang L, Li MC, Zhao M, Wang Y, Wu Q. Proposing a novel molecular subtyping scheme for predicting distant recurrence-free survival in breast cancer post-neoadjuvant chemotherapy with close correlation to metabolism and senescence. Front Endocrinol (Lausanne) 2023; 14:1265520. [PMID: 37900131 PMCID: PMC10602753 DOI: 10.3389/fendo.2023.1265520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 09/12/2023] [Indexed: 10/31/2023] Open
Abstract
Background High relapse rates remain a clinical challenge in the management of breast cancer (BC), with distant recurrence being a major driver of patient deterioration. To optimize the surveillance regimen for distant recurrence after neoadjuvant chemotherapy (NAC), we conducted a comprehensive analysis using bioinformatics and machine learning approaches. Materials and methods Microarray data were retrieved from the GEO database, and differential expression analysis was performed with the R package 'Limma'. We used the Metascape tool for enrichment analyses, and 'WGCNA' was utilized to establish co-expression networks, selecting the soft threshold power with the 'pickSoftThreshold' algorithm. We integrated ten machine learning algorithms and 101 algorithm combinations to identify key genes associated with distant recurrence in BC. Unsupervised clustering was performed with the R package 'ConsensusCluster Plus'. To further screen the key gene signature of residual cancer burden (RCB), multiple knockdown studies were analyzed with the Genetic Perturbation Similarity Analysis (GPSA) database. Single-cell RNA sequencing (scRNA-seq) analysis was conducted through the Tumour Immune Single-cell Hub (TISCH) database, and the XSum algorithm was used to screen candidate small molecule drugs based on the Connectivity Map (CMAP) database. Molecular docking processes were conducted using Schrodinger software. GMT files containing gene sets associated with metabolism and senescence were obtained from GSEA MutSigDB database. The GSVA score for each gene set across diverse samples was computed using the ssGSEA function implemented in the GSVA package. Results Our analysis, which combined Limma, WGCNA, and machine learning approaches, identified 16 RCB-relevant gene signatures influencing distant recurrence-free survival (DRFS) in BC patients following NAC. We then screened GATA3 as the key gene signature of high RCB index using GPSA analysis. A novel molecular subtyping scheme was developed to divide patients into two clusters (C1 and C2) with different distant recurrence risks. This molecular subtyping scheme was found to be closely associated with tumor metabolism and cellular senescence. Patients in cluster C2 had a poorer DRFS than those in cluster C1 (HR: 4.04; 95% CI: 2.60-6.29; log-rank test p < 0.0001). High GATA3 expression, high levels of resting mast cell infiltration, and a high proportion of estrogen receptor (ER)-positive patients contributed to better DRFS in cluster C1. We established a nomogram based on the N stage, RCB class, and molecular subtyping. The ROC curve for 5-year DRFS showed excellent predictive value (AUC=0.91, 95% CI: 0.95-0.86), with a C-index of 0.85 (95% CI: 0.81-0.90). Entinostat was identified as a potential small molecule compound to reverse high RCB after NAC. We also provided a comprehensive review of the EDCs exposures that potentially impact the effectiveness of NAC among BC patients. Conclusion This study established a molecular classification scheme associated with tumor metabolism and cancer cell senescence to predict RCB and DRFS in BC patients after NAC. Furthermore, GATA3 was identified and validated as a key gene associated with BC recurrence.
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Affiliation(s)
- Jin Huang
- Department of Pathology, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Department of Pathology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Jian-Lin Zhang
- Department of Emergency Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Lin Ang
- Department of Pathology, The Second People’s Hospital of Hefei, Hefei Hospital Affiliated to Anhui Medical University, Hefei, Anhui, China
| | - Ming-Cong Li
- Department of Pathology, The Second People’s Hospital of Hefei, Hefei Hospital Affiliated to Anhui Medical University, Hefei, Anhui, China
| | - Min Zhao
- Department of Pathology, The Second People’s Hospital of Hefei, Hefei Hospital Affiliated to Anhui Medical University, Hefei, Anhui, China
| | - Yao Wang
- Digestive Endoscopy Department, Jiangsu Provincial People’s Hospital, The First Afliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qiang Wu
- Department of Pathology, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Department of Pathology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
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11
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Blanchard Z, Rush CM, Arnesen S, Vahrenkamp JM, Rodriguez AC, Jarboe EA, Brown C, Chang MEK, Flory MR, Mohammed H, Modzelewska K, Lum DH, Gertz J. Allele-Specific Gene Regulation, Phenotypes, and Therapeutic Vulnerabilities in Estrogen Receptor Alpha-Mutant Endometrial Cancer. Mol Cancer Res 2023; 21:1023-1036. [PMID: 37363949 DOI: 10.1158/1541-7786.mcr-22-0848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 05/12/2023] [Accepted: 06/23/2023] [Indexed: 06/28/2023]
Abstract
Activating estrogen receptor alpha (ER; also known as ESR1) mutations are present in primary endometrial and metastatic breast cancers, promoting estrogen-independent activation of the receptor. Functional characterizations in breast cancer have established unique molecular and phenotypic consequences of the receptor, yet the impact of ER mutations in endometrial cancer has not been fully explored. In this study, we used CRISPR-Cas9 to model the clinically prevalent ER-Y537S mutation and compared results with ER-D538G to discover allele-specific differences between ER mutations in endometrial cancer. We found that constitutive activity of mutant ER resulted in changes in the expression of thousands of genes, stemming from combined alterations to ER binding and chromatin accessibility. The unique gene expression programs resulted in ER-mutant cells developing increased cancer-associated phenotypes, including migration, invasion, anchorage-independent growth, and growth in vivo. To uncover potential treatment strategies, we identified ER-associated proteins via Rapid Immunoprecipitation and Mass Spectrometry of Endogenous Proteins and interrogated two candidates, CDK9 and NCOA3. Inhibition of these regulatory proteins resulted in decreased growth and migration, representing potential novel treatment strategies for ER-mutant endometrial cancer. IMPLICATIONS This study provides insight into mutant ER activity in endometrial cancer and identifies potential therapies for women with ER-mutant endometrial cancer.
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Affiliation(s)
- Zannel Blanchard
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Craig M Rush
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Spencer Arnesen
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Jeffery M Vahrenkamp
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Adriana C Rodriguez
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Elke A Jarboe
- Department of Pathology, University of Utah, Salt Lake City, Utah
| | - Callie Brown
- Preclinical Research Resource, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Matthew E K Chang
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Mark R Flory
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Hisham Mohammed
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Katarzyna Modzelewska
- Preclinical Research Resource, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - David H Lum
- Preclinical Research Resource, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Jason Gertz
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
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12
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Fu X, Pereira R, Liu CC, De Angelis C, Shea MJ, Nanda S, Qin L, Mitchell T, Cataldo ML, Veeraraghavan J, Sethunath V, Giuliano M, Gutierrez C, Győrffy B, Trivedi MV, Cohen O, Wagle N, Nardone A, Jeselsohn R, Rimawi MF, Osborne CK, Schiff R. High FOXA1 levels induce ER transcriptional reprogramming, a pro-metastatic secretome, and metastasis in endocrine-resistant breast cancer. Cell Rep 2023; 42:112821. [PMID: 37467106 DOI: 10.1016/j.celrep.2023.112821] [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: 11/17/2021] [Revised: 11/03/2022] [Accepted: 07/03/2023] [Indexed: 07/21/2023] Open
Abstract
Aberrant activation of the forkhead protein FOXA1 is observed in advanced hormone-related cancers. However, the key mediators of high FOXA1 signaling remain elusive. We demonstrate that ectopic high FOXA1 (H-FOXA1) expression promotes estrogen receptor-positive (ER+) breast cancer (BC) metastasis in a xenograft mouse model. Mechanistically, H-FOXA1 reprograms ER-chromatin binding to elicit a core gene signature (CGS) enriched in ER+ endocrine-resistant (EndoR) cells. We identify Secretome14, a CGS subset encoding ER-dependent cancer secretory proteins, as a strong predictor for poor outcomes of ER+ BC. It is elevated in ER+ metastases vs. primary tumors, irrespective of ESR1 mutations. Genomic ER binding near Secretome14 genes is also increased in mutant ER-expressing or mitogen-treated ER+ BC cells and in ER+ metastatic vs. primary tumors, suggesting a convergent pathway including high growth factor receptor signaling in activating pro-metastatic secretome genes. Our findings uncover H-FOXA1-induced ER reprogramming that drives EndoR and metastasis partly via an H-FOXA1/ER-dependent secretome.
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Affiliation(s)
- Xiaoyong Fu
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Resel Pereira
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chia-Chia Liu
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Carmine De Angelis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA; Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Martin J Shea
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sarmistha Nanda
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lanfang Qin
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tamika Mitchell
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Maria L Cataldo
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA; Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Jamunarani Veeraraghavan
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Vidyalakshmi Sethunath
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mario Giuliano
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Carolina Gutierrez
- Department of Pathology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, 1085 Budapest, Hungary; RCNS Cancer Biomarker Research Group, Institute of Enzymology, Magyar Tudósok körútja 2, 1117 Budapest, Hungary
| | - Meghana V Trivedi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pharmacy Practice and Translational Research, University of Houston, Houston, TX 77204, USA; Department of Pharmacological and Pharmaceutical Sciences, University of Houston, Houston, TX 77204, USA
| | - Ofir Cohen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02210, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University, Beer-Sheva 84105, Israel
| | - Nikhil Wagle
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02210, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Agostina Nardone
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02210, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02210, USA
| | - Rinath Jeselsohn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02210, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02210, USA
| | - Mothaffar F Rimawi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - C Kent Osborne
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rachel Schiff
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA.
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13
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Li Z, Vacanti NM. A Tale of Three Proteomes: Visualizing Protein and Transcript Abundance Relationships in the Breast Cancer Proteome Portal. J Proteome Res 2023; 22:2727-2733. [PMID: 37493333 DOI: 10.1021/acs.jproteome.3c00290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Molecular characterization is transforming research on novel therapeutics in breast cancer. High-throughput methodologies are unbiased to hypotheses; thus, data produced are relevant to address unlimited questions and provide resources for the experimental design process. However, the opportunity is often overlooked because data are not readily accessed or analyzed. Herein, the Breast Cancer Proteome Portal, the only online tool for analyzing protein and transcript abundances across the three breast cancer proteomics studies, is presented. The tool is applied to demonstrate that cofunctioning protein abundances are highly correlated and, conversely, high abundance correlation may be an indicator of cofunction. Furthermore, the cofunction-correlation relationship is less resolved at the transcript level. By applying analysis and visualization tools within the Breast Cancer Proteome Portal, insights are garnered about serine synthesis and the compartmentalization of one-carbon metabolism in breast cancer, and a transcription factor tumorigenic regulatory network of glutamine deamination and oxidation is proposed, illustrating that the Breast Cancer Proteome Portal provides an interface for garnering insights from the information-rich studies of the breast cancer proteome.
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Affiliation(s)
- Zhuoheng Li
- Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853-0001, United States
| | - Nathaniel M Vacanti
- Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853-0001, United States
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14
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Diniz-Gonçalves GS, Hielm-Björkman A, da Silva VB, Ribeiro LGR, da Costa Vieira-Filho CH, Silva LP, Barrouin-Melo SM, Cassali GD, Damasceno KA, Estrela-Lima A. GATA-3 expression and its correlation with prognostic factors and survival in canine mammary tumors. Front Vet Sci 2023; 10:1179808. [PMID: 37483298 PMCID: PMC10356988 DOI: 10.3389/fvets.2023.1179808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 06/19/2023] [Indexed: 07/25/2023] Open
Abstract
Introduction The transcription factor GATA-3 plays a significant role in mammary gland development and differentiation. Recent studies on human oncology have demonstrated its association with favorable pathologic factors in breast cancer. Canine mammary tumours, proposed as comparative and translational study models, have epidemiological, clinical, biological, and genetic characteristics similar to those of human breast cancers. Methods Here, we evaluated the frequency of GATA-3 expression in mammary tumors of dogs and its relationship with prognostic factors and survival. Tumor samples were obtained from 40 female dogs and grouped according to histological type into benign tumors (n = 10), carcinoma in mixed tumors (CMTs) (n = 20), and aggressive tumors (n = 10). CMTs were further separated according to histological grade, and data on clinical staging and diagnosis, histopathological grading, and survival rate were collected. Results GATA-3 and estrogen receptor (ER) expression were higher in benign and well-differentiated carcinomas than in aggressive tumors, which showed greater Ki-67 expression. The expression rate of ER in the studied groups was equivalent to that of GATA-3. We identified a strong positive correlation between GATA-3 and ER expression frequencies and a negative correlation between those of GATA-3 and Ki-67. There were associations between GATA-3 (p < 0.001), Ki-67 (p = 0.003), tumor size (p < 0.001), clinical stage (p = 0.002), lymph node metastasis (p < 0.001), and histological grade (p < 0.001) by univariate survival analysis. The parameters ER (p = 0.015) and GATA-3 (p = 0.005) also influenced survival in a multifactorial manner. Discussion Kaplan-Meier analysis of survival curves validated our previous findings that dogs with GATA-3 expression in ≥79.4% of cells had significantly higher survival rates (p < 0.001). The performance analysis showed that the expression of GATA-3 in ≥79.4% of cells effectively predicted survival or death in dogs with mammary tumors. Collectively, these results suggest that GATA-3 can be a relevant marker in the study of mammary tumor progression and has potential as a prognosis marker for predicting outcomes in canine mammary tumors.
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Affiliation(s)
| | - Anna Hielm-Björkman
- DogRisk Research Group, Department of Equine and Small Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Vanessa Bonfim da Silva
- Research Center on Mammary Oncology NPqOM/HOSPMEV, Federal University of Bahia, Salvador, Brazil
| | - Lorena Gabriela Rocha Ribeiro
- Laboratory of Animal Pathology, Department of Veterinary Medicine, Federal University of Sergipe, São Cristóvão, Brazil
| | | | - Laís Pereira Silva
- Research Center on Mammary Oncology NPqOM/HOSPMEV, Federal University of Bahia, Salvador, Brazil
| | - Stella Maria Barrouin-Melo
- DogRisk Research Group, Department of Equine and Small Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Anatomy, Pathology and Clinics, School of Veterinary Medicine and Zootechny, Federal University of Bahia, Salvador, Brazil
| | - Geovanni Dantas Cassali
- Laboratory of Comparative Pathology, Department of General Pathology, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Karine Araújo Damasceno
- Experimental Pathology Laboratory (LAPEX), Gonçalo Moniz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Brazil
| | - Alessandra Estrela-Lima
- Research Center on Mammary Oncology NPqOM/HOSPMEV, Federal University of Bahia, Salvador, Brazil
- DogRisk Research Group, Department of Equine and Small Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Anatomy, Pathology and Clinics, School of Veterinary Medicine and Zootechny, Federal University of Bahia, Salvador, Brazil
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15
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Bobbitt JR, Seachrist DD, Keri RA. Chromatin Organization and Transcriptional Programming of Breast Cancer Cell Identity. Endocrinology 2023; 164:bqad100. [PMID: 37394919 PMCID: PMC10370366 DOI: 10.1210/endocr/bqad100] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 07/04/2023]
Abstract
The advent of sequencing technologies for assessing chromosome conformations has provided a wealth of information on the organization of the 3-dimensional genome and its role in cancer progression. It is now known that changes in chromatin folding and accessibility can promote aberrant activation or repression of transcriptional programs that can drive tumorigenesis and progression in diverse cancers. This includes breast cancer, which comprises several distinct subtypes defined by their unique transcriptomes that dictate treatment response and patient outcomes. Of these, basal-like breast cancer is an aggressive subtype controlled by a pluripotency-enforcing transcriptome. Meanwhile, the more differentiated luminal subtype of breast cancer is driven by an estrogen receptor-dominated transcriptome that underlies its responsiveness to antihormone therapies and conveys improved patient outcomes. Despite the clear differences in molecular signatures, the genesis of each subtype from normal mammary epithelial cells remains unclear. Recent technical advances have revealed key distinctions in chromatin folding and organization between subtypes that could underlie their transcriptomic and, hence, phenotypic differences. These studies also suggest that proteins controlling particular chromatin states may be useful targets for treating aggressive disease. In this review, we explore the current state of understanding of chromatin architecture in breast cancer subtypes and its potential role in defining their phenotypic characteristics.
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Affiliation(s)
- Jessica R Bobbitt
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Darcie D Seachrist
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Ruth A Keri
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
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16
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Wu Y, Li Z, Wedn AM, Casey AN, Brown D, Rao SV, Omarjee S, Hooda J, Carroll JS, Gertz J, Atkinson JM, Lee AV, Oesterreich S. FOXA1 Reprogramming Dictates Retinoid X Receptor Response in ESR1-Mutant Breast Cancer. Mol Cancer Res 2023; 21:591-604. [PMID: 36930833 PMCID: PMC10239325 DOI: 10.1158/1541-7786.mcr-22-0516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 01/27/2023] [Accepted: 03/15/2023] [Indexed: 03/19/2023]
Abstract
Estrogen receptor alpha (ER/ESR1) mutations occur in 30% to 40% of endocrine resistant ER-positive (ER+) breast cancer. Forkhead box A1 (FOXA1) is a key pioneer factor mediating ER-chromatin interactions and endocrine response in ER+ breast cancer, but its role in ESR1-mutant breast cancer remains unclear. Our previous FOXA1 chromatin immunoprecipitation sequencing (ChIP-seq) identified a large portion of redistributed binding sites in T47D genome-edited Y537S and D538G ESR1-mutant cells. Here, we further integrated FOXA1 genomic binding profile with the isogenic ER cistrome, accessible genome, and transcriptome data of T47D cell model. FOXA1 redistribution was significantly associated with transcriptomic alterations caused by ESR1 mutations. Furthermore, in ESR1-mutant cells, FOXA1-binding sites less frequently overlapped with ER, and differential gene expression was less associated with the canonical FOXA1-ER axis. Motif analysis revealed a unique enrichment of retinoid X receptor (RXR) motifs in FOXA1-binding sites of ESR1-mutant cells. Consistently, ESR1-mutant cells were more sensitive to growth stimulation with the RXR agonist LG268. The mutant-specific response was dependent on two RXR isoforms, RXR-α and RXR-β, with a stronger dependency on the latter. In addition, T3, the agonist of thyroid receptor (TR) also showed a similar growth-promoting effect in ESR1-mutant cells. Importantly, RXR antagonist HX531 blocked growth of ESR1-mutant cells and a patient-derived xenograft (PDX)-derived organoid with an ESR1 D538G mutation. Collectively, our data support the evidence for a stronger RXR response associated with FOXA1 reprograming in ESR1-mutant cells, suggesting development of therapeutic strategies targeting RXR pathways in breast tumors with ESR1 mutation. IMPLICATIONS It provides comprehensive characterization of the role of FOXA1 in ESR1-mutant breast cancer and potential therapeutic strategy through blocking RXR activation.
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Affiliation(s)
- Yang Wu
- School of Medicine, Tsinghua University, Beijing, China
- Women’s Cancer Research Center, UPMC Hillman Cancer Center, Magee-Womens Research Institute, Pittsburgh PA, USA
| | - Zheqi Li
- Women’s Cancer Research Center, UPMC Hillman Cancer Center, Magee-Womens Research Institute, Pittsburgh PA, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
| | - Abdalla M. Wedn
- Women’s Cancer Research Center, UPMC Hillman Cancer Center, Magee-Womens Research Institute, Pittsburgh PA, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
| | - Allison N. Casey
- Women’s Cancer Research Center, UPMC Hillman Cancer Center, Magee-Womens Research Institute, Pittsburgh PA, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
| | - Daniel Brown
- Institute for Precision Medicine, University of Pittsburgh, Pittsburgh PA, USA
| | - Shalini V. Rao
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Soleilmane Omarjee
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Jagmohan Hooda
- Women’s Cancer Research Center, UPMC Hillman Cancer Center, Magee-Womens Research Institute, Pittsburgh PA, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
| | - Jason S. Carroll
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Jason Gertz
- Department of Oncological Sciences, University of Utah, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Jennifer M. Atkinson
- Women’s Cancer Research Center, UPMC Hillman Cancer Center, Magee-Womens Research Institute, Pittsburgh PA, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
- Institute for Precision Medicine, University of Pittsburgh, Pittsburgh PA, USA
| | - Adrian V. Lee
- Women’s Cancer Research Center, UPMC Hillman Cancer Center, Magee-Womens Research Institute, Pittsburgh PA, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
- Institute for Precision Medicine, University of Pittsburgh, Pittsburgh PA, USA
| | - Steffi Oesterreich
- Women’s Cancer Research Center, UPMC Hillman Cancer Center, Magee-Womens Research Institute, Pittsburgh PA, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
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17
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Zhu Z, Shen H, Xu J, Fang Z, Wo G, Ma Y, Yang K, Wang Y, Yu Q, Tang JH. GATA3 mediates doxorubicin resistance by inhibiting CYB5R2-catalyzed iron reduction in breast cancer cells. Drug Resist Updat 2023; 69:100974. [PMID: 37230023 DOI: 10.1016/j.drup.2023.100974] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 04/26/2023] [Accepted: 05/04/2023] [Indexed: 05/27/2023]
Abstract
AIMS Neoadjuvant chemotherapy (NAC) is the primary preoperative therapy for breast cancer. The luminal subtype of breast cancer shows less NAC response than the basal subtype, with an inefficient NAC treatment effect. Understanding of the molecular and cellular mechanisms responsible for this chemoresistance is an important issue when determining optimal treatment. METHODS Doxorubicin-induced apoptosis and ferroptosis was investigated using cytotoxicity, western blotting, and flow cytometry assays. The role of GATA3 in modulating doxorubicin-induced cell death was investigated both in vitro and in vivo. RNA-seq, qPCR, ChIP, and luciferase assay and association analyses were performed to investigate the regulation of CYB5R2 by GATA3. The function of GATA3 and CYB5R2 in regulating doxorubicin-induced ferroptosis was evaluated with iron, ROS, and lipid peroxidation detection assays. Immunohistochemistry was performed for results validation. RESULTS Doxorubicin-induced basal breast cancer cell death is dependent on iron-mediated ferroptosis. Overexpression of the luminal signature transcriptional factor GATA3 mediates doxorubicin resistance. GATA3 promotes cell viability by decreasing ferroptosis-related gene CYB5R2 expression and by maintaining iron homeostasis. Analyzing data from the public and our cohorts demonstrates that GATA3 and CYB5R2 are associated with NAC response. CONCLUSIONS GATA3 promotes doxorubicin resistance by inhibiting CYB5R2-mediated iron metabolism and ferroptosis. Therefore, patients with breast cancer who display high GATA3 expression do not benefit from doxorubicin-based NAC regimens.
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Affiliation(s)
- Zhen Zhu
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China.
| | - Hongyu Shen
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China; Gusu School, the Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou 215026, PR China
| | - Jialin Xu
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
| | - Zheng Fang
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
| | - Guanqun Wo
- Nanjing University of Chinese Medicine, Nanjing 210023, PR China
| | - Ying Ma
- Foreign Language Teaching Department, Nanjing University of Chinese Medicine, Nanjing 210023, PR China
| | - Kai Yang
- The People's Hospital of Pizhou, Xuzhou 221300, PR China
| | - Yalin Wang
- First Clinical Medical College, Xuzhou Medical University, Xuzhou 221004, PR China
| | - Qiang Yu
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China.
| | - Jin-Hai Tang
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China; Gusu School, the Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou 215026, PR China.
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18
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Sun G, Wei Y, Zhou B, Wang M, Luan R, Bai Y, Li H, Wang S, Zheng D, Wang C, Wang S, Zeng K, Liu S, Lin L, He M, Zhang Q, Zhao Y. BAP18 facilitates CTCF-mediated chromatin accessible to regulate enhancer activity in breast cancer. Cell Death Differ 2023; 30:1260-1278. [PMID: 36828916 PMCID: PMC10154423 DOI: 10.1038/s41418-023-01135-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 02/09/2023] [Accepted: 02/14/2023] [Indexed: 02/26/2023] Open
Abstract
The estrogen receptor alpha (ERα) signaling pathway is a crucial target for ERα-positive breast cancer therapeutic strategies. Co-regulators and other transcription factors cooperate for effective ERα-related enhancer activation. Recent studies demonstrate that the transcription factor CTCF is essential to participate in ERα/E2-induced enhancer transactivation. However, the mechanism of how CTCF is achieved remains unknown. Here, we provided evidence that BAP18 is required for CTCF recruitment on ERα-enriched enhancers, facilitating CTCF-mediated chromatin accessibility to promote enhancer RNAs transcription. Consistently, GRO-seq demonstrates that the enhancer activity is positively correlated with BAP18 enrichment. Furthermore, BAP18 interacts with SMARCA1/BPTF to accelerate the recruitment of CTCF to ERα-related enhancers. Interestingly, BAP18 is involved in chromatin accessibility within enhancer regions, thereby increasing enhancer transactivation and enhancer-promoter looping. BAP18 depletion increases the sensitivity of anti-estrogen and anti-enhancer treatment in MCF7 cells. Collectively, our study indicates that BAP18 coordinates with CTCF to enlarge the transactivation of ERα-related enhancers, providing a better understanding of BAP18/CTCF coupling chromatin remodeling and E-P looping in the regulation of enhancer transcription.
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Affiliation(s)
- Ge Sun
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Yuntao Wei
- Department of Breast Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang City, 110042, Liaoning Province, China
| | - Baosheng Zhou
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Manlin Wang
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Ruina Luan
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Yu Bai
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Hao Li
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Shan Wang
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Dantong Zheng
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Chunyu Wang
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Shengli Wang
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Kai Zeng
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Shuchang Liu
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Lin Lin
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Mingcong He
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Qiang Zhang
- Department of Breast Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang City, 110042, Liaoning Province, China
| | - Yue Zhao
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China.
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19
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Anstine LJ, Majmudar PR, Aponte A, Singh S, Zhao R, Weber-Bonk KL, Abdul-Karim FW, Valentine M, Seachrist DD, Grennel-Nickelson KE, Cuellar-Vite L, Sizemore GM, Sizemore ST, Webb BM, Thompson CL, Keri RA. TLE3 Sustains Luminal Breast Cancer Lineage Fidelity to Suppress Metastasis. Cancer Res 2023; 83:997-1015. [PMID: 36696357 PMCID: PMC10089698 DOI: 10.1158/0008-5472.can-22-3133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/28/2022] [Accepted: 01/20/2023] [Indexed: 01/26/2023]
Abstract
Breast cancer subtypes and their phenotypes parallel different stages of the mammary epithelial cell developmental hierarchy. Discovering mechanisms that control lineage identity could provide novel avenues for mitigating disease progression. Here we report that the transcriptional corepressor TLE3 is a guardian of luminal cell fate in breast cancer and operates independently of the estrogen receptor. In luminal breast cancer, TLE3 actively repressed the gene-expression signature associated with highly aggressive basal-like breast cancers (BLBC). Moreover, maintenance of the luminal lineage depended on the appropriate localization of TLE3 to its transcriptional targets, a process mediated by interactions with FOXA1. By repressing genes that drive BLBC phenotypes, including SOX9 and TGFβ2, TLE3 prevented the acquisition of a hybrid epithelial-mesenchymal state and reduced metastatic capacity and aggressive cellular behaviors. These results establish TLE3 as an essential transcriptional repressor that sustains the more differentiated and less metastatic nature of luminal breast cancers. Approaches to induce TLE3 expression could promote the acquisition of less aggressive, more treatable disease states to extend patient survival. SIGNIFICANCE Transcriptional corepressor TLE3 actively suppresses SOX9 and TGFβ transcriptional programs to sustain the luminal lineage identity of breast cancer cells and to inhibit metastatic progression.
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Affiliation(s)
- Lindsey J. Anstine
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Parth R. Majmudar
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio
| | - Amy Aponte
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio
| | - Salendra Singh
- Department of Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio
| | - Ran Zhao
- Department of Qualitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Kristen L. Weber-Bonk
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Fadi W. Abdul-Karim
- Department of Pathology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Mitchell Valentine
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio
| | - Darcie D. Seachrist
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | | | - Leslie Cuellar-Vite
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio
| | - Gina M. Sizemore
- Department of Radiation Oncology and the James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Steven T. Sizemore
- Department of Radiation Oncology and the James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Bryan M. Webb
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio
- Department of Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio
| | - Cheryl L. Thompson
- Department of Public Health Sciences and the Penn State Cancer Institute, Hershey, Pennsylvania
| | - Ruth A. Keri
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
- Department of Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio
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20
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Păun O, Tan YX, Patel H, Strohbuecker S, Ghanate A, Cobolli-Gigli C, Llorian Sopena M, Gerontogianni L, Goldstone R, Ang SL, Guillemot F, Dias C. Pioneer factor ASCL1 cooperates with the mSWI/SNF complex at distal regulatory elements to regulate human neural differentiation. Genes Dev 2023; 37:218-242. [PMID: 36931659 PMCID: PMC10111863 DOI: 10.1101/gad.350269.122] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/28/2023] [Indexed: 03/19/2023]
Abstract
Pioneer transcription factors are thought to play pivotal roles in developmental processes by binding nucleosomal DNA to activate gene expression, though mechanisms through which pioneer transcription factors remodel chromatin remain unclear. Here, using single-cell transcriptomics, we show that endogenous expression of neurogenic transcription factor ASCL1, considered a classical pioneer factor, defines a transient population of progenitors in human neural differentiation. Testing ASCL1's pioneer function using a knockout model to define the unbound state, we found that endogenous expression of ASCL1 drives progenitor differentiation by cis-regulation both as a classical pioneer factor and as a nonpioneer remodeler, where ASCL1 binds permissive chromatin to induce chromatin conformation changes. ASCL1 interacts with BAF SWI/SNF chromatin remodeling complexes, primarily at targets where it acts as a nonpioneer factor, and we provide evidence for codependent DNA binding and remodeling at a subset of ASCL1 and SWI/SNF cotargets. Our findings provide new insights into ASCL1 function regulating activation of long-range regulatory elements in human neurogenesis and uncover a novel mechanism of its chromatin remodeling function codependent on partner ATPase activity.
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Affiliation(s)
- Oana Păun
- Neural Stem Cell Biology Laboratory, the Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Yu Xuan Tan
- Neural Stem Cell Biology Laboratory, the Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Harshil Patel
- Bioinformatics and Biostatistics Science and Technology Platform, the Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Stephanie Strohbuecker
- Bioinformatics and Biostatistics Science and Technology Platform, the Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Avinash Ghanate
- Bioinformatics and Biostatistics Science and Technology Platform, the Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Clementina Cobolli-Gigli
- Neural Stem Cell Biology Laboratory, the Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Miriam Llorian Sopena
- Bioinformatics and Biostatistics Science and Technology Platform, the Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Lina Gerontogianni
- Bioinformatics and Biostatistics Science and Technology Platform, the Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Robert Goldstone
- Bioinformatics and Biostatistics Science and Technology Platform, the Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Siew-Lan Ang
- Neural Stem Cell Biology Laboratory, the Francis Crick Institute, London NW1 1AT, United Kingdom
| | - François Guillemot
- Neural Stem Cell Biology Laboratory, the Francis Crick Institute, London NW1 1AT, United Kingdom;
| | - Cristina Dias
- Neural Stem Cell Biology Laboratory, the Francis Crick Institute, London NW1 1AT, United Kingdom;
- Medical and Molecular Genetics, School of Basic and Medical Biosciences, Faculty of Life Sciences and Medicine, King's College London, London SE1 9RT, United Kingdom
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21
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Zheng C, Wei Y, Zhang P, Xu L, Zhang Z, Lin K, Hou J, Lv X, Ding Y, Chiu Y, Jain A, Islam N, Malovannaya A, Wu Y, Ding F, Xu H, Sun M, Chen X, Chen Y. CRISPR/Cas9 screen uncovers functional translation of cryptic lncRNA-encoded open reading frames in human cancer. J Clin Invest 2023; 133:e159940. [PMID: 36856111 PMCID: PMC9974104 DOI: 10.1172/jci159940] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 01/19/2023] [Indexed: 03/02/2023] Open
Abstract
Emerging evidence suggests that cryptic translation within long noncoding RNAs (lncRNAs) may produce novel proteins with important developmental/physiological functions. However, the role of this cryptic translation in complex diseases (e.g., cancer) remains elusive. Here, we applied an integrative strategy combining ribosome profiling and CRISPR/Cas9 screening with large-scale analysis of molecular/clinical data for breast cancer (BC) and identified estrogen receptor α-positive (ER+) BC dependency on the cryptic ORFs encoded by lncRNA genes that were upregulated in luminal tumors. We confirmed the in vivo tumor-promoting function of an unannotated protein, GATA3-interacting cryptic protein (GT3-INCP) encoded by LINC00992, the expression of which was associated with poor prognosis in luminal tumors. GTE-INCP was upregulated by estrogen/ER and regulated estrogen-dependent cell growth. Mechanistically, GT3-INCP interacted with GATA3, a master transcription factor key to mammary gland development/BC cell proliferation, and coregulated a gene expression program that involved many BC susceptibility/risk genes and impacted estrogen response/cell proliferation. GT3-INCP/GATA3 bound to common cis regulatory elements and upregulated the expression of the tumor-promoting and estrogen-regulated BC susceptibility/risk genes MYB and PDZK1. Our study indicates that cryptic lncRNA-encoded proteins can be an important integrated component of the master transcriptional regulatory network driving aberrant transcription in cancer, and suggests that the "hidden" lncRNA-encoded proteome might be a new space for therapeutic target discovery.
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Affiliation(s)
- Caishang Zheng
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yanjun Wei
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Peng Zhang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Longyong Xu
- Department of Molecular and Cellular Biology
- Lester and Sue Smith Breast Center, and
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Zhenzhen Zhang
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina, USA
| | - Kangyu Lin
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jiakai Hou
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Xiangdong Lv
- Department of Molecular and Cellular Biology
- Lester and Sue Smith Breast Center, and
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Yao Ding
- Department of Molecular and Cellular Biology
- Lester and Sue Smith Breast Center, and
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Yulun Chiu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | | | - Anna Malovannaya
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
- Mass Spectrometry Proteomics Core and
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Yun Wu
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina, USA
| | - Han Xu
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center
- Genetics and Epigenetics Program, and
- Quantitative Sciences Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Ming Sun
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Xi Chen
- Department of Molecular and Cellular Biology
- Lester and Sue Smith Breast Center, and
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Yiwen Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Quantitative Sciences Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA
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22
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DiDonna SC, Nagornyuk A, Adhikari N, Takada M, Takaku M. P4HTM: A Novel Downstream Target of GATA3 in Breast Cancer. RESEARCH SQUARE 2023:rs.3.rs-2622989. [PMID: 36909571 PMCID: PMC10002838 DOI: 10.21203/rs.3.rs-2622989/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Breast cancer continues to be a major cause of death among women. The GATA3 gene is often overexpressed in breast cancer and is widely used to support a diagnosis. However, lower expression of GATA3 has been linked to poorer prognosis along with frequent gene mutations. Therefore, the role of GATA3 in breast cancer appears to be context specific. This study aims to identify a new downstream target of GATA3 to better understand its regulatory network. Clinical data analysis identified the prolyl 4-hydroxylase transmembrane protein (P4HTM) as one of the most highly co-expressed genes with GATA3. Immunohistochemical staining of breast tumors confirms co-expression between GATA3 and P4HTM at the protein level. Similar to GATA3, P4HTM expression levels are linked to patient prognosis, with lower levels indicating poorer survival. Genomics data found that GATA3 binds to the P4HTM locus, and that ectopic expression of GATA3 in basal breast cancer cells increases the P4HTM transcript level. These results collectively suggest that P4HTM is a novel downstream target of GATA3 in breast cancer and is involved in tumor progression.
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Affiliation(s)
- Sarah C DiDonna
- University of North Dakota School of Medicine and Health Sciences
| | - Aerica Nagornyuk
- University of North Dakota School of Medicine and Health Sciences
| | - Neeta Adhikari
- University of North Dakota School of Medicine and Health Sciences
| | | | - Motoki Takaku
- University of North Dakota School of Medicine and Health Sciences
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23
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Mohammed Ismail W, Mazzone A, Ghiraldini FG, Kaur J, Bains M, Munankarmy A, Bagwell MS, Safgren SL, Moore-Weiss J, Buciuc M, Shimp L, Leach KA, Duarte LF, Nagi CS, Carcamo S, Chung CY, Hasson D, Dadgar N, Zhong J, Lee JH, Couch FJ, Revzin A, Ordog T, Bernstein E, Gaspar-Maia A. MacroH2A histone variants modulate enhancer activity to repress oncogenic programs and cellular reprogramming. Commun Biol 2023; 6:215. [PMID: 36823213 PMCID: PMC9950461 DOI: 10.1038/s42003-023-04571-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 02/09/2023] [Indexed: 02/25/2023] Open
Abstract
Considerable efforts have been made to characterize active enhancer elements, which can be annotated by accessible chromatin and H3 lysine 27 acetylation (H3K27ac). However, apart from poised enhancers that are observed in early stages of development and putative silencers, the functional significance of cis-regulatory elements lacking H3K27ac is poorly understood. Here we show that macroH2A histone variants mark a subset of enhancers in normal and cancer cells, which we coined 'macro-Bound Enhancers', that modulate enhancer activity. We find macroH2A variants localized at enhancer elements that are devoid of H3K27ac in a cell type-specific manner, indicating a role for macroH2A at inactive enhancers to maintain cell identity. In following, reactivation of macro-bound enhancers is associated with oncogenic programs in breast cancer and their repressive role is correlated with the activity of macroH2A2 as a negative regulator of BRD4 chromatin occupancy. Finally, through single cell epigenomic profiling of normal mammary stem cells derived from mice, we show that macroH2A deficiency facilitates increased activity of transcription factors associated with stem cell activity.
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Affiliation(s)
- Wazim Mohammed Ismail
- Division of Experimental Pathology, Department of Lab Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Epigenomics program, Mayo Clinic, Rochester, MN, USA
| | - Amelia Mazzone
- Division of Experimental Pathology, Department of Lab Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Epigenomics program, Mayo Clinic, Rochester, MN, USA
| | - Flavia G Ghiraldini
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jagneet Kaur
- Division of Experimental Pathology, Department of Lab Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Epigenomics program, Mayo Clinic, Rochester, MN, USA
| | - Manvir Bains
- Division of Experimental Pathology, Department of Lab Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Epigenomics program, Mayo Clinic, Rochester, MN, USA
| | - Amik Munankarmy
- Division of Experimental Pathology, Department of Lab Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Epigenomics program, Mayo Clinic, Rochester, MN, USA
| | - Monique S Bagwell
- Division of Experimental Pathology, Department of Lab Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Epigenomics program, Mayo Clinic, Rochester, MN, USA
| | - Stephanie L Safgren
- Division of Experimental Pathology, Department of Lab Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Epigenomics program, Mayo Clinic, Rochester, MN, USA
| | - John Moore-Weiss
- Division of Experimental Pathology, Department of Lab Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Epigenomics program, Mayo Clinic, Rochester, MN, USA
| | - Marina Buciuc
- Division of Experimental Pathology, Department of Lab Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Epigenomics program, Mayo Clinic, Rochester, MN, USA
| | - Lynzie Shimp
- Division of Experimental Pathology, Department of Lab Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Epigenomics program, Mayo Clinic, Rochester, MN, USA
| | - Kelsey A Leach
- Division of Experimental Pathology, Department of Lab Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Epigenomics program, Mayo Clinic, Rochester, MN, USA
| | - Luis F Duarte
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Chandandeep S Nagi
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Saul Carcamo
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute Bioinformatics for Next Generation Sequencing (BiNGS) Shared Resource Facility, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Chi-Yeh Chung
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dan Hasson
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute Bioinformatics for Next Generation Sequencing (BiNGS) Shared Resource Facility, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Neda Dadgar
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - Jian Zhong
- Center for Individualized Medicine, Epigenomics program, Mayo Clinic, Rochester, MN, USA
| | - Jeong-Heon Lee
- Division of Experimental Pathology, Department of Lab Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Epigenomics program, Mayo Clinic, Rochester, MN, USA
| | - Fergus J Couch
- Division of Experimental Pathology, Department of Lab Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Alexander Revzin
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - Tamas Ordog
- Center for Individualized Medicine, Epigenomics program, Mayo Clinic, Rochester, MN, USA
| | - Emily Bernstein
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexandre Gaspar-Maia
- Division of Experimental Pathology, Department of Lab Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
- Center for Individualized Medicine, Epigenomics program, Mayo Clinic, Rochester, MN, USA.
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Kaddoura R, Alqutami F, Asbaita M, Hachim M. In Silico Analysis of Publicly Available Transcriptomic Data for the Identification of Triple-Negative Breast Cancer-Specific Biomarkers. Life (Basel) 2023; 13:life13020422. [PMID: 36836779 PMCID: PMC9965976 DOI: 10.3390/life13020422] [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: 01/02/2023] [Revised: 01/28/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Breast cancer is the most common type of cancer among women and is classified into multiple subtypes. Triple-negative breast cancer (TNBC) is the most aggressive subtype, with high mortality rates and limited treatment options such as chemotherapy and radiation. Due to the heterogeneity and complexity of TNBC, there is a lack of reliable biomarkers that can be used to aid in the early diagnosis and prognosis of TNBC in a non-invasive screening method. AIM This study aims to use in silico methods to identify potential biomarkers for TNBC screening and diagnosis, as well as potential therapeutic markers. METHODS Publicly available transcriptomic data of breast cancer patients published in the NCBI's GEO database were used in this analysis. Data were analyzed with the online tool GEO2R to identify differentially expressed genes (DEGs). Genes that were differentially expressed in more than 50% of the datasets were selected for further analysis. Metascape, Kaplan-Meier plotter, cBioPortal, and the online tool TIMER were used for functional pathway analysis to identify the biological role and functional pathways associated with these genes. Breast Cancer Gene-Expression Miner v4.7 was used to validify the obtained results in a larger cohort of datasets. RESULTS A total of 34 genes were identified as differentially expressed in more than half of the datasets. The DEG GATA3 had the highest degree of regulation, and it plays a role in regulating other genes. The estrogen-dependent pathway was the most enriched pathway, involving four crucial genes, including GATA3. The gene FOXA1 was consistently down-regulated in TNBC in all datasets. CONCLUSIONS The shortlisted 34 DEGs will aid clinicians in diagnosing TNBC more accurately as well as developing targeted therapies to improve patient prognosis. In vitro and in vivo studies are further recommended to validate the results of the current study.
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Du C, Jiang J, Li Y, Yu M, Jin J, Chen S, Fan H, Macfarlan TS, Cao B, Sun MA. Regulation of endogenous retrovirus-derived regulatory elements by GATA2/3 and MSX2 in human trophoblast stem cells. Genome Res 2023; 33:197-207. [PMID: 36806146 PMCID: PMC10069462 DOI: 10.1101/gr.277150.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 01/10/2023] [Indexed: 02/19/2023]
Abstract
The placenta is an organ with extraordinary phenotypic diversity in eutherian mammals. Recent evidence suggests that numerous human placental enhancers are evolved from lineage-specific insertions of endogenous retroviruses (ERVs), yet the transcription factors (TFs) underlying their regulation remain largely elusive. Here, by first focusing on MER41, a primate-specific ERV family previously linked to placenta and innate immunity, we uncover the binding motifs of multiple crucial trophoblast TFs (GATA2/3, MSX2, GRHL2) in addition to innate immunity TFs STAT1 and IRF1. Integration of ChIP-seq data confirms the binding of GATA2/3, MSX2, and their related factors on the majority of MER41-derived enhancers in human trophoblast stem cells (TSCs). MER41-derived enhancers that are constitutively active in human TSCs are distinct from those activated upon interferon stimulation, which is determined by the binding of relevant TFs and their subfamily compositions. We further demonstrate that GATA2/3 and MSX2 have prevalent binding to numerous other ERV families - indicating their broad impact on ERV-derived enhancers. Functionally, the derepression of many syncytiotrophoblast genes after MSX2 knockdown is likely to be mediated by regulatory elements derived from ERVs - suggesting ERVs are also important for mediating transcriptional repression. Overall, this study characterizes the regulation of ERV-derived regulatory elements by GATA2/3, MSX2, and their cofactors in human TSCs, and provides mechanistic insights into the importance of ERVs in human trophoblast regulatory network.
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Affiliation(s)
- Cui Du
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Jing Jiang
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Yuzhuo Li
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Miao Yu
- Fujian Provincial Key Laboratory of Reproductive Health Research, School of Medicine, Xiamen University, Xiamen, Fujian 361102, China
| | - Jian Jin
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Shuai Chen
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Hairui Fan
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Todd S Macfarlan
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland 20892, USA
| | - Bin Cao
- Fujian Provincial Key Laboratory of Reproductive Health Research, School of Medicine, Xiamen University, Xiamen, Fujian 361102, China;
| | - Ming-An Sun
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; .,Joint International Research Laboratory of Important Animal Infectious Diseases and Zoonoses of Jiangsu Higher Education Institutions, Yangzhou, Jiangsu 225009, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu 225009, China
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26
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Sgroi DC, Treuner K, Zhang Y, Piper T, Salunga R, Ahmed I, Doos L, Thornber S, Taylor KJ, Brachtel E, Pirrie S, Schnabel CA, Rea D, Bartlett JMS. Correlative studies of the Breast Cancer Index (HOXB13/IL17BR) and ER, PR, AR, AR/ER ratio and Ki67 for prediction of extended endocrine therapy benefit: a Trans-aTTom study. Breast Cancer Res 2022; 24:90. [PMID: 36527133 PMCID: PMC9758861 DOI: 10.1186/s13058-022-01589-x] [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: 08/24/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Multiple clinical trials demonstrate consistent but modest benefit of adjuvant extended endocrine therapy (EET) in HR + breast cancer patients. Predictive biomarkers to identify patients that benefit from EET are critical to balance modest reductions in risk against potential side effects of EET. This study compares the performance of the Breast Cancer Index, BCI (HOXB13/IL17BR, H/I), with expression of estrogen (ER), progesterone (PR), and androgen receptors (AR), and Ki67, for prediction of EET benefit. METHODS Node-positive (N+) patients from the Trans-aTTom study with available tissue specimen and BCI results (N = 789) were included. Expression of ER, PR, AR, and Ki67 was assessed by quantitative immunohistochemistry. BCI (H/I) gene expression analysis was conducted by quantitative RT-PCR. Statistical significance of the treatment by biomarker interaction was evaluated by likelihood ratio tests based on multivariate Cox proportional models, adjusting for age, tumor size, grade, and HER2 status. Pearson's correlation coefficients were calculated to evaluate correlations between BCI (H/I) versus ER, PR, AR, Ki67 and AR/ER ratio. RESULTS EET benefit, measured by the difference in risk of recurrence between patients treated with tamoxifen for 10 versus 5 years, is significantly associated with increasing values of BCI (H/I) (interaction P = 0.01). In contrast, expression of ER (P = 0.83), PR (P = 0.66), AR (P = 0.78), Ki67 (P = 0.87) and AR/ER ratio (P = 0.84) exhibited no significant relationship with EET benefit. BCI (H/I) showed a very weak negative correlation with ER (r = - 0.18), PR (r = - 0.25), and AR (r = - 0.14) expression, but no correlation with either Ki67 (r = 0.04) or AR/ER ratio (r = 0.02). CONCLUSION These findings are consistent with the growing body of evidence that BCI (H/I) is significantly predictive of response to EET and outcome. Results from this direct comparison demonstrate that expression of ER, PR, AR, Ki67 or AR/ER ratio are not predictive of benefit from EET. BCI (H/I) is the only clinically validated biomarker that predicts EET benefit.
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Affiliation(s)
- Dennis C Sgroi
- Molecular Pathology Research Unit, Department of Pathology, Harvard Medical School, Massachusetts General Hospital East, 149 13th Street, Charlestown, MA, 02129, USA.
- Massachusetts General Hospital Center for Cancer Research, Harvard Medical School, Boston, MA, USA.
| | - Kai Treuner
- Biotheranostics, A Hologic Company, San Diego, CA, USA
| | - Yi Zhang
- Biotheranostics, A Hologic Company, San Diego, CA, USA
| | | | | | - Ikhlaaq Ahmed
- Cancer Research UK Clinical Trials Unit, University of Birmingham, Birmingham, UK
| | - Lucy Doos
- Cancer Research UK Clinical Trials Unit, University of Birmingham, Birmingham, UK
| | - Sarah Thornber
- Cancer Research UK Clinical Trials Unit, University of Birmingham, Birmingham, UK
| | | | - Elena Brachtel
- Molecular Pathology Research Unit, Department of Pathology, Harvard Medical School, Massachusetts General Hospital East, 149 13th Street, Charlestown, MA, 02129, USA
- Massachusetts General Hospital Center for Cancer Research, Harvard Medical School, Boston, MA, USA
| | - Sarah Pirrie
- Cancer Research UK Clinical Trials Unit, University of Birmingham, Birmingham, UK
| | | | - Daniel Rea
- Cancer Research UK Clinical Trials Unit, University of Birmingham, Birmingham, UK
| | - John M S Bartlett
- University of Edinburgh, Edinburgh, UK
- Ontario Institute for Cancer Research, Ontario, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
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27
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Discovery of synthetic lethal interactions from large-scale pan-cancer perturbation screens. Nat Commun 2022; 13:7748. [PMID: 36517508 PMCID: PMC9751287 DOI: 10.1038/s41467-022-35378-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 11/29/2022] [Indexed: 12/15/2022] Open
Abstract
The development of cancer therapies is limited by the availability of suitable drug targets. Potential candidate drug targets can be identified based on the concept of synthetic lethality (SL), which refers to pairs of genes for which an aberration in either gene alone is non-lethal, but co-occurrence of the aberrations is lethal to the cell. Here, we present SLIdR (Synthetic Lethal Identification in R), a statistical framework for identifying SL pairs from large-scale perturbation screens. SLIdR successfully predicts SL pairs even with small sample sizes while minimizing the number of false positive targets. We apply SLIdR to Project DRIVE data and find both established and potential pan-cancer and cancer type-specific SL pairs consistent with findings from literature and drug response screening data. We experimentally validate two predicted SL interactions (ARID1A-TEAD1 and AXIN1-URI1) in hepatocellular carcinoma, thus corroborating the ability of SLIdR to identify potential drug targets.
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28
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Nardone A, Qiu X, Spisak S, Nagy Z, Feiglin A, Feit A, Cohen Feit G, Xie Y, Font-Tello A, Guarducci C, Hermida-Prado F, Syamala S, Lim K, Munoz Gomez M, Pun M, Cornwell M, Liu W, Ors A, Mohammed H, Cejas P, Brock JB, Freedman ML, Winer EP, Fu X, Schiff R, Long HW, Metzger Filho O, Jeselsohn R. A Distinct Chromatin State Drives Therapeutic Resistance in Invasive Lobular Breast Cancer. Cancer Res 2022; 82:3673-3686. [PMID: 35950920 PMCID: PMC9588703 DOI: 10.1158/0008-5472.can-21-3186] [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: 09/20/2021] [Revised: 02/04/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022]
Abstract
Most invasive lobular breast cancers (ILC) are of the luminal A subtype and are strongly hormone receptor-positive. Yet, ILC is relatively resistant to tamoxifen and associated with inferior long-term outcomes compared with invasive ductal cancers (IDC). In this study, we sought to gain mechanistic insights into these clinical findings that are not explained by the genetic landscape of ILC and to identify strategies to improve patient outcomes. A comprehensive analysis of the epigenome of ILC in preclinical models and clinical samples showed that, compared with IDC, ILC harbored a distinct chromatin state linked to gained recruitment of FOXA1, a lineage-defining pioneer transcription factor. This resulted in an ILC-unique FOXA1-estrogen receptor (ER) axis that promoted the transcription of genes associated with tumor progression and poor outcomes. The ILC-unique FOXA1-ER axis led to retained ER chromatin binding after tamoxifen treatment, which facilitated tamoxifen resistance while remaining strongly dependent on ER signaling. Mechanistically, gained FOXA1 binding was associated with the autoinduction of FOXA1 in ILC through an ILC-unique FOXA1 binding site. Targeted silencing of this regulatory site resulted in the disruption of the feed-forward loop and growth inhibition in ILC. In summary, ILC is characterized by a unique chromatin state and FOXA1-ER axis that is associated with tumor progression, offering a novel mechanism of tamoxifen resistance. These results underscore the importance of conducting clinical trials dedicated to patients with ILC in order to optimize treatments in this breast cancer subtype. SIGNIFICANCE A unique FOXA1-ER axis in invasive lobular breast cancer promotes disease progression and tamoxifen resistance, highlighting a potential therapeutic avenue for clinical investigations dedicated to this disease. See related commentary by Blawski and Toska, p. 3668.
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Affiliation(s)
- Agostina Nardone
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Xintao Qiu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Sandor Spisak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts.,Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Zsuzsanna Nagy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ariel Feiglin
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Avery Feit
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Gabriela Cohen Feit
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Yingtian Xie
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Alba Font-Tello
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Cristina Guarducci
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Francisco Hermida-Prado
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Sudeepa Syamala
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Klothilda Lim
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Miguel Munoz Gomez
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Matthew Pun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - MacIntosh Cornwell
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Weihan Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Aysegul Ors
- Knight Cancer Early Detection Advanced Research Center, Oregon Health and Science University, Portland, Oregon
| | - Hisham Mohammed
- Knight Cancer Early Detection Advanced Research Center, Oregon Health and Science University, Portland, Oregon
| | - Paloma Cejas
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jane B Brock
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Eric P Winer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Susan F. Smith Center for Women's Cancers, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Xiaoyong Fu
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Rachel Schiff
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Otto Metzger Filho
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Susan F. Smith Center for Women's Cancers, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Rinath Jeselsohn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts.,Susan F. Smith Center for Women's Cancers, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
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29
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Wang Y, Zhang C, Wang Y, Liu X, Zhang Z. Enhancer RNA (eRNA) in Human Diseases. Int J Mol Sci 2022; 23:ijms231911582. [PMID: 36232885 PMCID: PMC9569849 DOI: 10.3390/ijms231911582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/22/2022] [Accepted: 09/24/2022] [Indexed: 11/16/2022] Open
Abstract
Enhancer RNAs (eRNAs), a class of non-coding RNAs (ncRNAs) transcribed from enhancer regions, serve as a type of critical regulatory element in gene expression. There is increasing evidence demonstrating that the aberrant expression of eRNAs can be broadly detected in various human diseases. Some studies also revealed the potential clinical utility of eRNAs in these diseases. In this review, we summarized the recent studies regarding the pathological mechanisms of eRNAs as well as their potential utility across human diseases, including cancers, neurodegenerative disorders, cardiovascular diseases and metabolic diseases. It could help us to understand how eRNAs are engaged in the processes of diseases and to obtain better insight of eRNAs in diagnosis, prognosis or therapy. The studies we reviewed here indicate the enormous therapeutic potency of eRNAs across human diseases.
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Affiliation(s)
- Yunzhe Wang
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Chenyang Zhang
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yuxiang Wang
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Xiuping Liu
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
- Correspondence: author: (X.L.); (Z.Z.); Tel.: +86-21-5423-7896 (Z.Z.)
| | - Zhao Zhang
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
- Correspondence: author: (X.L.); (Z.Z.); Tel.: +86-21-5423-7896 (Z.Z.)
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30
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Ingebriktsen LM, Finne K, Akslen LA, Wik E. A novel age-related gene expression signature associates with proliferation and disease progression in breast cancer. Br J Cancer 2022; 127:1865-1875. [PMID: 35995935 DOI: 10.1038/s41416-022-01953-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 08/01/2022] [Accepted: 08/05/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND AND OBJECTIVE Breast cancer (BC) diagnosed at ages <40 years presents with more aggressive tumour phenotypes and poorer clinical outcome compared to older BC patients. Here, we explored transcriptional BC alterations to gain a better understanding of age-related tumour biology, also subtype-stratified. METHODS We studied publicly available global BC mRNA expression (n = 3999) and proteomics data (n = 113), exploring differentially expressed genes, enriched gene sets, and gene networks in the young compared to older patients. RESULTS We identified transcriptional patterns reflecting increased proliferation and oncogenic signalling in BC of the young, also in subtype-stratified analyses. Six up-regulated hub genes built a novel age-related score, significantly associated with aggressive clinicopathologic features. A high 6 Gene Proliferation Score (6GPS) demonstrated independent prognostic value when adjusted for traditional clinicopathologic variables and the molecular subtypes. The 6GPS significantly associated also with disease-specific survival within the luminal, lymph node-negative and Oncotype Dx intermediate subset. CONCLUSIONS We here demonstrate evidence of higher tumour cell proliferation in young BC patients, also when adjusting for molecular subtypes, and identified a novel age-based six-gene signature pointing to aggressive tumour features, tumour proliferation, and reduced survival-also in patient subsets with expected good prognosis.
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Affiliation(s)
- L M Ingebriktsen
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, Section for Pathology, University of Bergen, Bergen, Norway
| | - K Finne
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, Section for Pathology, University of Bergen, Bergen, Norway
| | - L A Akslen
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, Section for Pathology, University of Bergen, Bergen, Norway.,Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - E Wik
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, Section for Pathology, University of Bergen, Bergen, Norway. .,Department of Pathology, Haukeland University Hospital, Bergen, Norway.
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31
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Xia Y, He X, Renshaw L, Martinez-Perez C, Kay C, Gray M, Meehan J, Parker JS, Perou CM, Carey LA, Dixon JM, Turnbull A. Integrated DNA and RNA Sequencing Reveals Drivers of Endocrine Resistance in Estrogen Receptor-Positive Breast Cancer. Clin Cancer Res 2022; 28:3618-3629. [PMID: 35653148 PMCID: PMC7613305 DOI: 10.1158/1078-0432.ccr-21-3189] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 03/04/2022] [Accepted: 05/31/2022] [Indexed: 01/07/2023]
Abstract
PURPOSE Endocrine therapy resistance (ETR) remains the greatest challenge in treating patients with hormone receptor-positive breast cancer. We set out to identify molecular mechanisms underlying ETR through in-depth genomic analysis of breast tumors. EXPERIMENTAL DESIGN We collected pre-treatment and sequential on-treatment tumor samples from 35 patients with estrogen receptor-positive breast cancer treated with neoadjuvant then adjuvant endocrine therapy; 3 had intrinsic resistance, 19 acquired resistance, and 13 remained sensitive. Response was determined by changes in tumor volume neoadjuvantly and by monitoring for adjuvant recurrence. Twelve patients received two or more lines of endocrine therapy, with subsequent treatment lines being initiated at the time of development of resistance to the previous endocrine therapy. DNA whole-exome sequencing and RNA sequencing were performed on all samples, totalling 169 unique specimens. DNA mutations, copy-number alterations, and gene expression data were analyzed through unsupervised and supervised analyses to identify molecular features related to ETR. RESULTS Mutations enriched in ETR included ESR1 and GATA3. The known ESR1 D538G variant conferring ETR was identified, as was a rarer E380Q variant that confers endocrine hypersensitivity. Resistant tumors which acquired resistance had distinct gene expression profiles compared with paired sensitive tumors, showing elevated pathways including ER, HER2, GATA3, AKT, RAS, and p63 signaling. Integrated analysis in individual patients highlighted the diversity of ETR mechanisms. CONCLUSIONS The mechanisms underlying ETR are multiple and characterized by diverse changes in both somatic genetic and transcriptomic profiles; to overcome resistance will require an individualized approach utilizing genomic and genetic biomarkers and drugs tailored to each patient.
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Affiliation(s)
- Youli Xia
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Xiaping He
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Lorna Renshaw
- Edinburgh Breast Unit Western General Hospital, Edinburgh, United Kingdom
| | - Carlos Martinez-Perez
- Edinburgh Cancer Research Center, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Charlene Kay
- Edinburgh Cancer Research Center, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Mark Gray
- Edinburgh Cancer Research Center, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - James Meehan
- Edinburgh Cancer Research Center, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Joel S. Parker
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Charles M. Perou
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Lisa A. Carey
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Division of Hematology-Oncology, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - J. Michael Dixon
- Edinburgh Breast Unit Western General Hospital, Edinburgh, United Kingdom.,Edinburgh Cancer Research Center, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Arran Turnbull
- Edinburgh Cancer Research Center, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom.,Corresponding Author: Arran Turnbull, Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital, 2XU Crewe Road South, Edinburgh, United Kingdom. Phone: 4413-1651-8694; E-mail:
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32
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Tecalco-Cruz AC, Ramírez-Jarquín JO, Macías-Silva M, Sosa-Garrocho M, López-Camarillo C. Novel Breast Cancer Treatment by Targeting Estrogen Receptor-Alpha Stability Using Proteolysis-Targeting Chimeras (PROTACs) Technology. Breast Cancer 2022. [DOI: 10.36255/exon-publications-breast-cancer-protacs] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Messier TL, Boyd JR, Gordon JAR, Tye CE, Page NA, Toor RH, Zaidi SK, Komm BS, Frietze S, Stein JL, Lian JB, Stein GS. Epigenetic and transcriptome responsiveness to ER modulation by tissue selective estrogen complexes in breast epithelial and breast cancer cells. PLoS One 2022; 17:e0271725. [PMID: 35862394 PMCID: PMC9302754 DOI: 10.1371/journal.pone.0271725] [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: 11/08/2021] [Accepted: 07/06/2022] [Indexed: 01/07/2023] Open
Abstract
Selective estrogen receptor modulators (SERMs), including the SERM/SERD bazedoxifene (BZA), are used to treat postmenopausal osteoporosis and may reduce breast cancer (BCa) risk. One of the most persistent unresolved questions regarding menopausal hormone therapy is compromised control of proliferation and phenotype because of short- or long-term administration of mixed-function estrogen receptor (ER) ligands. To gain insight into epigenetic effectors of the transcriptomes of hormone and BZA-treated BCa cells, we evaluated a panel of histone modifications. The impact of short-term hormone treatment and BZA on gene expression and genome-wide epigenetic profiles was examined in ERαneg mammary epithelial cells (MCF10A) and ERα+ luminal breast cancer cells (MCF7). We tested individual components and combinations of 17β-estradiol (E2), estrogen compounds (EC10) and BZA. RNA-seq for gene expression and ChIP-seq for active (H3K4me3, H3K4ac, H3K27ac) and repressive (H3K27me3) histone modifications were performed. Our results show that the combination of BZA with E2 or EC10 reduces estrogen-mediated patterns of histone modifications and gene expression in MCF-7ERα+ cells. In contrast, BZA has minimal effects on these parameters in MCF10A mammary epithelial cells. BZA-induced changes in histone modifications in MCF7 cells are characterized by altered H3K4ac patterns, with changes at distal enhancers of ERα-target genes and at promoters of non-ERα bound proliferation-related genes. Notably, the ERα target gene GREB1 is the most sensitive to BZA treatment. Our findings provide direct mechanistic-based evidence that BZA induces epigenetic changes in E2 and EC10 mediated control of ERα regulatory programs to target distinctive proliferation gene pathways that restrain the potential for breast cancer development.
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Affiliation(s)
- Terri L. Messier
- Department of Biochemistry, University of Vermont Larner College of Medicine, Burlington, VT, United States of America
- University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, VT, United States of America
| | - Joseph R. Boyd
- Department of Biochemistry, University of Vermont Larner College of Medicine, Burlington, VT, United States of America
| | - Jonathan A. R. Gordon
- Department of Biochemistry, University of Vermont Larner College of Medicine, Burlington, VT, United States of America
- University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, VT, United States of America
| | - Coralee E. Tye
- Department of Biochemistry, University of Vermont Larner College of Medicine, Burlington, VT, United States of America
- University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, VT, United States of America
| | - Natalie A. Page
- Department of Biochemistry, University of Vermont Larner College of Medicine, Burlington, VT, United States of America
| | - Rabail H. Toor
- Department of Biochemistry, University of Vermont Larner College of Medicine, Burlington, VT, United States of America
| | - Sayyed K. Zaidi
- Department of Biochemistry, University of Vermont Larner College of Medicine, Burlington, VT, United States of America
- University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, VT, United States of America
| | - Barry S. Komm
- Komm Pharma Consulting LLC, San Francisco, CA, United States of America
| | - Seth Frietze
- University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, VT, United States of America
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT, United States of America
| | - Janet L. Stein
- Department of Biochemistry, University of Vermont Larner College of Medicine, Burlington, VT, United States of America
- University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, VT, United States of America
| | - Jane B. Lian
- Department of Biochemistry, University of Vermont Larner College of Medicine, Burlington, VT, United States of America
- University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, VT, United States of America
| | - Gary S. Stein
- Department of Biochemistry, University of Vermont Larner College of Medicine, Burlington, VT, United States of America
- University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, VT, United States of America
- Department of Surgery, University of Vermont, Burlington, VT, United States of America
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Portuguez AS, Grbesa I, Tal M, Deitch R, Raz D, Kliker L, Weismann R, Schwartz M, Loza O, Cohen L, Marchenkov-Flam L, Sung MH, Kaplan T, Hakim O. Ep300 sequestration to functionally distinct glucocorticoid receptor binding loci underlie rapid gene activation and repression. Nucleic Acids Res 2022; 50:6702-6714. [PMID: 35713523 PMCID: PMC9262608 DOI: 10.1093/nar/gkac488] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 05/18/2022] [Accepted: 05/26/2022] [Indexed: 12/24/2022] Open
Abstract
The rapid transcriptional response to the transcription factor, glucocorticoid receptor (GR), including gene activation or repression, is mediated by the spatial association of genes with multiple GR binding sites (GBSs) over large genomic distances. However, only a minority of the GBSs have independent GR-mediated activating capacity, and GBSs with independent repressive activity were rarely reported. To understand the positive and negative effects of GR we mapped the regulatory environment of its gene targets. We show that the chromatin interaction networks of GR-activated and repressed genes are spatially separated and vary in the features and configuration of their GBS and other non-GBS regulatory elements. The convergence of the KLF4 pathway in GR-activated domains and the STAT6 pathway in GR-repressed domains, impose opposite transcriptional effects to GR, independent of hormone application. Moreover, the ROR and Rev-erb transcription factors serve as positive and negative regulators, respectively, of GR-mediated gene activation. We found that the spatial crosstalk between GBSs and non-GBSs provides a physical platform for sequestering the Ep300 co-activator from non-GR regulatory loci in both GR-activated and -repressed gene compartments. While this allows rapid gene repression, Ep300 recruitment to GBSs is productive specifically in the activated compartments, thus providing the basis for gene induction.
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Affiliation(s)
| | | | - Moran Tal
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Ramat-Gan 5290002, Israel
| | - Rachel Deitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Ramat-Gan 5290002, Israel
| | - Dana Raz
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Ramat-Gan 5290002, Israel
| | - Limor Kliker
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Ramat-Gan 5290002, Israel
| | - Ran Weismann
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Ramat-Gan 5290002, Israel
| | - Michal Schwartz
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Ramat-Gan 5290002, Israel
| | - Olga Loza
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Ramat-Gan 5290002, Israel
| | - Leslie Cohen
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Ramat-Gan 5290002, Israel
| | - Libi Marchenkov-Flam
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Ramat-Gan 5290002, Israel
| | - Myong-Hee Sung
- Laboratory of Molecular Biology and Immunology, NIA, National Institutes of Health, Baltimore, MD 21224, USA
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 91904, Israel,Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91121, Israel
| | - Ofir Hakim
- To whom correspondence should be addressed. Tel: +972 3 738 4295; Fax: +972 3 738 4296;
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35
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Arruabarrena-Aristorena A, Toska E. Epigenetic Mechanisms Influencing Therapeutic Response in Breast Cancer. Front Oncol 2022; 12:924808. [PMID: 35774123 PMCID: PMC9239340 DOI: 10.3389/fonc.2022.924808] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/05/2022] [Indexed: 12/13/2022] Open
Abstract
The majority of breast cancers are estrogen receptor (ER)+ and agents targeting the ER signaling pathway have markedly increased survival for women with breast cancer for decades. However, therapeutic resistance eventually emerges, especially in the metastatic setting. In the past decade disrupted epigenetic regulatory processes have emerged as major contributors to carcinogenesis in many cancer types. Aberrations in chromatin modifiers and transcription factors have also been recognized as mediators of breast cancer development and therapeutic outcome, and new epigenetic-based therapies in combination with targeted therapies have been proposed. Here we will discuss recent progress in our understanding of the chromatin-based mechanisms of breast tumorigenesis, how these mechanisms affect therapeutic response to standard of care treatment, and discuss new strategies towards therapeutic intervention to overcome resistance.
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Affiliation(s)
- Amaia Arruabarrena-Aristorena
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- Traslational Prostate Cancer Research Lab, CIC bioGUNE-Basurto, Biocruces Bizkaia Health Research Institute, Derio, Spain
- *Correspondence: Amaia Arruabarrena-Aristorena, ; Eneda Toska,
| | - Eneda Toska
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Biochemistry and Molecular Biology, Johns Hopkins School of Public Health, Baltimore, MD, United States
- *Correspondence: Amaia Arruabarrena-Aristorena, ; Eneda Toska,
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36
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Wang J, Bando M, Shirahige K, Nakato R. Large-scale multi-omics analysis suggests specific roles for intragenic cohesin in transcriptional regulation. Nat Commun 2022; 13:3218. [PMID: 35680859 PMCID: PMC9184728 DOI: 10.1038/s41467-022-30792-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 05/14/2022] [Indexed: 12/19/2022] Open
Abstract
Cohesin, an essential protein complex for chromosome segregation, regulates transcription through a variety of mechanisms. It is not a trivial task to assign diverse cohesin functions. Moreover, the context-specific roles of cohesin-mediated interactions, especially on intragenic regions, have not been thoroughly investigated. Here we perform a comprehensive characterization of cohesin binding sites in several human cell types. We integrate epigenomic, transcriptomic and chromatin interaction data to explore the context-specific functions of intragenic cohesin related to gene activation. We identify a specific subset of cohesin binding sites, decreased intragenic cohesin sites (DICs), which are negatively correlated with transcriptional regulation. A subgroup of DICs is enriched with enhancer markers and RNA polymerase II, while the others are more correlated to chromatin architecture. DICs are observed in various cell types, including cells from patients with cohesinopathy. We also implement machine learning to our data and identified genomic features for isolating DICs from all cohesin sites. These results suggest a previously unidentified function of cohesin on intragenic regions for transcriptional regulation.
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Affiliation(s)
- Jiankang Wang
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masashige Bando
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Katsuhiko Shirahige
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Ryuichiro Nakato
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
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Werner RL, Nekritz EA, Yan KK, Ju B, Shaner B, Easton J, Yu PJ, Silva J. Single-cell analysis reveals Comma-1D as a unique cell model for mammary gland development and breast cancer. J Cell Sci 2022; 135:275228. [PMID: 35502723 DOI: 10.1242/jcs.259329] [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: 09/02/2021] [Accepted: 04/11/2022] [Indexed: 11/20/2022] Open
Abstract
The mammary epithelial tree contains two distinct populations, luminal and basal. The investigation of how this heterogeneity is developed and how it influences tumorigenesis has been hampered by the need to perform these studies using animal models. Comma-1D is an immortalized mouse mammary epithelial cell line that has unique morphogenetic properties. By performing single-cell RNA-seq studies we found that Comma-1D cultures consist of two main populations with luminal and basal features and a smaller population with mixed lineage and bipotent characteristics. We demonstrated that multiple transcription factors associated with the differentiation of the mammary epithelium in vivo also modulate this process in Comma-1D cultures. Additionally, we found that only cells with luminal features were able to acquire transformed characteristics after an oncogenic HER2 mutant was introduced in their genomes. Overall, our studies characterize at a single-cell level the heterogeneity of the Comma-1D cell line and illustrate how Comma-1D cells can be used as an experimental model to study both the differentiation and the transformation processes in vitro.
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Affiliation(s)
- Rachel L Werner
- Graduate School, Department of Pathology, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, USA
| | - Erin A Nekritz
- Graduate School, Department of Pathology, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, USA
| | - Koon-Kiu Yan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Bensheng Ju
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Bridget Shaner
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Partha Jiyang Yu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jose Silva
- Graduate School, Department of Pathology, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, USA
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38
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GATA3 and MDM2 are synthetic lethal in estrogen receptor-positive breast cancers. Commun Biol 2022; 5:373. [PMID: 35440675 PMCID: PMC9018745 DOI: 10.1038/s42003-022-03296-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 03/18/2022] [Indexed: 11/08/2022] Open
Abstract
Synthetic lethal interactions, where the simultaneous but not individual inactivation of two genes is lethal to the cell, have been successfully exploited to treat cancer. GATA3 is frequently mutated in estrogen receptor (ER)-positive breast cancers and its deficiency defines a subset of patients with poor response to hormonal therapy and poor prognosis. However, GATA3 is not yet targetable. Here we show that GATA3 and MDM2 are synthetically lethal in ER-positive breast cancer. Depletion and pharmacological inhibition of MDM2 significantly impaired tumor growth in GATA3-deficient models in vitro, in vivo and in patient-derived organoids/xenograft (PDOs/PDX) harboring GATA3 somatic mutations. The synthetic lethality requires p53 and acts via the PI3K/Akt/mTOR pathway. Our results present MDM2 as a therapeutic target in the substantial cohort of ER-positive, GATA3-mutant breast cancer patients. With MDM2 inhibitors widely available, our findings can be rapidly translated into clinical trials to evaluate in-patient efficacy.
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Bommi-Reddy A, Park-Chouinard S, Mayhew DN, Terzo E, Hingway A, Steinbaugh MJ, Wilson JE, Sims RJ, Conery AR. CREBBP/EP300 acetyltransferase inhibition disrupts FOXA1-bound enhancers to inhibit the proliferation of ER+ breast cancer cells. PLoS One 2022; 17:e0262378. [PMID: 35353838 PMCID: PMC8967035 DOI: 10.1371/journal.pone.0262378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/01/2022] [Indexed: 12/19/2022] Open
Abstract
Therapeutic targeting of the estrogen receptor (ER) is a clinically validated approach for estrogen receptor positive breast cancer (ER+ BC), but sustained response is limited by acquired resistance. Targeting the transcriptional coactivators required for estrogen receptor activity represents an alternative approach that is not subject to the same limitations as targeting estrogen receptor itself. In this report we demonstrate that the acetyltransferase activity of coactivator paralogs CREBBP/EP300 represents a promising therapeutic target in ER+ BC. Using the potent and selective inhibitor CPI-1612, we show that CREBBP/EP300 acetyltransferase inhibition potently suppresses in vitro and in vivo growth of breast cancer cell line models and acts in a manner orthogonal to directly targeting ER. CREBBP/EP300 acetyltransferase inhibition suppresses ER-dependent transcription by targeting lineage-specific enhancers defined by the pioneer transcription factor FOXA1. These results validate CREBBP/EP300 acetyltransferase activity as a viable target for clinical development in ER+ breast cancer.
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Affiliation(s)
- Archana Bommi-Reddy
- Constellation Pharmaceuticals, a Morphosys Company, Cambridge, Massachusetts, United States of America
| | - Sungmi Park-Chouinard
- Constellation Pharmaceuticals, a Morphosys Company, Cambridge, Massachusetts, United States of America
| | - David N. Mayhew
- Constellation Pharmaceuticals, a Morphosys Company, Cambridge, Massachusetts, United States of America
| | - Esteban Terzo
- Constellation Pharmaceuticals, a Morphosys Company, Cambridge, Massachusetts, United States of America
| | - Aparna Hingway
- Constellation Pharmaceuticals, a Morphosys Company, Cambridge, Massachusetts, United States of America
| | - Michael J. Steinbaugh
- Constellation Pharmaceuticals, a Morphosys Company, Cambridge, Massachusetts, United States of America
| | - Jonathan E. Wilson
- Constellation Pharmaceuticals, a Morphosys Company, Cambridge, Massachusetts, United States of America
| | - Robert J. Sims
- Constellation Pharmaceuticals, a Morphosys Company, Cambridge, Massachusetts, United States of America
| | - Andrew R. Conery
- Constellation Pharmaceuticals, a Morphosys Company, Cambridge, Massachusetts, United States of America
- * E-mail:
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40
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Hao C, Wang C, Lu N, Zhao W, Li S, Zhang L, Meng W, Wang S, Tong Z, Zeng Y, Lu L. Gene Mutations Associated With Clinical Characteristics in the Tumors of Patients With Breast Cancer. Front Oncol 2022; 12:778511. [PMID: 35494043 PMCID: PMC9046571 DOI: 10.3389/fonc.2022.778511] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 03/14/2022] [Indexed: 11/16/2022] Open
Abstract
Background Clinical characteristics including estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor 2 (HER2) are important biomarkers in the treatment of breast cancer, but how genomic mutations affect their status is rarely studied. This study aimed at finding genomic mutations associated with these clinical characteristics. Methods There were 160 patients with breast cancer enrolled in this study. Samples from those patients were used for next-generation sequencing, targeting a panel of 624 pan-cancer genes. Short nucleotide mutations, copy number variations, and gene fusions were identified for each sample. Fisher’s exact test compared each pair of genes. A similarity score was constructed with the resulting P-values. Genes were clustered with the similarity scores. The identified gene clusters were compared to the status of clinical characteristics including ER, PR, HER2, and a family history of cancer (FH) in terms of the mutations in patients. Results Gene-by-gene analysis found that CCND1 mutations were positively correlated with ER status while ERBB2 and CDK12 mutations were positively correlated with HER2 status. Mutation-based clustering identified four gene clusters. Gene cluster 1 (ADGRA2, ZNF703, FGFR1, KAT6A, and POLB) was significantly associated with PR status; gene cluster 2 (COL1A1, AXIN2, ZNF217, GNAS, and BRIP1) and gene cluster 3 (FGF3, FGF4, FGF19, and CCND1) were significantly associated with ER status; gene cluster 2 was also negatively associated with a family history of cancer; and gene cluster 4 was significantly negatively associated with age. Patients were classified into four corresponding groups. Patient groups 1, 2, 3, and 4 had 24.1%, 36.5%, 38.7%, and 41.3% of patients with an FDA-recognized biomarker predictive of response to an FDA-approved drug, respectively. Conclusion This study identified genomic mutations positively associated with ER and PR status. These findings not only revealed candidate genes in ER and PR status maintenance but also provided potential treatment targets for patients with endocrine therapy resistance.
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Affiliation(s)
- Chunfang Hao
- Department of Breast Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Chen Wang
- Department of Breast Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Ning Lu
- Department of Breast Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Weipeng Zhao
- Department of Breast Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Shufen Li
- Department of Breast Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Li Zhang
- Department of Breast Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Wenjing Meng
- Department of Breast Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Shuling Wang
- Department of Breast Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Zhongsheng Tong
- Department of Breast Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
- *Correspondence: Zhongsheng Tong, ; Yanwu Zeng, ; Leilei Lu,
| | - Yanwu Zeng
- Department of Breast Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
- Operations Department, Shanghai OrigiMed Co., Ltd., Shanghai, China
- *Correspondence: Zhongsheng Tong, ; Yanwu Zeng, ; Leilei Lu,
| | - Leilei Lu
- Department of Breast Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
- Operations Department, Shanghai OrigiMed Co., Ltd., Shanghai, China
- *Correspondence: Zhongsheng Tong, ; Yanwu Zeng, ; Leilei Lu,
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Li Z, Wu Y, Yates ME, Tasdemir N, Bahreini A, Chen J, Levine KM, Priedigkeit NM, Nasrazadani A, Ali S, Buluwela L, Arnesen S, Gertz J, Richer JK, Troness B, El-Ashry D, Zhang Q, Gerratana L, Zhang Y, Cristofanilli M, Montanez MA, Sundd P, Wallace CT, Watkins SC, Fumagalli C, Guerini-Rocco E, Zhu L, Tseng GC, Wagle N, Carroll JS, Jank P, Denkert C, Karsten MM, Blohmer JU, Park BH, Lucas PC, Atkinson JM, Lee AV, Oesterreich S. Hotspot ESR1 Mutations Are Multimodal and Contextual Modulators of Breast Cancer Metastasis. Cancer Res 2022; 82:1321-1339. [PMID: 35078818 PMCID: PMC8983597 DOI: 10.1158/0008-5472.can-21-2576] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/03/2021] [Accepted: 01/18/2022] [Indexed: 11/16/2022]
Abstract
Constitutively active estrogen receptor α (ER/ESR1) mutations have been identified in approximately one-third of ER+ metastatic breast cancers. Although these mutations are known as mediators of endocrine resistance, their potential role in promoting metastatic disease has not yet been mechanistically addressed. In this study, we show the presence of ESR1 mutations exclusively in distant but not local recurrences in five independent breast cancer cohorts. In concordance with transcriptomic profiling of ESR1-mutant tumors, genome-edited ESR1 Y537S and D538G-mutant cell models exhibited a reprogrammed cell adhesive gene network via alterations in desmosome/gap junction genes and the TIMP3/MMP axis, which functionally conferred enhanced cell-cell contacts while decreasing cell-extracellular matrix adhesion. In vivo studies showed ESR1-mutant cells were associated with larger multicellular circulating tumor cell (CTC) clusters with increased compactness compared with ESR1 wild-type CTCs. These preclinical findings translated to clinical observations, where CTC clusters were enriched in patients with ESR1-mutated metastatic breast cancer. Conversely, context-dependent migratory phenotypes revealed cotargeting of Wnt and ER as a vulnerability in a D538G cell model. Mechanistically, mutant ESR1 exhibited noncanonical regulation of several metastatic pathways, including secondary transcriptional regulation and de novo FOXA1-driven chromatin remodeling. Collectively, these data provide evidence for ESR1 mutation-modulated metastasis and suggest future therapeutic strategies for targeting ESR1-mutant breast cancer. SIGNIFICANCE Context- and allele-dependent transcriptome and cistrome reprogramming in mutant ESR1 cell models elicit diverse metastatic phenotypes related to cell adhesion and migration, which can be pharmacologically targeted in metastatic breast cancer.
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Affiliation(s)
- Zheqi Li
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
| | - Yang Wu
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
- School of Medicine, Tsinghua University, Beijing, China
| | - Megan E. Yates
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
- Integrative Systems Biology Program, University of Pittsburgh, Pittsburgh, PA, USA
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Nilgun Tasdemir
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
| | - Amir Bahreini
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
- Department of Human Genetics, University of Pittsburgh, Pittsburgh PA, USA
| | - Jian Chen
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
| | - Kevin M. Levine
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
- Department of Pathology, University of Pittsburgh, Pittsburgh PA, USA
| | - Nolan M. Priedigkeit
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
| | - Azadeh Nasrazadani
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
| | - Simak Ali
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Laki Buluwela
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Spencer Arnesen
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Jason Gertz
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Jennifer K. Richer
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Benjamin Troness
- University of Minnesota Masonic Cancer Center, Minneapolis, MN, USA
| | - Dorraya El-Ashry
- University of Minnesota Masonic Cancer Center, Minneapolis, MN, USA
| | - Qiang Zhang
- Robert H. Lurie Cancer Center of Northwestern University, Feinberg School of Medicine, Chicago, IL, US
| | - Lorenzo Gerratana
- Robert H. Lurie Cancer Center of Northwestern University, Feinberg School of Medicine, Chicago, IL, US
- Department of Medicine (DAME) University of Udine, Udine, Italy
| | - Youbin Zhang
- Robert H. Lurie Cancer Center of Northwestern University, Feinberg School of Medicine, Chicago, IL, US
| | - Massimo Cristofanilli
- Robert H. Lurie Cancer Center of Northwestern University, Feinberg School of Medicine, Chicago, IL, US
| | - Maritza A. Montanez
- Pittsburgh Heart, Lung and Blood Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh PA, USA
| | - Prithu Sundd
- Pittsburgh Heart, Lung and Blood Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh PA, USA
| | - Callen T. Wallace
- Center for Biological Imaging, University of Pittsburgh, Pittsburgh PA, USA
| | - Simon C. Watkins
- Center for Biological Imaging, University of Pittsburgh, Pittsburgh PA, USA
| | - Caterina Fumagalli
- Division of Pathology and Laboratory Medicine, IEO, European Institute of Oncology, IRCCS, Milan, Italy
| | - Elena Guerini-Rocco
- Division of Pathology and Laboratory Medicine, IEO, European Institute of Oncology, IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Li Zhu
- Department of Biostatistics, University of Pittsburgh, Pittsburgh PA, USA
| | - George C. Tseng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh PA, USA
| | - Nikhil Wagle
- Department of Medical Oncology and Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, USA
| | - Jason S. Carroll
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Paul Jank
- Institut of Pathology, Philipps-University Marburg, UKGM - Universitätsklinikum Marburg, Marburg, Germany
| | - Carsten Denkert
- Institut of Pathology, Philipps-University Marburg, UKGM - Universitätsklinikum Marburg, Marburg, Germany
| | - Maria M Karsten
- Department of Gynecology with Breast Center, Charité – Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humbold-Univeristät zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Jens-Uwe Blohmer
- Department of Gynecology with Breast Center, Charité – Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humbold-Univeristät zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Ben H. Park
- Vanderbilt University Ingraham Cancer Center, Nashville, TN, USA
| | - Peter C. Lucas
- Department of Pathology, University of Pittsburgh, Pittsburgh PA, USA
| | - Jennifer M. Atkinson
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
| | - Adrian V. Lee
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
- Integrative Systems Biology Program, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh, Pittsburgh PA, USA
| | - Steffi Oesterreich
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
- Integrative Systems Biology Program, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh, Pittsburgh PA, USA
- Department of Pathology, University of Pittsburgh, Pittsburgh PA, USA
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Detilleux D, Spill YG, Balaramane D, Weber M, Bardet AF. Pan-cancer predictions of transcription factors mediating aberrant DNA methylation. Epigenetics Chromatin 2022; 15:10. [PMID: 35331302 PMCID: PMC8944071 DOI: 10.1186/s13072-022-00443-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 03/04/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Aberrant DNA methylation is a hallmark of cancer cells. However, the mechanisms underlying changes in DNA methylation remain elusive. Transcription factors initially thought to be repressed from binding by DNA methylation, have recently emerged as being able to shape DNA methylation patterns. RESULTS Here, we integrated the massive amount of data available from The Cancer Genome Atlas to predict transcription factors driving aberrant DNA methylation in 13 cancer types. We identified differentially methylated regions between cancer and matching healthy samples, searched for transcription factor motifs enriched in those regions and selected transcription factors with corresponding changes in gene expression. We predict transcription factors known to be involved in cancer as well as novel candidates to drive hypo-methylated regions such as FOXA1 and GATA3 in breast cancer, FOXA1 and TWIST1 in prostate cancer and NFE2L2 in lung cancer. We also predict transcription factors that lead to hyper-methylated regions upon transcription factor loss such as EGR1 in several cancer types. Finally, we validate that FOXA1 and GATA3 mediate hypo-methylated regions in breast cancer cells. CONCLUSION Our work highlights the importance of some transcription factors as upstream regulators shaping DNA methylation patterns in cancer.
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Affiliation(s)
- Dylane Detilleux
- UMR7242 Biotechnology and Cell Signaling, CNRS, University of Strasbourg, 67412, Illkirch, France
| | - Yannick G Spill
- UMR7242 Biotechnology and Cell Signaling, CNRS, University of Strasbourg, 67412, Illkirch, France
| | - Delphine Balaramane
- UMR7242 Biotechnology and Cell Signaling, CNRS, University of Strasbourg, 67412, Illkirch, France
| | - Michaël Weber
- UMR7242 Biotechnology and Cell Signaling, CNRS, University of Strasbourg, 67412, Illkirch, France.
| | - Anaïs Flore Bardet
- UMR7242 Biotechnology and Cell Signaling, CNRS, University of Strasbourg, 67412, Illkirch, France.
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Epigenetic Factors as Etiological Agents, Diagnostic Markers, and Therapeutic Targets for Luminal Breast Cancer. Biomedicines 2022; 10:biomedicines10040748. [PMID: 35453496 PMCID: PMC9031900 DOI: 10.3390/biomedicines10040748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/16/2022] [Accepted: 03/21/2022] [Indexed: 11/16/2022] Open
Abstract
Luminal breast cancer, an etiologically heterogeneous disease, is characterized by high steroid hormone receptor activity and aberrant gene expression profiles. Endocrine therapy and chemotherapy are promising therapeutic approaches to mitigate breast cancer proliferation and recurrence. However, the treatment of therapy-resistant breast cancer is a major challenge. Recent studies on breast cancer etiology have revealed the critical roles of epigenetic factors in luminal breast cancer tumorigenesis and drug resistance. Tumorigenic epigenetic factor-induced aberrant chromatin dynamics dysregulate the onset of gene expression and consequently promote tumorigenesis and metastasis. Epigenetic dysregulation, a type of somatic mutation, is a high-risk factor for breast cancer progression and therapy resistance. Therefore, epigenetic modulators alone or in combination with other therapies are potential therapeutic agents for breast cancer. Several clinical trials have analyzed the therapeutic efficacy of potential epi-drugs for breast cancer and reported beneficial clinical outcomes, including inhibition of tumor cell adhesion and invasiveness and mitigation of endocrine therapy resistance. This review focuses on recent findings on the mechanisms of epigenetic factors in the progression of luminal breast cancer. Additionally, recent findings on the potential of epigenetic factors as diagnostic biomarkers and therapeutic targets for breast cancer are discussed.
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Hsieh YP, Naler LB, Ma S, Lu C. Cell-type-specific epigenomic variations associated with BRCA1 mutation in pre-cancer human breast tissues. NAR Genom Bioinform 2022; 4:lqac006. [PMID: 35118379 PMCID: PMC8808540 DOI: 10.1093/nargab/lqac006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 12/13/2021] [Accepted: 01/24/2022] [Indexed: 11/24/2022] Open
Abstract
BRCA1 germline mutation carriers are predisposed to breast cancers. Epigenomic regulations have been known to strongly interact with genetic variations and potentially mediate biochemical cascades involved in tumorigenesis. Due to the cell-type specificity of epigenomic features, profiling of individual cell types is critical for understanding the molecular events in various cellular compartments within complex breast tissue. Here, we produced cell-type-specific profiles of genome-wide histone modifications including H3K27ac and H3K4me3 in basal, luminal progenitor, mature luminal and stromal cells extracted from a small pilot cohort of pre-cancer BRCA1 mutation carriers (BRCA1mut/+) and non-carriers (BRCA1+/+), using a low-input ChIP-seq technology that we developed. We discovered that basal and stromal cells present the most extensive epigenomic differences between mutation carriers (BRCA1mut/+) and non-carriers (BRCA1+/+), while luminal progenitor and mature luminal cells are relatively unchanged with the mutation. Furthermore, the epigenomic changes in basal cells due to BRCA1 mutation appear to facilitate their transformation into luminal progenitor cells. Taken together, epigenomic regulation plays an important role in the case of BRCA1 mutation for shaping the molecular landscape that facilitates tumorigenesis.
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Affiliation(s)
- Yuan-Pang Hsieh
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Lynette B Naler
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Sai Ma
- Department of Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, VA 24061, USA
| | - Chang Lu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA
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Azfaralariff A, Farahfaiqah F, Shahid M, Sanusi SA, Law D, Mohd Isa AR, Muhamad M, Tsui TT, Fazry S. Marantodes pumilum: Systematic computational approach to identify their therapeutic potential and effectiveness. JOURNAL OF ETHNOPHARMACOLOGY 2022; 283:114751. [PMID: 34662662 DOI: 10.1016/j.jep.2021.114751] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/30/2021] [Accepted: 10/13/2021] [Indexed: 06/13/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Marantodes pumilum (MP) herbs, locally known as Kacip Fatimah, are widely used traditionally to improve women's health. The herb is frequently used for gynecological issues such as menstrual problems, facilitating and quickening delivery, post-partum medication, treats flatulence and dysentery, and. MP extracts are thought to aid in the firming and toning of abdominal muscles, tighten breasts and vaginal muscles, and anti-dysmenorrhea. It also was used for the treatment of gonorrhea and hemorrhoids. As MP product has been produced commercially recently, more in-depth studies should be conducted. The presence of numerous active compounds in MP might provide a synergistic effect and potentially offer other health benefits than those already identified and known. AIM OF THE STUDY This study aimed to use a computational target fishing approach to predict the possible therapeutic effect of Marantodes pumilum and evaluated their effectivity. MATERIALS AND METHODS This study involves a computational approach to identify the potential targets by using target fishing. Several databases were used: PubChem database to obtain the chemical structure of interested compounds; Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) server and the SWISSADME web tool to identify and select the compounds having drug-likeness properties; PharmMapper was used to identify top ten target protein of the selected compounds and Online Mendelian Inheritance in Man (OMIM) was used to predict human genetic problems; the gene id of top-10 proteins was obtained from UniProtKB to be analyzed by using GeneMANIA server to check the genes' function and their co-expression; Gene Pathway established by Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) of the selected targets were analyzed by using EnrichR server and confirmed by using DAVID (The Database for Annotation, Visualization and Integrated Discovery) version 6.8 and STRING database. All the interaction data was analyzed by Cytoscape version 3.7.2 software. The protein structure of most putative proteins was obtained from the RCSB protein data bank. Thedocking analysis was conducted using PyRx biological software v0.8 and illustrated by BIOVIA Discovery Studio Visualizer version 20.1.0. As a preliminary evaluation, a cell viability assay using Sulforhodamine B was conducted to evaluate the potential of the predicted therapeutic effect. RESULTS It was found that four studied compounds are highly correlated with three proteins: EFGR, CDK2, and ESR1. These proteins are highly associated with cancer pathways, especially breast cancer and prostate cancer. Qualitatively, cell proliferation assay conducted shown that the extract has IC50 of 88.69 μg/ml against MCF-7 and 66.51 μg/ml against MDA-MB-231. CONCLUSIONS Natural herbs are one of the most common forms of complementary and alternative medicine, and they play an important role in disease treatment. The results of this study show that in addition to being used traditionally to maintain women's health, the use of Marantodes pumilum indirectly has the potential to protect against the development of cancer cells, especially breast cancer. Therefore, further research is necessary to confirm the potential of this plant to be used in the development of anti-cancer drugs, especially for breast cancer.
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Affiliation(s)
- Ahmad Azfaralariff
- Department of Food Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Fazial Farahfaiqah
- Faculty of Chemical Engineering Technology, Universiti Malaysia Perlis (UNIMAP), Perlis, Malaysia
| | - Muhamad Shahid
- Department of Food Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Siti Aisyah Sanusi
- Department of Food Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Douglas Law
- Department of Food Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia; Faculty of Health and Life Sciences, Inti International University, Persiaran Perdana BBN Putra Nilai, 71800, Nilai, Negeri Sembilan, Malaysia
| | - Abdul Razak Mohd Isa
- Medika Natura Sdn. Bhd., No 44B, Jalan Bola Tampar, 13/14, Seksyen 13, Shah Alam, Selangor, Malaysia
| | - Mustadza Muhamad
- Medika Natura Sdn. Bhd., No 44B, Jalan Bola Tampar, 13/14, Seksyen 13, Shah Alam, Selangor, Malaysia
| | - Tee Thiam Tsui
- ZACH Biotech Depot Sdn. Bhd., No. 19-2, Jalan SC 5/A, Kawasan Perindustrian Sg. Chua, 43000, Kajang, Selangor, Malaysia
| | - Shazrul Fazry
- Department of Food Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia; Tasik Chini Research Centre, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
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46
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Saotome M, Poduval DB, Nair R, Cooper M, Takaku M. GATA3 Truncation Mutants Alter EMT Related Gene Expression via Partial Motif Recognition in Luminal Breast Cancer Cells. Front Genet 2022; 13:820532. [PMID: 35154280 PMCID: PMC8831884 DOI: 10.3389/fgene.2022.820532] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/10/2022] [Indexed: 12/13/2022] Open
Abstract
GATA3 is known to be one of the most frequently mutated genes in breast cancer. More than 10% of breast tumors carry mutations in this gene. However, the functional consequence of GATA3 mutations is still largely unknown. Clinical data suggest that different types of GATA3 mutations may have distinct roles in breast cancer characterization. In this study, we have established three luminal breast cancer cell lines that stably express different truncation mutants (X308 splice site deletion, C321 frameshift, and A333 frameshift mutants) found in breast cancer patients. Transcriptome analysis identified common and distinct gene expression patterns in these GATA3 mutant cell lines. In particular, the impacts on epithelial-to-mesenchymal transition (EMT) related genes are similar across these mutant cell lines. Chromatin localization of the mutants is highly overlapped and exhibits non-canonical motif enrichment. Interestingly, the A333 frameshift mutant expressed cells displayed the most significant impact on the GATA3 binding compared to X308 splice site deletion and C321fs mutants expressed cells. Our results suggest the common and different roles of GATA3 truncation mutations during luminal breast cancer development.
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47
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Patel JM, Jeselsohn RM. Estrogen Receptor Alpha and ESR1 Mutations in Breast Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1390:171-194. [DOI: 10.1007/978-3-031-11836-4_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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48
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El Ghamrasni S, Quevedo R, Hawley J, Mazrooei P, Hanna Y, Cirlan I, Zhu H, Bruce JP, Oldfield LE, Yang SYC, Guilhamon P, Reimand J, Cescon DW, Done SJ, Lupien M, Pugh TJ. Mutations in Noncoding Cis-Regulatory Elements Reveal Cancer Driver Cistromes in Luminal Breast Cancer. Mol Cancer Res 2022; 20:102-113. [PMID: 34556523 PMCID: PMC9398156 DOI: 10.1158/1541-7786.mcr-21-0471] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/31/2021] [Accepted: 09/17/2021] [Indexed: 01/07/2023]
Abstract
Whole-genome sequencing of primary breast tumors enabled the identification of cancer driver genes and noncoding cancer driver plexuses from somatic mutations. However, differentiating driver from passenger events among noncoding genetic variants remains a challenge. Herein, we reveal cancer-driver cis-regulatory elements linked to transcription factors previously shown to be involved in development of luminal breast cancers by defining a tumor-enriched catalogue of approximately 100,000 unique cis-regulatory elements from 26 primary luminal estrogen receptor (ER)+ progesterone receptor (PR)+ breast tumors. Integrating this catalog with somatic mutations from 350 publicly available breast tumor whole genomes, we uncovered cancer driver cistromes, defined as the sum of binding sites for a transcription factor, for ten transcription factors in luminal breast cancer such as FOXA1 and ER, nine of which are essential for growth in breast cancer with four exclusive to the luminal subtype. Collectively, we present a strategy to find cancer driver cistromes relying on quantifying the enrichment of noncoding mutations over cis-regulatory elements concatenated into a functional unit. IMPLICATIONS: Mapping the accessible chromatin of luminal breast cancer led to discovery of an accumulation of mutations within cistromes of transcription factors essential to luminal breast cancer. This demonstrates coopting of regulatory networks to drive cancer and provides a framework to derive insight into the noncoding space of cancer.
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Affiliation(s)
- Samah El Ghamrasni
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Rene Quevedo
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - James Hawley
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Parisa Mazrooei
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Genentech, South San Francisco, California
| | - Youstina Hanna
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Iulia Cirlan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Helen Zhu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Vector Institute, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Jeff P Bruce
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Leslie E Oldfield
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - S Y Cindy Yang
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Paul Guilhamon
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jüri Reimand
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Dave W Cescon
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Susan J Done
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
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Ahmed M, Lai TH, Kim W, Kim DR. A Functional Network Model of the Metastasis Suppressor PEBP1/RKIP and Its Regulators in Breast Cancer Cells. Cancers (Basel) 2021; 13:6098. [PMID: 34885208 PMCID: PMC8657175 DOI: 10.3390/cancers13236098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/26/2021] [Accepted: 11/30/2021] [Indexed: 12/12/2022] Open
Abstract
Drug screening strategies focus on quantifying the phenotypic effects of different compounds on biological systems. High-throughput technologies have the potential to understand further the mechanisms by which these drugs produce the desired outcome. Reverse causal reasoning integrates existing biological knowledge and measurements of gene and protein abundances to infer their function. This approach can be employed to appraise the existing biological knowledge and data to prioritize targets for cancer therapies. We applied text mining and a manual literature search to extract known interactions between several metastasis suppressors and their regulators. We then identified the relevant interactions in the breast cancer cell line MCF7 using a knockdown dataset. We finally adopted a reverse causal reasoning approach to evaluate and prioritize pathways that are most consistent and responsive to drugs that inhibit cell growth. We evaluated this model in terms of agreement with the observations under treatment of several drugs that produced growth inhibition of cancer cell lines. In particular, we suggested that the metastasis suppressor PEBP1/RKIP is on the receiving end of two significant regulatory mechanisms. One involves RELA (transcription factor p65) and SNAI1, which were previously reported to inhibit PEBP1. The other involves the estrogen receptor (ESR1), which induces PEBP1 through the kinase NME1. Our model was derived in the specific context of breast cancer, but the observed responses to drug treatments were consistent in other cell lines. We further validated some of the predicted regulatory links in the breast cancer cell line MCF7 experimentally and highlighted the points of uncertainty in our model. To summarize, our model was consistent with the observed changes in activity with drug perturbations. In particular, two pathways, including PEBP1, were highly responsive and would be likely targets for intervention.
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Affiliation(s)
| | | | | | - Deok Ryong Kim
- Department of Biochemistry and Convergence Medical Science, Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju 527-27, Korea; (M.A.); (T.H.L.); (W.K.)
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50
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Lu S, Yakirevich E, Yang D, Xiao Y, Wang LJ, Wang Y. Wnt Family Member 9b (Wnt9b) Is a New Sensitive and Specific Marker for Breast Cancer. Am J Surg Pathol 2021; 45:1633-1640. [PMID: 34324458 DOI: 10.1097/pas.0000000000001784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Confirming the tumor origin is often a diagnostic challenge in pathology and carries significant therapeutic impacts. Cytokeratin 7, estrogen receptor, and GATA binding protein 3 (GATA3) are well-established diagnostic markers frequently used to support a tumor's breast origin. However, their specificities still have room to improve. Many nonbreast tumors express cytokeratin 7 and estrogen receptor, and urothelial tumors frequently express GATA3. There is a practical need for a new breast lineage marker that is sensitive and specific. Wnt family member proteins play critical roles in embryo development, tissue homeostasis and tumor development through β-catenin dependent and independent pathways. The current study evaluated Wnt9b and GATA3 expression in 163 primary breast cancers, 63 metastatic breast cancers, and 525 nonbreast epithelial tumors. The positive rates of Wnt9b and GATA3 in primary breast cancer were both 98.7%. The positive rates in metastatic breast cancer were 87.3% for Wnt9b and 96.8% for GATA3. For nonbreast tumors, including 64 cases of urothelial carcinoma, Wnt9b was negative in all except salivary gland carcinomas. The study demonstrated that Wnt9b is a breast cancer marker with similar sensitivity as GATA3 but with greater specificity than GATA3 and may ultimately become a useful diagnostic tool in routine surgical pathology practice.
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Affiliation(s)
- Shaolei Lu
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School of Brown University, Providence, RI
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